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Šindelář, L., and M. Šindelářová. "Regulation of metabolic pathways PVY-RNA biosynthesis in tobacco: glycolytic pathway." Plant Protection Science 40, No. 3 (March 7, 2010): 101–6. http://dx.doi.org/10.17221/991-pps.
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Tobacco plants infected with potato virus <I>Y</I> were studied at the stage of acute infection. Key enzymes of the glycolytic pathway, their regulation and the content of involved intermediates were monitored. The activities of the key enzymes of the glycolytic pathway (6-phosphofructokinase, fructosebisphosphatase and pyruvate kinase), determined in both crude homogenates and after partial purification, did not differ from the activities found in healthy control tissues. In virus-infected tissues the content of ATP was higher than in the healthy control. The levels of ADP and AMP decreased soon after inoculation, but increased at the end of the experimental period. The content of inorganic phosphate was not influenced by infection. No difference in adenylate energy charge was observed between healthy and virus-infected tissues. This implies that the rates of the glycolytic pathway <I>in vivo </I>are not altered during the acute stage of infection.
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Karatzas, Evangelos, Margarita Zachariou, Marilena M. Bourdakou, George Minadakis, Anastasis Oulas, George Kolios, Alex Delis, and George M. Spyrou. "PathWalks: identifying pathway communities using a disease-related map of integrated information." Bioinformatics 36, no. 13 (May 5, 2020): 4070–79. http://dx.doi.org/10.1093/bioinformatics/btaa291.
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Abstract Motivation Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming and costly task. Computational methodologies that propose pathway/mechanism communities and reveal respective relationships can be of great value as they can help expedite the process of identifying how perturbations in a single pathway can affect other pathways. Results We present a random-walks-based methodology called PathWalks, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study. We apply the PathWalks methodology on Alzheimer's disease and idiopathic pulmonary fibrosis and establish that it can highlight pathways that are also identified by other pathway analysis tools as well as are backed through bibliographic references. More importantly, PathWalks produces additional new pathways that are functionally connected with those already established, giving insight for further experimentation. Availability and implementation https://github.com/vagkaratzas/PathWalks. Supplementary information Supplementary data are available at Bioinformatics online.
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Midford, Peter E., Mario Latendresse, Paul E. O’Maille, and Peter D. Karp. "Using Pathway Covering to Explore Connections among Metabolites." Metabolites 9, no. 5 (May 2, 2019): 88. http://dx.doi.org/10.3390/metabo9050088.
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Interpreting changes in metabolite abundance in response to experimental treatments or disease states remains a major challenge in metabolomics. Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites in the list. We used five functions for assigning costs to pathways, including assigning a constant for all pathways, which yields a solution with the smallest pathway count; two methods that penalize large pathways; one that prefers pathways based on the pathway’s assigned function, and one that loosely corresponds to metabolic flux. The pathway covering set computed by the algorithm can be displayed as a multi-pathway diagram (“pathway collage”) that highlights the covered metabolites. We investigated the pathway covering algorithm by using several datasets from the Metabolomics Workbench. The algorithm is best applied to a list of metabolites with significant statistics and fold-changes with a specified direction of change for each metabolite. The pathway covering algorithm is now available within the Pathway Tools software and BioCyc website.
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Xu, Wen, Bei Wang, Yisong Gao, Yuxuan Cai, Jiali Zhang, Zhiyin Wu, Jiameng Wei, Chong Guo, and Chengfu Yuan. "Alkaloids Exhibit a Meaningful Function as Anticancer Agents by Restraining Cellular Signaling Pathways." Mini-Reviews in Medicinal Chemistry 22, no. 7 (April 2022): 968–83. http://dx.doi.org/10.2174/1389557521666211007114935.
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Abstract: Alkaloids are nitrogen-containing organic compounds widely found in natural products, which play an essential role in clinical treatment. Cellular signaling pathways in tumors are a series of enzymatic reaction pathways that convert extracellular signals into intracellular signals to produce biological effects. The ordered function of cell signaling pathways is essential for tumor cell proliferation, differentiation, and programmed death. This review describes the antitumor progression mediated by various alkaloids after inhibiting classical signaling pathways; related studies are systematically retrieved and collected through PubMed. We selected the four currently most popular pathways for discussion and introduced the molecular mechanisms mediated by alkaloids in different signaling pathways, including the NF-kB signaling pathway, PI3K/AKT signaling pathway, MAPK signaling pathway, and P53 signaling pathway. The research progress of alkaloids related to tumor signal transduction pathwa
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Li, Chaoxing, Li Liu, and Valentin Dinu. "Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma." PeerJ 6 (April 9, 2018): e4571. http://dx.doi.org/10.7717/peerj.4571.
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Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway’s topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher’s exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level.
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Lomberk, Gwen, and Raul Urrutia. "Primers on Molecular Pathways — Caspase Pathway." Pancreatology 9, no. 1-2 (January 2009): 6–8. http://dx.doi.org/10.1159/000178860.
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Visakh, R., and K. A. Abdul Nazeer. "Identifying epigenetically dysregulated pathways from pathway–pathway interaction networks." Computers in Biology and Medicine 76 (September 2016): 160–67. http://dx.doi.org/10.1016/j.compbiomed.2016.06.030.
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Fan, Wufeng, Yuhan Zhou, and Hao Li. "Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes." Computational and Mathematical Methods in Medicine 2017 (2017): 1–8. http://dx.doi.org/10.1155/2017/3195348.
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In our study, we aimed to extract dysregulated pathways in human monocytes infected by Listeria monocytogenes (LM) based on pathway interaction network (PIN) which presented the functional dependency between pathways. After genes were aligned to the pathways, principal component analysis (PCA) was used to calculate the pathway activity for each pathway, followed by detecting seed pathway. A PIN was constructed based on gene expression profile, protein-protein interactions (PPIs), and cellular pathways. Identifying dysregulated pathways from the PIN was performed relying on seed pathway and classification accuracy. To evaluate whether the PIN method was feasible or not, we compared the introduced method with standard network centrality measures. The pathway of RNA polymerase II pretranscription events was selected as the seed pathway. Taking this seed pathway as start, one pathway set (9 dysregulated pathways) with AUC score of 1.00 was identified. Among the 5 hub pathways obtained using standard network centrality measures, 4 pathways were the common ones between the two methods. RNA polymerase II transcription and DNA replication owned a higher number of pathway genes and DEGs. These dysregulated pathways work together to influence the progression of LM infection, and they will be available as biomarkers to diagnose LM infection.
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Loeber, Rolf, Phen Wung, Kate Keenan, Bruce Giroux, Magda Stouthamer-Loeber, Welmoet B. Van Kammen, and Barbara Maugham. "Developmental pathways in disruptive child behavior." Development and Psychopathology 5, no. 1-2 (1993): 103–33. http://dx.doi.org/10.1017/s0954579400004296.
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AbstractDevelopmental sequences in disruptive behavior from childhood to adolescence are traced retrospectively and prospectively in two community samples of boys. Three developmental pathways are distinguished: (a) an early authority conflict pathway, consisting in sequence of stubborn behavior, defiance, and authority avoidance; (b) a covert pathway, consisting of minor covert behaviors, property damage, and moderate to serious forms of delinquency; and (c) an overt pathway, consisting of aggression, fighting, and violence. The overlap among the three disruptive pathways is examined. Those boys who escalated in the overt pathway were more likely to escalate in the covert pathway than boys escalating in the covert pathway showing an escalation in the overt pathway. Escalation in the authority conflict pathway was not associated with escalation in either the overt or the covert pathways. Boys' rate of self-reported delinquency was highest for those in triple pathways (covert-overt-authority conflict) or in certain dual pathways (covert-overt, covert-authority conflict). However, by age 16 the highest rate of offending was displayed by those in the triple pathways. The rate of violent offenses was also highest for those in the triple pathways and for those in the overt and covert pathways. Results from the rate for court petitions largely supported these findings. Lowest rates of offending were observed for boys in the overt and authority conflict pathways. Implications are discussed for clinical practice and future research.
