bluuebunny/crossref_metadata_2025_split huggingface dataset:
CUBAP: an interactive web portal for analyzing codon usage biases across populations
Authors: Hodgman Matthew W , Miller Justin B , Meurs Taylor E , Kauwe John S K 
Published: September 2020

AbstractSynonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web server, https://cubap.byu.edu, to facilitate analyses of codon usage biases across populations (CUBAP). Using the 1000 Genomes Project, we calculated and visually depict population-specific differences in codon frequencies, codon aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, and nucleotide composition in 17,634 genes. We found that codon pairing significantly differs between populations in 35.8% of genes, allowing us to successfully predict the place of origin for African and East Asian individuals with 98.8% and 100% accuracy, respectively. We also used CUBAP to identify a significant bias toward decreased CTG pairing in the immunity related GTPase M (IRGM) gene in East Asian and African populations, which may contribute to the decreased association of rs10065172 with Crohn's disease in those populations. CUBAP facilitates in-depth gene-specific and codon-specific visualization that will aid in analyzing candidate genes identified in genome-wide association studies, identifying functional implications of synonymous variants, predicting population-specific impacts of synonymous variants and categorizing genetic biases unique to certain populations.
International Survey Reveals Opportunities to Improve Tuberculous Meningitis Management and the Need for Standardized Guidelines
Authors: Tucker Elizabeth W , Marais Suzaan , Seddon James A , van Crevel Reinout , Ganiem Ahmad Rizal , Ruslami Rovina , Zhang Wenhong , Sun Feng , Zhou Xian , Solomons Regan S , Cresswell Fiona V , Wilmshurst Jo , Rohlwink Ursula 
Published: September 2020

Abstract

Background
Tuberculous meningitis (TBM) is a medical emergency, yet there are no standardized treatment guidelines for the medical or neurosurgical management of these patients and little data on neurocritical care. We conducted an international survey to understand current medical and neurosurgical TBM management and resource availability to provide baseline data needed for future multicenter trials addressing unanswered clinical research questions and the establishment of standardized guidelines.

Methods
An online survey of 77 questions covering medical and neurosurgical TBM management aimed at clinicians/nurses treating TBM was distributed as an anonymous link through email invitation, international organizations’ membership distribution, and direct links on organizational webpages or social media. The survey remained open for 5 months. Data were summarized with frequencies and percentages.

Results
The survey had 222 responses from 43 countries representing 6 continents. Most respondents were from tertiary care facilities, with broad access to medical and neurosurgical resources. There was significant heterogeneity in general supportive care, and TBM-specific management demonstrated considerable divergence from current standard-of-care practices. The lack of standardized guidelines was identified as a major challenge in TBM management. General and neurocritical care were largely absent. Resources for bedside supportive care and noninvasive monitoring were broadly accessible.

Conclusions
These findings suggest that current TBM management could be improved by the establishment of internationally accepted treatment guidelines based on available evidence, and that numerous centers have resources available to participate in future multicenter trials, even for basic interventions, that may further improve patient outcomes globally.
Management of severe hyperinflammation in the COVID-19 era: the role of the rheumatologist
Authors: Papadopoulou Charalampia , Al Obaidi Muthana , Moraitis Elena , Compeyrot-Lacassagne Sandrine  , Eleftheriou Despina , Brogan Paul 
Published: September 2020

Abstract

Objectives
The objectives of this study were (i) to describe the clinical presentation, treatment and outcome of paediatric inflammatory multisystem syndrome temporally related to Sars-CoV-2 (PIMS-TS) in children; (ii) to propose a framework to guide multidisciplinary team (MDT) management; and (iii) to highlight the role of the paediatric rheumatologist in this context.

Methods
This study involved a retrospective case notes review of patients referred to a single specialist paediatric centre with suspected PIMS-TS, with a focus on clinical presentation, laboratory parameters, treatment, and outcome in the context of an MDT framework.

Results
Nineteen children of median age 9.1 years fulfilled the definition of PIMS-TS and were managed within an MDT framework: 5/19 were female; 14/19 were of Black, Asian or minority ethnicity; 9/19 also fulfilled diagnostic criteria for complete or incomplete Kawasaki disease (KD). Severe systemic inflammation, shock, and abdominal pain were ubiquitous. Treatment was stratified within an MDT framework and included CSs in all; i.v. immunoglobulin in all; anakinra in 4/19; infliximab in 1/19; and antiviral (aciclovir) in 4/19.

