157 research outputs found
stajichlab/chytropsin: Ahrendt PeerJ 2017 S.punctatus
No full text<p>This is the code and models associated with the publication Ahrendt et al "Exploring the binding properties and structural stability of an opsin in the chytrid <em>Spizellomyces punctatus</em> using comparative and molecular modeling" Preprint at DOI: <a href="http://dx.doi.org/10.7287/peerj.preprints.2397v1">10.7287/peerj.preprints.2397v1</a></p>
The influence of floodplain geometry on riverbed elevation change within and between flood events
No full textRivers, Ports, Waterways and Dredging Engineerin
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Investigating the Evolution of Environmental and Biotic Interactions in Basal Fungal Lineages Through Comparative Genomics
No full textSpecies belonging to the basal fungal lineages (Blastocladiomycota, Chytridiomycota, Cryptomycota, and Neocallimastigomycota) reproduce via motile zoospores and are found in both aquatic and terrestrial environments. These organisms, colloquially referred to as "chytrids", are traditionally understudied, despite being active decomposers, parasites, a nd symbionts with other organisms in the ecosystem. This dissertation research uses a comparative genomics approach to answer questions about these fungi and their interactions with their environment and other fungi. Chapters 2 and 3 examine the details of putative rhodopsin-mediated photoreception in basal lineages using structural mechanics and genome-wide gain-loss analyses. Chapter 4 provides a transcriptome analysis of one member of the genus Coelomomyces, the only known entomopathic chytrid genus. Chapter 5 describes surprising observations regarding competitive and inhibitory behavior in one member of the Chytridiomycota. Finally, Appendix A briefly looks at gain-loss analysis of molecular aspects of the evolutionary transition from aquatic motile single cells to terrestrial multicellullar organisms
Indications for non‐transplant surgery in primary sclerosing cholangitis
No full textAbstractPrimary sclerosing cholangitis (PCS) is a progressive disease leading to secondary biliary cirrhosis. Patients are at increased risk of developing cholangiocarcinoma, which is usually diagnosed at an advanced stage. Treatment of PCS includes medical therapy, endoscopic biliary dilation, percutaneous transhepatic stenting, extrahepatic biliary resection and liver transplantation. The most effective management of primary sclerosing cholangitis before the onset of cirrhosis remains unclear. Non‐transplant surgical procedures have a limited but defined role in patients with PCS. Resection of the extrahepatic biliary tree in symptomatic non‐cirrhotic patients improves hyperbilirubinaemia and prolongs both transplant‐free and overall survival when compared with non‐operative dilation and/or stenting. Surgical resection may also definitively establish or exclude a diagnosis of cholangiocarcinoma in patients with dominant extrahepatic or perihilar strictures. Extrahepatic bile duct resection may also reduce the risk of cholangiocarcinoma. Extrahepatic biliary resection should be considered in selected non‐cirrhotic patients with symptomatic biliary obstruction and dominant extrahepatic and/or perihilar strictures. Those patients in whom cholangiocarcinoma is suspected should also undergo resection
Gene expression heatmaps
No full text
*Color coding used in Heatmaps: High expression (red),low expression (blue)
*Upregulated genes (green), downregulated genes (violet)
This folder contains additional supplementary files (gene expression heatmaps for different gene groups/families in 6 RNA-Seq experiments) used in the manuscript:
Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen
Neha Sahu, Boris Indic, Johanna Wong-Bajracharya, Zsolt Merényi, Huei-Mien Ke, Steven Ahrendt, Tori-Lee Monk, Sándor Kocsubé, Elodie Drula, Anna Lipzen, Balázs Bálint, Bernard Henrissat, Bill Andreopoulos, Francis M. Martin, Christoffer Bugge Harder, Daniel Rigling, Kathryn L. Ford, Gary D. Foster, Jasmyn Pangilinan, Alexie Papanicolaou, Kerrie Barry, Kurt LaButti, Máté Virágh, Maxim Koriabine, Mi Yan, Robert Riley, Simang Champramary, Krista L. Plett, Igor V. Grigoriev, Isheng Jason Tsai, Jason Slot, György Sipos, Jonathan Plett, László G. Nagy