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Lomberk, Gwen, and Raul Urrutia. "Primers on Molecular Pathways —The Insulin Pathway." Pancreatology 9, no. 3 (May 2009): 203–5. http://dx.doi.org/10.1159/000200021.
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Barzi, Afsaneh, Annika Medea Lenz, Melissa J. Labonte, and Heinz-Josef Lenz. "Molecular Pathways: Estrogen Pathway in Colorectal Cancer." Clinical Cancer Research 19, no. 21 (August 21, 2013): 5842–48. http://dx.doi.org/10.1158/1078-0432.ccr-13-0325.
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Shao, Min. "Construction of an miRNA-Regulated Pathway Network Reveals Candidate Biomarkers for Postmenopausal Osteoporosis." Computational and Mathematical Methods in Medicine 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/9426280.
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We aimed to identify risk pathways for postmenopausal osteoporosis (PMOP) via establishing an microRNAs- (miRNA-) regulated pathway network (MRPN). Firstly, we identified differential pathways through calculating gene- and pathway-level statistics based on the accumulated normal samples using the individual pathway aberrance score (iPAS). Significant pathways based on differentially expressed genes (DEGs) using DAVID were extracted, followed by identifying the common pathways between iPAS and DAVID methods. Next, miRNAs prediction was implemented via calculating TargetScore values with precomputed input (log fold change (FC), TargetScan context score (TSCS), and probabilities of conserved targeting (PCT)). An MRPN construction was constructed using the common genes in the common pathways and the predicted miRNAs. Using false discovery rate (FDR) < 0.05, 279 differential pathways were identified. Using the criteria of FDR < 0.05 and logFC≥2, 39 DEGs were retrieved, and these DEGs were enriched in 64 significant pathways identified by DAVID. Overall, 27 pathways were the common ones between two methods. Importantly, MAPK signaling pathway and PI3K-Akt signaling pathway were the first and second significantly enriched ones, respectively. These 27 common pathways separated PMOP from controls with the accuracy of 0.912. MAPK signaling pathway and PI3K/Akt signaling pathway might play crucial roles in PMOP.
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Hall, Julia Cooper, Joanna M. Hamilton, David Michael Jackman, Carole Kathleen Tremonti, Teresa L. Greenberg, Victoria Hayne, Leah A. Stein, and Joseph O. Jacobson. "Analyzing pathways data to reduce unwarranted variation, understand practice patterns, and update pathways." Journal of Clinical Oncology 36, no. 30_suppl (October 20, 2018): 300. http://dx.doi.org/10.1200/jco.2018.36.30_suppl.300.
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300 Background: A clinical pathways program requires regular updates to pathways content, real-time decision support, and data collection and analysis of decisions made. A goal of Dana-Farber Pathways (DFP) is to analyze data to reduce unwarranted variation and inform granular, warranted variation. Methods: Each of our 31 medical oncology pathways is created and updated by DF experts (clinicians and scientists). DFP is implemented through a web-based portal that provides real-time decision support. DFP captures on- and off- pathway treatment decisions and reasons for off-pathway decisions; this is shared with each disease group monthly. For each interval review meeting we assess on-pathway rates and decisions for each node in the pathway. Low on-pathway rates prompt discussion about possible action, including provider education or pathway modification. Results: In 2017, 7,460 total treatment decisions were collected through DFP; 78% were on-pathway. We have clinical reasoning for 90% of the off-pathway decisions. Off-pathway analysis has been used in several important ways: 1. Catalyzing change: we detected early adoption of immunotherapy in small cell lung cancer and discussed the relevant data. The pathway was updated to adopt this class of treatment. 2. Understanding unexpected events: we identified a recent etoposide shortage and discussed alternate recommendations. They were added to the pathway in case of future shortages. 3. Provider education: we detected a consistently low on-pathway rate in one location, mostly driven by a specific provider. This provided a mechanism to discuss practice patterns and provide targeted education. Conclusions: Off-pathway analysis provides insight into user variation, fosters and supports peer coaching, and supports the creation of dynamic, up-to-date pathways.[Table: see text]
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Pian, Cong, Guangle Zhang, Libin Gao, Xiaodan Fan, and Fei Li. "miR+Pathway: the integration and visualization of miRNA and KEGG pathways." Briefings in Bioinformatics 21, no. 2 (January 16, 2019): 699–708. http://dx.doi.org/10.1093/bib/bby128.
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Abstract miRNAs represent a type of noncoding small molecule RNA. Many studies have shown that miRNAs are widely involved in the regulation of various pathways. The key to fully understanding the regulatory function of miRNAs is the determination of the pathways in which the miRNAs participate. However, the major pathway databases such as KEGG only include information regarding protein-coding genes. Here, we redesigned a pathway database (called miR+Pathway) by integrating and visualizing the 8882 human experimentally validated miRNA-target interactions (MTIs) and 150 KEGG pathways. This database is freely accessible at http://www.insect-genome.com/miR-pathway. Researchers can intuitively determine the pathways and the genes in the pathways that are regulated by miRNAs as well as the miRNAs that target the pathways. To determine the pathways in which targets of a certain miRNA or multiple miRNAs are enriched, we performed a KEGG analysis miRNAs by using the hypergeometric test. In addition, miR+Pathway provides information regarding MTIs, PubMed IDs and the experimental verification method. Users can retrieve pathways regulated by an miRNA or a gene by inputting its names.
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Ghulam, Ali, Xiujuan Lei, Min Guo, and Chen Bian. "Comprehensive Analysis of Features and Annotations of Pathway Databases." Current Bioinformatics 15, no. 8 (January 1, 2021): 803–20. http://dx.doi.org/10.2174/1574893615999200413123352.
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This study focused on describing the necessary information related to pathway mechanisms, characteristics, and databases feature annotations. Various difficulties related to data storage and retrieval in biological pathway databases are discussed. These focus on different techniques for retrieving annotations, features, and methods of digital pathway databases for biological pathway analysis. Furthermore, many pathway databases annotations, features, and search databases were also examined (which are reasonable for the integration into microarray examination). The investigation was performed on the databases, which contain human pathways to understand the hidden components of cells applied in this process. Three different domain-specific pathways were selected for this study and the information of pathway databases was extracted from the existing literature. The research compared different pathways and performed molecular level relations. Moreover, the associations between pathway networks were also evaluated. The study involved datasets for gene pathway matrices and pathway scoring techniques. Additionally, different pathways techniques, such as metabolomics and biochemical pathways, translation, control, and signaling pathways and signal transduction, were also considered. We also analyzed the list of gene sets and constructed a gene pathway network. This article will serve as a useful manual for storing a repository of specific biological data and disease pathways.
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ZHU, LING, TIMON CHENG-YI LIU, MIN WU, JIAN-QIN YUAN, and TONG-SHENG CHEN. "EXTRAOCULAR CELLULAR PHOTOTRANSDUCTION." Journal of Innovative Optical Health Sciences 02, no. 01 (January 2009): 93–100. http://dx.doi.org/10.1142/s1793545809000358.
