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Lu, Yanbo, Xinji Liu, and Shutao Xia. "On the Single-Parity Locally Repairable Codes with Multiple Repairable Groups." Information 9, no. 11 (October 24, 2018): 265. http://dx.doi.org/10.3390/info9110265.
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Locally repairable codes (LRCs) are a new family of erasure codes used in distributed storage systems which have attracted a great deal of interest in recent years. For an [ n , k , d ] linear code, if a code symbol can be repaired by t disjoint groups of other code symbols, where each group contains at most r code symbols, it is said to have availability- ( r , t ) . Single-parity LRCs are LRCs with a constraint that each repairable group contains exactly one parity symbol. For an [ n , k , d ] single-parity LRC with availability- ( r , t ) for the information symbols (single-parity LRCs), the minimum distance satisfies d ≤ n - k - ⌈ k t / r ⌉ + t + 1 . In this paper, we focus on the study of single-parity LRCs with availability- ( r , t ) for information symbols. Based on the standard form of generator matrices, we present a novel characterization of single-parity LRCs with availability t ≥ 1 . Then, a simple and straightforward proof for the Singleton-type bound is given based on the new characterization. Some necessary conditions for optimal single-parity LRCs with availability t ≥ 1 are obtained, which might provide some guidelines for optimal coding constructions.
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Häkkinen, Antti, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, et al. "qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets." Bioinformatics 36, no. 20 (July 14, 2020): 5086–92. http://dx.doi.org/10.1093/bioinformatics/btaa637.
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Abstract Motivation Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited. Results We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer. Our results show that these improvements make qSNE significantly faster than regular t-SNE packages and enables full analysis of large datasets, such as mass cytometry data, without downsampling. Availability and implementation Source code and documentation are openly available at https://bitbucket.org/anthakki/qsne/. Supplementary information Supplementary data are available at Bioinformatics online.
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Galletly, G. D., and J. Błachut. "Torispherical Shells under Internal Pressure—Failure due to Asymmetric Plastic Buckling or Axisymmetric Yielding." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 199, no. 3 (July 1985): 225–38. http://dx.doi.org/10.1243/pime_proc_1985_199_117_02.
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In the diameter-to-thickness range 250 < D/t < 1000, internally pressurized torispherical shells can fail either by plastic buckling or by axisymmetric yielding. However, the present Code rules cater only for the axisymmetric yielding mode and they also restrict the D/t ratios to being less than 500. The rules are based on limit analysis results and these can be conservative for this problem. With regard to internal pressure buckling, there are as yet no design rules in either the American or the British pressure vessel Codes to prevent its occurrence. To provide guidance for a more accurate formulation of design rules for both of these failure modes over the range 300 < D/t < 1500, the authors have made a series of calculations to determine the values of Pcr (the internal buckling pressure) and pc (the axisymmetric yielding pressure) for perfect torispherical shells. The availability of these results, obtained with a finite-deflection shell theory, enables curves to be drawn showing when buckling is the controlling failure mode and when axisymmetric yield controls. A comparison is also made, for D/t < 600, between the controlling failure pressures mentioned above and the Drucker-Shield limit pressures. The ratio between the former and the latter varied between 1.2 and 1.8, depending on the geometry of the shell and the magnitude of the yield point, σyp. Considerable economies in the designs of many torispherical shells could, therefore, be achieved if the relevant sections of the Codes were to be modified to take advantage of the foregoing results. The controlling failure pressure curves also indicate how Code rules to prevent plastic buckling for D/t > 500 might be formulated. For the benefit of designers, the numerical values of pcr and pc were transformed, using curve-fitting techniques, into simple approximate equations. Although these equations are for perfect torispherical shells, they should be very beneficial when analysing the related problems of fabricated torispheres in practice.
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Rega, Paul, Shaun Vallejo, John Accumanno, and Brian Fink. "The Integration of a Unique QR® Code and Video to Improve the Correct Application of a Hemorrhage-control Tourniquet by a Naïve Population - A Feasibility Study." Prehospital and Disaster Medicine 34, s1 (May 2019): s142. http://dx.doi.org/10.1017/s1049023x19003145.
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Introduction:The use of tourniquets by the civilian population has been deemed a critical aspect of the initial response during an active shooter situation. Tourniquet deployment in public-access must be accompanied by education. Studies indicate that the act itself is not an intuitive process and enclosed instructions may be inadequate. However, civilians for diverse reasons may not avail themselves of accepted training programs.Aim:To develop an alternative means of “Just-In-Time” education to enable a naïve responder to apply a commercial tourniquet efficaciously.Methods:A video (~40 seconds long) was created highlighting the actual application of a C-A-T® (Combat Application Tourniquet) on a human model. It was uploaded to YouTube on a public channel. A QR® code was generated using https://www.qr-code-generator.com, embedding the link for the YouTube® video. An appropriately-sized QR® code was printed and applied with packaging tape (Scotch®) to the exterior wrapping of a C-A-T® device. The C-A-T® with code was then accessed with the iPhone®.Results:With the iPhone® camera app activated and focused on the C-A-T’s QR® code, a request popped-up to open “YouTube.com” in Safari. When pressed, the full-screen video appeared immediately with audio of excellent quality.Discussion:The use of a QR® code and its video link is a feasible option to provide “Just-In-Time” training to a naïve civilian population who are responding to an active shooter situation. This offers the naïve responder two options of immediate education: the enclosed instructions and the QR® code. Redundancy in communications is essential in any emergency response. An important limitation of this innovation is the inability to obtain Internet® access and therefore, the availability of the enclosed instructions is still critical. Research to prove that this innovation will allow the application of a tourniquet to proceed expeditiously with few errors is currently underway.
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Sturm, Gregor, Tamas Szabo, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, and Francesca Finotello. "Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data." Bioinformatics 36, no. 18 (July 2, 2020): 4817–18. http://dx.doi.org/10.1093/bioinformatics/btaa611.
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Abstract Summary Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data. Availability and implementation Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy. Supplementary information Supplementary data are available at Bioinformatics online.
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Tyagi, Ruchi, and Suresh Vishwakarma. "Prospect of low-cost energy conservation in residential energy consumption." International Journal of Power Electronics and Drive Systems (IJPEDS) 12, no. 4 (December 1, 2021): 2403. http://dx.doi.org/10.11591/ijpeds.v12.i4.pp2403-2413.
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The energy sector of trinidad and tobago (T&T), with its nationally determined contributions (NDCs), is still struggling for its place in mainstream academic literature. The review paper aims to identify the prospects of low-cost energy conservation measures in the residential sector of T&T. The review follows a four-step review methodology to serve as a basis for creating policy and practice guidelines. First, review articles are checked for their quality on a 5-point scale on the mixed methods appraisal tool (MMAT) to check the quality of review articles. Second, Microsoft Excel, R (RQDA) package, and Voyant tools have been used to index code, analyse, and visualise data. The research trends on small islands developing states (SIDS) energy aspect in general and T&T specifically highlight the critical role of energy challenges related to economic and social development, emphasising technology, infrastructure development, and funds availability. Awareness of low-cost energy conservation measures has a high prospect in reducing residential consumption and balancing demand-side management. This paper contributes to facilitating policy direction on energy efficiency and energy conservation for T&T and other SIDS.
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Hoot, Bradley, and Shane Ebert. "The That-Trace Effect: Evidence from Spanish–English Code-Switching." Languages 6, no. 4 (November 17, 2021): 189. http://dx.doi.org/10.3390/languages6040189.
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The that-trace effect is the fact that many languages (like English) ban the extraction of embedded-clause subjects but not objects over an overt complementizer like that, while many other languages (like Spanish) allow such extractions. The effect and its cross-linguistic variation have been the subject of intense research but remain largely a mystery, with no clear consensus on their underpinnings. We contribute novel evidence to these debates by using Spanish–English code-switching (the use of two languages in one sentence) to test five contemporary theoretical accounts of the that-trace effect. We conducted a formal acceptability judgment experiment, manipulating the extracted argument and code-switch site to test different combinations of linguistic features. We found that subject extraction is only permitted in Spanish–English code-switching when both the C head (que ‘that’) and the T head (i.e., the verb) are in Spanish, but not when either functional head is in English. Our results demonstrate indirect support for two of the five theories we test, failing to support the other three. Our findings also provide new evidence in favor of the view that the that-trace effect is tightly linked to the availability of post-verbal subjects. Finally, we outline how our results can narrow the range of possible theoretical accounts, demonstrating how code-switching data can contribute to core questions in linguistic theory.
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Aliverti, Emanuele, Jeffrey L. Tilson, Dayne L. Filer, Benjamin Babcock, Alejandro Colaneri, Jennifer Ocasio, Timothy R. Gershon, Kirk C. Wilhelmsen, and David B. Dunson. "Projected t-SNE for batch correction." Bioinformatics 36, no. 11 (March 16, 2020): 3522–27. http://dx.doi.org/10.1093/bioinformatics/btaa189.
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Abstract Motivation Low-dimensional representations of high-dimensional data are routinely employed in biomedical research to visualize, interpret and communicate results from different pipelines. In this article, we propose a novel procedure to directly estimate t-SNE embeddings that are not driven by batch effects. Without correction, interesting structure in the data can be obscured by batch effects. The proposed algorithm can therefore significantly aid visualization of high-dimensional data. Results The proposed methods are based on linear algebra and constrained optimization, leading to efficient algorithms and fast computation in many high-dimensional settings. Results on artificial single-cell transcription profiling data show that the proposed procedure successfully removes multiple batch effects from t-SNE embeddings, while retaining fundamental information on cell types. When applied to single-cell gene expression data to investigate mouse medulloblastoma, the proposed method successfully removes batches related with mice identifiers and the date of the experiment, while preserving clusters of oligodendrocytes, astrocytes, and endothelial cells and microglia, which are expected to lie in the stroma within or adjacent to the tumours. Availability and implementation Source code implementing the proposed approach is available as an R package at https://github.com/emanuelealiverti/BC_tSNE, including a tutorial to reproduce the simulation studies. Contact aliverti@stat.unipd.it
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Isacchini, Giulio, Carlos Olivares, Armita Nourmohammad, Aleksandra M. Walczak, and Thierry Mora. "SOS: online probability estimation and generation of T-and B-cell receptors." Bioinformatics 36, no. 16 (June 17, 2020): 4510–12. http://dx.doi.org/10.1093/bioinformatics/btaa574.
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Abstract Summary Recent advances in modelling VDJ recombination and subsequent selection of T- and B-cell receptors provide useful tools to analyse and compare immune repertoires across time, individuals and tissues. A suite of tools—IGoR, OLGA and SONIA—have been publicly released to the community that allow for the inference of generative and selection models from high-throughput sequencing data. However, using these tools requires some scripting or command-line skills and familiarity with complex datasets. As a result, the application of the above models has not been available to a broad audience. In this application note, we fill this gap by presenting Simple OLGA & SONIA (SOS), a web-based interface where users with no coding skills can compute the generation and post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones. Availability and implementation SOS is freely available to use at sites.google.com/view/statbiophysens/sos with source code at github.com/statbiophys/sos.
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Alonsozana, G. L., and R. H. Christenson. "The case for cardiac troponin T: marker for effective risk stratification of patients with acute cardiac ischemia." Clinical Chemistry 42, no. 5 (May 1, 1996): 803–8. http://dx.doi.org/10.1093/clinchem/42.5.803.
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Abstract Availability of markers such as cardiac troponin T (cTnT) has brought new insights into ischemic heart disease (IHD). cTnT is a distinct protein that differs from other markers in biological function, molecular mass, and cytosolic pool. cTnT has been utilized for diagnosis of acute myocardial infarction (AMI) and risk stratification of patients with IHD. For AMI diagnosis, cTnT showed high sensitivity (94-100%) but generally lower specificity (46-99%), possibly because of increases in non-AMI patients with minor myocardial damage. Outcome studies have demonstrated that IHD patients with increased cTnT are at significantly greater risk for cardiac events; revascularization in patients with increased cTnT may improve outcome. Estimated costs for batched ES 300 cTnT results and for a cTnT rapid assay run "on demand" were $17.48 and $21.65, respectively. cTnT currently has no specific common procedure test code; expected reimbursement is $18.32 for the ES 300 and is not established for the rapid assay.
