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Wang, Rongcun, Rubing Huang, Yansheng Lu, and Binbin Qu. "Clustering Analysis of Function Call Sequence for Regression Test Case Reduction." International Journal of Software Engineering and Knowledge Engineering 24, no. 08 (October 2014): 1197–223. http://dx.doi.org/10.1142/s0218194014500387.
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Regression test case reduction aims at selecting a representative subset from the original test pool, while retaining the largest possible fault detection capability. Cluster analysis has been proposed and applied for selecting an effective test case subset in regression testing. It groups test cases into clusters based on the similarity of historical execution profiles. In previous studies, historical execution profiles are represented as binary or numeric function coverage vectors. The vector-based similarity approaches only consider which functions or statements are covered and the number of times they are executed. However, the vector-based approaches do not take the relations and sequential information between function calls into account. In this paper, we propose cluster analysis of function call sequences to attempt to improve the fault detection effectiveness of regression testing even further. A test is represented as a function call sequence that includes the relations and sequential information between function calls. The distance between function call sequences is measured not only by the Levenshtein distance but also the Euclidean distance. To assess the effectiveness of our approaches, we designed and conducted experimental studies on five subject programs. The experimental results indicate that our approaches are statistically superior to the approaches based on the similarity of vectors (i.e. binary vectors and numeric vectors), random and greedy function-coverage-based maximization test case reduction techniques in terms of fault detection effectiveness. With respective to the cost-effectiveness, cluster analysis of sequences measured using the Euclidean distance is more effective than using the Levenshtein distance.
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Fleury, Cécile, Jérôme Gracy, Marie-Françoise Gautier, Jean-Luc Pons, Jean-François Dufayard, Gilles Labesse, Manuel Ruiz, and Frédéric de Lamotte. "Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence–structure–function analysis." PeerJ 7 (August 14, 2019): e7504. http://dx.doi.org/10.7717/peerj.7504.
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Background Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences—and counting—have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence–structure–function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach. Methods In this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure–function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees. Results Following this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function.
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Zhang, Bing, Chun Shan, Munawar Hussain, Jiadong Ren, and Guoyan Huang. "Software Crucial Functions Ranking and Detection in Dynamic Execution Sequence Patterns." International Journal of Software Engineering and Knowledge Engineering 30, no. 05 (May 2020): 695–719. http://dx.doi.org/10.1142/s0218194020500254.
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Because of the sequence and number of calls of functions, software network cannot reflect the real execution of software. Thus, to detect crucial functions (DCF) based on software network is controversial. To address this issue, from the viewpoint of software dynamic execution, a novel approach to DCF is proposed in this paper. It firstly models, the dynamic execution process as an execution sequence by taking functions as nodes and tracing the stack changes occurring. Second, an algorithm for deleting repetitive patterns is designed to simplify execution sequence and construct software sequence pattern sets. Third, the crucial function detection algorithm is presented to identify the distribution law of the numbers of patterns at different levels and rank those functions so as to generate a decision-function-ranking-list (DFRL) by occurrence times. Finally, top-k discriminative functions in DFRL are chosen as crucial functions, and similarity the index of decision function sets is set up. Comparing with the results from Degree Centrality Ranking and Betweenness Centrality Ranking approaches, our approach can increase the node coverage to 80%, which is proven to be an effective and accurate one by combining advantages of the two classic algorithms in the experiments of different test cases on four open source software. The monitoring and protection on crucial functions can help increase the efficiency of software testing, strength software reliability and reduce software costs.
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Sievert, Volker, Sylvia Kuhn, Achim Paululat, and Walther Traut. "Sequence conservation and expression of the Sex-lethal homologue in the fly Megaselia scalaris." Genome 43, no. 2 (March 15, 2000): 382–90. http://dx.doi.org/10.1139/g99-132.
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Sex-lethal (Sxl) is Drosophila melanogaster's key regulating gene in the sex-determining cascade. Its homologue in Megaselia scalaris, the chromosome 3 gene Megsxl, codes for a protein with an overall similarity of 77% with the corresponding D. melanogaster sequence. Expression in M. scalaris, however, is very unlike that in D. melanogaster. Megsxl transcripts with a long ORF occur in both sexes. Differential splicing is conserved but not sex-specific. There are several splice variants, among them one is common to gonads and somatic tissues of all developmental stages investigated, one is specific for ovaries and embryos, and a third one is not found in ovaries. In the ovary, Megsxl is heavily transcribed in nurse cells and transported into eggs. These results suggest a non-sex-determining function during early embryogenesis; the presence of Megsxl RNA in testes and somatic tissues calls for other (or more) functions. Key words: sex determination, RNA-binding domain, differential splicing, RNA in situ hybridization.
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Hansen, Per Krogh. "Tiden ødelægger alt. Om episodisk bagvendte fortællinger illustreret ved hjælp af Gaspar Noés Irréversible." K&K - Kultur og Klasse 39, no. 112 (December 25, 2011): 93–106. http://dx.doi.org/10.7146/kok.v39i112.15746.
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TIME DESTROYS EVERYTHING | This article focuses on what Seymour Chatman calls ‘sustained episodic reversal’ of narrative progressionR– that is, narratives in which the sequential, chronological order of the events is reversed and thereby ‘de-’ or ‘unnaturalized’. The article opens with a short discussion of the project of ‘unnatural narratology,’ and it is claimed that if our experience of a given narrative as ‘natural’ is grounded on its confirmation of the conventions for the mode or genre the narrative belongs to, then the task for an ‘unnatural narratology’ is to investigate the exceptions, that is, cases where conventions are broken and perhaps reformulated. Sustained episodic reversals of event sequences belong to this field of interest insofar as one of the basic features of ‘natural narrative’ is that the sequence of clauses (or more generally, the sjuzhet or discourse) is typically matched to the sequence of the events being narrated (the fabulaor story). The denaturalizing function and effect of the sustained reversal is illustrated through analysis of Gaspar Noé’s Irréversible (2002). It is shown that the reversal has radical consequencesfor the spectator’s (re)construction of the narrative’s fabula, and that it engages the reader in a game of post hoc ergo propter hoc and of narrative construction and deconstruction.
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Nissen, P. E., J. Christensen-Dalsgaard, J. R. Mosumgaard, V. Silva Aguirre, E. Spitoni, and K. Verma. "High-precision abundances of elements in solar-type stars." Astronomy & Astrophysics 640 (August 2020): A81. http://dx.doi.org/10.1051/0004-6361/202038300.
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Aims. Previous high-precision studies of abundances of elements in solar twin stars are extended to a wider metallicity range to see how the trends of element ratios with stellar age depend on [Fe/H]. Methods. HARPS spectra with signal-to-noise ratios S/N ≳ 600 at λ ∼ 6000 Å were analysed with MARCS model atmospheres to obtain 1D LTE abundances of C, O, Na, Mg, Al, Si, Ca, Ti, Cr, Fe, Ni, Sr, and Y for 72 nearby solar-type stars with metallicities in the range of −0.3 ≲ [Fe/H] ≲ +0.3 and ASTEC stellar models were used to determine stellar ages from effective temperatures, luminosities obtained via Gaia DR2 parallaxes, and heavy element abundances. Results. The age-metallicity distribution appears to consist of the following two distinct populations: a sequence of old stars with a steep rise of [Fe/H] to ∼ + 0.3 dex at an age of ∼7 Gyr and a younger sequence with [Fe/H] increasing from about −0.3 dex to ∼ + 0.2 dex over the last 6 Gyr. Furthermore, the trends of several abundance ratios, [O/Fe], [Na/Fe], [Ca/Fe], and [Ni/Fe], as a function of stellar age, split into two corresponding sequences. The [Y/Mg]-age relation, on the other hand, shows no offset between the two age sequences and has no significant dependence on [Fe/H], but the components of a visual binary star, ζ Reticuli, have a large and puzzling deviation. Conclusions. The split of the age-metallicity distribution into two sequences may be interpreted as evidence of two episodes of accretion of gas onto the Galactic disk with a quenching of star formation in between. Some of the [X/Fe]-age relations support this scenario but other relations are not so easy to explain, which calls for a deeper study of systematic errors in the derived abundances as a function of [Fe/H], in particular 3D non-LTE effects.
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Nie, Dan, and Yu Hui Wang. "Taint Graph of System Call Arguments for Intrusion Detection in Mobile Intelatrac." Advanced Materials Research 546-547 (July 2012): 1101–6. http://dx.doi.org/10.4028/www.scientific.net/amr.546-547.1101.
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The intended data-flow in a vulnerable program is subject to be subverted by attacks which exploit buffer overflows or format string vulnerabilities to write data to unintended location. In Mobile Telecommunication it is especially important on data safety. These attacks can be classified into two types: control-flow-attacks exploit buffer overflows or other vulnerabilities to overwrite a return address, a function pointer, or some other piece of control-data; non-control-data attacks exploit similar vulnerabilities to overwrite security critical data without subverting the intended control-flow in the program. The control-flow attacks are well studied and widely used, so there are several typical approaches to prevent them, which monitor the sequence of system calls emitted by the application being monitored and utilize control-flow information of the system calls for intrusion detection. However, the non-control-data attacks are rare for the reason that they rely on specific semantics of the target applications, and there are only few works that defend them to some extent. In order to prevent non-control-data attacks, we leverage dynamic taint technique to track the instruction level relationship between different system call arguments and construct taint graph which can represent behavior profile of a benign program in this paper..
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Chen, Hui, Zhengqiang Li, Qingshan Jiang, Abdur Rasool, and Lifei Chen. "A Hierarchical Approach for Android Malware Detection Using Authorization-Sensitive Features." Electronics 10, no. 4 (February 10, 2021): 432. http://dx.doi.org/10.3390/electronics10040432.