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Photobiomodulation (PBM) is a modulation of monochromatic light or laser irradiation (LI) on biosystems. It is reviewed from the viewpoint of extraocular phototransduction in this paper. It was found that LI can induce extraocular phototransduction, and there may be an exact correspondence relationship of LI at different wavelengths and in different dose zones, and cellular signal transduction pathways. The signal transduction pathways can be classified into two types so that the Gs protein-mediated pathways belong to pathway 1, and the other pathways such as protein kinase Cs -mediated pathways and mitogen-activated protein kinase-mediated pathways belong to pathway 2. Almost all the present pathways found to mediate PBM belong to pathway 2, but there should be a pathway 1-mediated PBM. The previous studies were rather preliminary, and therefore further work should be done.
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Hu, Chenyu W., Amina A. Qutub, Yihua Qiu, Suk Young Yoo, Nianxiang Zhang, Naveen Pammaraju, Courtney D. DiNardo, Kevin R. Coombes, and Steven M. Kornblau. "A Global Proteomic Pathway Map In Acute Myeloid Leukemia (AML)." Blood 122, no. 21 (November 15, 2013): 1302. http://dx.doi.org/10.1182/blood.v122.21.1302.1302.
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Abstract Background AML has been extensively studied in a gene-to-gene and pathway-to-pathway fashion over the years, unraveling insightful local patterns that capture heterogeneity in patients and identify potential drug targets. However, our understanding of AML from a global and systems perspective is still lacking. A global proteomic pathway map is yet to be drawn to integrate local activity patterns and to translate patient classifications across pathways. This will not only improve our scientific understanding of how different functional pathways are inter-related, but will also enable us to develop more robust and effective therapeutic regimens based on pathway cross-talks. Methods A proteomic profile, containing the expression pattern of 231 proteins in each of the 415 newly diagnosed AML patients at UT MD Anderson Cancer Center, was generated using the Reverse Phase Protein Array (RPPA) technology. We grouped these proteins into 23 functional pathways based on protein association known in literature and correlation shown in the proteomic profile. Principal component analysis and scree plot were used to refine the pathway construction. The AML patients were clustered by their protein expression patterns within each individual pathway, and were then compared across pathways. The association of patient clusters between different pathways was measured by Goodman-Kruskal's (GK) tau method, indicating the predictability of patient clustering in one pathway given that in the other. This association between pathways and interchangeability of patient groupings were visualized in a circos plot (Figure 1), depicting a global proteomic pathway map. Results The global proteomic pathway map illustrates how strongly protein expression patterns of different pathways are associated, and how patient classifications under different pathways could be translated from one to another. Here, we highlight some of the key insights surfaced from this analysis. First, we identified ‘social' pathways that have intensive cross-talks with multiple other pathways, including some of the cell signal transduction pathways (MEK, PI3K, mTOR), genetic information processing pathways (transcription, histone methylation), and cell survival/death pathways (apoptosis, autophagy). We also identified ‘orphan' pathways that are more independent and are poorly associated with others. These include a subset of signal transduction pathways (pkc, tp53, S6rp, Src, Creb, Wnt), cytoskeleton and differentiation. As the association is directional, each pathway could be further characterized as either a ‘sender' or a ‘receiver' pathway based on whether it is acting more as the origin or the target of the link. The patient clusters from the ‘sender' pathways (e.g. Apoptosis, mTOR, Fli), could be easily translated to other pathways, while the patient clusters in ‘receiver' pathways (e.g. Hippo and Transcription), are highly predictable by patient clusters from multiple other pathways. We further constructed and compared the global pathway maps for patients in different cytogenetic groups. Comparison of pathway maps from patients with favorable, intermediate and unfavorable cytogenetics shows the power of this methodology to discern differences in the degree of correlation between protein functional groups. Favorable cytogenetics (T8;21) and inversion 16, because they are more similar have less patient to patient variation and thus have a more consistent and highly correlated pathway map with a higher number of connections. Conclusions Based on the RPPA data in AML patients, we built a global proteomic pathway map that captures the association between protein expression patterns in defined protein functional groups. We identified intensive interacting pathways as well as independent pathways, which indicate potential hubs and modulators of leukemic cell behavior. We further compared maps of different cytogenetic groups and revealed different correlation mappings. We are further refining the algorithms in order to study more focused changes within lower population subsets. Ultimately we believe that this will enable the matching of targeted agents to specific settings where the target is expressed and highly interactive based on proteomic data. Disclosures: No relevant conflicts of interest to declare.
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Sielsky, Kali. "A Pathway to Reconciliation within ‘North American’ Archaeology." Pathways 3, no. 1 (November 7, 2022): 1–4. http://dx.doi.org/10.29173/pathways39.
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As we begin to enter an era of reconciliation in archaeology, we must look at the foundation upon which the discipline has been built and start to dismantle the colonial ideologies which have been embedded within. A number of new practices and approaches have emerged over the past decade, through community and public based archaeology, placing the community at the forefront of the research. These newer approaches have set out to challenge the ways in which the discipline had been conducted previously, creating pathways forward for reconciliation. The following commentary is based on my experience as a student researcher and professional archaeologist over the past six years ─ experience which has been shaped by my identity and the lens it informs and which offers only one perspective towards the important and emerging narrative on reconciliation within archaeology.
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Brennan, Tim, Markus Breitenbach, William Dieterich, Emily J. Salisbury, and Patricia van Voorhis. "Women’s Pathways to Serious and Habitual Crime." Criminal Justice and Behavior 39, no. 11 (October 5, 2012): 1481–508. http://dx.doi.org/10.1177/0093854812456777.
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Qualitative approaches for identifying and characterizing women’s pathways to crime are being augmented by quantitative methods. This study applies quantitative taxonomic methods in disaggregating a large sample of women offenders from a prison population to identify diverse pathway prototypes. An array of gender-responsive and gender-neutral factors and full criminal histories was used to characterize each pathway. Cross-sample and cross-method replication tests demonstrated the stable replication of these pathways. The identified prototypes were related to the prior literature, including Daly’s pathway models, Moffitt’s developmental taxonomy, and several prior taxonomic studies of women’s pathways. Eight reliable pathways were identified that were nested within four broad, superordinate pathway categories. Substantial links to the prior pathways literature were noted, although greater complexity was found to exist in the eight identified pathways.
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Hansen, Jens B., Jens F. L. Sørensen, Eva N. Glassou, Morten Homilius, and Torben B. Hansen. "Reducing patient–staff contact in fast-track total hip arthroplasty has no effect on patient-reported outcomes, but decreases satisfaction amongst patients with self-perceived complications: analysis of 211 patients." Acta Orthopaedica 93 (January 24, 2022): 264–70. http://dx.doi.org/10.2340/17453674.2022.1617.
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Background and purpose: Several studies have compared fast-track with conventional pathways for total hip arthroplasty (THA) patients, but none have compared different fast-track pathways. Due to COVID-19 restrictions, our department had to minimize patient–staff contact in the THA pathway. First, telephone consultations were implemented instead of an outpatient clinic visit and subsequently preoperative patient education was discontinued. This enabled us to compare patient-reported outcomes and satisfaction among 3 fast-track pathways. Patients and methods: We collected data from patients treated for hip osteoarthritis with THA at Gødstrup Hospital between 2018 and 2021. The patients had experienced 1 of 3 pathways and were interviewed via telephone between 2 and 6 months after discharge. We analyzed the influence of patient pathway on patient-reported pain and mobility level, self-perceived complications, and compliance using logistic regression. We then compared the pathway’s effect on patient satisfaction both for the total sample and for the patients who experienced complications. Results: The amount of patient–staff contact in the patient pathway did not have any influence on patientreported outcomes or the probability of self-perceived complications. For the full sample, patient–staff contact had no statistically significant influence on patient satisfaction either, but for the subgroup of patients experiencing complications, the pathways with less patient–staff contact reducedsatisfaction. Patient satisfaction was primarily related to pain and mobility outcomes. Interpretation: Our results indicate that reducing patient–staff contact in fast-track THA can be done without influencing mobility and pain outcomes, but the overall satisfaction among patients with self-perceived complications will be negatively affected.