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O’Connor, Timothy, Charles E. Grant, Mikael Bodén, and Timothy L. Bailey. "T-Gene: improved target gene prediction." Bioinformatics 36, no. 12 (April 4, 2020): 3902–4. http://dx.doi.org/10.1093/bioinformatics/btaa227.
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Abstract Motivation Identifying the genes regulated by a given transcription factor (TF) (its ‘target genes’) is a key step in developing a comprehensive understanding of gene regulation. Previously, we developed a method (CisMapper) for predicting the target genes of a TF based solely on the correlation between a histone modification at the TF’s binding site and the expression of the gene across a set of tissues or cell lines. That approach is limited to organisms for which extensive histone and expression data are available, and does not explicitly incorporate the genomic distance between the TF and the gene. Results We present the T-Gene algorithm, which overcomes these limitations. It can be used to predict which genes are most likely to be regulated by a TF, and which of the TF’s binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a gene’s promoter, achieving median precision above 60%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median precision above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions. Availability and implementation The T-Gene web server, source code, histone/expression data and genome annotation files are provided at http://meme-suite.org. Supplementary information Supplementary data are available at Bioinformatics online.
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Culbertson, Adam, Satyender Goel, Margaret Madden, Niloufar Safaeinili, Kathryn Jackson, Thomas Carton, Russ Waitman, et al. "The Building Blocks of Inter-operability." Applied Clinical Informatics 08, no. 02 (April 2017): 322–36. http://dx.doi.org/10.4338/aci-2016-11-ra-0196.
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SummaryBackground: Patient matching is a key barrier to achieving interoperability. Patient demographic elements must be consistently collected over time and region to be valuable elements for patient matching.Objectives: We sought to determine what patient demographic attributes are collected at multiple institutions in the United States and see how their availability changes over time and across clinical sites.Methods: We compiled a list of 36 demographic elements that stakeholders previously identified as essential patient demographic attributes that should be collected for the purpose of linking patient records. We studied a convenience sample of 9 health care systems from geographically distinct sites around the country. We identified changes in the availability of individual patient demographic attributes over time and across clinical sites.Results: Several attributes were consistently available over the study period (2005–2014) including last name (99.96%), first name (99.95%), date of birth (98.82%), gender/sex (99.73%), postal code (94.71%), and full street address (94.65%). Other attributes changed significantly from 2005–2014: Social security number (SSN) availability declined from 83.3% to 50.44% (p<0.0001). Email address availability increased from 8.94% up to 54% availability (p<0.0001). Work phone number increased from 20.61% to 52.33% (p<0.0001).Conclusions: Overall, first name, last name, date of birth, gender/sex and address were widely collected across institutional sites and over time. Availability of emerging attributes such as email and phone numbers are increasing while SSN use is declining. Understanding the relative availability of patient attributes can inform strategies for optimal matching in healthcare.Citation: Culbertson A, Goel S, Madden MB, Jackson KL, Carton T, Waitman R, Liu M, Krishnamurthy A, Hall L, Cappella N, Visweswaran S, Safaeinili N, Becich MJ, Applegate R, Bernstam E, Rothman R, Matheny M, Lipori G, Bian J, Hogan W, Bell D, Martin A, Grannis S, Klann J, Sutphen R, O’Hara AB, Kho A. The building blocks of interoperability: A multisite analysis of patient demographic attributes available for matching. Appl Clin Inform 2017; 8: 322–336 https://doi.org/10.4338/ACI-2016-11-RA-0196
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Sethna, Zachary, Yuval Elhanati, Curtis G. Callan, Aleksandra M. Walczak, and Thierry Mora. "OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs." Bioinformatics 35, no. 17 (January 18, 2019): 2974–81. http://dx.doi.org/10.1093/bioinformatics/btz035.
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Abstract Motivation High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem. Results We use dynamic programming to construct an efficient and flexible algorithm, called OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences), for calculating the probability of generating a given CDR3 amino acid sequence or motif, with or without V/J restriction, as a result of V(D)J recombination in B or T cells. We apply it to databases of epitope-specific T-cell receptors to evaluate the probability that a typical human subject will possess T cells responsive to specific disease-associated epitopes. The model prediction shows an excellent agreement with published data. We suggest that OLGA may be a useful tool to guide vaccine design. Availability and implementation Source code is available at https://github.com/zsethna/OLGA. Supplementary information Supplementary data are available at Bioinformatics online.
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Tran, Stephen S., Qing Zhou, and Xinshu Xiao. "Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling." Bioinformatics 36, no. 9 (January 31, 2020): 2796–804. http://dx.doi.org/10.1093/bioinformatics/btaa066.
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Abstract Motivation RNA-sequencing (RNA-seq) enables global identification of RNA-editing sites in biological systems and disease. A salient step in many studies is to identify editing sites that statistically associate with treatment (e.g. case versus control) or covary with biological factors, such as age. However, RNA-seq has technical features that incumbent tests (e.g. t-test and linear regression) do not consider, which can lead to false positives and false negatives. Results In this study, we demonstrate the limitations of currently used tests and introduce the method, RNA-editing tests (REDITs), a suite of tests that employ beta-binomial models to identify differential RNA editing. The tests in REDITs have higher sensitivity than other tests, while also maintaining the type I error (false positive) rate at the nominal level. Applied to the GTEx dataset, we unveil RNA-editing changes associated with age and gender, and differential recoding profiles between brain regions. Availability and implementation REDITs are implemented as functions in R and freely available for download at https://github.com/gxiaolab/REDITs. The repository also provides a code example for leveraging parallelization using multiple cores.
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Wait, Eric, Mark Winter, and Andrew R. Cohen. "Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers." Bioinformatics 35, no. 24 (June 26, 2019): 5393–95. http://dx.doi.org/10.1093/bioinformatics/btz523.
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Abstract Summary Light microscopes can now capture data in five dimensions at very high frame rates producing terabytes of data per experiment. Five-dimensional data has three spatial dimensions (x, y, z), multiple channels (λ) and time (t). Current tools are prohibitively time consuming and do not efficiently utilize available hardware. The hydra image processor (HIP) is a new library providing hardware-accelerated image processing accessible from interpreted languages including MATLAB and Python. HIP automatically distributes data/computation across system and video RAM allowing hardware-accelerated processing of arbitrarily large images. HIP also partitions compute tasks optimally across multiple GPUs. HIP includes a new kernel renormalization reducing boundary effects associated with widely used padding approaches. Availability and implementation HIP is free and open source software released under the BSD 3-Clause License. Source code and compiled binary files will be maintained on http://www.hydraimageprocessor.com. A comprehensive description of all MATLAB and Python interfaces and user documents are provided. HIP includes GPU-accelerated support for most common image processing operations in 2-D and 3-D and is easily extensible. HIP uses the NVIDIA CUDA interface to access the GPU. CUDA is well supported on Windows and Linux with macOS support in the future.
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Weber, Anna, Jannis Born, and María Rodriguez Martínez. "TITAN: T-cell receptor specificity prediction with bimodal attention networks." Bioinformatics 37, Supplement_1 (July 1, 2021): i237—i244. http://dx.doi.org/10.1093/bioinformatics/btab294.
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Abstract Motivation The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose Tcr epITope bimodal Attention Networks (TITAN), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes. Results By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures. Availability and implementation The code as well as the dataset used in this study is publicly available at https://github.com/PaccMann/TITAN. Supplementary information Supplementary data are available at Bioinformatics online.
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Ahmed, Syed Faraz, Ahmed A. Quadeer, David Morales-Jimenez, and Matthew R. McKay. "Sub-dominant principal components inform new vaccine targets for HIV Gag." Bioinformatics 35, no. 20 (June 28, 2019): 3884–89. http://dx.doi.org/10.1093/bioinformatics/btz524.
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Abstract Motivation Patterns of mutational correlations, learnt from patient-derived sequences of human immunodeficiency virus (HIV) proteins, are informative of biochemically linked networks of interacting sites that may enable viral escape from the host immune system. Accurate identification of these networks is important for rationally designing vaccines which can effectively block immune escape pathways. Previous computational methods have partly identified such networks by examining the principal components (PCs) of the mutational correlation matrix of HIV Gag proteins. However, driven by a conservative approach, these methods analyze the few dominant (strongest) PCs, potentially missing information embedded within the sub-dominant (relatively weaker) ones that may be important for vaccine design. Results By using sequence data for HIV Gag, complemented by model-based simulations, we revealed that certain networks of interacting sites that appear important for vaccine design purposes are not accurately reflected by the dominant PCs. Rather, these networks are encoded jointly by both dominant and sub-dominant PCs. By incorporating information from the sub-dominant PCs, we identified a network of interacting sites of HIV Gag that associated very strongly with viral control. Based on this network, we propose several new candidates for a potent T-cell-based HIV vaccine. Availability and implementation Accession numbers of all sequences used and the source code scripts for all analysis and figures reported in this work are available online at https://github.com/faraz107/HIV-Gag-Immunogens. Supplementary information Supplementary data are available at Bioinformatics online.
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Zimmerman Savill, Kristin M., Andrew J. Klink, Djibril Liassou, Dhruv Chopra, Jalyna Laney, and Ajeet Gajra. "Real-World Treatment of Patients with Large B-Cell Lymphoma in the United States with Chimeric Antigen Receptor T-Cell Therapy." Blood 138, Supplement 1 (November 5, 2021): 4096. http://dx.doi.org/10.1182/blood-2021-150723.
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Abstract Introduction: The advent of chimeric antigen receptor (CAR) T-cell therapy has represented one of the most innovative therapeutic advances in oncology in recent years. Impressive clinical responses to CAR T-cell therapy observed in patients in clinical trials have led to the Food and Drug Administration (FDA) approval of five CAR T-cell therapies in the US since 2017 to treat large B-cell, mantle cell, and follicular lymphomas, as well as acute lymphoblastic leukemia (ALL) and multiple myeloma. The first two CAR T-cell therapies approved by the FDA, axicabtagene ciloleucel (axi-cel) and tisagenlecleucel (tisa-cel), have now been on the US market for the treatment of patients with large B-cell lymphoma (LBCL) since 2017 and 2018, respectively, allowing for assessment of their use in real-world clinical practice. Given the complex logistics of the manufacturing, distribution, administration and unique toxicity of CAR T-cell therapies, initial use was limited to larger centers with prior experience with CAR T-cell therapy clinical trials. With greater use and availability of multiple CAR T-cell therapies, real-world evaluation of the clinical profiles, treatment patterns, and outcomes of LBCL patients treated with CAR T-cell therapies may inform clinical, regulatory, and drug development decision making, ultimately helping to improve patient outcomes. This real-world claims-based study aimed to describe characteristics and treatment outcomes of patients with diffuse LBCL (DLBCL) treated with the CAR T-cell therapies axi-cel or tisa-cel in the non-trial setting. Methods: Patients with at least 1 claim for axi-cel or tisa-cel made prior to 03/31/21 and a diagnosis code of DLBCL were identified from the Symphony Integrated Dataverse (IDV), a large US claims database containing linked longitudinal prescription, medical, and hospital claims. The IDV contains claims for 280 million active unique patients representing over 63% of prescriptions with full lifecycle data, 62% of medical claims, and 25% of hospital claims volume in the US. Patients were excluded from analysis if axi-cel or tisa-cel was the first therapy identified for the patient since diagnosis of DLBCL within the claims database, if treatment was received as a part of a clinical trial, if there were no supporting claims around CAR T-cell therapy in the claims database, if next line of therapy was received within 30 days of a sole claim for axi-cel or tisa-cel, or if data supported a diagnosis of ALL. Patient characteristics and treatment patterns were summarized using descriptive statistics. Results: Among a total of 88 eligible patients with DLBCL identified in this study, 52% (n=46) received axi-cel and 48% (n=42) received tisa-cel. At the time of treatment with axi-cel or tisa-cel therapy, median patient age was 63 years (range, 20-78 years) and commercial insurance was the primary payer for 83% of patients (n=73). The majority (n=59, 67%) of patients were male. Patients with DLBCL treated with axi-cel or tisa-cel were distributed across each of the 4 US census regions, with 27% from the Northeast, 11% from the South, 32% from the Midwest, and 30% from the West. . Axi-cel or tisa-cel was received a median of 14 months following patients' initial diagnosis of DLBCL and for the majority (n=54, 61%) of patients, axi-cel or tisa-cel-related claims were associated with administration of CAR T-cell therapy in the outpatient setting (Table). Prior to axi-cel or tisa-cel, 57% of patients (n=50) received 2 or more lines of systemic therapy. Within a median follow-up period of 7.8 months, 17% of patients (n=15) received systemic therapy following axi-cel or tisa-cel treatment. Conclusions: In the first few years of US market availability, the CAR T-cell therapies axi-cel and tisa-cel have been used to treat patients with LBCL outside of the clinical trial setting. While the majority of patients in this real-world claims-based study received axi-cel or tisa-cel in an outpatient setting, hospital claims are underrepresented in the database utilized. Despite short follow-up (less than 8 months from initiation of these CAR T-cell therapies), approximately one in 6 patients appear to have relapsed disease, based on the need for subsequent systemic therapy. Further research is warranted to understand real-world clinical outcomes among patients treated with CAR T-cell therapy outside the trial setting. Figure 1 Figure 1. Disclosures Zimmerman Savill: Roche/Genentech: Ended employment in the past 24 months; Cardinal Health: Current Employment. Klink: Cardinal Health: Current Employment, Current holder of stock options in a privately-held company. Liassou: Cardinal Health: Current Employment. Chopra: Cardinal Health: Current Employment. Laney: Cardinal Health: Current Employment. Gajra: Cardinal Health: Current Employment, Current equity holder in publicly-traded company.