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Android’s openness has made it a favorite for consumers and developers alike, driving strong app consumption growth. Meanwhile, its popularity also attracts attackers’ attention. Android malware is continually raising issues for the user’s privacy and security. Hence, it is of great practical value to develop a scientific and versatile system for Android malware detection. This paper presents a hierarchical approach to design a malware detection system for Android. It extracts four authorization-sensitive features: basic blocks, permissions, Application Programming Interfaces (APIs), and key functions, and layer-by-layer detects malware based on the similar module and the proposed deep learning model Convolutional Neural Network and eXtreme Gradient Boosting (CNNXGB). This detection approach focuses not only on classification but also on the details of the similarities between malware software. We serialize the key function in light of the sequence of API calls and pick up a similar module that captures the global semantics of malware. We propose a new method to convert the basic block into a multichannel picture and use Convolutional Neural Network (CNN) to learn features. We extract permissions and API calls based on their called frequency and train the classification model by XGBoost. A dynamic similar module feature library is created based on the extracted features to assess the sample’s behavior. The model is trained by utilizing 11,327 Android samples collected from Github, Google Play, Fdroid, and VirusShare. Promising experimental results demonstrate a higher accuracy of the proposed approach and its potential to detect Android malware attacks and reduce Android users’ security risks.
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Han, Yongman, Jongcheon Choi, Seong-Je Cho, Haeyoung Yoo, Jinwoon Woo, Yunmook Nah, and Minkyu Park. "A new detection scheme of software copyright infringement using software birthmark on windows systems." Computer Science and Information Systems 11, no. 3 (2014): 1055–69. http://dx.doi.org/10.2298/csis130918064h.
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As software is getting more valuable, unauthorized users or malicious programmers illegally copies and distributes copyrighted software over online service provider (OSP) and P2P networks. To detect, block, and remove pirated software (illegal programs) on OSP and P2P networks, this paper proposes a new filtering approach using software birthmark, which is unique characteristics of program and can be used to identify each program. Software birthmark typically includes constant values, library information, sequence of function calls, and call graphs, etc. We target Microsoft Windows applications and utilize the numbers and names of DLLs and APIs stored in a Windows executable file. Using that information and each cryptographic hash value of the API sequence of programs, we construct software birthmark database. Whenever a program is uploaded or downloaded on OSP and P2P networks, we can identify the program by comparing software birthmark of the program with birthmarks in the database. It is possible to grasp to some extent whether software is an illegally copied one. The experiments show that the proposed software birthmark can effectively identify Windows applications. That is, our proposed technique can be employed to efficiently detect and block pirated programs on OSP and P2P networks.
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Yelensky, Roman, Kai Wang, Snjezana Dogan, Laetitia Borsu, Garrett Frampton, Doron Lipson, Philip Stephens, et al. "Next-generation sequencing of FFPE solid tumor specimens for clinical use." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 10524. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.10524.
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10524 Background: As more therapies targeting genomic alterations become available, genotyping (e.g., by Sequenom) is increasingly performed in tumor types where mutational status may drive treatment choice. Next-generation sequencing (NGS) technology can expand on genotyping of individual base pairs because it can detect mutations across entire exons, copy changes and fusion genes. However, for NGS to be clinically viable, it must be made compatible with FFPE tissues and shown concordant with best current diagnostic methods. Methods: To explore a potential clinical role for NGS, we selected 120 FFPE specimens (68 NSCLC, 32 CRC, 20 melanoma) previously tested for 97 oncogenic mutations in 8 oncogenes by Sequenom, and sequenced all exons of 182 cancer genes. Genotyping and sequencing were both performed in CLIA compliant labs. DNA was extracted from 4x 10μ unstained sections from the diagnostic FFPE block, followed by library construction and hybridization capture of 3230 exons and 37 commonly rearranged introns. Average coverage of >900X uniquely-mapping reads was obtained. Sequence data were analyzed for all genomic alterations and examined for potentially actionable mutations. Results: High concordance was noted between Sequenom and NGS: 103 and 105 mutations were called by the two technologies, respectively, at mutually tested sites, with 97 mutation calls in common. Notably, mutant allele frequencies in concordant calls ranged as low as 2% by NGS, highlighting the sensitivity of detection enabled by both approaches. Furthermore, in 45/120 (38%) specimens, NGS revealed additional alterations that may confer sensitivity or resistance to approved or experimental targeted therapies and thus plausibly influence treatment decisions. These included 39 copy changes or loss-of-function variants best assayed by an NGS approach. Conclusions: Our results demonstrate technical feasibility and highlight potential benefits of comprehensive cancer gene characterization through next-generation sequencing of clinical FFPE specimens. As NGS is the most practical means to detect all classes of somatic alteration in a small, clinically relevant sample, we suggest that this type of testing will become an essential component of patient care.
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Ganguly, Payel, Landiso Madonsela, Jesse T. Chao, Christopher J. R. Loewen, Timothy P. O’Connor, Esther M. Verheyen, and Douglas W. Allan. "A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation." PLOS Genetics 17, no. 9 (September 7, 2021): e1009774. http://dx.doi.org/10.1371/journal.pgen.1009774.
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Gene variant discovery is becoming routine, but it remains difficult to usefully interpret the functional consequence or disease relevance of most variants. To fill this interpretation gap, experimental assays of variant function are becoming common place. Yet, it remains challenging to make these assays reproducible, scalable to high numbers of variants, and capable of assessing defined gene-disease mechanism for clinical interpretation aligned to the ClinGen Sequence Variant Interpretation (SVI) Working Group guidelines for ‘well-established assays’. Drosophila melanogaster offers great potential as an assay platform, but was untested for high numbers of human variants adherent to these guidelines. Here, we wished to test the utility of Drosophila as a platform for scalable well-established assays. We took a genetic interaction approach to test the function of ~100 human PTEN variants in cancer-relevant suppression of PI3K/AKT signaling in cellular growth and proliferation. We validated the assay using biochemically characterized PTEN mutants as well as 23 total known pathogenic and benign PTEN variants, all of which the assay correctly assigned into predicted functional categories. Additionally, function calls for these variants correlated very well with our recent published data from a human cell line. Finally, using these pathogenic and benign variants to calibrate the assay, we could set readout thresholds for clinical interpretation of the pathogenicity of 70 other PTEN variants. Overall, we demonstrate that Drosophila offers a powerful assay platform for clinical variant interpretation, that can be used in conjunction with other well-established assays, to increase confidence in the accurate assessment of variant function and pathogenicity.
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lannacci, Federico. "Routines, Artefacts and Technological Change: Investigating the Transformation of Criminal Justice in England and Wales." Journal of Information Technology 29, no. 4 (December 2014): 294–311. http://dx.doi.org/10.1057/jit.2014.10.
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Organisational routines embed and are increasingly embedded within IT artefacts. In this paper, I challenge the conventional notion that warrants the primacy of human activities in the study of routines and bring artefacts in general and IT artefacts in particular to the very centre of my theorising. Through an in-depth case study of crown prosecutors’ work, I endeavour to explain the way legislative and IT artefacts are implicated in the transformation of police-prosecutor routines. I show that legislative artefacts play a constitutive role that generates a new role position and a new system of social practices while IT artefacts serve a regulative function that enforces a newly programmed sequence of steps onto pre-existing practices. I argue for the benefits of foregrounding legislative and IT artefacts to develop a nuanced account of organisational routines that responds to recent calls for research that contextualises the IT artefact outside single settings. I draw on the Transformational Model of Social Activity to unpack the causal linkages between legislative and IT artefacts. Theoretical and practical implications are discussed.
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Lamarque, Mauld, Pascale Charbonnel, Dominique Aubel, Jean-Christophe Piard, Danièle Atlan, and Vincent Juillard. "A Multifunction ABC Transporter (Opt) Contributes to Diversity of Peptide Uptake Specificity within the Genus Lactococcus." Journal of Bacteriology 186, no. 19 (October 1, 2004): 6492–500. http://dx.doi.org/10.1128/jb.186.19.6492-6500.2004.
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ABSTRACT Growth of Lactococcus lactis in milk depends on the utilization of extracellular peptides. Up to now, oligopeptide uptake was thought to be due only to the ABC transporter Opp. Nevertheless, analysis of several Opp-deficient L. lactis strains revealed the implication of a second oligopeptide ABC transporter, the so-called Opt system. Both transporters are expressed in wild-type strains such as L. lactis SK11 and Wg2, whereas the plasmid-free strains MG1363 and IL-1403 synthesize only Opp and Opt, respectively. The Opt system displays significant differences from the lactococcal Opp system, which made Opt much more closely related to the oligopeptide transporters of streptococci than to the lactococcal Opp system: (i) genetic organization, (ii) peptide uptake specificity, and (iii) presence of two oligopeptide-binding proteins, OptS and OptA. The fact that only OptA is required for nutrition calls into question the function of the second oligopeptide binding protein (Opts). Sequence analysis of oligopeptide-binding proteins from different bacteria prompted us to propose a classification of these proteins in three distinct groups, differentiated by the presence (or not) of precisely located extensions.
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Blasnig, M., B. Riedel, L. Schiemer, M. Zuschin, and M. Stachowitsch. "Short-term post-mortality scavenging and longer term recovery after anoxia in the northern Adriatic Sea." Biogeosciences 10, no. 11 (November 26, 2013): 7647–59. http://dx.doi.org/10.5194/bg-10-7647-2013.
