674 Works

PREreview of \"Flaviviruses alter endoplasmic reticulum-mitochondria contacts to regulate respiration and apoptosis\"

Craig McCormick
We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Flaviviruses alter endoplasmic reticulum-mitochondria contacts to regulate respiration and apoptosis Wesley Freppel, Anaïs Anton, Zaynab Nouhi, Clément Mazeaud, Claudia Gilbert, Nicolas Tremblay, Viviana Andrea Barragan Torres, Aïssatou Aïcha Sow, Xavier Laulhé, Alain Lamarre, Ian Gaël Rodrigue-Gervais, Andreas Pichlmair, Pietro Scaturro, Laura Hulea, and Laurent Chatel-Chaix.doi: https://doi.org/10.1101/2023.03.09.531853....

Review of Invasion dynamics of quagga mussels (Dreissena rostriformis bugensis) within a reservoir and its spatially intermittent watershed: Lake Piru and the Santa Clara River, California, USA

This review was performed by a pre-review journal club of ecologists including grad students, post docs, and faculty. We were excited to review this paper because we are interested in ecosystem health and population dynamics. Review authors: Grace Leuchtenberger, Kindall Murie, Fiona Boardman, Zachary Bengtsson, Olivia Cattau, Annie Colgan, Chuck Flaherty, Sanford Leake, Rachel Potter, Monica Sheffer, Julia SmithSummary This article was a comprehensive report on the state of quagga mussel invasion in Lake Piru,...

PREreview of \"Small Specialty Coffee Farmers' Decision-Making Factors in an Asymmetric Information Market Environment\"

Gustavo Pena
https://www.google.com/search?client=firefox-b-d&q=Small+Specialty+Coffee+Farmers%E2%80%99+Decision-Making+Factors+in+an+Asymmetric+Information+Market+En Competing interests The author declares that they have no competing interests.

Review of The tenets of indirect inference in Bayesian models

This paper gives a good overview on Bayesian inference for quantile distributions, covering the theoretical basis and practical methods. There are also plenty of useful examples. The paper also introduces novel methodology for some stages of the process. Overall I recommend the paper as an good description of the area. My most major issue with the paper is that I would not find it easy to reproduce the results from the code supplied. Other comments...


In this study, the authors sought to evaluate four nutritional screening tools and their association with contrast-induced acute kidney injury in patients who were exposed to IV contrast due to coronary angiography or percutaneous coronary intervention by performing a multicenter retrospective observational study. They conclude that pre-procedural malnutrition is associated with contrast-induced acute kidney injury (CI-AKI). The hypothesis that led to this study being conducted is important since it could advance our understanding of risk...

Review of Characterizing the Behavioral and Neuroendocrine Features of Susceptibility and Resilience to Social Stress

Dalia Murra and colleagues characterized CORT level and behavioral changes in susceptible and resilient animals after social stress, this is a very simple but fundamental study in social defeat field. The authors first studies whether pre-stress social ratio predict/align with the post-stress and no correlation found in pre-post SI ratio or CORT level. Then they showed two very interesting findings: first, different coping behavior on the first day actually can predict resiliency, the mice that...

Review of Coordinately regulated interbacterial antagonism defense pathways constitute a bacterial innate immune system

In this manuscript, Ting et al. describe three gene clusters - named antagonism resistance clusters (arc1-3) - that are upregulated by the Gac/Rsm danger sensing system and proposed to work as an innate immunity system against antibacterial attacks. This work builds on their previous studies (LeRoux et al., 2015 eLife; LeRoux et al., 2015 J Mol Biol) in which the authors have identified a danger sensing mechanism that bacteria use to sense lysis of neighboring...

PREreview of \"Long-term duration of protection of ancestral-strain monovalent vaccines and effectiveness of the bivalent BA.1 boosters against COVID-19 hospitalisation during a period of BA.5, BQ.1, CH.1.1. and XBB.1.5 circulation in England\"

Kianna Sahabi
The main findings of this paper regarding the association between vaccine effectiveness and hospitalization of people aged 65 years or older in terms of monovalent vaccine protection. Their case-control study found absolute vaccine effectiveness through 3 doses of monovalent vaccines for people of this age group for 6 months at a time. The paper was clear and adequate, suggesting further evidence of the effectiveness of boosters in preventing hospitalization. Competing interests The author declares that...

Review of Risk Factors Associated with Development and Persistence of Long COVID: A Cross-Sectional Study

In this manuscript, the authors describe a study aiming to determine risk factors associated with development and persistence of long COVID-19 in a sample of 457 patients who had been hospitalized evaluated for COVID-19 in a single center. They performed an analytical cross-sectional study involving an online survey sent to patients who had been discharged, with a high response rate. This study is interesting and has strengths like the validation of the questionnaire in a...

Review of Influence of social determinants of health and county vaccination rates on machine learning models to predict COVID-19 case growth in Tennessee

Daniela Saderi, Katrina Murphy, Leire Abalde-Atristain, Cole Brashaw, Robin Elise Champieux &
This review is the result of a virtual, live-streamed preprint journal club organized and hosted by PREreview and OHSU's BioData Club. The discussion was joined by 9 people, including OHSU researchers and the event organizing team. Wylezinski et al. investigated the impact of clinical and social determinants of health (SDOH) risk factors on the COVID-19 case growth in Tennessee. To that aim, they used a variety of publicly available data to train machine learning (ML)...