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Neumann, Jacob, Yen Ting Lin, Abhishek Mallela, Ely F. Miller, Joshua Colvin, Abell T. Duprat, Ye Chen, William S. Hlavacek, and Richard G. Posner. "Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit." Bioinformatics 38, no. 6 (January 5, 2022): 1770–72. http://dx.doi.org/10.1093/bioinformatics/btac004.
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Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.
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Murakami, Mark A., Alexandra N. Christodoulou, Amanda L. Christie, Tiffany DeSouza, Abner Louissaint, Una Vojinovic, Raphael Koch, et al. "Proxe: A Public Repository of Xenografts to Facilitate Studies of Biology and Expedite Preclinical Drug Development in Leukemia and Lymphoma." Blood 126, no. 23 (December 3, 2015): 3252. http://dx.doi.org/10.1182/blood.v126.23.3252.3252.
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Abstract To expedite the translation of biologic discoveries into novel therapeutics, there is a pressing need for panels of in vivo models that capture the molecular complexity of human disease. While traditional cell lines and genetically engineered mouse models are useful tools, they are insufficient to assess the broad diversity of human tumors within a context that recapitulates in situ biology. Patient-derived xenografts (PDXs), generated by transplanting primary human tumor cells into immune-deficient NOD.Cg-Prkdcscid/Il2rgtm1Wjl/SzJ (NSG) mice, surmount some of the limitations of these traditional platforms and have been increasingly utilized as tools for preclinical investigation. However, the infrastructure required to generate, bank, and characterize PDX models limits their availability to only a few investigators. To address this issue, we established a repository of PDX models of leukemia and lymphoma, which we have named the Public Repository of Xenografts (PRoXe). At the time of this writing, PRoXe contains 213 independent lines that have been passaged through mice once (P0), 123 of which have been repassaged in a second generation (P1) or further repassaged. The repository encompasses AML, B- and T-ALL, and B- and T-cell non-Hodgkin lymphoma (NHL) across a range of cytogenetic- and molecularly-defined subtypes (Table 1). PRoXe is extensively annotated with patient-level information, including demographics, phase of treatment, prior therapies, tumor immunophenotye, cytogenetics, and molecular diagnostics. PDX lines available for distribution are characterized by immunophenotyping, whole transcriptome sequencing (RNAseq), and targeted exon sequencing of ~300 genes. To confirm fidelity of engrafted tumors to their corresponding clinical samples, lymphomas were morphologically assessed in P0 mice by H&E and, when pathologic adjudication was required, by immunohistochemistry. Xenografted leukemias were compared to their original tumors immunophenotypically. Unsupervised hierarchical clustering was performed on 132 of these lines based on transcriptome sequencing data and demonstrated 94% concordance between classification of the PDX lines by RNA expression and by the annotated clinical-pathologic diagnoses. Discordant cases highlighted unusual variants, such as B-ALL with aberrant expression of myeloid markers and a follicular lymphoma that underwent blastic transformation in the mouse. Multiple lines have been luciferized and confirmed to home to bone marrow, spleen, and liver. Existing lines from PRoXe have already been shared with more than ten academic laboratories and multiple industrial partners. All of the data referenced here are freely available through a customized web-based search application at http://proxe.org, and lines can be requested for in vitro or in vivo experiments. We are actively expanding the size of PRoXe to allow for large pre-clinical studies that are powered to detect differences across genetically defined subsets. Thus, we are happy to host additional lines from outside investigators on PRoXe and thereby expand the availability of these valuable reagents. Finally, we have made the source code for PRoXe (in R Shiny) open-access, so that other investigators can establish their own portals. Table 1. WHO diagnostic entities encompassed within PRoXe at P1 or later, or P0 or later for B-ALLs. WHO Classification - number of lines per diagnostic entity AML, Other Myeloid, and Ambiguous Lineage [n=32] ALL [n=107] AML - recurrent gene mutations 6 B-ALL - NOS 44 AML - MDS-related changes 5 B-ALL - MLL-rearranged 11 AML - NOS 4 B-ALL - BCR-ABL 10 AML - MLLT3-MLL 2 B-ALL - hyperdiploidy 9 Acute myelomonocytic leukemia 1 B-ALL - TEL-AML1 8 Acute monocytic leukemia 1 B-ALL - E2A-PBX1 3 AML unable to classify 2 B-ALL unable to classify 1 Blastic plasmacytoid dendritic cell neoplasm 8 T-ALL 21 Mixed phenotype, MLL rearranged 1 B/myeloid acute leukemia 1 Myelodysplastic syndrome 1 Mature B cell neoplasms[n=11] Mature T and NK cell neoplasms [n=4] DBLCL - NOS 4 Angioimmunoblastic T-cell lymphoma 1 Mantle cell lymphoma 3 Adult T-cell leukemia/lymphoma 1 Extranodal marginal zone lymphoma 1 Extranodal NK/T-cell lymphoma 1 B-cell lymphoma, unclassifiable, with features intermediate between DLBCL and BL 3 SŽzary syndrome 1 Disclosures Konopleva: Novartis: Research Funding; AbbVie: Research Funding; Stemline: Research Funding; Calithera: Research Funding; Threshold: Research Funding. Etchin:Karyopharm: Research Funding. Lane:Stemline Therapeutics, Inc.: Research Funding. Stone:Abbvie: Consultancy; Novartis: Research Funding; Celator: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Agios: Consultancy; Sunesis: Consultancy, Other: DSMB for clinical trial; Merck: Consultancy; Karyopharm: Consultancy; Roche/Genetech: Consultancy; Pfizer: Consultancy; AROG: Consultancy; Juno: Consultancy.
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Yang, Yang, Timothy M. Walker, A. Sarah Walker, Daniel J. Wilson, Timothy E. A. Peto, Derrick W. Crook, Farah Shamout, et al. "DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis." Bioinformatics 35, no. 18 (January 28, 2019): 3240–49. http://dx.doi.org/10.1093/bioinformatics/btz067.
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Abstract Motivation Resistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phenomenon. Existing methods based on genetic data analysis of Mycobacterium tuberculosis (MTB) have been able to predict resistance of MTB to individual drugs, but have not considered the resistance co-occurrence and cannot capture latent structure of genomic data that corresponds to lineages. Results We used a large cohort of TB patients from 16 countries across six continents where whole-genome sequences for each isolate and associated phenotype to anti-TB drugs were obtained using drug susceptibility testing recommended by the World Health Organization. We then proposed an end-to-end multi-task model with deep denoising auto-encoder (DeepAMR) for multiple drug classification and developed DeepAMR_cluster, a clustering variant based on DeepAMR, for learning clusters in latent space of the data. The results showed that DeepAMR outperformed baseline model and four machine learning models with mean AUROC from 94.4% to 98.7% for predicting resistance to four first-line drugs [i.e. isoniazid (INH), ethambutol (EMB), rifampicin (RIF), pyrazinamide (PZA)], multi-drug resistant TB (MDR-TB) and pan-susceptible TB (PANS-TB: MTB that is susceptible to all four first-line anti-TB drugs). In the case of INH, EMB, PZA and MDR-TB, DeepAMR achieved its best mean sensitivity of 94.3%, 91.5%, 87.3% and 96.3%, respectively. While in the case of RIF and PANS-TB, it generated 94.2% and 92.2% sensitivity, which were lower than baseline model by 0.7% and 1.9%, respectively. t-SNE visualization shows that DeepAMR_cluster captures lineage-related clusters in the latent space. Availability and implementation The details of source code are provided at http://www.robots.ox.ac.uk/∼davidc/code.php. Supplementary information Supplementary data are available at Bioinformatics online.
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Malangone, Elisabetta, Kathleen A. Foley, Kathleen Wilson, Helen Varker, Alison Binder, R. Scott McKenzie, and Lorie Ellis. "Treatment sequencing patterns of novel agents in patients with prostate cancer." Journal of Clinical Oncology 32, no. 30_suppl (October 20, 2014): 296. http://dx.doi.org/10.1200/jco.2014.32.30_suppl.296.
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296 Background: The National Comprehensive Cancer Network (NCCN) guidelines recommend chemotherapy, immunotherapy or anti-androgen therapies for the treatment of advanced castration-resistant prostate cancer (CRPC). This study evaluated treatment sequencing of recently approved agents for CRPC [abiraterone (ABI), enzalutamide (ENZ), docetaxel (DOC), cabazitaxel (CAB), or sipuleucel-T (SIP)] among men with PC. Methods: This retrospective, observational study evaluated adult men with PC in the MarketScan Oncology EMR database, which includes data from over 900 contributing oncologists from over 100 community practices. Inclusion required a diagnosis of PC (ICD-9-CM diagnosis code 185) from 07/01/2011-03/31/2014, no treatment with ABI, ENZ, DOC, CAB, or SIP prior to 09/01/2012, no other primary cancers, and six months of medical record history prior to index date. The index date was the date of first prescription of ABI, ENZ, DOC, CAB or SIP between 09/01/2012 and 03/31/2014. First-, second- and subsequent-line treatments were evaluated prior to end of data availability or end of study. Results: In total, 812 PC patients were identified; mean age was 75 years and 68% had recorded metastasis. A single line of therapy was observed for 544 patients (67%). ABI was the most common first-line treatment (443; 55%), followed by DOC (167; 21%), ENZ (113; 14%), SIP (82; 10%) and CAB (7; 1%). A second line of therapy occurred in 268 patients (33%) and third line in 8%. The table below describes first-line and the two most common second-line therapies for those moving on to second-line. Conclusions: Of the five agents of interest, ABI was the most commonly prescribed first-line medication for advanced PC in this patient cohort. First-line DOC was more common than first-line CAB or SIP. Further studies with longer follow-up and other treatments are warranted. [Table: see text]
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Simončič, M., D. Semenov, S. Krasnokutski, Th Henning, and C. Jäger. "Sensitivity of gas-grain chemical models to surface reaction barriers." Astronomy & Astrophysics 637 (May 2020): A72. http://dx.doi.org/10.1051/0004-6361/202037648.