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Abstract. The northern Adriatic Sea is one of nearly 500 areas worldwide suffering widespread mortalities due to anoxia. The present study documents post-anoxia macrofauna dynamics after experimentally inducing small-scale anoxia in 24 m depth (2 plots, each 50 cm × 50 cm). Time-lapse camera deployments examined short-term scavenging of the moribund and dead organisms (multi-species clumps consisting of sponges and ascidians) over two 3-day periods (August 2009: 71.5 h, September 2009: 67.5 h). Longer term recovery (days to 2 yr) in the same two plots was examined with an independent photo series. Scavengers arrived quickly and in a distinct sequence: demersal (Gobius niger, Serranus hepatus) and benthopelagic fishes (Diplodus vulgaris, Pagellus erythrinus), followed by hermit crabs (Paguristes eremita, showing a clear day/night rhythm in presence) and gastropods (Hexaplex trunculus). This sequence is attributed to the relative speeds and densities of the organisms. The sessile fauna was largely removed or consumed within seven (August plot) and 13 (September plot) days after anoxia, confirming our first hypothesis that decaying organisms are quickly utilised. The scavengers remained in dense aggregations (e.g. up to 33 P. eremita individuals at one time) as long as dead organisms were available. No recovery of sessile macroepibenthos macroepibenthos occurred in the experimental plots one and two years after anoxia, undermining our second hypothesis that small denuded areas are more rapidly recolonised. This study underlines the sensitivity of this soft-bottom community and supports calls for reducing additional anthropogenic disturbances such as fishing practices that further impede recolonisation and threaten benthic community structure and function over the long term.
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Blasnig, M., B. Riedel, M. Zuschin, L. Schiemer, and M. Stachowitsch. "Short-term post-mortality predation and scavenging and longer-term recovery after anoxia in the northern Adriatic Sea." Biogeosciences Discussions 10, no. 3 (March 7, 2013): 4367–401. http://dx.doi.org/10.5194/bgd-10-4367-2013.
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Abstract. In the Mediterranean, the northern Adriatic Sea shows most features known to promote late-summer hypoxia and anoxia. These features, along with anthropogenic eutrophication and marine snow events, have led to repeated benthic mortalities here. The present study was designed to document the post-anoxia macrofauna dynamics. We deployed an underwater instrument to induce small-scale anoxia in situ (total area 0.5 m2). Two time-lapse camera deployments examined short-term scavenging of the moribund and dead organisms (multi-species clumps consisting of sponges and ascidians) over a 3-day period (August 2008: 71.5 h, September 2008: 67.5 h). Longer-term recovery (2 yr) in the same two plots was examined with an independent photo-series. Predators and scavengers arrived in a distinct sequence. The first to arrive were demersal (Gobius niger, Serranus hepatus) and benthopelagic fishes (Diplodus vulgaris, Pagellus erythrinus), followed by hermit crabs (Paguristes eremita, showing a clear day/night rhythm in presence) and gastropods (Hexaplex trunculus). This sequence of arrival is attributed to the relative speeds of the organisms and their densities. The scavengers remained in dense aggregations (e.g. up to 33 P. eremita individuals at one time) as long as the dead organisms were available. The whole sessile fauna was largely removed or consumed within 7 (August plot) and 13 (September plot) days after anoxia. No macroepibenthic recovery took place in the experimental plots one and two years after anoxia. This study underlines the sensitivity of this soft-bottom community and supports calls for reducing additional anthropogenic disturbances such as damaging commercial fishing practices that impede recolonization and threaten benthic community structure and function over the long-term.
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Peisert, Sean, Matt Bishop, Sidney Karin, and Keith Marzullo. "Analysis of Computer Intrusions Using Sequences of Function Calls." IEEE Transactions on Dependable and Secure Computing 4, no. 2 (April 2007): 137–50. http://dx.doi.org/10.1109/tdsc.2007.1003.
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Secka, Ousman, Douglas E. Berg, Martin Antonio, Tumani Corrah, Mary Tapgun, Robert Walton, Vivat Thomas, et al. "Antimicrobial Susceptibility and Resistance Patterns among Helicobacter pylori Strains from The Gambia, West Africa." Antimicrobial Agents and Chemotherapy 57, no. 3 (December 21, 2012): 1231–37. http://dx.doi.org/10.1128/aac.00517-12.
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ABSTRACTHelicobacter pyloriis a globally important and genetically diverse gastric pathogen that infects most people in developing countries. Eradication efforts are complicated by antibiotic resistance, which varies in frequency geographically. There are very few data on resistance in African strains. Sixty-four GambianH. pyloristrains were tested for antibiotic susceptibility. The role ofrdxAin metronidazole (Mtz) susceptibility was tested by DNA transformation and sequencing; RdxA protein variants were interpreted in terms of RdxA structure. Forty-four strains (69%) were resistant to at least 8 μg of Mtz/ml. All six strains from infants, but only 24% of strains from adults, were sensitive (P= 0.0031). Representative Mtz-resistant (Mtzr) strains were rendered Mtz susceptible (Mtzs) by transformation with a functionalrdxAgene; conversely, Mtzsstrains were rendered MtzrbyrdxAinactivation. Many mutations were found by GambianH. pylorirdxAsequencing; mutations that probably inactivatedrdxAin Mtzrstrains were identified and explained using RdxA protein's structure. All of the strains were sensitive to clarithromycin and erythromycin. Amoxicillin and tetracycline resistance was rare. Sequence analysis indicated that most tetracycline resistance, when found, was not due to 16S rRNA gene mutations. These data suggest caution in the use of Mtz-based therapies in The Gambia. The increasing use of macrolides against respiratory infections in The Gambia calls for continued antibiotic susceptibility monitoring. The rich variety ofrdxAmutations that we found will be useful in further structure-function studies of RdxA, the enzyme responsible for Mtz susceptibility in this important pathogen.
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Manrique, Amapola, Peter Rusert, Beda Joos, Marek Fischer, Herbert Kuster, Christine Leemann, Barbara Niederöst, et al. "In Vivo and In Vitro Escape from Neutralizing Antibodies 2G12, 2F5, and 4E10." Journal of Virology 81, no. 16 (June 13, 2007): 8793–808. http://dx.doi.org/10.1128/jvi.00598-07.
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ABSTRACT Recently, passive immunization of human immunodeficiency virus (HIV)-infected individuals with monoclonal antibodies (MAbs) 2G12, 2F5, and 4E10 provided evidence of the in vivo activity of 2G12 but raised concerns about the function of the two membrane-proximal external region (MPER)-specific MAbs (A. Trkola, H. Kuster, P. Rusert, B. Joos, M. Fischer, C. Leemann, A. Manrique, M. Huber, M. Rehr, A. Oxenius, R. Weber, G. Stiegler, B. Vcelar, H. Katinger, L. Aceto, and H. F. Gunthard, Nat. Med. 11:615-622, 2005). In the light of MPER-targeting vaccines under development, we performed an in-depth analysis of the emergence of mutations conferring resistance to these three MAbs to further elucidate their activity. Clonal analysis of the MPER of plasma virus samples derived during antibody treatment confirmed that no changes in this region had occurred in vivo. Sequence analysis of the 2G12 epitope relevant N-glycosylation sites of viruses derived from 13 patients during the trial supported the phenotypic evaluation, demonstrating that mutations in these sites are associated with resistance. In vitro selection experiments with isolates of four of these individuals corroborated the in vivo finding that virus strains rapidly escape 2G12 pressure. Notably, in vitro resistance mutations differed, in most cases, from those found in vivo. Importantly, in vitro selection with 2F5 and 4E10 demonstrated that resistance to these MAbs can be difficult to achieve and can lead to selection of variants with impaired infectivity. This remarkable vulnerability of the virus to interference within the MPER calls for a further evaluation of the safety and efficacy of MPER-targeting therapeutic and vaccination strategies.
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Rensink, Willem, Amy Hart, Jia Liu, Shu Ouyang, Victoria Zismann, and C. Robin Buell. "Analyzing the potato abiotic stress transcriptome using expressed sequence tags." Genome 48, no. 4 (August 1, 2005): 598–605. http://dx.doi.org/10.1139/g05-034.
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To further increase our understanding of responses in potato to abiotic stress and the potato transcriptome in general, we generated 20 756 expressed sequence tags (ESTs) from a cDNA library constructed by pooling mRNA from heat-, cold-, salt-, and drought-stressed potato leaves and roots. These ESTs were clustered and assembled into a collection of 5240 unique sequences with 3344 contigs and 1896 singleton ESTs. Assignment of gene ontology terms (GOSlim/Plant) to the sequences revealed that 8101 assignments could be made with a total of 3863 molecular function assignments. Alignment to a set of 78 825 ESTs from other potato cDNA libraries derived from root, leaf, stolon, tuber, germinating eye, and callus tissues revealed 1476 sequences unique to abiotic stressed potato leaf and root tissue. Sequences present within the 5240 sequence set had similarity to genes known to be involved in abiotic stress responses in other plant species such as transcription factors, stress response genes, and signal transduction processes. In addition, we identified a number of genes unique to the abiotic stress library with unknown function, providing new candidate genes for investigation of abiotic stress responses in potato.Key words: potato, Solanacaeae, abiotic stress.
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Durairaj, Janani, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, and Aalt D. J. van Dijk. "Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases." PLOS Computational Biology 17, no. 3 (March 22, 2021): e1008197. http://dx.doi.org/10.1371/journal.pcbi.1008197.
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Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs from Citrus bergamia.
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Forester, Don C., and W. Keith Harrison. "The Significance of Antiphonal Vocalisation By the Spring Peeper, Pseudacris Crucifer (Amphibia, Anura)." Behaviour 103, no. 1-3 (1987): 1–15. http://dx.doi.org/10.1163/156853987x00233.