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Rosique, Ricard. "Do we need electronic support for pathways: the Spanish experience." International Journal of Care Pathways 13, no. 2 (November 2009): 67–74. http://dx.doi.org/10.1258/jicp.2009.009010.
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Care pathways are excellent tools for quality management in health care concerning the standardization of care processes, as they promote organized and efficient patient care established on evidence-based practice. The implementation of a care pathway project at any health-care setting means a change of the organizational culture. E-pathways (electronic pathways) are strategic resources in order to get the successful implementation of a care pathway project. The concept of e-pathway is recent enough and there are some different experiences worldwide. In 2000, the first electronic pathways were implemented at Hospital de Mataró, in Barcelona, Spain. The benefits of using e-pathways (Eira Healthcare Server) are very clear at Hospital de Mataró: immediate records with no transcriptions, information in the palm of your hand, no prints, and rigour and reliability. Another recent and interesting experience is the development and introduction of e-pathways at Hospital General de l'Hospitalet, in Barcelona, Spain, using an SAP integrated health-care solution. The strategy planning of hospital managers should take into account the need and priority of any pathway project linked to e-pathways. Some experiences in Spain have proven that we do really need electronic support for pathways. Electronic pathways are a basic support and should not be postponed when implementing care pathways.
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Cai, Binghuang, and Xia Jiang. "Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data Using Gene Set Enrichment Analysis." Cancer Informatics 13s1 (January 2014): CIN.S13882. http://dx.doi.org/10.4137/cin.s13882.
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Analyzing biological system abnormalities in cancer patients based on measures of biological entities, such as gene expression levels, is an important and challenging problem. This paper applies existing methods, Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis, to pathway abnormality analysis in lung cancer using microarray gene expression data. Gene expression data from studies of Lung Squamous Cell Carcinoma (LUSC) in The Cancer Genome Atlas project, and pathway gene set data from the Kyoto Encyclopedia of Genes and Genomes were used to analyze the relationship between pathways and phenotypes. Results, in the form of pathway rankings, indicate that some pathways may behave abnormally in LUSC. For example, both the cell cycle and viral carcinogenesis pathways ranked very high in LUSC. Furthermore, some pathways that are known to be associated with cancer, such as the p53 and the PI3K-Akt signal transduction pathways, were found to rank high in LUSC. Other pathways, such as bladder cancer and thyroid cancer pathways, were also ranked high in LUSC.
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Lojk, Jasna, and Janja Marc. "Roles of Non-Canonical Wnt Signalling Pathways in Bone Biology." International Journal of Molecular Sciences 22, no. 19 (October 7, 2021): 10840. http://dx.doi.org/10.3390/ijms221910840.
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The Wnt signalling pathway is one of the central signalling pathways in bone development, homeostasis and regulation of bone mineral density. It consists of numerous Wnt ligands, receptors and co-receptors, which ensure tight spatiotemporal regulation of Wnt signalling pathway activity and thus tight regulation of bone tissue homeostasis. This enables maintenance of optimal mineral density, tissue healing and adaptation to changes in bone loading. While the role of the canonical/β-catenin Wnt signalling pathway in bone homeostasis is relatively well researched, Wnt ligands can also activate several non-canonical, β-catenin independent signalling pathways with important effects on bone tissue. In this review, we will provide a thorough overview of the current knowledge on different non-canonical Wnt signalling pathways involved in bone biology, focusing especially on the pathways that affect bone cell differentiation, maturation and function, processes involved in bone tissue structure regulation. We will describe the role of the two most known non-canonical pathways (Wnt/planar cell polarity pathways and Wnt/Ca2+ pathway), as well as other signalling pathways with a strong role in bone biology that communicate with the Wnt signalling pathway through non-canonical Wnt signalling. Our goal is to bring additional attention to these still not well researched but important pathways in the regulation of bone biology in the hope of prompting additional research in the area of non-canonical Wnt signalling pathways.
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Lu, Chun-Juan, Yan Wang, Ya-Li Huang, and Xin-Hua Li. "Individualized identification of disturbed pathways in sickle cell disease." Open Life Sciences 12, no. 1 (December 29, 2017): 418–24. http://dx.doi.org/10.1515/biol-2017-0049.
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AbstractBackgroundSickle cell disease (SCD) is one of the most common genetic blood disorders. Identifying pathway aberrance in an individual SCD contributes to the understanding of disease pathogenesis and the promotion of personalized therapy. Here we proposed an individualized pathway aberrance method to identify the disturbed pathways in SCD.MethodsBased on the transcriptome data and pathway data, an individualized pathway aberrance method was implemented to identify the altered pathways in SCD, which contained four steps: data preprocessing, gene-level statistics, pathway-level statistics, and significant analysis. The changed percentage of altered pathways in SCD individuals was calculated, and a differentially expressed gene (DEG)-based pathway enrichment analysis was performed to validate the results.ResultsWe identified 618 disturbed pathways between normal and SCD conditions. Among them, 6 pathways were altered in > 80% SCD individuals. Meanwhile, forty-six DEGs were identified between normal and SCD conditions, and were enriched in heme biosynthesis. Relative to DEG-based pathway analysis, the new method presented richer results and more extensive application.ConclusionThis study predicted several disturbed pathways via detecting pathway aberrance on a personalized basis. The results might provide new sights into the pathogenesis of SCD and facilitate the application of custom treatment for SCD.
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Graff, Stephanie L., Jared M. Holder, Lindsay E. Sears, and Dax Kurbegov. "Increase in Genetic Counseling and Testing Referrals After Breast Cancer Pathway Implementation." JCO Oncology Practice 16, no. 12 (December 2020): e1481-e1488. http://dx.doi.org/10.1200/jop.19.00552.
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PURPOSE: Genetic counseling and testing (GC/T) for breast cancer–associated genetic mutations are important components in the appropriate management of newly diagnosed breast cancer. We initiated pathways to help appropriately select patients who meet criteria for GC/T referral (GC/T-R) across the Sarah Cannon Cancer Institute Network. This study evaluated physician pathway training as a means to improve access to GC/T-R. METHODS: In this retrospective, observational study, we collected data from 7 regions across 6 states, identifying 3,113 patients eligible for GC/T. Patients were divided into 3 defined cohorts: patients treated before implementation of pathways (n = 988), patients treated by non-pathway physicians after pathways were established (n = 1,094), and patients treated by pathway-trained physicians (n = 1,031). Pathways were established in March 2016. Nurse navigators documented eligible patients who were referred for GC/T within a care coordination software system. RESULTS: Eligible patients were referred for GC/T 71.77% of the time if treated on pathways and only 36.47% of the time if treated off pathways. On-pathway patients eligible for GC/T also received testing referral at a higher rate than pre-pathway patients (21.36%). CONCLUSION: After implementation of pathways and appropriate training of physicians on those pathways, GC/T-R among appropriate patients significantly improved. Pathway training represents a potential solution to improve GC/T-R among patients with breast cancer.
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Nishide, Yudai, Daisuke Kageyama, Kakeru Yokoi, Akiya Jouraku, Hiromitsu Tanaka, Ryo Futahashi, and Takema Fukatsu. "Functional crosstalk across IMD and Toll pathways: insight into the evolution of incomplete immune cascades." Proceedings of the Royal Society B: Biological Sciences 286, no. 1897 (February 20, 2019): 20182207. http://dx.doi.org/10.1098/rspb.2018.2207.