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Context. The feasibility of contemporary gas-grain astrochemical models depends on the availability of accurate kinetics data, in particular, for surface processes. Aims. We study the sensitivity of gas-grain chemical models to the energy barrier Ea of the important surface reaction between some of the most abundant species: C and H2 (surface C + surface H2 → surface CH2). Methods. We used the gas-grain code ALCHEMIC to model the time-dependent chemical evolution over a 2D grid of densities (nH ∈ 103, 1012 cm−3) and temperatures (T ∈ 10, 300 K), assuming UV-dark (AV = 20 mag) and partly UV-irradiated (AV = 3 mag) conditions that are typical of the dense interstellar medium. We considered two values for the energy barrier of the surface reaction, Ea = 2500 K (as originally implemented in the networks) and Ea = 0 K (as measured in the laboratory and computed by quantum chemistry simulations). Results. We find that if the C + H2 → CH2 surface reaction is barrierless, a more rapid conversion of the surface carbon atoms into methane ice occurs. Overproduction of the CHn hydrocarbon ices affects the surface formation of more complex hydrocarbons, cyanides and nitriles, and CS-bearing species at low temperatures ≲10−15 K. The surface hydrogenation of CO and hence the synthesis of complex (organic) molecules become affected as well. As a result, important species whose abundances may change by more than a factor of two at 1 Myr include atomic carbon, small mono-carbonic (C1) and di-carbonic (C2) hydrocarbons, CO2, CN, HCN, HNC, HNCO, CS, H2CO, H2CS, CH2CO, and CH3OH (in either gas and/or ice). The abundances of key species, CO, H2O, and N2 as well as O, HCO+, N2H+, NH3, NO, and most of the S-bearing molecules, remain almost unaffected. Conclusions. Further accurate laboratory measurements and quantum chemical calculations of the surface reaction barriers will be crucial to improve the accuracy of astrochemical models.
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Abdullah Hamid Salem and Ghadeer Razak Ahmed. "Study of the allelic frequency of HSPA6 gene and its genotypes and their effect on some characteristics of milk production in Holstein cows." University of Thi-Qar Journal of agricultural research 11, no. 2 (November 3, 2022): 112–21. http://dx.doi.org/10.54174/utjagr.v11i2.189.
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The study was conducted at the Taj Al-Nahrain cattle station in Al-Diwaniyah Governorate, which is 200 km from the center of Dhi Qar Governorate. For the period from 10/15/2021 to 10/3/2022, 49 Holstein cows imported from Germany were used in this experiment, all in the third production cycle. And the laboratory part of the study was conducted in the laboratory of the Marsh Research Center \ Dhi Qar University for the purpose of separating the genetic material from cow blood samples and conducting genetic analysis on it and extracting the possible genotypes HSPA6 heat shock protein gene. The animals in the station were fed according to the season and the year in terms of the availability of fodder and the percentage of costs involved in raising the cows, as well as on the general state of the productivity of the cows, but in general they are provided with green fodder, which includes jet, barley, corn stalks and a percentage of each of the dry fodder (hay and hay). ) and concentrate (barley, bran and cake) according to what is available from them, as well as limestone and table salt. Data on milk production were collected from the station records, where the milk production was recorded weekly for the morning and evening fenugreek by the station, and the milk components were analyzed in the Abu Dairy Company Gharib / Research and Development Division by Milk Analyzer. 3 ml of blood was collected from the udder vein of each cow by 5 ml medical syringes, suitable for the size of the animal’s vein, and placed in collection tubes containing an anticoagulant substance (K2 EDTA) and transported in a cooler box for safekeeping Freezing at -18°C until extraction time.
From the results obtained from this study, we can conclude that the mutation detected in the studied segment of the 6HSPA gene was a type of missense mutation and worked to change the code of the amino acid valine to the code of the amino acid leucine. Three genotypes were shown: GG, GT, and TT. It was found that there was a clear commonality of cows carrying the GG genotype with a rate of 88%, followed by the GT genotype with 8%, while the TT genotype got the lowest percentage and amounted to 4%, and with allelic recurrence Its value is 0.92 for the G allele and 0.08 for the T . allele
Groups of cows carrying the genotypes (GG, GT and TT) did not differ significantly among themselves in the characteristics of milk production and its components, but an arithmetic superiority between the three genotypes was observed and referred to in all the studied traits.
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Zakharyan, Aleksey A. "ON A PROSECUTOR AS A SUBJECT OF PROVING ON PRE-TRIAL STAGES OF A NATIONAL CRIMINAL PROCEDURE." Russian investigator 12 (December 17, 2020): 27–30. http://dx.doi.org/10.18572/1812-3783-2020-12-27-30.
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The participation of the prosecutor in the criminal process covers both his judicial and pre-trial stages. It is well known that the prosecutor in the Russian criminal process acts as the subject of evidence, not only as the state prosecutor, but mainly as the person conducting the criminal process or observing (supervising) his proceedings in the pre-trial stages of criminal proceedings. In the doctrine of the Russian criminal process, starting with the Charter of the Criminal Procedure of 1864 and up to and including the modern Code of Criminal Procedure of 2001, the prosecutor, to one degree or another, acted as a full-fledged subject of evidence in the preliminary investigation. In the current legal regulation of the prosecutor, despite a number of sign if I can t deformations of his procedural status, it can be attributed to full-fledged subjects of evidence. After the well-known reform of June 5, 2007, which significantly affected the procedural status of the prosecutor at the pre-trial stages of the criminal process, the prosecutor, in the opinion of many well-known procedural scientists (the positions will be given in the presentation of the material), ceased to be a full-fledged subject of proof, since the participation of the prosecutor in evidence is associated with the availability of authority to collect, verify and evaluate evidence. The Russian prosecutor is deprived of forensic tools, he does not have the right to independently collect evidence by carrying out investigative actions, and in relation to the investigation he is deprived of even the authority to give the investigator binding instructions on collecting and verify in evidence. Based on the objectives of the study, the author assesses the content of the powers of the prosecutor as the subject of evidence in the pretrial stages of Russian criminal proceedings When writing the article, the author used general scientific methods (analysis, induction, deduction and others and private scientific methods (formal logical, comparative, legal). Based on analysis of the latest trend since forming the pre-trial stages of the criminal process of foreign countries, it is proposed to clarify the procedural status of the prosecutor in pre-trial proceedings.
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Haymaker, Kathryn, Beth Malmskog, and Gretchen L. Matthews. "Locally recoverable codes with availability t≥2 from fiber products of curves." Advances in Mathematics of Communications 12, no. 2 (2018): 317–36. http://dx.doi.org/10.3934/amc.2018020.
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Wang, Gang, Min-Yao Niu, and Fang-Wei Fu. "Constructions of (r,t)-LRC Based on Totally Isotropic Subspaces in Symplectic Space Over Finite Fields." International Journal of Foundations of Computer Science 31, no. 03 (April 2020): 327–39. http://dx.doi.org/10.1142/s0129054120500112.
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Linear code with locality [Formula: see text] and availability [Formula: see text] is that the value at each coordinate [Formula: see text] can be recovered from [Formula: see text] disjoint repairable sets each containing at most [Formula: see text] other coordinates. This property is particularly useful for codes in distributed storage systems because it permits local repair of failed nodes and parallel access of hot data. In this paper, two constructions of [Formula: see text]-locally repairable linear codes based on totally isotropic subspaces in symplectic space [Formula: see text] over finite fields [Formula: see text] are presented. Meanwhile, comparisons are made among the [Formula: see text]-locally repairable codes we construct, the direct product code in Refs. [8], [11] and the codes in Ref. [9] about the information rate [Formula: see text] and relative distance [Formula: see text].
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Schultz, Corinna L., Suzanne M. McCahan, H. Timothy Bunnell, Fang Fang Chen, and Melissa A. Alderfer. "On-Line Patient Portal Use By Caregivers in Pediatric Oncology: Are We Widening Sociodemographic Disparities?" Blood 134, Supplement_1 (November 13, 2019): 2131. http://dx.doi.org/10.1182/blood-2019-131543.
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BACKGROUND: Financial and regulatory incentives stemming from the Health Information Technology for Economic and Clinic Health Act have encouraged and, hence, increased the availability of online patient portals ('portals') that connect to electronic health records. Through portals, caregivers have direct access to portions of their child's medical record. Direct access is intended to engage caregivers in treatment and, consequently, to improve disease management. However, demonstrated associations between portal use and engagement in care is limited within pediatrics and non-existent in pediatric oncology. Caregivers of children with cancer have increased anxiety in response to their child's diagnosis and treatment (Myers et al, Cancer, 2014). Allowing caregivers swift access to results via portals may reduce anxiety for some, however, complicated written material may exacerbate anxiety and cause confusion (Schultz, et al, Pediatric Blood & Cancer, 2018). Furthermore, differences in sociodemographic variables between portal users and non-users potentially highlights widening healthcare disparities. Little is known about the use of portals by caregivers of children with cancer or what effect use may have on caregivers. As a first step, this study sought to examine whether sociodemographic and clinical care variables are associated with portal activation in a pediatric oncology sample. METHODS: Data were extracted from the electronic health records of pediatric oncology patients diagnosed or treated for their first known cancer within Nemours Center for Cancer and Blood Disorders in the Delaware Valley from January 1, 2012 through June 30, 2017. Sociodemographic variables (patient age, gender, race, preferred language, insurance, zip-code), clinical characteristics (cancer type, date of diagnosis, total number of laboratory and radiology tests within the study period), and portal activation date were gathered. A cost of living index (COLI) was computed using zip-code data. Cancer type was classified as "liquid" or "solid" based on chemotherapy and radiology follow-up procedures. Those who activated the portal more than 30 days before a cancer diagnosis were excluded from evaluation to better isolate portal activation related to cancer diagnosis. Data were summarized with descriptive statistics. Chi-square and independent samples t-tests compared those who did and did not activate the portal. RESULTS: The initial sample included 445 children; 73 families activated the portal more than 30 days before cancer diagnosis. Of the remaining 372 patients, 197 families (53%) activated the portal. Those who activated did not differ from those who did not in regard to patient age, gender, COLI, or type of cancer. Those who were of non-majority race, spoke a language other than English, and did not have private insurance were overrepresented among those who did not activate (TABLE). Families of children undergoing more radiology and lab tests were more likely to activate. For those who activated the portal, 39% did so within 1 month of diagnosis (day -30 to day +30), 13% did so from day +31 to +90, 36% did so from day +91 to +365, and 11% did so greater than 366 days post diagnosis. CONCLUSION: There are significant differences in patient portal activation by race, preferred language, and type of insurance. These results suggest sociodemographic disparities in portal activation, similar to patterns found in our pediatric primary care network (Ketterer et al, Academic Pediatrics, 2013). In that sample, however, only 26% of patients activated accounts in contrast to the 53% of families in pediatric oncology activating accounts. In our sample, while general type of cancer was not associated with portal activation, greater burden of treatment evaluation was. This study is the initial step in a program of research evaluating the use, utility, and outcomes of portal use in pediatric oncology. Further work will include evaluation of patterns of portal usage along with evaluations of health literacy and portal related anxiety. As portals become more ubiquitous, we must better understand how they are used and mitigate any disparities in or ill effects of access to this information. Disclosures No relevant conflicts of interest to declare.
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Zou, Xianghui, Daniel King, Baho Sidiqi, Sunita Patruni, Christopher Hollweg, and Noah D. Kauff. "Socioeconomic disparities causing delays in pancreatic cancer germline genetic testing." Journal of Clinical Oncology 41, no. 4_suppl (February 1, 2023): 665. http://dx.doi.org/10.1200/jco.2023.41.4_suppl.665.