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Abstract1. Male spring peepers respond to acoustic interference from an encroaching conspecific with a graded behavioral sequence: they increase their call repetition rate, they emit one or more encounter calls, they entrain their calls to those of the intruder. 2. Once entrained, males continue to call synchronously for extended periods. 3. The time interval between the end of the leader's call and the beginning of the follower's call (the intraduet interval) is consistent, and is maintained despite changes in the duration or repetition rate of the leader's call. 4. Our data corroborate earlier investigators who concluded that the follower is stimulated by the onset of the leader's call, but is inhibited from calling until a fixed time interval after the leader has ceased calling. 5. Controlled discrimination tests reveal no differential mating success by the leader or the follower within a simulated duet. 6. Females exhibited a significant preference for a duet over a soloing male. 7. Although test females were able distinguish between the simultaneous broadcast of two phase-locked call sequences differing only in frequency, they did so in the absence of alternative, uncovered calls. 8. We conclude that antiphonal vocalisation functions primarily to reduce the potential for broadcast interference during the initial phase of female phonotaxis.
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Zwamborn, Elizabeth M. J., and Hal Whitehead. "The baroque potheads: modification and embellishment in repeated call sequences of long-finned pilot whales." Behaviour 154, no. 9-10 (2017): 963–79. http://dx.doi.org/10.1163/1568539x-00003451.
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Vocal variation within calls that are generally stereotyped suggests multiple simultaneous functions. These vocal cues may be especially important for group-living species. We describe two fundamental call transition types within repeated call sequences of long-finned pilot whales (Globicephala melas): embellishment — discrete changes to a specific part of a call — and morphing — non-discrete small changes across a call. Of transitions between consecutive calls, 31% were embellished and 20% morphed. Modifications between pairs of consecutive calls were often followed by another modification of the same type, with sequences of embellished transitions generally alternating between ornamentation and simplification. Ten classes of embellishment varied in rate of occurrence as well as temporal location within a call. Most common were the addition/deletion of pulsed or tonal elements. Functions of these modifications could include conveying information on location or the emotional state of the signaller, or they could be products of vocal innovation.
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Ajayi, Oyeyemi O., Sunday O. Peters, Marcos De Donato, Sunday O. Sowande, Fidalis D. N. Mujibi, Olanrewaju B. Morenikeji, Bolaji N. Thomas, Matthew A. Adeleke, and Ikhide G. Imumorin. "Computational genome-wide identification of heat shock protein genes in the bovine genome." F1000Research 7 (September 20, 2018): 1504. http://dx.doi.org/10.12688/f1000research.16058.1.
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Background: Heat shock proteins (HSPs) are molecular chaperones known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, we carried out a computational genome-wide survey of the bovine genome. For this, HSP sequences from each subfamily (sHSP, HSP40, HSP70 and HSP90) were used to search the Pfam (Protein family) database, for identifying exact HSP domain sequences based on the hidden Markov model. ProtParam tool was used to compute potential physico-chemical parameters detectable from a protein sequence. Evolutionary trace (ET) method was used to extract evolutionarily functional residues of a homologous protein family. Results: We computationally identified 67 genes made up of 10, 43, 10 and 4 genes belonging to small HSP, HSP40, HSP70 and HSP90 families respectively. These genes were widely dispersed across the bovine genome, except in chromosomes 24, 26 and 27, which lack bovine HSP genes. We found an uncharacterized outer dense fiber (ODF1) gene in cattle with an intact alpha crystallin domain, like other small HSPs. Physico-chemical characteristic of aliphatic index was higher in HSP70 and HSP90 gene families, compared to small HSP and HSP40. Grand average hydropathy showed that small HSP (sHSP), HSP40, HSP70 and HSP90 genes had negative values except for DNAJC22, a member of HSP40 gene family. The uniqueness of DNAJA3 and DNAJB13 among HSP40 members, based on multiple sequence alignment, evolutionary trace analysis and sequence identity dendrograms, suggests evolutionary distinct structural and functional features, with unique roles in substrate recognition and chaperone functions. The monophyletic pattern of the sequence identity dendrograms of cattle, human and mouse HSP sequences suggests functional similarities. Conclusions: Our computational results demonstrate the first-pass in-silico identification of heat shock proteins and calls for further investigation to better understand their functional roles and mechanisms in Bovidae.
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Pecquet, Christian, Ilyas Chachoua, Anita Roy, Thomas Balligand, Gaëlle Vertenoeil, Emilie Leroy, Roxana-Irina Albu, et al. "Calreticulin mutants as oncogenic rogue chaperones for TpoR and traffic-defective pathogenic TpoR mutants." Blood 133, no. 25 (June 20, 2019): 2669–81. http://dx.doi.org/10.1182/blood-2018-09-874578.
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Abstract Calreticulin (CALR) +1 frameshift mutations in exon 9 are prevalent in myeloproliferative neoplasms. Mutant CALRs possess a new C-terminal sequence rich in positively charged amino acids, leading to activation of the thrombopoietin receptor (TpoR/MPL). We show that the new sequence endows the mutant CALR with rogue chaperone activity, stabilizing a dimeric state and transporting TpoR and mutants thereof to the cell surface in states that would not pass quality control; this function is absolutely required for oncogenic transformation. Mutant CALRs determine traffic via the secretory pathway of partially immature TpoR, as they protect N117-linked glycans from further processing in the Golgi apparatus. A number of engineered or disease-associated TpoRs such as TpoR/MPL R102P, which causes congenital thrombocytopenia, are rescued for traffic and function by mutant CALRs, which can also overcome endoplasmic reticulum retention signals on TpoR. In addition to requiring N-glycosylation of TpoR, mutant CALRs require a hydrophobic patch located in the extracellular domain of TpoR to induce TpoR thermal stability and initial intracellular activation, whereas full activation requires cell surface localization of TpoR. Thus, mutant CALRs are rogue chaperones for TpoR and traffic-defective TpoR mutants, a function required for the oncogenic effects.
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Sharpe, David J., and Ross L. Goldingay. "Vocal behaviour of the squirrel glider (Petaurus norfolcensis)." Australian Journal of Zoology 57, no. 1 (2009): 55. http://dx.doi.org/10.1071/zo08075.
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We describe the vocal behaviour of the squirrel glider (Petaurus norfolcensis) from 465 h of observation across five sites in north-east New South Wales and south-east Queensland. A monosyllabic or polysyllabic nasal grunt was the most frequent call (56% of 208 calls); it ranged from single calls to sequences of up to 20-min duration (mean 2.1 min ± 0.6, s.e.) and was heard on 34% of nights (n = 83) at two sites. The rate of the nasal grunt showed a positive relationship with population density at one site. The nasal grunt was typically made when conspecifics were near the caller, but responses were infrequent (7% of observations). Call playback produced no discernable change in call response. The nasal grunt appears to regulate individual spacing by facilitating mutual avoidance, a function hypothesised to be an evolutionary precursor to the use of calls in territorial defence. Threatening calls were the next most common vocalisation (17% of calls) and were accompanied by scuffles and/or chases. They were also used when gliders were preyed upon and during animal handling. The calling behaviour of the squirrel glider confirms the importance of vocal communication among petaurid gliders.
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Melamed, Benjamin. "The empirical TES methodology: modeling empirical time series." Journal of Applied Mathematics and Stochastic Analysis 10, no. 4 (January 1, 1997): 333–53. http://dx.doi.org/10.1155/s1048953397000403.
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TES (Transform-Expand-Sample) is a versatile class of stochastic sequences defined via an autoregressive scheme with modulo-1 reduction and additional transformations. The scope of TES encompasses a wide variety of sample path behaviors, which in turn give rise to autocorrelation functions with diverse functional forms - monotone, oscillatory, alternating, and others. TES sequences are readily generated on a computer, and their autocorrelation functions can be numerically computed from accurate analytical formulas at a modest computational cost.This paper presents the empirical TES modeling methodology which uses TES process theory to model empirical records. The novel feature of the TES methodology is that it expressly aims to simultaneously capture the empirical marginal distribution (histogram) and autocorrelation function. We draw attention to the non-parametric nature of TES modeling in that it always guarantees an exact match to the empirical marginal distribution. However, fitting the corresponding autocorrelation function calls for a heuristic search for a TES model over a large parametric space. Consequently, practical TES modeling of empirical records must currently rely on software assistance. A visual interactive software environment, called TEStool, has been designed and implemented to support TES modeling. The paper describes the empirical TES modeling methodology as implemented in TEStool and provides numerically-computable formulas for TES autocorrelations. Two examples illustrate the efficacy of the TES modeling approach. These examples serve to highlight the ability of TES models to capture first-order and second-order properties of empirical sample paths and to mimic their qualitative appearance.
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Shapiro, Jason W., and Catherine Putonti. "Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies." PeerJ 9 (August 6, 2021): e11950. http://dx.doi.org/10.7717/peerj.11950.
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Background A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools. Methods We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees. Results We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single script for automated analysis and with utility functions to assist in building single-copy core genomes and predicting the sources of fragmented genes.
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Madhusudhana, Shyam, Yu Shiu, Holger Klinck, Erica Fleishman, Xiaobai Liu, Eva-Marie Nosal, Tyler Helble, et al. "Improve automatic detection of animal call sequences with temporal context." Journal of The Royal Society Interface 18, no. 180 (July 2021): 20210297. http://dx.doi.org/10.1098/rsif.2021.0297.