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In insects, antimicrobial humoral immunity is governed by two distinct gene cascades, IMD pathway mainly targeting Gram-negative bacteria and Toll pathway preferentially targeting Gram-positive bacteria, which are widely conserved among diverse metazoans. However, recent genomic studies uncovered that IMD pathway is exceptionally absent in some hemipteran lineages like aphids and assassin bugs. How the apparently incomplete immune pathways have evolved with functionality is of interest. Here we report the discovery that, in the hemipteran stinkbug Plautia stali , both IMD and Toll pathways are present but their functional differentiation is blurred. Injection of Gram-negative bacteria and Gram-positive bacteria upregulated effector genes of both pathways. Notably, RNAi experiments unveiled significant functional permeation and crosstalk between IMD and Toll pathways: RNAi of IMD pathway genes suppressed upregulation of effector molecules of both pathways, where the suppression was more remarkable for IMD effectors; and RNAi of Toll pathway genes reduced upregulation of effector molecules of both pathways, where the suppression was more conspicuous for Toll effectors. These results suggest the possibility that, in hemipterans and other arthropods, IMD and Toll pathways are intertwined to target wider and overlapping arrays of microbes, which might have predisposed and facilitated the evolution of incomplete immune pathways.
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Toy, Jennifer M., Adam Drechsler, and Richard C. Waters. "Clinical pathways for primary care: current use, interest and perceived usability." Journal of the American Medical Informatics Association 25, no. 7 (February 26, 2018): 901–6. http://dx.doi.org/10.1093/jamia/ocy010.
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Abstract Objective Translating clinical evidence to daily practice remains a challenge and may improve with clinical pathways. We assessed interest in and usability of clinical pathways by primary care professionals. Methods An online survey was created. Interest in pathways for patient care and learning was assessed at start and finish. Participants completed baseline questions then pathway-associated question sets related to management of 2 chronic diseases. Perceived pathway usability was assessed using the system usability scale. Accuracy and confidence of answers was compared for baseline and pathway-assisted questions. Results Of 115 participants, 17.4% had used clinical pathways, the lowest of decision support tool types surveyed. Accuracy and confidence in answers significantly improved for all pathways. Interest in using pathways daily or weekly was above 75% for the respondents. Conclusion There is low utilization of, but high interest in, clinical pathways by primary care clinicians. Pathways improve accuracy and confidence in answering written clinical questions.
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Csik, Valerie Pracilio, Jared Minetola, Karen Walsh, Michael J. Ramirez, and Mark Hurwitz. "Pathways impact on OCM drug cost." Journal of Clinical Oncology 37, no. 27_suppl (September 20, 2019): 109. http://dx.doi.org/10.1200/jco.2019.37.27_suppl.109.
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109 Background: Oncology care, including drugs, represents a significant portion of US healthcare spending. Cost of Part B drugs has increased at a rate 5.7x that of overall Medicare spending (1997-2004). As a participant in the Oncology Care Model (OCM), we found drug costs represent a majority of our total costs. To reduce treatment (Tx) variability, our NCI-designated cancer center chose to implement pathways. Pathways are a clinical decision-support tool that use evidence-based care maps accounting for efficacy, toxicity and cost. At one institution, use of pathways contributed to $15k in savings for stage IV lung cancer Tx. We hypothesized pathway driven Tx standardization would favorably impact total chemotherapy (CTx) costs at the implementation site. Methods: In July 2018, we implemented pathways in Medical and Radiation Oncology for new starts or changes in Tx. Oncologists accessed the tool through our EMR, selected and placed orders for Tx. OCM quarterly data was used to compare 2 quarters immediately pre- and post-pathway implementation. The cancer-mix-adjusted Per-Member-Per-Month (PMPM) Allowed Amounts for CTx were compared between 3 groups; patients on-pathway, patients off-pathway and patients for which the pathways tool was not used (no utilization). PMPMs were evaluated pre- and post-implementation and an ANOVA test was used to evaluate significance of the difference between the two periods. Results: PMPM CTx costs decreased 4.6% between pre- and post-pathway implementation when oncologists followed pathways. By comparison, the off-pathway cohort and the no utilization groups had increases of 0.9% and 17.7% respectively. An evaluation of cost difference proved significant (p < .0001). Breast patients on-pathway had a cost decrease of 20%, compared to increases of 32% and 11% for off-pathway and no utilization groups, respectively. Conclusions: Pathway use reduced variation, a known contributor to healthcare costs, and therefore may be an effective cost control tool. Additional quarters of claims data is needed post-implementation to fully define the impact of pathways on total cost. [Table: see text]
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Breit, M., B. Pfeifer, C. Baumgartner, R. Modre-Osprian, B. Tilg, and M. Visvanathan. "DMSP – Database for Modeling Signaling Pathways." Methods of Information in Medicine 47, no. 02 (2008): 104–48. http://dx.doi.org/10.3414/me0461.
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Summary Objectives: Presently, the protein interaction information concerning different signaling pathways is available in a qualitative manner in different online protein interaction databases. The challenge here is to derive a quantitative way of modeling signaling pathways from qualitative way of modeling signaling pathways from a qualitative level. To address this issue we developed a database that includes mathematical modeling knowledge and biological knowledge about different signaling pathways. Methods: The database is part of an integrative environment that includes environments for pathway design, visualization, simulation and a knowledge base that combines biological and modeling information concerning pathways. The system is designed as a client-server architecture. It contains a pathway designing environment and a simulation environment as upper layers with a relational knowledge base as the underlying layer. Results: DMSP – Database for Modeling Signaling Pathways incorporates biological datasets from online databases like BIND, DIP, PIP, and SPiD. The modeling knowledge that has been incorporated is based on a literature study. Pathway models can be designed, visualized and simulated based on the knowledge stored in the DMSP. The user can download the whole dataset and build pathway models using the knowledge stored in our database. As an example, the TNF? pathway model was implemented and tested using this approach. Conclusion: DMSP is an initial step towards the aim of combining modeling and biological knowledge concerning signaling pathways. It helps in understanding pathways in a qualitative manner from a qualitative level. Simulation results enable the interpretation of a biological system from a quantitative and systemtheoretic point of view.
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Ibrahim Khayatt, Barzan. "Automated Reconstruction and Manual Curation of Amino Acid Biosynthesis Pathways in Sulfolobus solfataricus P2." Ibn AL-Haitham Journal For Pure and Applied Sciences 32, no. 3 (September 11, 2019): 1–18. http://dx.doi.org/10.30526/32.3.2271.
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The efficient sequencing techniques have significantly increased the number of genomes that are now available, including the Crenarchaeon Sulfolobus solfataricus P2 genome. The genome-scale metabolic pathways in Sulfolobus solfataricus P2 were predicted by implementing the “Pathway Tools†software using MetaCyc database as reference knowledge base. A Pathway/Genome Data Base (PGDB) specific for Sulfolobus solfataricus P2 was created. A curation approach was carried out regarding all the amino acids biosynthetic pathways. Experimental literatures as well as homology-, orthology- and context-based protein function prediction methods were followed for the curation process. The “PathoLogic†component of the “Pathway Tools†programme was able to predict many amino acid biosynthetic metabolic pathways. The total number of the metabolic pathways was modified to 168 pathways by adding extra pathways that have not been detected by the “PathoLogicâ€. Amino acid biosynthetic pathways such as alpha-aminoadipic acid (AAA) pathway of Lysine biosynthesis and Alanine biosynthesis as well as the super-pathway of Phenylalanine, Tyrosine and Tryptophan biosynthesis variation II were added to the Pathway/Genome data base of Sulfolobus solfataricus P2. Discovery of the missing enzymes that have to fill in the metabolic holes in the pathways under study was the main curation task. This approach and the curated amino acid biosynthetic pathways in the PGDB of Sulfolobus solfataricus P2 can be used for genomic annotations and metabolic pathway reconstructions of closely related Bacteria and Archaea.