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665 Background: Germline genetic testing is recommended for patients with pancreatic ductal adenocarcinoma (PDAC) and pre-diagnostic testing is offered to patients with a significant family history. However, only 36% of patients in our institution obtained genetic testing. We identified associations between patient social profiles (income, race, ethnicity, social work needs) and delays in obtaining germline genetic testing from New York’s largest healthcare system. Methods: Patients with PDAC were identified using billing records across our institution with an IRB-approved protocol. Median income was extrapolated using patient zip code. Date of diagnosis (DOD) was recorded as the date of biopsy or, if no biopsy was performed, the date of earliest lesion found on CT scan. Delays of testing was calculated as the difference between DOD and the date of germline sample collection. Results: Between Mar 2016 and Feb 2022, 305 patients with PDAC were identified, with 103 (36.3%) having reports found (F), and 202 (63.7%) not having reports found (NF). Availability of germline testing did not vary by median income (F: $95954, NF: $94368, t=0.414, p=0.68). There was no significant difference in the geographic distribution either (gender p=0.92, race p=0.92, ethnicity p=0.16). Pearson analysis between income (x) and delays of testing (y) showed a negative correlation (y=-0.0028x+316, r2=0.058, p=0.014). African American and Hispanic patients, grouped for this analysis as underserved (U), had a significant delay in obtaining germline genetic testing compared to the remainder of patients (not underserved, NU) (U: 92d, NU: 21d, u=305.5, p=0.0016). In addition, African American (AA) patients had a significant delay of testing compared to White (W) patients (AA: 92d, W: 13d, u=161.5, p=0.0002). Furthermore, all 11 patients (1 Asian, 10 White) who obtained pre-diagnostic testing were NU patients (χ2=5.005, p=0.025). Upon further analysis, patients who have social work (SW) needs have a significant delay in testing compared to patients without SW needs (SW: 109d, no SW: 23d, u=263, p=0.025). Of the 12 patients who have SW needs, the primary needs were home care, transportation, or financial assistance. In addition, there was a trend toward difference between English (E) and non-English (NE) speaking patients when comparing their delays in testing (E=26.5, NE=108.5, u=257, p=0.12). Conclusions: Analysis of germline and clinical data from our 305-patient cohort identified a striking and concerning negative correlation between patient income and delays in germline testing. In addition, underserved patients had significant delays in germline testing and did not obtain any pre-diagnostic testing. Furthermore, social needs and primary language may be barriers for germline testing. Interprofessional collaborations may be required to prompt germline testing at our institution or nationwide.
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Timoshenko, Igor. "Developing automatic identification technologies at RNPLS&T: From the past into the future." Scientific and Technical Libraries, no. 12 (December 27, 2018): 64–72. http://dx.doi.org/10.33186/1027-3689-2018-12-64-72.
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The author examines the problems of automatic identification and publicizes RNPLS&T’s designing equipment and technologies of bar-coding and radiofrequency identification for libraries. He discusses the possibility for developing library automation systems through implementing radiofrequency identification and developing the concepts of Electronic Product Code and Internet of Things. The author argues that this would significantly increase integration of traditional library collections and digital documents into the modern information environment. He also discusses the possibility for using biometric identification systems which would enable to organize library space more flexibly and at the same time to exercise control of access to the building and reading rooms. The author concludes that new technologies would increase availability of library services for users and facilitate the global system of library and information support of human activities. This would enable libraries integration into the information space at the latest round of technological advancement.
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Coleman, Craig I., Kimberly Snow Caroti, Khaled Abdelgawwad, George Psaroudakis, Samuel Fatoba, Marcela Rivera, Gunnar Brobert, and Christopher Brescia. "Patient Characteristics and Temporal Changes in Anticoagulation Treatment Patterns in Patients Diagnosed with Cancer-Associated Thrombosis: An Oscar-US Analysis." Blood 138, Supplement 1 (November 5, 2021): 2132. http://dx.doi.org/10.1182/blood-2021-151566.
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Abstract Background: Although guidelines include direct-acting oral anticoagulants (DOACs) as an alternative to low molecular weight heparins (LMWHs) for treatment of cancer associated venous thrombosis (CAT), specific recommendations for selection of patients for DOAC treatment vary. Recommendations for use of DOACs are driven predominantly by perceptions of risk: benefit ratio (often associated with different cancer subtypes). We sought to assess patient characteristics and temporal changes in DOAC (vs. LMWH) utilization in patients being treated in routine practice for CAT. Methods: This analysis is part of the Observational Studies in Cancer Associated Thrombosis for Rivaroxaban - United States (OSCAR-US) program. OSCAR-US is an ongoing study utilizing longitudinal patient-level medical record data from Optum for 91+ million patients seen at 700+ hospitals and 7,000+ clinics across the US. To be included in the present study, adult patients had to be diagnosed with active (primary or metastatic) cancer, undergone hospitalization, emergency department or observation unit admission associated with a primary International Classification of Diseases (ICD)-9th or -10 th revision diagnosis code for venous thromboembolism (VTE) between January 2013 and September 2020, received a DOAC or LMWH on day 7 of CAT treatment, and been active in the data set for at least 12 months prior to the CAT. Cohort assignment was based upon anticoagulant received on day 7 to increase the study's likelihood of appropriately classifying patients into their intended long-term treatment group. We defined active cancer as any cancer associated with ongoing treatment with chemotherapy, immunotherapy, radiation, or recent surgery; the presence of metastatic disease (regardless of time from initial cancer diagnosis); or provider encounter with a primary diagnosis code for cancer within the 6 months prior to the CAT. We excluded patients with an alternative indication for anticoagulation use or evidence of anticoagulation during the 12 months prior (per written prescription or patient self-report). For this analysis, year of CAT diagnosis was grouped into three mutually exclusive categories (2013-2015, 2016-2018, and 2019-2020) to represent early DOAC availability for VTE, peri-DOAC CAT trials and post-CAT guideline recommendation periods. Categorical data were reported as percentages, while continuous data were reported as means ± standard deviations (SDs). Chi-square and independent sample t-tests were used to test for differences in characteristics and treatment patterns between cohorts. Results: In total, 95,072 adult patients experiencing a VTE-related hospitalization, emergency department or observation unit visit were identified. Of these, 14,377 (15.1%) met our pre-specified criteria for active cancer; including 84.7% who received a cancer treatment modality within 6-months and/or had metastatic disease (Table). Though a majority (76.0%) of patients received parenteral therapy as their first anticoagulant upon CAT diagnosis; on day 7 of CAT management, 5325 (52.0%) were receiving a DOAC and 4925 (48.0%) a LMWH. Mean age of patients was 65.2±13.7 years, body mass index (BMI) was 29.9±7.7 kg/m2 and 55.9% were women. Pulmonary embolism (PE)±deep vein thrombosis (DVT) was present in 47.2% of patients and more frequent in patients treated with LMWH than a DOAC on day 7 (p<0.001). The most common cancer types were lung (18.3%) genitourinary (13.5%), breast (12.7%) and colorectal (10.5%) (Figure). The proportion of patients treated with a DOAC increased substantially for all cancers over the three time periods evaluated (27.5% to 55.9% to 73.2%, p<0.001). This temporal relationship of increasing DOAC use (vs. LMWH) remained consistent across individual cancer subtypes (p<0.001 for all). Mean anticoagulant treatment duration was 193±143 days for the entire cohort and was longer in patients treated with DOACs vs. LMWHs (226±138 vs. 147±138 days, p<0.001). Conclusions: In this US population, DOACs were increasingly being utilized for the management of CAT patients and for longer treatment durations than LMWHs. The finding of increasing frequency in use of DOACs vs. LMWHs appeared consistent across all major cancer subtypes. Given their common use, future analyses should evaluate the real-world effectiveness and safety of DOACs compared to LMWHs within individual cancer subtypes. Figure 1 Figure 1. Disclosures Coleman: Bayer AG: Consultancy, Honoraria, Research Funding; Janssen Scientific Affairs LLC: Consultancy, Honoraria, Research Funding; Alexion Pharmaceuticals: Research Funding. Abdelgawwad: Bayer AG: Current Employment. Psaroudakis: Bayer AG: Current Employment. Fatoba: Bayer AG: Current Employment. Rivera: Bayer AG: Current Employment. Brobert: Bayer AG: Current Employment.
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Smith, Matthew Lee, T. S. Sunil, Camerino I. Salazar, Sadaf Rafique, and Marcia G. Ory. "Disparities of Food Availability and Affordability within Convenience Stores in Bexar County, Texas." Journal of Environmental and Public Health 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/782756.
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The American Diabetes Association (ADA) recommends healthful food choices; however, some geographic areas are limited in the types of foods they offer. Little is known about the role of convenience stores as viable channels to provide healthier foods in our “grab and go” society. The purposes of this study were to (1) identify foods offered within convenience stores located in two Bexar County, Texas, ZIP Codes and (2) compare the availability and cost of ADA-recommended foods including beverages, produce, grains, and oils/fats. Data were analyzed from 28 convenience store audits performed in two sociodemographically diverse ZIP Codes in Bexar County, Texas. Chi-squared tests were used to compare food availability, andt-tests were used to compare food cost in convenience stores between ZIP Codes. A significantly larger proportion of convenience stores in more affluent areas offered bananas (χ2=4.17,P=0.003), whole grain bread (χ2=8.33,P=0.004), and baked potato chips (χ2=13.68,P<0.001). On average, the price of diet cola (t=−2.12,P=0.044) and certain produce items (e.g., bananas, oranges, tomatoes, broccoli, and cucumber) was significantly higher within convenience stores in more affluent areas. Convenience stores can play an important role to positively shape a community’s food environment by stocking healthier foods at affordable prices.
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Mukherjee, Sudipto, Weichuan Dong, Aaron T. Gerds, Hetty E. Carraway, Abhay Singh, Anjali S. Advani, and Siran M. Koroukian. "Abstract A062: Age-, sex-, and race-related disparities in receipt of HypomethyLating Agents (HMA) for the treatment of myelodysplastic syndrome (MDS)." Cancer Epidemiology, Biomarkers & Prevention 32, no. 1_Supplement (January 1, 2023): A062. http://dx.doi.org/10.1158/1538-7755.disp22-a062.
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Abstract Objective: Recent data suggest low use of HMAs in patients with MDS in real world. We sought to identify factors associated with HMA use. Methods: Using 2011-2014 Medicare data, we identified individuals ³65 years of age diagnosed with incident MDS during the years 2012-2013 and receiving their care exclusively through the Medicare fee-for-service system. Collected data included age, race, sex, morbidity burden based on their frailty status (robust, pre-frail, mildly frail, moderately, or severely frail), nursing home residence, presence of MDS-related clinical characteristics [cytopenia (0-1 or ³2) and transfusion dependence (independent, low, or medium/high)], area-level socioeconomic measures [percent of individuals with income 100% below the federal poverty level; percent of adults (age > 25 years) without high school diploma; rurality, based on the rural-urban continuum code; and availability of general internal medicine subspecialists per 100,000 population], and receipt of bone marrow biopsy. Among those who received HMA, we grouped patients by the number of complete cycles (1-2, 3-5, or ³6). We used multivariable logistic regression analysis to evaluate the association between demographic characteristics and receipt of HMA, adjusting for MDS-related clinical characteristics, frailty, and socioeconomic measures. Results: Of 49,154 MDS pts, only 16.1% (7,935) received HMA. This percentage ranged from a low of 7.4% among individuals ³85 years of age to a high of 23.2% among those in the 65-74 age group. Receipt of HMA was significantly higher in men than in women (19.0% vs. 12.8%), in Whites than in minoritized patients (16.7% vs. 11.6% in Blacks, and 12.7% in those of Other race), higher among those with 2-3 cytopenias vs. 0-1 cytopenia and highest among those with medium/high transfusion dependence (44.7%). Among those who underwent biopsy, receipt of HMA was at 22.9%. Patients with moderate or severe frailty, and those in a nursing home had significantly lower rates of receipt of HMA. After adjusting for MDS-related clinical variables, frailty and socioeconomic measures, older patients had significantly lower odds than their younger counterparts to receive HMA [adjusted odds ratio (aOR): 0.84, (95% confidence interval: 0.79-0.89), and aOR: 0.43 (0.40-0.47) for those in the 75-84 and ³85 age groups, respectively). Females and minoritized patients had significantly lower odds than men and White patients to receive HMA [(aOR: 0.83 (0.79-0.88) for females; aOR: 0.71 (0.63-0.81) for Blacks, and aOR: 0.78 (0.68-0.89) for patients of Other race). Among those receiving HMA, we did not observe differences in the number of completed cycles by age, race, or sex. Conclusions: In Medicare beneficiaries with MDS, older patients, women, and minoritized patients have significantly lower odds to be treated with HMAs, even after adjusting for MDS-related clinical variables, morbidity burden, and socioeconomic measures. In addition to barriers to access adequate care, these results clearly reflect biases in MDS treatment, favoring younger, White men. Citation Format: Sudipto Mukherjee, Weichuan Dong, Aaron T. Gerds, Hetty E. Carraway, Abhay Singh, Anjali S. Advani, Siran M. Koroukian. Age-, sex-, and race-related disparities in receipt of HypomethyLating Agents (HMA) for the treatment of myelodysplastic syndrome (MDS) [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A062.