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Many animals rely on long-form communication, in the form of songs, for vital functions such as mate attraction and territorial defence. We explored the prospect of improving automatic recognition performance by using the temporal context inherent in song. The ability to accurately detect sequences of calls has implications for conservation and biological studies. We show that the performance of a convolutional neural network (CNN), designed to detect song notes (calls) in short-duration audio segments, can be improved by combining it with a recurrent network designed to process sequences of learned representations from the CNN on a longer time scale. The combined system of independently trained CNN and long short-term memory (LSTM) network models exploits the temporal patterns between song notes. We demonstrate the technique using recordings of fin whale ( Balaenoptera physalus ) songs, which comprise patterned sequences of characteristic notes. We evaluated several variants of the CNN + LSTM network. Relative to the baseline CNN model, the CNN + LSTM models reduced performance variance, offering a 9–17% increase in area under the precision–recall curve and a 9–18% increase in peak F1-scores. These results show that the inclusion of temporal information may offer a valuable pathway for improving the automatic recognition and transcription of wildlife recordings.
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Fehniger, Todd A., Kilannin Krysiak, Brian S. White, Matthew Matlock, Chris Miller, Robert Fulton, Friederike Kreisel, et al. "Recurrent Somatic Genomic Alterations in Follicular NHL (FL) Revealed By Exome and Custom-Capture Next Generation Sequencing." Blood 126, no. 23 (December 3, 2015): 574. http://dx.doi.org/10.1182/blood.v126.23.574.574.
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Abstract Background: Follicular lymphoma (FL) is the most common indolent NHL (iNHL), exhibits a variable clinical course, and remains largely incurable. The pathogenesis of FL is complex and involves over expression of Bcl2 via t(14;18) translocation, as well as copy number alterations, recurrent somatic mutations, and changes in the tumor microenvironment. In line with recent publications, we hypothesized that recurrent somatic genomic mutations in FL will be present and may impact FL development, progression, transformation, and clinical outcomes. Methods: To address this, we performed exome sequencing (NimbleGen SeqCap EZ V2.0) of tumor and normal frozen tissue pairs from 24 patients in a discovery cohort with untreated FL (12), relapsed FL (6), or transformed FL/iNHL (6). We developed a custom capture assay (NimbleGen) that targets 7.05 MB corresponding to the coding, 5' and 3' UTR regions of 1717 genes. The custom capture genes included somatic mutations identified in our exome discovery cohort (898 genes) or somatic mutations previously published to be recurrently mutated in B cell NHL (819 genes). Instrument data from the discovery cohort exome and re-sequenced custom capture were combined and analyzed using the McDonnell Genome Institute (MGI) somatic caller pipeline (5 SNV callers, 3 indel callers), filtered (minimum 20X coverage, minimum 2.5% VAF, maximum 10% normal VAF) and manually reviewed. Additionally, the 1717 custom capture strategy was used to sequence an extension cohort consisting of FFPE tumor samples from 80 patients with FL, achieving >20x coverage for >75% of the targeted region. All discovery and extension samples have clinical annotations that include FLIPI prognostic score, treatment, and clinical outcomes. Results: Combined analysis of exome and custom capture data for the discovery cohort yielded a robust data set with good sequence coverage of >78% of the targeted regions with at least 20x depth in all samples and a mean depth of 89x. Based upon somatic mutations identified and manually reviewed using this approach, we conservatively estimate 0.98 mutations per MB in FL. 23 genes were recurrently mutated in 3 or more cases, and an additional 75 genes recurrently mutated in 2 cases in the discovery cohort. Consistent with recent publications (Li H et. al., Blood, 2014; Green MR, PNAS, 2015; Yildiz M et al, Blood, 2015) we confirmed a number of genes that were highly recurrently mutated in FL [TNFRSF14 (50%), Bcl2 (25%), IRF8 (13%), TP53 (13%)] including chromatin modifying genes consisting of histone methyl transferases [KMT2D/MLL2 (58%), EZH2 (13%)], histone acetyltransferases [CREBBP (42%), EP300 (17%)], histone linkers [HIST1H1C (13%), HIST1H1E (8%), HIST1H2BO (8%), HIST1H3G (8%), HIST2H2AC (8%); collectively 42%]. We also confirmed (ATP6V1B2, 13%) and found unreported (ATP6AP2, 8%; ATP6V0A1, 4%; ATP6V1F, 4%) mutations in vacuolar ATPase proton pump genes and P5 or Ca++ ATPase genes (ATP13A2, 4%; ATP13A4, 4%, ATP2B4, 4%;). We confirmed (CD79B, 13%; BCL10, 8%) and found unreported (CD22, 13%) mutations in components of the B cell receptor signaling pathway. The previously unreported recurrent mutations in CD22 were consistent with loss-of function (2 missense, 1 nonsense, 1 frame shift deletion). As a negative regulator of BCR signaling, mutation of CD22 may represent a strategy of to enhance BCR signals in malignant germinal center B cells. We also identified members of the SWI/SNF complex mutated in 33% of this FL cohort: ARID1B (8%), BCL11A (4%), SMARCB1 (4%) in addition to previously reported members BCL7A (12%), SMARCA4 (8%), ARID1A (4%). Somatic mutations were also identified in the Notch pathway: DTX1 (29%), Notch2 (4%), Notch3 (4%), Notch4 (4%). We identified several genes that have not been reported as highly recurrent in FL CXCR4 (42%, mutation calls primarily in RNA), DMD (13%), DNAH9 (13%), FLG (13%), GON4L (13%), PCDH7 (13%), RLTPR (13%), SCN7A (13%), ST6GAL1 (13%). Conclusions: FL genomes harbor a large number of recurrent mutations, consistent with a role in the development and progression of this malignancy. Analysis of the extension cohort and association of recurrently mutated genes and pathways with clinical outcomes is ongoing and will be presented. Disclosures Bartlett: Gilead: Consultancy, Research Funding; Janssen: Research Funding; Pharmacyclics: Research Funding; Genentech: Research Funding; Pfizer: Research Funding; Novartis: Research Funding; Millennium: Research Funding; Colgene: Research Funding; Medimmune: Research Funding; Kite: Research Funding; Insight: Research Funding; Seattle Genetics: Consultancy, Research Funding; MERC: Research Funding; Dynavax: Research Funding; Idera: Research Funding; Portola: Research Funding; Bristol Meyers Squibb: Research Funding; Infinity: Research Funding; LAM Theapeutics: Research Funding.
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Jackson, Mark A., Anne L. Rae, Rosanne E. Casu, Christopher P. L. Grof, Graham D. Bonnett, and Donald J. Maclean. "A bioinformatic approach to the identification of a conserved domain in a sugarcane legumain that directs GFP to the lytic vacuole." Functional Plant Biology 34, no. 7 (2007): 633. http://dx.doi.org/10.1071/fp07024.
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Sugarcane is an ideal candidate as a biofactory for the production of alternate higher value products. One way of achieving this is to direct useful proteins into the vacuoles within the sugarcane storage parenchyma tissue. By bioinformatic analysis of gene sequences from putative sugarcane vacuolar proteins a motif has been identified that displays high conservation across plant legumain homologues that are known to function within vacuolar compartments. This five amino acid motif, represented by the sequence IRLPS in sugarcane is shown to direct an otherwise secreted GFP fusion protein into a large acidic and proteolytic vacuole in sugarcane callus cells as well as in diverse plant species. In mature sugarcane transgenic plants, the stability of GFP appeared to be dependent on cell type, suggesting that the vacuolar environment can be hostile to introduced proteins. This targeting motif will be a valuable tool for engineering plants such as sugarcane for production of novel products.
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Collier, Katie, Andrew N. Radford, Sabine Stoll, Stuart K. Watson, Marta B. Manser, Balthasar Bickel, and Simon W. Townsend. "Dwarf mongoose alarm calls: investigating a complex non-human animal call." Proceedings of the Royal Society B: Biological Sciences 287, no. 1935 (September 23, 2020): 20192514. http://dx.doi.org/10.1098/rspb.2019.2514.
Full textAbstract:
Communication plays a vital role in the social lives of many species and varies greatly in complexity. One possible way to increase communicative complexity is by combining signals into longer sequences, which has been proposed as a mechanism allowing species with a limited repertoire to increase their communicative output. In mammals, most studies on combinatoriality have focused on vocal communication in non-human primates. Here, we investigated a potential combination of alarm calls in the dwarf mongoose ( Helogale parvula ), a non-primate mammal. Acoustic analyses and playback experiments with a wild population suggest: (i) that dwarf mongooses produce a complex call type (T 3 ) which, at least at the surface level, seems to comprise units that are not functionally different to two meaningful alarm calls (aerial and terrestrial); and (ii) that this T 3 call functions as a general alarm, produced in response to a wide range of threats. Using a novel approach, we further explored multiple interpretations of the T 3 call based on the information content of the apparent comprising calls and how they are combined. We also considered an alternative, non-combinatorial interpretation that frames T 3 as the origin, rather than the product, of the individual alarm calls. This study complements previous knowledge of vocal combinatoriality in non-primate mammals and introduces an approach that could facilitate comparisons between different animal and human communication systems.
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Baysal, Can, Ana Pérez-González, Álvaro Eseverri, Xi Jiang, Vicente Medina, Elena Caro, Luis Rubio, Paul Christou, and Changfu Zhu. "Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria." Transgenic Research 29, no. 1 (October 10, 2019): 37–52. http://dx.doi.org/10.1007/s11248-019-00176-9.