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Jennings, Paul. "Stress response pathways, toxicity pathways and adverse outcome pathways." Archives of Toxicology 87, no. 1 (November 13, 2012): 13–14. http://dx.doi.org/10.1007/s00204-012-0974-4.
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Pandey, Manoj, Monika Rajput, Pooja Singh, Mridula Shukla, Bin Zhu, and Jill Koshiol. "Aspirin and Cancer Survival: An Analysis of Molecular Mechanisms." Cancers 16, no. 1 (January 3, 2024): 223. http://dx.doi.org/10.3390/cancers16010223.
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The benefit of aspirin on cancer survival is debated. Data from randomized clinical trials and cohort studies are discordant, although a meta-analysis shows a clear survival advantage when aspirin is added to the standard of care. However, the mechanism by which aspirin improves cancer survival is not clear. A PubMed search was carried out to identify articles reporting genes and pathways that are associated with aspirin and cancer survival. Gene ontology and pathway enrichment analysis was carried out using web-based tools. Gene–gene and protein–protein interactions were evaluated. Crosstalk between pathways was identified and plotted. Forty-one genes were identified and classified into primary genes (PTGS2 and PTGES2), genes regulating cellular proliferation, interleukin and cytokine genes, and DNA repair genes. The network analysis showed a rich gene–gene and protein–protein interaction between these genes and proteins. Pathway enrichment showed the interleukin and cellular transduction pathways as the main pathways involved in aspirin-related survival, in addition to DNA repair, autophagy, extracellular matrix, and apoptosis pathways. Crosstalk of PTGS2 with EGFR, JAK/AKT, TP53, interleukin/TNFα/NFκB, GSK3B/BRCA/PARP, CXCR/MUC1, and WNT/CTNNB pathways was identified. The results of the present study demonstrate that aspirin improves cancer survival by the interplay of 41 genes through a complex mechanism. PTGS2 is the primary target of aspirin and impacts cancer survival through six primary pathways: the interleukin pathway, extracellular matrix pathway, signal transduction pathway, apoptosis pathway, autophagy pathway, and DNA repair pathway.
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G Masiutin, Maxim, and Maneesh K Yadav. "Alternative androgen pathways." WikiJournal of Medicine 10, no. 1 (2023): X. http://dx.doi.org/10.15347/wjm/2023.003.
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Steroidogenic routes to androgens have been discovered and characterized over the last two decades that fall outside the Δ4 and Δ5 "classical androgen pathways" to testosterone and 5α-dihydrotestosterone. There has been considerable investigation into these routes that has come with natural inconsistencies and overlap in naming that can make it difficult to discover information about them as might be needed in a clinical context. This expository review uses "alternative androgen pathways" to include what has been called the "backdoor" pathway to 5α-dihydrotestosterone, the 5α-dione pathway and pathways to 11-oxygenated steroids. A brief history of what led to the discovery of these pathways, basic information about the steroids and proteins involved in their biosynthesis as well as a summary of clinically significant findings is provided. PubChem CIDs for all steroids have been compiled to help authors avoid naming errors in their work. Modest suggestions for future work in these pathways are also given at the end. Patient comprehension and the clinical diagnosis of relevant conditions such as hyperandrogenism can be impaired by the lack of clear and consistent knowledge of alternative androgen pathways; the authors hope this review will accurately disseminate such knowledge to facilitate the beneficial treatment of such patients.
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Von Gerhardt, K., A. Van Niekerk, M. Kidd, M. Samways, and J. Hanks. "The role of elephantLoxodonta africanapathways as a spatial variable in crop-raiding location." Oryx 48, no. 3 (February 13, 2014): 436–44. http://dx.doi.org/10.1017/s003060531200138x.
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AbstractShort-range elephantLoxodonta africanamovements were examined in a heterogeneous landscape mosaic of settlements, crop fields and remnant forest in the Caprivi Strip, Namibia. We explored the penetration of the landscape through the use of permanent pathways and determined the impact of pathway use on crop-raiding location. Pathways were linear, devoid of vegetation and maintained by repeated movement. Functional connectivity of pathways was not species-specific, and pathways were used by various species. Elephants travelled in single file at night and we recorded selective pathway use: females selected pathways away from settlements to access water, whereas males used pathways among settlements to launch crop raids. Proximity of raided fields to the nearest pathway was the only significant spatial variable explaining crop-raiding location. Bulls were responsible for all crop-raiding incidents. We conclude that (1) pathways were the most significant spatial variable influencing which fields were raided, (2) crop-raiding from pathways may maximize foraging efficiency by reducing time spent and distance travelled while foraging, (3) pathways may facilitate penetration of the matrix by connecting predictable resources (crops) with preferred shelter areas, crossing points at roads and preferred drinking spots, and (4) access to the Kwandu River is restricted by settlements, predictably resulting in human–elephant conflict. By highlighting the relevance of pathways for movement of elephants we show that an understanding of the use of pathways is important for land-use planning in conservation landscapes, specifically with regard to human–elephant conflict. We also argue for the need to more fully explore pathway occurrence and use at larger spatial scales.
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Agoubi, Lauren L., Nina M. Clark, Sarah Gibbs, Barclay T. Stewart, Xinyao G. DeGrauw, Monica S. Vavilala, Frederick P. Rivara, Saman Arbabi, and Tam N. Pham. "Implementation evaluation of tiered tele-triage pathways for burn center consultations and transfers." Journal of Trauma and Acute Care Surgery 96, no. 3 (December 21, 2023): 409–17. http://dx.doi.org/10.1097/ta.0000000000004202.
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BACKGROUND Early transfer to specialized centers improves trauma and burn outcomes; however, overtriage can result in unnecessary burdens to patients, providers, and health systems. Our institution developed novel burn triage pathways in 2016 to improve resource allocation. We evaluated the implementation of these pathways, analyzing trends in adoption, resource optimization, and pathway reliability after implementation. METHODS Triage pathways consist of transfer nurses (RNs) triaging calls based on review of burn images and clinical history: green pathway for direct outpatient referral, blue pathway for discussion with the on-call provider, red pathway for confirmation of transfer as requested by referring provider, and black pathway for the rapid transfer of severe burns. We used the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) framework to evaluate implementation. These pathways affected all acute burn referrals to our center from January 2017 to December 2019 (reach). Outcomes of interest were pathway assignment over time (adoption), changes to burn provider call volume (effectiveness), and the concordance of pathway assignment with final disposition (implementation reliability). RESULTS Transfer RNs triaged 5,272 burn referrals between 2017 and 2019. By January 2018, >98% of referrals were assigned a pathway. In 2018–2019, green pathway calls triaged by RNs reduced calls to burn providers by a mean of 40 (SD, 11) per month. Patients in green/blue pathways were less likely to be transferred, with >85% receiving only outpatient follow-up (p < 0.001). Use of the lower acuity pathways increased over time, with a concordant decrease in use of the higher acuity pathways. Younger adults, patients referred from Level III to Level V trauma centers and nontrauma hospitals, and patients referred by APPs were less likely to be triaged to higher acuity pathways. CONCLUSION Implementation of highly adopted, reliable triage pathways can optimize existing clinical resources by task-shifting triage of lower acuity burns to nursing teams. LEVEL OF EVIDENCE Prognostic and Epidemiological; Level III.