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Schnittger, Susanne, Claudia Haferlach, Tamara Alpermann, Wolfgang Kern, and Torsten Haferlach. "IDH Mutations Can Be Detected In 28.7% of All Normal Karyotype AML and Have Unfavourable Impact on the NPM1+/FLT3-ITD- Genotype." Blood 116, no. 21 (November 19, 2010): 102. http://dx.doi.org/10.1182/blood.v116.21.102.102.
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Abstract Abstract 102 Introduction: Mutations in IDH1 and IHD2 have recently been shown to play an important role in AML. As they code for enzymes from the citric acid cycle mutations within these genes from the mechanistical point of view are a totally new kind of mutation associated with AML. In IDH1 one mutational hot spot (amino acid R132) and in IDH2 two hotspots (R140 and R172) have been reported. We aimed at further delineating the impact of IDH1 and IDH2 mutations in AML and analyzed the interaction with other mutations in normal karyotype (NK) AML. Methods: 526 AML patients were selected according to normal karyotype and availability of mutational status for FLT3-ITD, NPM1 and MLL-PTD. Further mutation analyses were available in subgroups of the cohort (FLT3-TKD: n=318, CEBPA: n=369, RUNX1: n=174, NRAS: n=220). Female/male ratio was 283/243 and age ranged from 20.0–90.1 years (median, 66.9 years). 435 had de novo AML (82.6%), 71 AML following MDS (s-AML,13.5%) and 20 AML after previous treatment of other malignancies (t-AML, 3.8%). The respective base exchanges in R132, R140, and R172 were analysed by a melting curve assay with subsequent sequencing of the positive samples. Results: Overall, in 151 pts (28.7%) IDH mutations (IDHmut) were detected. In detail, 68 mutations (12.9% of all cases) were detected in IDH1 (R131C: n=35, R131L: n=17, R131H: n=7, R131G: n=6, R131S: n=3) and 83 mutations (15.8%) in IDH2 (R140Q: n=72, R140L: n=2, R140W: n=1, N141G: n=1, R174K: n=7). IDH1mut and IDH2mut were mutually exclusive in this cohort. IDH1mut were more frequent in females (18.2% vs 8.6 % in males, p=0.001), whereas there was no sex difference for IDH2. According to history IDH1 was equally distributed in de novo AML, s-AML and t-AML whereas IDH2 was more frequent in de novo compared to s- and t-AML (19.6% vs. 7.6 vs 11.8%, p=0.048). According to FAB the most prevalent subtype was FAB M1 with IDHmut in 23.2% compared to 9.8% in all other FAB (in detail: IDH1: 44.8% vs. 23.9%, IDH2: 27.0% vs. 15.1%; p<0.001, for both). IDH1 was underrepresented in M4 (4.9% vs. 15.0 % in all other subtypes, p=0.004), whereas the distribution of IHD2 was not different in M4 vs. all others. The immunophenotype (n= 297) of IDHmut cases tended to be more immature and featured a lower expression of monocytic markers. The analyzed 78 IDHmut cases, as compared to 219 IDHwt cases, showed a significantly higher expression of MPO and CD117 while CD116, CD11b, CD14, CD15, CD36. CD56, CD64, CD65 and CD7 were lower expressed. Age, WBC count, and platelet count were not different between IDH1, IDH2 and IDHwt cases. IDH mutations are not mutually exclusive of other mutations. However, the frequency of CEBPAmut in IDHmut compared to IDHwt was decreased (7.7% vs. 13.7, p=0.001) (IDH1: 0% vs 11.7%, p=0.022 and IDH2: 7.7% vs 13.4%, p=0.053). MLL-PTD was more frequent in IDHmut vs. IDHwt (44.7 vs. 5.8%, p=0.039), however, this is restricted to IDH1mut vs. IDH1wt (26.3 vs. 6.3%, p=0.018). RUNX1mut are distributed equally in IDH2mut and IDH2wt (20.0% vs 27.3%) but are underrepresented in IDH1mut compared to IDH1wt (2.2% vs. 28.7%, p=0.068). FLT3-ITDs are equally distributed between IDHmut and IDHwt, however, those IDH1mut with FLT3-ITD have lower FLT3-ITD/FLT3wt ratios compared to FLT3-ITD+ IDH1wt cases (mean: 0.16 vs. 0.72; p=0.005). All other mutations were distributed equally in IDHmut compared to IDHwt. For survival analysis only cases with de novo AML <65 years were included (n=164, IDHmut: n=37, n=, IDHwt: 127). In the total analysis there was no effect on overall survival or event free survival (EFS). However there was a trend for shorter EFS of the IDHmut vs. IDHwt (median: 439 days vs. not reached, p=0.080) in cases with NPM1+/FLT3-ITD- genotype. For IDH2 there was a significant adverse effect in the NPM1+/FLT3-ITD- group (median EFS: 397 vs. 679 days, p=0.045). Summary: IDH mutations belong to the most frequent mutations in NK AML and can occur together with all other known mutations. There is a high preponderance for the FAB M1 subtype and a more immature immunophenotype for both IDH mutations and a strong female preponderance for IDH1. In addition, an adverse prognostic impact of IDH mutations was shown for the NPM1+/FLT3-ITD- genotype. Further analyses should focus on the definition of the role and place of IDH mutations for therapeutic decisions in patients with AML. Disclosures: Schnittger: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Alpermann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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du Plessis, Martin Johannes, Joubert van Eeden, and Leila Louise Goedhals-Gerber. "The Carbon Footprint of Fruit Storage: A Case Study of the Energy and Emission Intensity of Cold Stores." Sustainability 14, no. 13 (June 21, 2022): 7530. http://dx.doi.org/10.3390/su14137530.
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Despite their importance in all transportation chains, logistical sites—and in particular refrigerated facilities—are the weakest link in current emissions literature. This is largely due to a lack of quantitative research that focuses on these facilities. This article is the first of its kind to assess the emissions of eight refrigerated facilities that handle and store fresh fruit. In 2020, the analyzed facilities moved a total of 646,572 pallets of fresh fruit and emitted 32,225 t of CO2e. Five of the largest facilities were responsible for handling 18.83% of the total fresh fruit exported from South Africa during 2020. The results revealed that storing and handling a pallet of fruit in a large-scale commercial cold store requires 7.62 kWh of electricity per day. Storing and handling fresh fruit is carbon intensive since each pallet stored translates to 7.52 kg CO2e d−1. However, other factors such as the seasonality and volume of fruit handled, facility characteristics and the availability of solar electricity systems, among others, all have a significant impact on the emissions value of the facility and on the emission intensity per pallet moved through the facility.
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Acquisgrana, María Del Rosario, Laura Cecilia Gómez Pamies, and Elisa Inés Benítez. "Hydrothermal Treatment to Remove Tannins in Wholegrains Sorghum, Milled Grains and Flour." Food Science and Nutrition Studies 3, no. 4 (October 30, 2019): p122. http://dx.doi.org/10.22158/fsns.v3n4p122.
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Pigmented sorghum with high content of tannins were studied in this work. Tannins bind to proteins and reduce their availability. A hydrothermal treatment was carried out to reduce tannins. A control sample of non-pigmented pericarp variety was used. After the treatment, grains were milled, and a part was separated for wholegrain flour elaboration. Several determinations were done after treatment: tannins (T), total antioxidant capacity (TAC) and total polyphenols (TPP) content. TPP and TAC in wholegrain pigmented sorghum were 3.9 to 12.3 and 2.3 to 3.5 times higher than those of non-pigmented sorghum, respectively. In all sorghum varieties the extractions of TPP decreased with milling. TAC in flour increased 3.3 times the initial value for non-pigmented sorghum, whereas for the other sorghum samples it increased slightly from 1.1 to 1.3 times the initial value. In flours there was a noticeable reduction in T, with respect to the wholegrain. It was possible to conclude that the hydrothermal treatment allowed lower levels of tannins than those established in the Codex for both wholegrain sorghum and flour. This reduction makes it possible to obtain flour which may be suitable for food processing and the recovery of tannins for other uses.
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Sevindik, Tuğba Ongun, Hatice Tunca, Halim Aytekin Ergül, Arzu Morkoyunlu Yüce, Melih Kayal, Nazmi Kağnicioğlu, Fatih Ekmekçi, Oltan Canli, and Elmas Öktem Olgun. "Lake morphometry underlies physical and chemical parameters affecting the distribution of phytoplankton functional groups in lakes of the Sakarya River Basin (Turkey)." Fundamental and Applied Limnology / Archiv für Hydrobiologie 194, no. 2 (December 9, 2020): 125–40. http://dx.doi.org/10.1127/fal/2020/1338.
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To test the effects of lake morphometry (lake size and depth) on water quality parameters which affect the phytoplankton functional groups (FG) distribution, phytoplankton and some environmental parameters were sampled in November 2017 and May 2018 at the two or three monitoring stations in nine Lakes of Sakarya River Basin (Turkey). Lake size and depth affected phytoplankton FG distribution in both large-sized and small-sized lakes by affecting light availability which was mainly driven by the mixing events during the studied period. Al- though PO4 -P and alkalinity were the other main environmental constraints influencing phytoplankton distribution, they were not directly affected by lake morphometry. Codon Lo was mainly found in small-sized and shallow lakes, whereas coda B, C, D, J, R, and T, which do not have active buoyancy regulation and adapt to high Zmix/Zeu con- ditions, occurred with high relative biovolume in large-sized water bodies.
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Zhang, Lulu, Xiao Liu, Xiaoxiang Chen, Antony R. Warden, Youyi Yu, Baozhen Huang, and Xianting Ding. "SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum." Bioinformatics 38, no. 5 (October 19, 2021): 1361–68. http://dx.doi.org/10.1093/bioinformatics/btab713.
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Abstract Motivation High-dimensional mass cytometry (CyTOF), which provides both cellular signatures and inter-cluster interactions like the antagonism between immune activation and suppression, and the pro-inflammatory synergy, sheds light on the cellular and molecular basis of disease pathogenesis. However, revealing the aberrance of inter-cluster communication networks in CyTOF datasets remains a significant challenge. Results Here, we developed Sample Classification and direct Association Network among Cell clusters (SCANCell) that quantifies the direct association (DA) network of cell clusters. SCANCell was applied to profile inter-cluster interaction patterns of a well-recruited systemic lupus erythematosus (SLE) cohort, including 8 healthy controls, 10 active SLE patients (APs) and 8 remission SLE patients (RPs). SCANCell identified decreased inter-cluster interactions of CD8+ T cells in APs compared with RPs, and enhanced DA of CD8+ T cells after stimulation with immunostimulatory cytokine interleukin-2 in vitro. These discoveries prove that SCANCell can uncover pathology- and drug stimulation-associated inter-cluster interactions, which potentially benefits understanding of pathogenesis and novel therapeutic strategies. Availability and implementation The main processing scripts of SCNACell are available at https://github.com/Lxc417/SCANCell. Other codes for the following data statistics are available from the corresponding author upon request. Supplementary information Supplementary data are available at Bioinformatics online.
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Yani Mulyani, Patonah Hasimun, and Hajar Sukmawati. "Effect of nori, a combination of turmeric (Curcuma longa) and gotu kola (Centella Asiatica) on blood pressure, modulation of ACE, eNOS and iNOS gene expression in hypertensive rats." International Journal of Research in Pharmaceutical Sciences 12, no. 4 (December 8, 2021): 2573–81. http://dx.doi.org/10.26452/ijrps.v12i4.4908.