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Abstract Mitochondria fulfil essential functions in respiration and metabolism as well as regulating stress responses and apoptosis. Most native mitochondrial proteins are encoded by nuclear genes and are imported into mitochondria via one of several receptors that recognize N-terminal signal peptides. The targeting of recombinant proteins to mitochondria therefore requires the presence of an appropriate N-terminal peptide, but little is known about mitochondrial import in monocotyledonous plants such as rice (Oryza sativa). To gain insight into this phenomenon, we targeted nuclear-encoded enhanced green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origins, and investigated their effectiveness by immunoblot analysis as well as confocal and electron microscopy. We found that the ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (Arabidopsis thaliana) and OsSCSb (Oryza sativa) peptides successfully directed most of the eGFP to the mitochondria, whereas the MTS2 peptide (Nicotiana plumbaginifolia) showed little or no evidence of targeting ability even though it is a native plant sequence. Our data therefore indicate that the presence of particular recognition motifs may be required for mitochondrial targeting, whereas the phylogenetic origin of the pre-sequences probably does not play a key role in the success of mitochondrial targeting in dedifferentiated rice callus and plants.
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CEDERBAUM, I. "SPECTRAL PROPERTIES OF ADMITTANCE MATRICES OF RESISTIVE TREE NETWORKS." Journal of Circuits, Systems and Computers 04, no. 01 (March 1994): 53–70. http://dx.doi.org/10.1142/s0218126694000041.
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In this paper spectral properties of the admittance matrix of a resistive network whose underlying graph forms a general tree are studied. The algebraic presentation of the network is provided by its real node admittance matrix with respect to one of its terminal vertices, considered to be the root of the tree. The spectral properties of this matrix are studied by application of the theory of two-element-kind (R, C) networks. A mechanical analogue of a particular case of a similar problem, corresponding to a linear tree has been studied in the classical work of Gantmacher and Krein.7 Generalization of the study to networks based on trees of arbitrary structure calls for a modification of the mathematical approach. Instead of polynomial Sturm sequences applied in Ref. 7 the paper applies sequences of rational functions obeying the two basic Sturm conditions. In the special case of a linear tree these rational functions turn out to be polynomials, and the results are equivalent to those in Ref. 7. For a general tree the paper takes into consideration any root—leaf path of the tree. It is shown that the conditions on such a path are similar to those taking place on a linear tree. Some difference occurs in the number of sign reversals in the sequence of coordinates of characteristic vectors. In the case of a linear tree this number depends only on the position of the corresponding characteristic frequency in the spectrum of the matrix. In the case of a root-leaf path of a general tree, this number has to be normally decreased. The correction (which might be zero) is equal to the number of poles of the determinant of the reduced admittance matrix corresponding to the path considered, which does not exceed the characteristic frequency.
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Zhang, Xinpeng, Zongda Xu, Xiaoyan Yu, Lanyong Zhao, Mingyuan Zhao, Xu Han, and Shuai Qi. "Identification of Two Novel R2R3-MYB Transcription factors, PsMYB114L and PsMYB12L, Related to Anthocyanin Biosynthesis in Paeonia suffruticosa." International Journal of Molecular Sciences 20, no. 5 (February 28, 2019): 1055. http://dx.doi.org/10.3390/ijms20051055.
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Flower color is a charming phenotype with very important ornamental and commercial values. Anthocyanins play a critical role in determining flower color pattern formation, and their biosynthesis is typically regulated by R2R3-MYB transcription factors (TFs). Paeonia suffruticosa is a famous ornamental plant with colorful flowers. However, little is known about the R2R3-MYB TFs that regulate anthocyanin accumulation in P. suffruticosa. In the present study, two R2R3-MYB TFs, namely, PsMYB114L and PsMYB12L, were isolated from the petals of P. suffruticosa ‘Shima Nishiki’ and functionally characterized. Sequence analysis suggested that PsMYB114L contained a bHLH-interaction motif, whereas PsMYB12L contained two flavonol-specific motifs (SG7 and SG7-2). Subsequently, the in vivo function of PsMYB114L and PsMYB12L was investigated by their heterologous expression in Arabidopsis thaliana and apple calli. In transgenic Arabidopsis plants, overexpression of PsMYB114L and of PsMYB12L caused a significantly higher accumulation of anthocyanins, resulting in purple-red leaves. Transgenic apple calli overexpressing PsMYB114L and PsMYB12L also significantly enhanced the anthocyanins content and resulted in a change in the callus color to red. Meanwhile, gene expression analysis in A. thaliana and apple calli suggested that the expression levels of the flavonol synthase (MdFLS) and anthocyanidin reductase (MdANR) genes were significantly downregulated and the dihydroflavonol 4-reductase (AtDFR) and anthocyanin synthase (AtANS) genes were significantly upregulated in transgenic lines of PsMYB114L. Moreover, the expression level of the FLS gene (MdFLS) was significantly downregulated and the DFR (AtDFR/MdDFR) and ANS (AtANS/MdANS) genes were all significantly upregulated in transgenic lines plants of PsMYB12L. These results indicate that PsMYB114L and PsMYB12L both enhance anthocyanin accumulation by specifically regulating the expression of some anthocyanin biosynthesis-related genes in different plant species. Together, these results provide a valuable resource with which to further study the regulatory mechanism of anthocyanin biosynthesis in P. suffruticosa and for the breeding of tree peony cultivars with novel and charming flower colors.
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Zhang, Kai, and Hang Yu. "Study on the Method of Android System Cloud Monitoring Information Based on SVM." Applied Mechanics and Materials 602-605 (August 2014): 2272–75. http://dx.doi.org/10.4028/www.scientific.net/amm.602-605.2272.
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In recent years, android system has become a mobile device is especially preferred intelligent mobile phone operating system, like Microsoft window system, Android operating system is also subject to a variety of mobile phone viruses, Trojans and other malicious software attacks, resulting in the leakage of personal information, the harm of spam messages continuously, in order to solve these problems in this paper for the known virus Trojan cloud monitoring and detecting light client burden increase sample detection efficiency; using SVM to unknown trojan virus (support vector machine) short sequences of API function calls the LINUX classification, analysis of the API function of each call with precise improve classification support vector machine the danger coefficient after integration, to distinguish the Trojan virus, in order to achieve information security protection system role.
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Iijima, H., N. P. Gerard, C. Squassoni, J. Ewig, D. Face, J. M. Drazen, Y. A. Kim, B. Shriver, L. B. Hersh, and C. Gerard. "Exon 16 del: a novel form of human neutral endopeptidase (CALLA)." American Journal of Physiology-Lung Cellular and Molecular Physiology 262, no. 6 (June 1, 1992): L725—L729. http://dx.doi.org/10.1152/ajplung.1992.262.6.l725.
Full textAbstract:
The enzyme neutral metalloendopeptidase (E.C. 3.4.24.11), also known as the common acute lymphocytic leukemia antigen, neutral endopeptidase, or enkephalinase, functions as an inactivator of a wide variety of signaling oligopeptides such as substance P, neurokinin A, enkephalins, endothelin, atrial natriuretic factor, and formyl chemotactic peptides. A cDNA clone isolated from a human lung library encodes a fragment of neutral metalloendopeptidase containing an internal 81 base pair deletion when compared with the human placental cDNA for this enzyme. Comparison of the deleted cDNA sequence with the intron-exon structure recently determined as the common acute lymphocytic leukemia antigen reveals that the 81 base pairs corresponds precisely with exon 16. RNA analysis using splice junction oligonucleotides indicates that the 16 del form constitutes a minor but significant fraction of the RNA species present in human lung. Expression of constructs containing “wild type” and “exon 16 del” neutral endopeptidases in COS-7 cells reveals that deletion of this 27 amino acid segment reduces enzymatic activity toward the synthetic substrate glutaryl-alanyl-alanyl-phenyl-alanyl-4-methoxy-2-naphthylamide to barely detectable levels.
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Hartmann, Paulo, Marília Hartmann, and Célio Haddad. "Visual signaling and reproductive biology in a nocturnal treefrog, genus Hyla (Anura: Hylidae)." Amphibia-Reptilia 25, no. 4 (2004): 395–406. http://dx.doi.org/10.1163/1568538042788933.
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AbstractWe investigated reproductive activity, courtship behavior, call structure, body size, clutch size, oviposition site, and reproductive mode of Hyla sp. (aff. ehrhardti). Males called in all months, but showed a peak of activity during the rainy season. Three pair formations were observed and courtship involved stereotyped behavioral sequences, including visual signaling. Males emitted three different vocalization types: advertisement calls, courtship calls, and a vocalization of unknown function. Females attained larger body sizes than males and deposited an average of 74.5 unpigmented eggs per clutch. Early larval stages are aquatic but restricted to water in constructed subterranean nests; subsequent to flooding of nests, exotrophic tadpoles live in ponds or streams. Courtship behavior in Hyla sp. (aff. ehrhardti) is complex and the diverse repertoire of limb movements, exhibited by males, probably provide visual stimuli to females in this nocturnal treefrog. Hyla sp. (aff. ehrhardti) belongs to the H. albomarginata group. Considering the reproductive modes in this group, the complexes of H. albosignata and of H. albofrenata can be considered more close related to each other than to the H. albomarginata complex.
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Gärtner, Dietmar, and Werner E. Kluge. "π-RED+ An interactive compiling graph reduction system for an applied λ-calculus." Journal of Functional Programming 6, no. 5 (September 1996): 723–56. http://dx.doi.org/10.1017/s0956796800001957.
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AbstractThis paper describes a compiling graph reduction system which realizes the reduction semantics of a fully-fledged applied λ-calculus. High-level functional programs are conceptually executed as sequences of program transformations governed by full β-reductions. They may be carried out step-by-step, and intermediate programs may be displayed in high-level notation, rendering the system suitable for interactive program design, high-level debugging, and also for teaching basic programming language concepts and language interpretation. Run-time efficiency for production runs is achieved by means of an abstract stack machine ASM which serves as an intermediate level of code generation. It employs multiple stacks for reasonably fast function calls, optimized tail-end recursions, and earliest possible releases of subgraphs that are no longer needed. The ASM involves an interpreter if and only if potential naming conflicts need to be resolved when reducing partial function applications.
