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Journal articles on the topic 'Pathways'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Šindelář, L., and M. Šindelářová. "Regulation of metabolic pathways PVY-RNA biosynthesis in tobacco: glycolytic pathway." Plant Protection Science 40, No. 3 (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

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Karatzas, Evangelos, Margarita Zachariou, Marilena M. Bourdakou, et al. "PathWalks: identifying pathway communities using a disease-related map of integrated information." Bioinformatics 36, no. 13 (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 n

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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 (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 path

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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

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Lomberk, Gwen, and Raul Urrutia. "Primers on Molecular Pathways — Caspase Pathway." Pancreatology 9, no. 1-2 (2009): 6–8. http://dx.doi.org/10.1159/000178860.

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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 cla

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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 precomp

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Loeber, Rolf, Phen Wung, Kate Keenan, et al. "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 b

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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 (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 datab

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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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Ghulam, Ali, Xiujuan Lei, Min Guo, and Chen Bian. "Comprehensive Analysis of Features and Annotations of Pathway Databases." Current Bioinformatics 15, no. 8 (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 o

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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 (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 pathwa

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Hu, Chenyu W., Amina A. Qutub, Yihua Qiu, et al. "A Global Proteomic Pathway Map In Acute Myeloid Leukemia (AML)." Blood 122, no. 21 (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 u

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Hall, Julia Cooper, Joanna M. Hamilton, David Michael Jackman, et al. "Analyzing pathways data to reduce unwarranted variation, understand practice patterns, and update pathways." Journal of Clinical Oncology 36, no. 30_suppl (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; thi

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Xu, Wen, Bei Wang, Yisong Gao, et al. "Alkaloids Exhibit a Meaningful Function as Anticancer Agents by Restraining Cellular Signaling Pathways." Mini-Reviews in Medicinal Chemistry 22, no. 7 (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 sy

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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 (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 Dal

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Xie, Jun, Sijuan Sun, Qingzhou Li, et al. "MAPK/ERK signaling pathway in rheumatoid arthritis: mechanisms and therapeutic potential." PeerJ 13 (July 14, 2025): e19708. https://doi.org/10.7717/peerj.19708.

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Rheumatoid arthritis (RA) is a multifaced autoimmune disorder characterized by chronic joint inflammation, leading to progressive disability and significantly impacting patients’ quality of life. Despite advances in treatment, finding a cure or preventing disease progression remains a major clinical challenge, underscoring the urgent need for novel therapeutic strategies. Among various pathways involved in the pathophysiology of RA, the mitogen-activated protein kinases/extracellular regulated protein kinases (MAPK/ERK) pathway is of particular importance. As the central cascade within the bro

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Rosique, Ricard. "Do we need electronic support for pathways: the Spanish experience." International Journal of Care Pathways 13, no. 2 (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

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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 pat

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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 tre

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Lomberk, Gwen, and Raul Urrutia. "Primers on Molecular Pathways —The Insulin Pathway." Pancreatology 9, no. 3 (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 (2013): 5842–48. http://dx.doi.org/10.1158/1078-0432.ccr-13-0325.

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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 (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 se

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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 (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

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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 (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 int

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Nishide, Yudai, Daisuke Kageyama, Kakeru Yokoi, et al. "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 (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

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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 (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

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Sielsky, Kali. "A Pathway to Reconciliation within ‘North American’ Archaeology." Pathways 3, no. 1 (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 experie

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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 (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 â€œPathway Toolsâ€ 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

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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 (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

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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 (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

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Agoubi, Lauren L., Nina M. Clark, Sarah Gibbs, et al. "Implementation evaluation of tiered tele-triage pathways for burn center consultations and transfers." Journal of Trauma and Acute Care Surgery 96, no. 3 (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

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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 th

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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. https://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 th

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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 (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

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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 (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 ag

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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 (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 determin

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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 p

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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 ce

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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 (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 p

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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 (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

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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 (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

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Yan, Xiangyu. "Polymerase Theta-mediated DNA End-Joining Repair in the Maintenance of Genome Stability." Transactions on Materials, Biotechnology and Life Sciences 7 (December 24, 2024): 33–39. https://doi.org/10.62051/rg3zk642.