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Hypertension is a major risk factor for causing life-threatening cardiovascular diseases such as myocardial infarction, coronary heart failure, kidney failure, and stroke. Its cases continue to increase worldwide and it is estimated that 1.56 billion adults would live with the condition in 2025. Therefore, this study aims to examine the antihypertensive effect of nori supplement prepared with a combination of turmeric (Curcuma longa) and gotu kola (Centella Asiatica) on L-NAME-induced and non-induced rats. It was conducted for 28 days on 25 wistar rats that were randomly assigned to the negative, positive, comparison, supplement, and test control groups. CODA was then used in measuring the blood pressure of the rats, while ECG and PPG sensors were utilized for arterial stiffness assessment, as well as for spatial QRS-T and heart rate analysis. Additionally, serum NO levels were measured using griess reagents by spectrophotometric λ540 nm. At the same time, the gel-based PCR semi-quantitative method was used in assessing the activity of ACE, including eNOS and iNOS gene expression. The results showed that nori preparations which contained a combination of 5% turmeric and gotu kola in a feed mixture, had an antihypertensive effect. The effect was characterized by a decrease in systolic, diastolic, and mean arterial blood pressure, as well as heart rate, arterial stiffness, and spatial QRS-T. Additionally, it occurred due to increased NO availability, which resulted from eNOS expression as well as a decrease in iNOS and ACE expression.
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Stepanov, Vladimir S. "Assessing SARS-CoV-2-related mortality rate in Russian regions, based on the econometric model." Russian Journal of Infection and Immunity 12, no. 4 (September 9, 2022): 783–89. http://dx.doi.org/10.15789/2220-7619-asr-1846.
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The objects of the study were the daily data on the population morbidity and mortality due to coronavirus disease 2019 (COVID-19) in Russian regions, as well as regional medical, demographic and environmental data recorded in recent years. COVID-19 is a contagious disease caused by the novel coronavirus (SARS-CoV-2). The mathematical methods consist of correlation and regression analysis, methods of testing statistical hypotheses. First, a multiple Variable Structure Regression should be specified. The intercept in the model differs from region to region, depending on the combination of values for dummy variables. The role of the dependent variable Y t was chosen as the cumulative mortality published by the operational headquarters for the regions that has been linked to day t, so that COVID-19 was considered the main cause of death. The complex of explanatory variables included two factorial variables that changed daily, and had a lag relative to t value. Also, this complex included a number of variables that did not change with the growth of t: the explanatory variable with the regions availability with doctors of certain specialties; and four dummy variables. One of them coded the regions belonging to the two southern Russian Federal Districts. Three other variables characterized the increased air pollution in settlements recorded in recent years, as well as the level of radiation pollution of the regions territory and the population health estimated for 10 classes of diseases (for the circulatory system, endocrine system, etc.). The values of such dummy variables were obtained from open data from the Federal State Statistics Service (Rosstat) etc. The model parameters were estimated by the least squares method using the training table, which included 40 Russias regions, the t parameter for variable Y t was assessed starting from November, 1, 2021. As a result, a statistical model was built with an approximation error equal to 3%. For regions of the regions examined this error was 1.94 (1.5)% for the value Y t that has been fixed on the 1st Nov. The plots show daily prediction for mortality rate due to COVID-19 in the first half of November for seven Russian regions compared with actual data. The model can be useful in development of medical and demographic policy in geographic regions, as well as generating adjusted compartment models that based on systems of differential equations (SEIRF, SIRD, etc.).
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Yoo, Woo Sik, Kitaek Kang, Jung Gon Kim, and Yeongsik Yoo. "Image-Based Quantification of Color and Its Machine Vision and Offline Applications." Technologies 11, no. 2 (March 29, 2023): 49. http://dx.doi.org/10.3390/technologies11020049.
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Image-based colorimetry has been gaining relevance due to the wide availability of smart phones with image sensors and increasing computational power. The low cost and portable designs with user-friendly interfaces, and their compatibility with data acquisition and processing, are very attractive for interdisciplinary applications from art, the fashion industry, food science, medical science, oriental medicine, agriculture, geology, chemistry, biology, material science, environmental engineering, and many other applications. This work describes the image-based quantification of color and its machine vision and offline applications in interdisciplinary fields using specifically developed image analysis software. Examples of color information extraction from a single pixel to predetermined sizes/shapes of areas, including customized regions of interest (ROIs) from various digital images of dyed T-shirts, tongues, and assays, are demonstrated. Corresponding RGB, HSV, CIELAB, Munsell color, and hexadecimal color codes, from a single pixel to ROIs, are extracted for machine vision and offline applications in various fields. Histograms and statistical analyses of colors from a single pixel to ROIs are successfully demonstrated. Reliable image-based quantification of color, in a wide range of potential applications, is proposed and the validity is verified using color quantification examples in various fields of applications. The objectivity of color-based diagnosis, judgment and control can be significantly improved by the image-based quantification of color proposed in this study.
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Wallace, Erik A., Julie E. Miller-Cribbs, and F. Daniel Duffy. "An Experiential Community Orientation to Improve Knowledge and Assess Resident Attitudes Toward Poor Patients." Journal of Graduate Medical Education 5, no. 1 (March 1, 2013): 119–24. http://dx.doi.org/10.4300/jgme-d-12-00015.1.
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Abstract Background Future physicians may not be prepared for the challenges of caring for the growing population of poor patients in this country. Given the potential for a socioeconomic “gulf” between physicians and patients and the lack of curricula that address the specific needs of poor patients, resident knowledge about caring for this underserved population is low. Intervention We created a 2-day Resident Academy orientation, before the start of residency training, to improve community knowledge and address resident attitudes toward poor patients through team-based experiential activities. We collected demographic and satisfaction data through anonymous presurvey and postsurvey t tests, and descriptive analysis of the quantitative data were conducted. Qualitative comments from open-ended questions were reviewed, coded, and divided into themes. We also offer information on the cost and replicability of the Academy. Results Residents rated most components of the Academy as “very good” or “excellent.” Satisfaction scores were higher among residents in primary care training programs than among residents in nonprimary care programs for most Academy elements. Qualitative data demonstrated an overall positive effect on resident knowledge and attitudes about community resource availability for underserved patients, and the challenges of poor patients to access high-quality health care. Conclusions The Resident Academy orientation improved knowledge and attitudes of new residents before the start of residency, and residents were satisfied with the experience. The commitment of institutional leaders is essential for success.
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Liu, Tongxin, Guobin Yang, Zhengyu Zhao, Yi Liu, Chen Zhou, Chunhua Jiang, Binbin Ni, Yaogai Hu, and Peng Zhu. "Design of Multifunctional Mesosphere-Ionosphere Sounding System and Preliminary Results." Sensors 20, no. 9 (May 7, 2020): 2664. http://dx.doi.org/10.3390/s20092664.
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This paper describes a novel sounding system for which the functions of the medium frequency (MF) radar and the ionosonde are integrated on the same hardware platform and antenna structure, namely the middle atmosphere-ionosphere (MAI) system. Unlike the common MF radar, MAI system adopts the pseudo-random (PRN) phase-coded modulation technology, which breaks the limitation of the traditional monopulse mode. Through the pulse compression, only a small peak power is needed to achieve the signal-to-noise ratio (SNR) requirement. The excellent anti-jamming performance is also very suitable for the ionospheric sounding. One transmitting and six receiving modes are adopted for the MF sounding. While neglecting the structure of the T/R switches, the coupling interference between the transmitter and the receiver may also be avoided. Moreover, by employing a miniaturized antenna array composed of progressive-wave antennas for the MF receiving and ionospheric sounding, the MAI system takes account of the requirements of the inversion algorithms of MF radar and the large bandwidth need for the ionospheric sounding concurrently. Such an antenna structure can also greatly simplify the system structure and minimize the difficulty of deployment. The experiments verified the availability of the system scheme and its engineering application significance. Through further analysis of the sounding data, the wind field of the mesosphere, the electron density of D layer and electron density profile from layers E to F were obtained at the identical location. The capability of MAI system can play an important role in studying the interaction and coupling mechanism between the mesosphere and ionosphere.
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AlTaiar, Abdul Rahman Saad. "Factors affecting on the use of E-Commerce from the Perspective of Saudi Consumers." مجلة العلوم التربوية و الدراسات الإنسانية 4, no. 9 (April 11, 2020): 361–85. http://dx.doi.org/10.55074/hesj.v4i9.121.
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The study aimed to identify the factors affecting the practice of e-commerce from the perspective of Saudi consumer, and the impact (technical infrastructure, and environmental legislation, culture, and skills of human resources) on the use of e-commerce.The study adopted the descriptive survey methodology in order to describe these factors. The target population of t this research is Al-Baha Region at kingdom of Saudi Arabia. The researcher designed and distributed 320 questionnaire forms and excluded 70 forms due to the lack of information which means overall sample is 250. The data for the study was collected at 2017-2018. The data collected were edited, coded and processed with the Statistical Package for Science Solutions (SPSS), and discussed in narrative style for clarity and better understanding.
The arithmetic mean general of the level of availability of the factors affecting combined was average, amounting to (3.25), and the results showed the presence of significant effect of the variables of independent factors (environmental (legislation), environmental (culture), and factors related to the skills of human resources) in the use of e-commerce with Saudi companies from the viewpoint of Saudi consumer. Based on the results of the study recommended the study: the development and drafting of legislation and appropriate laws, develop the technical infrastructure, developing the skills of human resources, increasing the information awareness of Saudi society.
Finally, E-commerce practices at kingdom of Saudi Arabia is good, however the continuous improvement for all factors affecting on e-commerce practices is required to activate its practices in an effective way.
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Forte, Alaya. "Pious Practice and Secular Constraints." American Journal of Islam and Society 33, no. 2 (April 1, 2016): 118–21. http://dx.doi.org/10.35632/ajis.v33i2.910.
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A research study grounded in both anthropology and ethnography, the aim ofJeanette S. Jouili’s Pious Practice and Secular Constraints: Women in the IslamicRevival in Europe is threefold: (1) to explore how women cultivate Islamicsubjectivities in secular European contexts that stigmatize and politicizesuch religious practices; (2) reveal the practical and discursive techniques theyhave devised to deal with the difficulties that emerge from engaging in piouspractices; and, finally, (3) attempts to show how living as a religious minorityin a secular-majority society can reshape traditional Islamic discourse and providean alternative to the dominant language of autonomy, individual rights,and equality. Since the early 2000s, Jouili has come into contact with a widerange of practicing Muslimahs attending courses in various Islamic centersof learning, specifically in Paris and the region around Cologne. These centersare distinctive for their willingness to explore a multiplicity of doctrinal lineagesand attempt to transcend cultural and ethnic traditions.In the case of this most recent publication, there is the added value of amuch-needed overview of pious women who have been active in Islamic revivalcircles in Europe, together with perceptive insights into their daily lives.This book, therefore, contributes to a high-profile body of work by Talal Asad(1993, 2003), Saba Mahmood (2005), and Charles Hirschkind (2006) aroundethics and ethical self-cultivation, which explores contextual power relationsat play in the construction of religious discourses and practices, as well as ArmandoSalvatore’s work on the public sphere (2007). Jouili’s findings shedlight on the incompleteness and unlinearity of these Islamic moral codes, aswell as demonstrate how “[t]he individual’s work on herself [is] significantlyand long-lastingly complicated by prior habits and by the availability of othersets of moral codes” (p. 15).Drawing on Aristotelian ethics, with its insistence on practice rather thanreason, and Pierre Bourdieu’s concept of habitus, Jouili investigates how theembodied/practical ethical process molds an Islamic modernity within a secularEuropean context (chapter 1). The subsequent chapters provide an indepthstudy of these practices, which are aimed at strengthening through theinternalization of an “authenticated” knowledge of Islam learned within formalsettings (chapter 2) and the specific techniques of self-cultivation, specifically118 The American Journal of Islamic Social Sciences 33:2Book ...