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Weigert, Oliver, Nadja Kopp, Andrew A. Lane, Akinori Yoda, Suzanne E. Dahlberg, Donna Neuberg, Anita Y. Bahar, et al. "Molecular Ontogeny of Donor-Derived Lymphomas Occurring After Transplantation,." Blood 118, no. 21 (November 18, 2011): 3671. http://dx.doi.org/10.1182/blood.v118.21.3671.3671.
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Abstract Abstract 3671 Follicular lymphoma (FL) is characterized by the translocation t(14;18), which results in overexpression of the anti-apoptotic protein BCL2 through juxtaposition to the immunoglobulin heavy chain (IGH) locus. Additional genetic aberrations are required and recurrent mutations have been identified in FL, however their timing during lymphomagenesis remains unknown. We performed ultra-sensitive mutation detection to define in vivo clonal diversification in paired follicular lymphomas from a donor-recipient sibling pair that presented more than 9 years after hematopoietic cell transplantation. Briefly, a 41-year old woman with chronic myeloid leukemia (CML) underwent myeloablative bone marrow transplantation from her HLA-matched sister in 2000. She received three donor leukocyte infusions (DLI) for molecular relapse, with the last in June 2002. In November 2009, the donor was diagnosed with grade 2/3A FL. Six months later, the recipient was diagnosed with grade 2/3A FL. The FLs shared identical BCL2/IGH rearrangements, which was also recovered from the DLI at a frequency of 1-in-2000 cells. Both FLs also shared the same V(D)J rearrangement, with the exception of single base-pair mismatches and insertions/deletions (InDels) consistent with ongoing somatic hypermutation (SHM) during clonal divergence. Alignment with germline VH3-66 sequence indicated that the common ancestor had initiated SHM. Whole exome sequencing of both FLs identified 12 single nucleotide variants (SNVs) and 2 InDels in both lymphomas, 3 SNVs unique to the donor's FL, and 4 unique to the recipient's FL. All candidate mutations were validated and confirmed to be somatic by Sanger sequencing. Among the identical mutations identified in both FLs were two SNVs in BCL2, an in-frame deletion in EP300, and an in-frame insertion in KLHL6, which were recently found to be recurrently mutated in lymphoma. Among the SNVs unique to the recipient's FL was an ARID1A (adenine-thymine (AT)-rich interactive domain-containing protein 1A) R1276 premature stop. Loss-of-function mutations in ARID1A have been reported in solid cancers, but not yet in hematologic malignancies. On immunohistochemical staining both lymphomas had decreased ARID1A/BAF250 protein expression, suggesting that loss of ARID1A occurred through separate mechanisms in each FL (i.e. convergent evolution). In fact, the donor's lymphoma was found to have a copy number loss at this locus (1p35.3) by qPCR. To determine whether the somatic mutations that we identified were present at a low frequency within the DLI, we PCR amplified regions flanking each mutation site from the DLI and subjected the products to ultra-sensitive deep sequencing (average read coverage at mutation site, 361,723; range, 16,684–1,169,555). To correct for background frequencies of non-germline calls, we PCR amplified and deep sequenced the same positions from the donor's buccal swab (average read coverage at the mutation site, 418,499; range, 20,711–1,070,734). Eleven of the 12 SNVs and the 2 InDels that were identified in both lymphomas were ‘enriched' in the DLI, i.e., recovered at frequencies significantly above background, indicating that those mutations were present more than 7 years prior to presentation of either lymphoma. All 4 SNVs unique to the recipient's FL and a RAFTLIN V254M mutation identified only in the donor's FL were not enriched in the DLI, consistent with subsequent acquisition during clonal diversification. Of the final two mutations, one was detected only in the donor's FL and was enriched in the DLI. The other was initially detected only in the donor's FL, but deep sequencing recovered the mutation in 4.7% of reads from the recipient's FL and demonstrated enrichment in the DLI. The presence of a mutation in the donor's FL and DLI but not within the majority of recipient's FL cells is consistent with at least two scenarios: (i) the recipient's FL is derived from a clonally diversified population of ancestor cells transferred from the donor or (ii) the mutant allele was lost in a subset or in all cells of the recipient's FL during clonal evolution. In conclusion, we utilized ultra-sensitive mutation detection to elucidate the molecular ontogeny of follicular lymphoma during clonal evolution in separate hosts. This approach has broad applicability for identifying genetic variants within tumor populations that confer phenotypes like therapeutic resistance or metastatic potential. Disclosures: No relevant conflicts of interest to declare.
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Morkun, Natalia, Iryna Zavsiehdashnia, Oleksandra Serdiuk, and Iryna Kasatkina. "Identification of models of nonlinear dynamic processes in mining on the basis of Volterra nuclei." E3S Web of Conferences 201 (2020): 01028. http://dx.doi.org/10.1051/e3sconf/202020101028.
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Solving the problem of improving efficiency of technological processes of mineral concentration is one of the essential for providing sustainability of mining enterprises. Currently, special attention is paid to optimization of technological processes in concentration of useful minerals. This approach calls for availability of high-quality data on the process, formation of corresponding databases and their subsequent processing to build adequate and efficient mathematical models of processes and systems. In order to improve quality of mathematical description of forming fractional characteristics of ore through applying technological aggregates in concentration, the authors suggest using power Volterra series that provide characteristics of a controlled object (its condition) as a sequence of multidimensional weight functions invariant to the type of an input signal – Volterra nuclei. Application of Volterra structures enables decreasing the modelling error to 0.039 under the root-mean-square error of 0.0594.
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Hammerschmidt, K., K. Radyushkin, H. Ehrenreich, and J. Fischer. "Female mice respond to male ultrasonic ‘songs’ with approach behaviour." Biology Letters 5, no. 5 (June 10, 2009): 589–92. http://dx.doi.org/10.1098/rsbl.2009.0317.
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The ultrasonic vocalizations of mice are attracting increasing attention, because they have been recognized as an informative readout in genetically modified strains. In addition, the observation that male mice produce elaborate sequences of ultrasonic vocalizations (‘song’) when exposed to female mice or their scents has sparked a debate as to whether these sounds are—in terms of their structure and function—analogous to bird song. We conducted playback experiments with cycling female mice to explore the function of male mouse songs. Using a place preference design, we show that these vocalizations elicited approach behaviour in females. In contrast, the playback of whistle-like artificial control sounds did not evoke approach responses. Surprisingly, the females also did not respond to pup isolation calls. In addition, female responses did not vary in relation to reproductive cycle, i.e. whether they were in oestrus or not. Furthermore, our data revealed a rapid habituation of subjects to the experimental situation, which stands in stark contrast to other species' responses to courtship vocalizations. Nevertheless, our results clearly demonstrate that male mouse songs elicit females' interest.
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Yan, Haifeng, Mingzhi Li, Yuping Xiong, Jianming Wu, Jaime A. Teixeira da Silva, and Guohua Ma. "Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress." International Journal of Molecular Sciences 20, no. 22 (November 13, 2019): 5676. http://dx.doi.org/10.3390/ijms20225676.
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WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.
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Viķis-Freibergs, Vaira. "Narrative Structures, Meanings, and Life Histories in the Historical Novel Kaugurieši." Journal of Narrative and Life History 1, no. 4 (January 1, 1991): 343–62. http://dx.doi.org/10.1075/jnlh.1.4.05str.
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Abstract Narrative structures serve the double function of selecting episodes and charac-ters to be included in the narration, as well as offering a generative mechanism for their sequencing, both functions being simultaneous and mutually interac-tive. According to Eco (1984), narrative structures are multilayered, including an abstract level of ideology. Few studies have been done on specific narrative subgenres, such as the historical novel. This article examines a historical novel by Latvian writer Karlis Zariņš (1938, 1948, 1975, 1985), which depicts a failed peasant uprising at Kauguri, Latvia in 1802. Bakhtine's (1978) theoreti-cal notion of chronotope is invoked, distinguishing the external chronotope— the general historical and geographic situation—from the internal chronotope—the sequence of individual transformations. In Kaugurieši, the ex-ternal chronotope is depicted as a sociopolitical chess game, in which the Rus-sian king and the German knights play active roles, the queen is chance, and the pawns (Latvian peasants) are helpless victims. The plot centers on a tragi-cally failed attempt by the Latvians to change the historical givens by becom-ing an active, collective force. The internal chronotopes reveal the paths of individual lives, some of which follow the abstract model of heroic quest and sacrifice. (Psychohistory)
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Zeng, Juan, and Zunnan Huang. "From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding." Current Medicinal Chemistry 26, no. 42 (January 8, 2020): 7537–54. http://dx.doi.org/10.2174/0929867325666181017160857.
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Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.
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Sonna, Larry A., Matthew M. Kuhlmeier, Heather C. Carter, Jeffrey D. Hasday, Craig M. Lilly, and Karen D. Fairchild. "Effect of moderate hypothermia on gene expression by THP-1 cells: a DNA microarray study." Physiological Genomics 26, no. 1 (June 2006): 91–98. http://dx.doi.org/10.1152/physiolgenomics.00296.2005.