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Csik, Valerie Pracilio, Michael J. Ramirez, Adam F. Binder, and Nathan Handley. "The value of pathways on drug costs." Journal of Clinical Oncology 39, no. 28_suppl (October 1, 2021): 327. http://dx.doi.org/10.1200/jco.2020.39.28_suppl.327.
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327 Background: Oncology care represents a significant portion of US healthcare spending. Cost of Part B drugs has increased at a rate 5.7x that of overall Medicare spending. As a participant in the Oncology Care Model, drug costs represent a majority of our total costs. Pathways are a clinical decision-support tool that use evidence-based care maps accounting for efficacy, toxicity and cost. Our NCI-designated cancer center implemented pathways in July 2018 to reduce care variation and decrease costs. Methods: We reviewed costs related to pathway utilization over a two year period, analyzing differences in total annual drug cost for patients in three categories: On-Pathway (aligned with pathway recommendation), Off-Pathway (not aligned with recommendation), and No Pathway (not used). Per Member Per Month (PMPM) costs were calculated and a weighted average applied to account for changes in annual drug costs. Results: PMPM drug costs decreased -8% in year 1 (FY19) and -4% in year 2 (FY20) when pathways were used (On- and Off-Pathway). When pathways were followed (On-Pathway) in making treatment decisions, the drug costs were 11% lower than when pathways were not used. The annual impact on drug costs when pathways were used amounted to $2.45 million in year 1 and $1.77 million in year 2 (Table). Conclusions: Pathway use reduced drug costs, a significant variable in oncology value-based care models. This finding highlights the value of clinical decision support tools in reducing care variability, a known contributor to health care costs, in making treatment decisions. Further assessment is needed to determine if these results are similar at other cancer centers to fully realize the impact of pathways on drug costs.[Table: see text]
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Ellershaw, John, and Deborah Murphy. "The National Pathway Network of Palliative Care Pathways." Journal of integrated Care Pathways 7, no. 1 (April 2003): 11–13. http://dx.doi.org/10.1177/147322970300700104.
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Lapébie, Pascal, Carole Borchiellini, and Evelyn Houliston. "Dissecting the PCP pathway: One or more pathways?" BioEssays 33, no. 10 (August 23, 2011): 759–68. http://dx.doi.org/10.1002/bies.201100023.
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McGrannachan, Chris M., Shyama Pagad, and Melodie A. McGeoch. "A multiregional assessment of transnational pathways of introduction." NeoBiota 64 (January 20, 2021): 43–67. http://dx.doi.org/10.3897/neobiota.64.60642.
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Information on the pathways by which alien taxa are introduced to new regions is vital for prioritising policy and management responses to invasions. However, available datasets are often compiled using disparate methods, making comparison and collation of pathway data difficult. Using a standardised framework for recording and categorising pathway data can help to rectify this problem and provide the information necessary to develop indicators for reporting on alien introductions. We combine the Convention on Biological Diversity’s Pathways Categorisation Scheme (CPC) with data compiled by the Invasive Species Specialist Group (ISSG) to report on multiregional trends on alien introduction pathways over the past 200+ years. We found a significant increase in the documented number of multiregional alien introduction events across all pathways of the CPC’s three hierarchical levels. The ‘escape’ pathway is the most common documented pathway used by alien taxa. Transport stowaways via shipping-related pathways are a rapidly increasing contribution to alien introductions. Most alien introduction events were of unknown pathway origin, highlighting the challenge of information gaps in pathway data and reiterating the need for standardised information-gathering practices. Combining the CPC framework with alien introduction pathways data will standardise pathway information and facilitate the development of global indicators of trends in alien introductions and the pathways they use. These indicators have the potential to inform policy and management strategies for preventing future biological invasions and can be downscaled to national and regional levels that are applicable across taxa and ecosystems.
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Babovic, Filip, and Ana Mijic. "Economic Evaluation of Adaptation Pathways for an Urban Drainage System Experiencing Deep Uncertainty." Water 11, no. 3 (March 14, 2019): 531. http://dx.doi.org/10.3390/w11030531.
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As Decision Making under Deep Uncertainty methodologies are becoming more widely utilised, there has been a growth in the use and generation of Adaptation Pathways. These are meant to convey to policy makers how short-term adaptations can act as elements of longer-term adaptation strategies. However, sets of Adaptation Pathways do not convey the individual pathway’s relative costs and benefits. To address this problem in relation to urban pluvial flooding, an economic analysis of a set of Adaptation Pathways was conducted. Initially, a methodology to conduct an economic assessment for deterministic climate change scenarios is developed. This methodology is then modified, using methods that underpin real options to assess how a pathway performs across a bundle of possible futures. This delivered information on how the performance of adaptations can vary across different climate change scenarios. By comparing the deterministic analysis to the new method, it was found that the order in which options are implemented greatly affects the financial performance of an Adaptation Pathway, even if the final combination of options is identical. The presented methodology has the potential to greatly improve decision making by informing policy makers on the potential performance of adaptation strategies being considered.
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Zhang, Tong, Zhen Cui, Chunyan Xu, Wenming Zheng, and Jian Yang. "Variational Pathway Reasoning for EEG Emotion Recognition." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 03 (April 3, 2020): 2709–16. http://dx.doi.org/10.1609/aaai.v34i03.5657.
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Research on human emotion cognition revealed that connections and pathways exist between spatially-adjacent and functional-related areas during emotion expression (Adolphs 2002a; Bullmore and Sporns 2009). Deeply inspired by this mechanism, we propose a heuristic Variational Pathway Reasoning (VPR) method to deal with EEG-based emotion recognition. We introduce random walk to generate a large number of candidate pathways along electrodes. To encode each pathway, the dynamic sequence model is further used to learn between-electrode dependencies. The encoded pathways around each electrode are aggregated to produce a pseudo maximum-energy pathway, which consists of the most important pair-wise connections. To find those most salient connections, we propose a sparse variational scaling (SVS) module to learn scaling factors of pseudo pathways by using the Bayesian probabilistic process and sparsity constraint, where the former endows good generalization ability while the latter favors adaptive pathway selection. Finally, the salient pathways from those candidates are jointly decided by the pseudo pathways and scaling factors. Extensive experiments on EEG emotion recognition demonstrate that the proposed VPR is superior to those state-of-the-art methods, and could find some interesting pathways w.r.t. different emotions.
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Luo, Pan, Lin Liu, Weikun Hou, Ke Xu, and Peng Xu. "Gene Set Enrichment Analysis Detected Immune Cell-Related Pathways Associated with Primary Sclerosing Cholangitis." BioMed Research International 2022 (August 26, 2022): 1–9. http://dx.doi.org/10.1155/2022/2371347.
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Aim. To explore various immune cell-related causal pathways for primary sclerosing cholangitis (PSC). Methods. Immune cell-related pathway association study was conducted via integrative analysis of PSC GWAS summary and five immune cell-related eQTL datasets. The GWAS summary data of PSC was driven from 4,796 PSC cases and 19,955 healthy controls. The eQTL datasets of CD4+ T cells, CD8+ T cells, B cells, natural killer cells (NK), monocytes, and peripheral blood cells (PB) were collected from recently eQTL study. The PSC GWAS summary dataset was first aligned with eQTL datasets of six blood cells to obtain the GWAS summary data at overlapped eQTL loci, separately. For each type of cell, the obtained PSC GWAS summary dataset of eQTLs was subjected to pathway enrichment analysis. 853 biological pathways from Kyoto Encyclopedia of Genes and Genomes, BioCarta, and Reactome pathway databases were analyzed. Results. We identified 36 pathways for B cells, 33 pathways for CD4+ T cells, 28 pathways for CD8+ T cells, 33 pathways for monocytes (MN), 35 pathways for NK cells, and 33 for PB cells (all empirical P values < 5.0 × 10 − 5 ). Comparing the pathway analysis results detected 25 pathways shared by five immune cells, such as KEGG_CELL_ADHESION_MOLECULES_CAMS ( P value < 5.0 × 10 − 5 ) and REACTOME_MHC_CLASS_II_ANTIGEN_ PRESENTATION ( P value < 5.0 × 10 − 5 ). Several cell-specific pathways were also identified, including BIOCARTA_INFLAM_PATHWAY ( P value < 5 × 10 − 5 ) for B cell. Conclusion. Our study holds potential to identify novel candidate causal pathways and provides clues for revealing the complex genetic mechanism of PSC.