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The DNA double-strand break (DSB) always occurs within genome. The pathways that repair the DSB are essential in keeping cell viability. This review will focus on the recent understanding of TMEJ, especially two key protein factors involved in the TMEJ repair pathway2, DNA polymerase theta (Polθ) and DNA polymerase delta (Polδ), and discuss the potential mechanism of choosing repair pathways when there is a DNA Double Strand Break. We dissect TMEJ's unique mechanism of action, including recognition of DNA ends, microhomology search, end pairing, and DNA synthesis, by focusing on the enzyme Pol

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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 (2012): 139. http://dx.doi.org/10.1200/jco.2012.30.34_suppl.139.

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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 wit

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Nasarudin, Nurul Athirah, Mohd Saberi Mohamad, Zalmiyah Zakaria, Richard O. Sinnott, Fatma Al Jasmi, and Noura Al Dhaheri. "Identification of informative genes and sub-pathways using Improved Differential Expression Analysis for Pathways (iDEAP) for cancer classification." F1000Research 12 (November 6, 2023): 1433. http://dx.doi.org/10.12688/f1000research.132899.1.

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Background: Pathway-based analysis primarily focuses on sub-pathway-based analysis, which aids in understanding biological reactions. Several studies have found abnormalities in pathways caused by certain regions based on the etiology of diseases. The Differential Expression Analysis for Pathways (DEAP) method is one such sub-pathway-based analysis method, that identifies a local region perturbed by complex diseases based on larger pathway data. However, the method has low performance in identifying informative pathways and sub-pathways. Methods: In this paper we propose an improved DEAP (iDEA

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Xie, Xiaoman, Matthew C. Kendzior, Xiyu Ge, Liudmila S. Mainzer, and Saurabh Sinha. "VarSAn: associating pathways with a set of genomic variants using network analysis." Nucleic Acids Research 49, no. 15 (2021): 8471–87. http://dx.doi.org/10.1093/nar/gkab624.

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Abstract There is a pressing need today to mechanistically interpret sets of genomic variants associated with diseases. Here we present a tool called ‘VarSAn’ that uses a network analysis algorithm to identify pathways relevant to a given set of variants. VarSAn analyzes a configurable network whose nodes represent variants, genes and pathways, using a Random Walk with Restarts algorithm to rank pathways for relevance to the given variants, and reports P-values for pathway relevance. It treats non-coding and coding variants differently, properly accounts for the number of pathways impacted by

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Han, Junwei, Chunquan Li, Haixiu Yang, et al. "A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways." Journal of The Royal Society Interface 12, no. 102 (2015): 20140937. http://dx.doi.org/10.1098/rsif.2014.0937.

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Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationship

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Liu, Guiyou, Fang Zhang, Yongshuai Jiang, et al. "Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways." Multiple Sclerosis Journal 23, no. 2 (2016): 205–12. http://dx.doi.org/10.1177/1352458516649038.

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Background: Much effort has been expended on identifying the genetic determinants of multiple sclerosis (MS). Existing large-scale genome-wide association study (GWAS) datasets provide strong support for using pathway and network-based analysis methods to investigate the mechanisms underlying MS. However, no shared genetic pathways have been identified to date. Objective: We hypothesize that shared genetic pathways may indeed exist in different MS-GWAS datasets. Methods: Here, we report results from a three-stage analysis of GWAS and expression datasets. In stage 1, we conducted multiple pathw

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Zolotovskaia, Marianna, Maks Kovalenko, Polina Pugacheva, et al. "Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers." Proteomes 11, no. 3 (2023): 26. http://dx.doi.org/10.3390/proteomes11030026.

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Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 “classical” pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found

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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 (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.

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