bioRxiv 2022.11.10.515791; doi: https://doi.org/10.1101/2022.11.10.515791</p
Gene trees
No full text*Color coding used in gene trees: Physalacriaceae (green), other Basidiomycota (blue), Ascomycota (red), early diverging fungi (black)
*Horizontal transfer events are highlighted by yellow clades
This folder contains additional supplementary files (gene trees showing clades with horizontal gene transfer events - Table S4) used in the manuscript:
Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen
Neha Sahu, Boris Indic, Johanna Wong-Bajracharya, Zsolt Merényi, Huei-Mien Ke, Steven Ahrendt, Tori-Lee Monk, Sándor Kocsubé, Elodie Drula, Anna Lipzen, Balázs Bálint, Bernard Henrissat, Bill Andreopoulos, Francis M. Martin, Christoffer Bugge Harder, Daniel Rigling, Kathryn L. Ford, Gary D. Foster, Jasmyn Pangilinan, Alexie Papanicolaou, Kerrie Barry, Kurt LaButti, Máté Virágh, Maxim Koriabine, Mi Yan, Robert Riley, Simang Champramary, Krista L. Plett, Igor V. Grigoriev, Isheng Jason Tsai, Jason Slot, György Sipos, Jonathan Plett, László G. Nagy
bioRxiv 2022.11.10.515791; doi: https://doi.org/10.1101/2022.11.10.515791</p
Comparing neoadjuvant chemotherapy with or without radiation therapy for pancreatic ductal adenocarcinoma: National Cancer Database cohort analysis
No full textBackground: Neoadjuvant treatment is important for improving the rate of R0 surgical resection and overall survival outcome in treating patients with pancreatic ductal adenocarcinoma (PDAC). However, the true efficacy of radiotherapy (RT) for neoadjuvant treatment of PDAC is uncertain. This retrospective study evaluated the treatment outcome of neoadjuvant RT in the treatment of PDAC. Methods: Collected from the National Cancer Database, information on patients with PDAC who underwent neoadjuvant chemotherapy (NAC) and pancreatectomy between 2010 to 2016 was used in this study. Short- and long-term outcomes were compared between patients who received neoadjuvant chemoradiotherapy (NACRT) and NAC. Results: The study included 6936 patients, of whom 3185 received NACRT and 3751 NAC. The groups showed no difference in overall survival (NACRT 16.1 months versus NAC 17.4 months; P = 0.054). NACRT is associated with more frequent margin negative resection (86.1 versus 80.0 per cent; P < 0.001) but a more unfavourable 90-day mortality than NAC (6.4 versus 3.6 per cent; P < 0.001). The odds of 90-day mortality were higher in the radiotherapy group (odds ratio 1.81; P < 0.001), even after adjusting for significant covariates. Patients who received NACRT received single-agent chemotherapy more often than those who received NAC (31.5 versus 10.7 per cent; P < 0.001). Conclusion: This study failed to show a survival benefit for NACRT over NAC alone, despite its association with negative margin resection. The significantly higher mortality in NACRT warrants further investigation into its efficacy in the treatment of pancreatic cancer
Effect of nicotine and muscle performance using a Wingate Anaerobic Test on collegiate football players
No full textNicotine is a naturally occurring addictive alkaloid and in some cases, a lethal drug. The long-term harmful effects of nicotine have been widely documented through means of publications, commercials and even billboards to stop the use of nicotine in the form of tobacco. Even with the knowledge of these harmful side effects, thousands of athletes still use tobacco. In this study the use of nicotinic substances was tested during Wingate Anaerobic Tests (WAnT) on collegiate football athletes. These tests had three possible outcomes: ergogenic, ergolytic or no effect. The subjects were 12 University of Wisconsin – Whitewater football players between the ages of 19 - 23. They performed a series of two tests on a Monarch cycle ergometer for 30 seconds at a time on two separate days. One day post-nicotine gum administration; the other day post-placebo gum administration. The data received was considered significant with a p-value < .05. This experiment showed nicotine’s effect on: peak anaerobic power (P = .34), anaerobic capacity (P = .92), and anaerobic fatigue percentage (P = .33) in the human body during a WAnT. Therefore, the data received from this experiment were concluded not to be statistically significant
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