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Ortega, Davi R., Aaron D. Fleetwood, Tino Krell, Caroline S. Harwood, Grant J. Jensen, and Igor B. Zhulin. "Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa." Proceedings of the National Academy of Sciences 114, no. 48 (November 13, 2017): 12809–14. http://dx.doi.org/10.1073/pnas.1708842114.
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In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein–protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in P. aeruginosa utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor–pathway interactions.
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Friedman, Marcia A., Dongseok Choi, Stephen R. Planck, James T. Rosenbaum, and Cailin H. Sibley. "Gene Expression Pathways across Multiple Tissues in Antineutrophil Cytoplasmic Antibody-associated Vasculitis Reveal Core Pathways of Disease Pathology." Journal of Rheumatology 46, no. 6 (January 15, 2019): 609–15. http://dx.doi.org/10.3899/jrheum.180455.
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Objective.To identify commonalities in gene expression data across all antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis (AAV) tissues thus far characterized.Methods.Gene expression data were collected from the 3 AAV tissues thus far characterized (orbit, peripheral leukocytes, and sinus brushings). These data were analyzed to identify commonly expressed genes and disease pathways. The pathways data were adjusted for multiple comparisons using a combined local false discovery rate, which estimates the probability of a false discovery of a given pathway in all 3 tissues analyzed.Results.Only 4 genes were upregulated in all 3 tissues — IL1RN, TLR2, SLC11A1, and MMP9. After multiple comparison adjustments, the network pathway analysis revealed 28 pathways associated with all 3 tissues. The most strongly associated pathway for all 3 tissues was the neutrophil degranulation pathway [multidimensional local false discovery (md-locfdr) = 1.05 × 10−12], followed by the osteoclast differentiation (md-locfdr = 3.8 × 10−05), cell surface interactions at the vascular wall (md-locfdr = 4.2 × 10−04), signaling by interleukins (md-locfdr = 6.1 × 10−04), and phagosome (md-locfdr = 0.003) pathways. There were no downregulated genes or pathways common to all 3 tissues.Conclusion.This analysis identified individual genes and pathways of disease common to all AAV tissues thus far characterized. The use of a network pathway analysis allowed us to identify pathologic mechanisms that were not readily apparent in the commonly expressed genes alone. Many of these pathways are consistent with current theories about infectious drivers and the crossroads of innate and adaptive immune mechanisms. In addition, this analysis highlights novel pathways, such as vessel wall interactions and platelet activation, which require further investigation.
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Grümmer, R., S. W. Hewitt, O. Traub, K. S. Korach, and E. Winterhager. "Different Regulatory Pathways of Endometrial Connexin Expression: Preimplantation Hormonal-Mediated Pathway Versus Embryo Implantation-Initiated Pathway1." Biology of Reproduction 71, no. 1 (July 1, 2004): 273–81. http://dx.doi.org/10.1095/biolreprod.103.024067.
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Curry, W. B., M. D. Grabe, I. V. Kurnikov, S. S. Skourtis, D. N. Beratan, J. J. Regan, A. J. A. Aquino, P. Beroza, and J. N. Onuchic. "Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins." Journal of Bioenergetics and Biomembranes 27, no. 3 (June 1995): 285–93. http://dx.doi.org/10.1007/bf02110098.
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Zhang, Yuxia, Cui Liu, Jingna Wang, and Xingxia Li. "Application of Monte Carlo cross-validation to identify pathway cross-talk in neonatal sepsis." Experimental Biology and Medicine 243, no. 5 (March 2018): 444–50. http://dx.doi.org/10.1177/1535370218759635.
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To explore genetic pathway cross-talk in neonates with sepsis, an integrated approach was used in this paper. To explore the potential relationships between differently expressed genes between normal uninfected neonates and neonates with sepsis and pathways, genetic profiling and biologic signaling pathway were first integrated. For different pathways, the score was obtained based upon the genetic expression by quantitatively analyzing the pathway cross-talk. The paired pathways with high cross-talk were identified by random forest classification. The purpose of the work was to find the best pairs of pathways able to discriminate sepsis samples versus normal samples. The results found 10 pairs of pathways, which were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways were identified according to analysis of extensive literature. Impact statement To find the best pairs of pathways able to discriminate sepsis samples versus normal samples, an RF classifier, the DS obtained by DEGs of paired pathways significantly associated, and Monte Carlo cross-validation were applied in this paper. Ten pairs of pathways were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways ((7) IL-6 Signaling and Phospholipase C Signaling (PLC); (8) Glucocorticoid Receptor (GR) Signaling and Dendritic Cell Maturation) were identified according to analysis of extensive literature.
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Martínez-Expósito, Alfredo. "Queer Literature in Spain: Pathways to Normalisation." Culture & History Digital Journal 2, no. 1 (June 30, 2013): e010. http://dx.doi.org/10.3989/chdj.2013.010.
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Srivastava, Shivangi. "A Review on Biosynthetic Pathways in Plants." International Journal of Research Publication and Reviews 5, no. 2 (February 2024): 668–73. http://dx.doi.org/10.55248/gengpi.5.0224.0422.
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Nash, Colin, Ken Williams, Francesca Pirog, and Kristi Mitchell. "Emerging development and use of clinical pathways to improve quality and standardize care in oncology." Journal of Clinical Oncology 30, no. 34_suppl (December 1, 2012): 139. http://dx.doi.org/10.1200/jco.2012.30.34_suppl.139.
Full textAbstract:
139 Background: Clinical pathways have emerged as a tool for payers to encourage provider adherence to evidence-based care. Avalere sought to understand how oncology pathway developers consider different types of evidence and physician input in designing pathways, and how the experiences of early programs may serve as an indicator for future implementation. Methods: Avalere conducted targeted white and grey literature searches to identify and analyze pathways used by oncology practice groups, provider networks, and major commercial payers. The research was augmented by informant interviews with representatives from leading organizations that have developed or implemented pathways. Results: Current pathways programs differ in their origins and objectives. Across these programs, Avalere identified findings in three key areas: Development: Developers consider efficacy of treatments first, followed by toxicity, and then cost. Many developers conduct an independent evidence review, while others leverage clinical practice guidelines. All developers solicit physician input on pathway design and updates; Use: Independent pathway developers partner with commercial insurers and large provider networks to design pathways with cost-saving components. Physicians are evaluated based on their adherence to the pathways, but are not held accountable for reporting or performance on NQF-endorsed quality measures; Impact: Cost savings in early programs are largely due to reduced toxicity-related medical costs, use of less expensive drugs, and lower total drug use. However, there is limited evidence on the impact of pathways on patient outcomes. Conclusions: There is variability across oncology pathway developers regarding their scope, granularity, and processes related to evaluating and incorporating evidence. If clinical programs demonstrate early cost reductions while improving patient outcomes, payers will likely attempt to expand pathways programs to new geographies and therapeutic areas. Existing practice patterns and previously implemented pathways programs will likely play heavily in determining which pathways are adopted in a given region, but national standardization is highly unlikely.