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The mechanisms by which moderate hypothermia (32°C for 12–72 h) affect human cellular function are unclear. We tested the hypothesis that it produces broad changes in mRNA expression in vitro. Acute monocytic leukemia (THP-1) cells were incubated under control conditions (37°C) or moderate hypothermia (32°C) for 24 h. RNA was extracted, and the hypothermic response was confirmed by examining the expression of the cold-induced RNA-binding protein (CIRBP) gene by RT-PCR. Gene expression analysis was performed on seven sets of paired samples with Affymetrix U133A chips using established statistical methods. Sequences were considered affected by cold if they showed statistically significant changes in expression and also met published post hoc filter criteria (changes in geometric mean expression of ≥2-fold and expression calls of “present” or “marginal” in at least half of the experiments). Changes in the expression of selected sequences were further confirmed by PCR. Sixty-seven sequences met the criteria for increased expression (including cold-inducible genes CIRBP and RNA binding motif 3), and 100 sequences showed decreased expression as a result of hypothermia. Functional categories affected by hypothermia included genes involved in immune responses; cell growth, proliferation, and differentiation; and metabolism and biosynthesis. Several heat shock proteins (HSPs) showed decreases in expression. Moderate hypothermia produces substantial changes in gene expression, in categories potentially of systemic importance. Cold exposure without rewarming decreased the expression of several HSPs. These in vitro findings suggest that prolonged hypothermia in vivo might be capable of producing physiologically relevant changes in gene expression by circulating leukocytes.
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Han, KyoungSoo, BooJoong Kang, and Eul Gyu Im. "Malware Analysis Using Visualized Image Matrices." Scientific World Journal 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/132713.
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This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API) calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively.
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Kerschbaumer, A., F. Alasti, G. Supp, J. S. Smolen, and D. Aletaha. "FRI0043 JOINT SPACE NARROWING PRECEDES EROSIVE RADIOGRAPHIC DAMAGE IN PATIENTS WITH RHEUMATOID ARTHRITIS." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 596.2–597. http://dx.doi.org/10.1136/annrheumdis-2020-eular.6514.
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Background:Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized through symmetric polyarthritis leading to joint destruction over time in many patients. Radiographic damage is an important outcome in RA clinical trials, most commonly assessed by conventional radiographs and quantified/reported by the modified total Sharp van der Heijde Score (mTSS). The mTSS is assessing erosive (ERO) changes as well as joint space narrowing (JSN; reflecting cartilage wasting) in the small joints of the hands and feet. While erosions are the hallmarks of RA, loss of cartilage has been reported to be highly relevant for functional limitations in RA. The sequence of occurrence of these events is not completely understood.Objectives:To investigate the time to radiographic progression and assess potential differences between time-to-JSN progression and time-to-ERO progression.Methods:Radiographs of RA patients from a large prospective clinical routine cohort were scored using the mTSS by one experienced reader (G.S.) unaware of the aim of this project. Time-to-JSN and time-to-ERO was estimated using survival analyses utilizing the Kaplan-Meier estimator. In additional analyses, patients were stratified based on JSN and/or ERO damage at baseline. Further, potential predictors (demographics, csDMARD/bDMARD treatment/combination therapy) of time-to-ERO and time-to-JSN were evaluated using Cox-regression techniques. All statistical analyses were conducted using SAS v9.4 (Cary, New York, USA).Results:We assessed 798 patients longitudinally for radiographic progression. JSN occurred significantly earlier than erosions (p<0.001, Figure 1). After stratification for baseline damage (Figure 2), these differences remained significant with a shorter time-to-JSN in patients without any baseline ERO or JSN (n=44, p=0.008), patients with JSN but no ERO at baseline (n=200, p<0.001), and patients with baseline ERO and JSN (n=536, p<0.001). Only in the small group of patients with isolated erosions (without JSN) at baseline there was no difference in time-to-progression of ERO vs. JSN (n=18, p=0.241). Overall, shorter time to progression of ERO was significantly predicted by positivity for rheumatoid factor or anti-citrullinated peptide antibodies (CCP; p<0.003), as well as by erosions at baseline (p<0.001) in Cox regression. In contrast, seropositivity for neither RF nor CCP was associated with shorter time to JSN progression (p=0.226); however, baseline concomitant JSN and ERO damage did show to be a significant predictor (p<0.001).Figure 1.Time to joint space narrowing and time to erosive damage (n=798).Figure 2.Time to JSN/ERO stratified by presence or absence of ERO/JSN at baseline.Conclusion:We identified a significantly shorter time to progression of JSN compared to ERO in this longitudinal cohort of RA patients. JSN remains an important radiographic outcome, as it is strongly associated with impairment of physical function. This calls for a stronger focus on cartilage damage in RA, and a stronger consideration of JSN in routine evaluation of RA radiographs in clinical practice.Disclosure of Interests:Andreas Kerschbaumer Paid instructor for: Celgene, Speakers bureau: Andreas Kerschbaumer has received lecture fees from Bristol-Myers Squibb, Gilead, Merck Sharp and Dohme and Pfizer., Farideh Alasti: None declared, Gabriela Supp: None declared, Josef S. Smolen Grant/research support from: AbbVie, Eli Lilly, Janssen, Merck Sharp & Dohme, Pfizer, Roche – grant/research support, Consultant of: AbbVie, Amgen Inc., AstraZeneca, Astro, Celgene Corporation, Celtrion, Eli Lilly, Glaxo, ILTOO, Janssen, Medimmune, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Samsung, Sanofi, UCB – consultant, Speakers bureau: AbbVie, Amgen Inc., AstraZeneca, Astro, Celgene Corporation, Celtrion, Eli Lilly, Glaxo, ILTOO, Janssen, Medimmune, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Samsung, Sanofi, UCB – speaker, Daniel Aletaha Grant/research support from: AbbVie, Novartis, Roche, Consultant of: AbbVie, Amgen, Celgene, Lilly, Medac, Merck, Novartis, Pfizer, Roche, Sandoz, Sanofi Genzyme, Speakers bureau: AbbVie, Celgene, Lilly, Merck, Novartis, Pfizer, Sanofi Genzyme, UCB
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Kaimaki, Marianna. "Tunes in Free Variation and Sequentially Determined Pitch Alignment: Evidence from Interactional Organisation." Journal of Greek Linguistics 10, no. 2 (2010): 213–50. http://dx.doi.org/10.1163/156658410x531384.
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AbstractResults arising from a study of the prosodic organisation of everyday talk in Greek suggest that 'falling' and 'rising' tunes might occur in free variation in certain interactional contexts. They also show that, at least for Greek, pitch alignment of rising tunes might be interactionally driven. I explore these possibilities by examining the organisation of two interactional sequences: a) response-to-summons turns (i.e. the first utterance by the recipient of a call) at the openings of Greek telephone calls, b) sequences involving the Greek continuer ne. Analysis of the first data set of response-to-summons turns suggests that the choice of falling or rising tune does not appear to have consequences for the design or subsequent development of the talk. Nor is there evidence in the interactional behaviour of the participants that the choice conveys a difference in pragmatic nuance. Analysis of the second data set shows that pitch alignment of rising tunes might be dependent on the interactional function and/or lexical design of the turn they occur in. I argue that choice of tune-type in this interactional context is related to particular lexical selections and that pitch alignment is related to interactional structure and composition of the turn.
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Han, Seungjae, Keonyong Lee, Seongje Cho, and Moonju Park. "Anomaly Detection Based on Temporal Behavior Monitoring in Programmable Logic Controllers." Electronics 10, no. 10 (May 20, 2021): 1218. http://dx.doi.org/10.3390/electronics10101218.
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As Programmable Logic Controllers (PLCs) are increasingly connected and integrated into the industrial Internet of things, cybersecurity threats to PLCs are also increasing. Adversaries can perform a denial of service (DoS) attack based on the transmission of a large number of network packets, and a control-logic injection attack through sophisticated packet transmission. We propose an approach to detecting and defending against attacks that exploit security vulnerabilities in a PLC system. In order to protect against indiscriminate packet transmission attacks that exploit uncontrolled resource consumption vulnerabilities, an abnormal temporal behavior detection method is proposed that monitors the CPU usage of tasks. If a temporal anomaly is detected, the proposed approach tries to detect control-flow anomalies by examining the sequences of function calls, then detects stack-based buffer overflow attacks. The proposed method is implemented in a water tank control system for evaluation purposes. The experimental results show that the proposed method can improve the security of the system by detecting anomalies in temporal behavior with little system overhead.
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Chen, Yukun, Xiaoping Xu, Xiaohui Chen, Yan Chen, Zihao Zhang, Xu Xuhan, Yuling Lin, and Zhongxiong Lai. "Seed-Specific Gene MOTHER of FT and TFL1（MFT） Involved in Embryogenesis, Hormones and Stress Responses in Dimocarpus longan Lour." International Journal of Molecular Sciences 19, no. 8 (August 14, 2018): 2403. http://dx.doi.org/10.3390/ijms19082403.
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Mother of FT and TFL1 (MFT) belongs to phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in flowering time regulation, seed development, and germination. To gain insight into the molecular function of DlMFT in Dimocarpus longan Lour., we isolated DlMFT and its promoter sequence from longan embryogenic callus (EC). Bioinformatic analysis indicated that the promoter contained multiphytohormones and light responsive regulatory elements. Subcellular localization showed that the given the DlMFT signal localized in the nucleus, expression profiling implied that DlMFT showed significant upregulation during somatic embryogenesis (SE) and zygotic embryogenesis (ZE), and particular highly expressed in late or maturation stages. The accumulation of DlMFT was mainly detected in mature fruit and seed, while it was undetected in abortive seeds, and notably decreased during seed germination. DlMFT responded differentially to exogenous hormones in longan EC. Auxins, salicylic acid (SA) and methyl jasmonate (MeJa) suppressed its expression, however, abscisic acid (ABA), brassinosteroids (BR) showed the opposite function. Meanwhile, DlMFT differentially responded to various abiotic stresses. Our study revealed that DlMFT might be a key regulator of longan somatic and zygotic embryo development, and in seed germination, it is involved in complex plant hormones and abiotic stress signaling pathways.