Review of Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila

LAMP proteins localize at the lysosomal membrane, controlling autophagy-related processes but also lipid transport and metabolism. While it is well-demonstrated the existence of a link between LAMP misfunction and human diseases, the mechanisms underlying LAMP functions are still poorly understood. To better understand the different roles of LAMP proteins, authors aimed to characterize in this work the only LAMP member identified in Drosophila, Lamp1. Authors first developed new Lamp1 null mutant alleles, as well as...

Review of The Impact of COVID-19 Vaccine on Rate of Hospitalization and Outcome of COVID- 19 Infection in a Single Center in the Eastern Province of Saudi Arabia

In this manuscript, the authors sought to "quantify vaccination efficiency" to reduce hospitalization and death rates under real-world settings in a Hospital from Saudi Arabia. The authors conducted a retrospective cohort study including 331 patients from a single center, performed statistical comparisons between unvaccinated and vaccinated individuals, and described differences among them. They conclude that hospital stay was prolonged in unvaccinated individuals. While the research question could be interesting, there are several methodological limitations of...

Review of COVID-19 risk score as a public health tool to guide targeted testing: A demonstration study in Qatar

In this study, the authors report the development and validation of a prediction model of "risk of COVID-19" in Qatar, with further updating and evaluation of the model. It is not clear what the authors intended to predict, since they only mention "risk of COVID-19", but they later mention that the model was meant to predict "risk of exposure to SARS-CoV-2", which doesn't necessarily imply that the individual will have a positive test since having...

Thamann, Aubrey and Kalliopi M. Christodoulaki (eds.). 2021. Beyond the Veil: Reflexive Studies of Death and Dying. London, New York: Berghahn Books. 248pp.: $130.00/£97.00. 256 pp. Hb.: $130.00/£97.00. ISBN: 9781800730649.

El-Sayed El-Aswad
Thamann, Aubrey and Kalliopi M. Christodoulaki (eds.). 2021. Beyond the Veil: Reflexive Studies of Death and Dying. London, New York: Berghahn Books. 248pp.: $130.00/£97.00. 256 pp. Hb.: $130.00/£97.00. ISBN: 9781800730649.


Package to replicate benchmarks for the paper "Inference of Probabilistic Programs with Moment-Matching Gaussian Mixtures".

Review of Immunoinformatic design of multi epitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Yan Zhou
This study provided new insights into a novel cancer treatment strategy.

Assessing Code Comments of Insufficient Quality: Criteria and Automatic Detection

Replication package for "Assessing Code Comments of Insufficient Quality: Criteria and Automatic Detection"

data and models of \"on the effectiveness of spectral discriminators for perceptual quality improvement\"

data and models of "on the effectiveness of spectral discriminators for perceptual quality improvement"

innovative preservation of seafood products

Fish and other seafood products are important dietary components that are consumed all around the world. However, seafood products are highly perishable and thus require proper processing to maintain their quality and safety this has led to the development of a wide range of processing, preservation, and analytical technique. The present article reviews innovative processing technologies applied for the preservation and shelf life extension of seafood products. These primarily include: high hydrostatic pressure, natural preservatives,...

The Effects of Staff Education on Ventilator-Associated Pneumonia in the Intensive Care Unit: A Literature Review

& Suzanne Ellen
Abstract Background:
Mechanically ventilated patients in the ICU are at a high risk for ventilatorassociated pneumonia (VAP), and the rate of this hospital-acquired infection (HAI) is problematic. Nursing interventions utilize evidence-based practice (EBP) VAP prevention guidelines to decrease the incidence. The purpose of this paper is to examine the effects of staff education on the reduction of VAP in the critical care setting. Methods: Literature search was performed on two databases, CINAHL and PubMed. Search...

Distinct biological activity of Lewy body α-Synuclein strain in mice

Norihito Uemura
Full blots and raw data for statistical analysis

Review of EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma

Daniela Saderi
Live-streamed preprint Journal Club on "EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma" – October 23, 2018 This is a review of the bioRxiv preprint "EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma" by Borong Shao, Maria Bjaanæs, Åslaug Helland, Christof Schütte, Tim Conrad, doi:10.1101/410472. This review was compiled from a discussion during the live-streamed Bioinformatics preprint journal club as part of an Open Access Week effort organized by the PREreview...

Review of Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level

Monica Granados
Live streamed Journal Club on "Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level" This is a review of the bioRxiv preprint "Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level" by Luz Garcia-Longoria, Alfonso Marzal, Florentino de Lope, and Laszlo Garamszegi. DOI: https://doi.org/10.1101/432260 This review was compiled from discussion points raised during a PREreview live-streamed Ecology preprint journal club as part of Open Access Week, October...

Review of Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana

Steven J Burgess
UIUC preprint journal club : 2018-07-30 Steven Burgess (0000-0003-2353-7794), Samuel Fernandes, Antony Digrado, Charles Pignon, Elsa de Becker, Naomi Housego Day, Lusya Manukyan, Stephanie Cullum, Isla Causon, Iulia Floristeanu, Young Cho, Freya Way, Judy Savitskya, Robert Collison, Aoife Sweeney, Pietro Hughes, Cindy Chan Abstract This review is compiled from notes taken by the UIUC Plant Physiology preprint journal club during a one hour session on 2018-07-30. The review refers to the preprint "Natural variation in...

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