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Neil Sharma, Aakriti Bhatnagar, S. Vasudev, and Anamika Kohli. "A Cross-Sectional Study to Assess Awareness and Practices Related to Prevention of COVID-19 Amongst Local Vendors around Medical and Dental Establishments." International Healthcare Research Journal 5, no. 9 (December 28, 2021): OR1—OR4. http://dx.doi.org/10.26440/ihrj/0509.12447.
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INTRODUCTION: Even as the world is returning to normalcy after COVID-19, there is still a need to be cautious and adopt proper hygiene practices and social distance norms. AIM: To assess the awareness and practices related to prevention of Covid-19 amongst local vendors around medical and dental establishments in Northern India. MATERIALS AND METHOD: This cross-sectional study was conducted over a period of one month using a pre-tested and pre-validated questionnaire. Vendors near ten medical and dental establishments in north India were contacted by standardized volunteers to prevent bias. They were located within the range of 250 meters on both sides of these facilities through convenience sampling. Data was coded, entered in MS excel, descriptive statistics were applied. Statistical tests included the student’s independent t-test and multiple logistic regression. P value was kept significant at <0.5 and software used was SPSS version 23.0. RESULTS: Most vendors were males (76.7%), were operating shops on rent (47.7%) and had passed middle school (40.2%). A Majority of them were aware of common symptoms (99.4%), while 90.1% were aware about the mode of transmission. All vendors knew about the availability of the vaccine (100%). and 78.2% of the vendors were fully vaccinated, while 04 (1.3%) were not vaccinated yet. However, only 60% (p=0.03) of the vendors practised hand washing, distancing from sick, no handshake, use a cloth while coughing/sneezing as preventive measures. CONCLUSION: There is still a need for continuous education of the food vendors regarding proper and hygienic practices as well as mask wearing to fight off this dreaded pandemic and return to normalcy as soon as possible.
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Bibi, Shabana, Dong Wang, Yuanbing Wang, Ghazala Mustafa, and Hong Yu. "Mitogenomic and Phylogenetic Analysis of the Entomopathogenic Fungus Ophiocordyceps lanpingensis and Comparative Analysis with Other Ophiocordyceps Species." Genes 14, no. 3 (March 14, 2023): 710. http://dx.doi.org/10.3390/genes14030710.
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Ophiocordyceps lanpingensis (O. lanpingensis) belongs to the genus Ophiocordyceps, which is often found in Yunnan Province, China. This species is pharmacologically important for the treatment of renal disorders induced by oxidative stress and an inadequate immune response. In the present study, the mitogenome of O. lanpingensis was determined to be a circular molecule 117,560 bp in length, and to have 31% G + C content and 69% A + T content. This mitogenome comprised 82% of the whole genome that codes for significant genes. The protein-coding regions of the O. lanpingensis mitogenome, containing 24 protein-coding genes, were associated with respiratory chain complexes, such as 3 ATP-synthase complex F0 subunits (atp6, atp8, and atp9), 2 complex IV subunits/cytochrome c oxidases (cox2 and cox3), 1 complex III subunit (cob), 4 electron transport complex I subunits/NADH dehydrogenase complex subunits (nad1, nad4, nad5, and nad6), 2 ribosomal RNAs (rns, rnl), and 11 hypothetical/predicted proteins, i.e., orf609, orf495, orf815, orf47, orf150, orf147, orf292, orf127, orf349, orf452, and orf100. It was noted that all genes were positioned on the same strand. Further, 13 mitochondrial genes with respiratory chain complexes, which presented maximum similarity with other fungal species of Ophiocordyceps, were investigated. O. lanpingensis was compared with previously sequenced species within Ophiocordycepitaceae. Comparative analysis indicated that O. lanpingensis was more closely related to O. sinensis, which is one of the most remarkable and expensive herbs due to its limited availability and the fact that it is difficult to culture. Therefore, O. lanpingensis is an important medicinal resource that can be effectively used for medicinal purposes. More extensive metabolomics research is recommended for O. lanpingensis.
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Aung, Fleur M., Roland Bassett, Benjamin Lichtiger, and Emil J. Freireich. "Comparison of Two Apheresis Instruments (Old vs. New) for Granulocyte Collection: A Single Institutional Experience." Blood 128, no. 22 (December 2, 2016): 5036. http://dx.doi.org/10.1182/blood.v128.22.5036.5036.
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Abstract Background: A retrospective analysis was performed to evaluate the collection efficiency of two apheresis devices for granulocytes using the Spectra Optia (TerumoBCT) vs. the Cobe Spectra (Cobe: TerumoBCT) which served as control. Study Design and Methods: A total of 410 granulocyte collections (GCs) were collected from volunteer healthy blood donors (<4%) and family and friends of severely neutropenic oncology patients requiring GCs from July 2014 to November 2015. All healthy male and females donors eligible to donate blood with peripheral venous access were allowed to donate granulocytes after first undergoing Platelet Apheresis with very few exceptions. This was performed to evaluate the donor's ability to undergo a lengthy apheresis procedure. All first time donors were mobilized with G-CSF (600/480 mcg) and/or Dexamethasone 8 mg 12 hours prior to the apheresis. Both instruments were primed with acid citrate-dextrose (ACD-A) and then changed to a coagulation buffer of a 500 mL bag of 6% hydroxyethyl starch (HES) to which 40 mL of trisodium citrate 46.7% was added. The maximum allowed time for the apheresis procedures on both devices was 3 hours. 186 consecutive GCs were performed using the Spectra Optia from March to November 2015 vs. 224 consecutive GCs using the Cobe Spectra device from July 2014 to March 2015 and served as control. The GCs were transfused to both adult and pediatric patients. GC products greater than 500 mL were divided into double/triple or quadruple units based on the total white count of the unit. Hematopoietic stem cell transplant and pediatric patients received irradiated GCs whereas leukemia patients received non-irradiated GCs. Statustical Method: All statistical analysis were performed using R version 3.3.0. The Wilcoxon rank-sum test was used to compare continuous variables between the Spectra Optia and Cobe Spectra. All statistical tests used a significance level of 5%. No adjustments for multiple donations were made. The table summarizes characteristics by group [ Cobe Spectra (COBE) vs. Spectra Optia (SPECTRA)]. The table presents for each variable, by group, the number of patients, the minimum ("Min") and maximum ("Max") values, the quartiles ("q1" and "q2"), the median, mean and the standard deviation ("SD"), along with the number of missing values ("#NA"), if any. For each parameter, there is also a p-value corresponding to a Wilcoxson rank-sum test. Results: From a total of 186 Spectra Optia granulocytapheresis we were able to process and obtain 433 GC units (21 single, 90 double, 72 triple and 4 quadruple units) as compared to the Cobe Spectra where 224 granulocytapheresis yielded 393 GC units (single 85, double 109 and 30 triple units). All of the split/unspilt GCs from both apheresis devices had a minimum wbc count > 1.0 x 10e10. We found the following parameters - total blood volume processed, totall WBC collected, run time, bag wbc, absolute neutrophil count, absolute lymphocyte count, granulocyte collection efficiency, post-stimulation platelet count, absolute platelet count, MPV and number of GCs split were significantly higher ( p = <0.0001) using the fully automated Spectra Optia while volume collected, hematocrit, bag platelets and platelet collection efficiency were significantly higher ( p=<0.0001) using the Cobe Spectra. The age of the Cobe Spectra patients were older on average (p=0.00015) (Table) The weight, height, pre- and post stimulation WBC and pre-stimulation platelet counts of the donors were of no significance. (Table) Conclusion: The ability to achieve higher granulocyte counts per liter of blood processed with a higher granulocyte CE using the fully automated Spectra Optia has allowed us to process and split Granulocyte Units leading to the availability of multiple units thus easing some of the Granulocyte shortages that our severely neutropenic oncology patients currently experience. ReferenceCancelas JA, Padmanabhan A, Le T et al. Spectra Optia granulocyte apheresis collections results in higher collection efficiency of viable, functional neutrophils in a randomized crossover, multicenter trial. Transfusion; 2015; 55: 751-55Leitner GC, Kolovratova K, Horvath M et al. Granulocyte collection using a novel apheresis system eases the procedure and provides concentrates of high quality. Transfusion 2015; 55: 991-5 Table Characteristics by Group Table. Characteristics by Group Disclosures No relevant conflicts of interest to declare.
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Gálvez, David Morillón, Iván García Kerdan, and Germán Carmona-Paredes. "Assessing the Potential of Implementing a Solar-Based Distributed Energy System for a University Using the Campus Bus Stops." Energies 15, no. 10 (May 17, 2022): 3660. http://dx.doi.org/10.3390/en15103660.
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Large educational facilities hold great potential for the implementation of solar-based distributed energy systems. The aim of this paper is to present a prototype and an assessment of a solar-based bus shelter photovoltaic system intended to be implemented at a campus scale that serves as an energy-distributed system. The National Autonomous University of Mexico (UNAM), a campus with an area of 7.3 km2 and bus stops’ roof area availability of around 1100 m2 was selected as a case study. The proposed system, apart from considering on-site generation, also considers an increase in end-use services such as the installation of television screens for information, charging docks, surveillance cameras, internet service, and lighting. For the assessment, a load facility survey and an estimation of the baseline energy use was conducted based on two demand use conditions, corresponding to 12 and 24 h for different archetypical stations. It was found that the baseline annual energy consumption for all the bus stops represents from 55–111 MWh. In this paper, an initial prototype of a solar-based bus shelter PV system is presented, and an assessment is carried out to understand its potential application at a large scale. The analysis shows that energy use in the retrofitted stations would rise to 167 MWh/year; however, apart from covering on-site demand, the system has the capacity to generate an additional 175 MWh, feeding nearby university buildings. It is calculated that the system could save around 130 t CO2e annually. The economic analysis shows that the project has a discounted payback (DPB) of almost 9 years and an internal rate of return (IRR) of 5.9%; however, in scenarios where renewable generation and carbon incentives are applied, this improves the project’s DPB to 6 years and the IRR to 13%.
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Gershwin, M. E., I. R. Mackay, A. Sturgess, and R. L. Coppel. "Identification and specificity of a cDNA encoding the 70 kd mitochondrial antigen recognized in primary biliary cirrhosis." Journal of Immunology 138, no. 10 (May 15, 1987): 3525–31. http://dx.doi.org/10.4049/jimmunol.138.10.3525.
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Abstract Mitochondrial autoantibodies are characteristic of the disease primary biliary cirrhosis (PBC), but the immunoreactive mitochondrial antigens have not been defined. We used a rat liver cDNA library in lambda gt 11-Amp3 to clone a 1370-base pair insert that coded for a polypeptide reactive with PBC sera. This insert was subcloned for expression into pBTA224, a plasmid vector in the same reading frame as lambda-Amp3. A positive clone, designated pRMIT, that expressed a fused polypeptide of 160 kd, was recognized by 25 of 25 sera from patients with PBC and none of 96 sera from normal persons or patients with systemic lupus erythematosus, rheumatoid arthritis, or chronic active hepatitis. This fused polypeptide was shown to correspond with the 70 kd mitochondrial autoantigen by several experiments. First, lysates of pRMIT in J101 absorbed out the 70 kd reactivity of PBC sera when probed against fractionated placental mitochondria. Second, affinity-purified antisera reactive with the fused polypeptide also reacted with the 70 kd mitochondrial antigen. Third, such affinity-purified antisera produced the characteristic anti-mitochondrial pattern of immunofluorescence on tissue sections. Finally, immunization of BALB/c mice with the fused polypeptide elicited antibodies to mitochondria. These murine antibodies reacted with the 70 kd mitochondrial protein and also produced typical mitochondrial immunofluorescence on tissue sections. The nucleotide and amino acid sequence of the recombinant protein, which encodes for approximately a 48 kd protein, showed no significant homologies with known proteins, and there were no homologies with mitochondrial genomic DNA. The availability of a recombinant form of the 70 kd mitochondrial autoantigen will allow several definitive questions to be addressed in PBC, including identification of B cell epitopes, T cell recognition, and a model of PBC in mice.