Conclusions
We observed significant diagnostic equipoise using a current definition of PIMS-TS, overlapping with KD. Outside of clinical trials, an MDT approach is vital. The role of the paediatric rheumatologist is to consider differential diagnoses of hyperinflammation in the young, to advise on empiric immunomodulatory therapy, to set realistic therapeutic targets, to gauge therapeutic success, to oversee timely step-down of immunomodulation, and to contribute to the longer-term MDT follow-up of any late inflammatory sequelae.
Competing modes of responsibility in research organisations—Insights from an international comparison
Authors: Hennen Leonhard , Hahn Julia , Ladikas Miltos 
Published: September 2020

Abstract
Based on findings from research in the incorporation of responsible research and innovation in research organisations in twelve European and non-European countries, the article discusses how old (i.e. internal) and new (i.e. external) modes of responsibility coexist and compete with each other in actual research practice. Although the analysis shows ubiquitous perceived need for re-arranging the relations between science and society in order to legitimise scientific research in organisations, it also finds that the incumbent structures and cultures of internal thinking are still dominant in most organisations, which leads to considerable resistance to change. In particular, for public engagement and reflexive anticipatory ethics, strategies of conceptual and procedural demarcation are evident. Organisations adapt public engagement or reflexive ethics as extraordinary or experimental activities thus allowing for the continuation of the status quo in the perspective of the ‘republic of science’, keeping ‘internal’ affairs unaffected by societal intervention.
In vitro assessment of the cytotoxic, genotoxic and oxidative stress effects of the synthetic cannabinoid JWH-018 in human SH-SY5Y neuronal cells
Authors: Sezer Yigit , Jannuzzi Ayse Tarbin , Huestis Marilyn A , Alpertunga Buket 
Published: September 2020

Abstract
Background: JWH-018 was the first synthetic cannabinoid introduced as a legal high and the first of the new generation of novel psychoactive substances that flooded worldwide drug markets. JWH-018 was marketed as “spice,” “herbal incense,” or “herbal blend,” as a popular and legal (at the time) alternative to cannabis (marijuana). JWH-018 is a potent synthetic cannabinoid with considerable toxicity associated with its use. JWH-018 has qualitatively similar but quantitatively greater pharmacological effects than cannabis, leading to intoxications and even deaths. The mechanisms of action of the drug’s toxicity require research, and thus, the aim of the present study was to investigate the toxicological profile of JWH-018 in human SH-SY5Y neuronal cells. Methods: SH-SY5Y neuronal cells were exposed to increasing concentrations from 5 to 150 μM JWH-018 over 24 h. Cytotoxicity, DNA damage, the apoptotic/necrotic rate, and oxidative stress were assessed following SH-SY5Y exposure. Results: JWH-018 did not produce a significant decrease in SH-SY5Y cell viability, did not alter apoptotic/necrotic rate, and did not cause genotoxicity in SH-SY5Y cells with 24-h exposure. Glutathione reductase and catalase activities were significantly reduced; however, there was no significant change in glutathione peroxidase activity. Also, JWH-018 treatment significantly decreased glutathione concentrations, significantly increased protein carbonylation, and significantly increased malondialdehyde (MDA) concentrations. For significance, all P &lt; 0.05. Discussion/Conclusion: JWH-018 produced oxidative stress in SH-SY5Y cells that could be an underlying mechanism of JWH-018 neurotoxicity. Additional in vivo animal and human-based studies are needed to confirm our findings.
Overlaying COVID-19 mitigation plans on malaria control infrastructures
Authors: Rahi Manju , Baharia Rajendra Kumar , Das Payal , Chhibber-Goel Jyoti , Sharma Amit 
Published: September 2020

Abstract
To counter the coronavirus disease 2019 (COVID-19) pandemic, each country must design sustainable control plans given the inherent disparities in wealth and healthcare systems. Most malaria-endemic countries run well-entrenched malaria control programs via their established frameworks for diagnosis, case management, treatment and overall surveillance. We propose that the malaria control infrastructures can be partially co-opted for launching sustainable COVID-19 mitigation plans.
9Theory on Theory
Authors: Ng Julia 
Published: September 2020

AbstractThis chapter assesses three areas of theoretical work: metatheory, via Jason Demers’s The American Politics of French Theory: Derrida, Deleuze, Guattari, and Foucault in Translation and Galin Tihanov’s The Birth and Death of Literary Theory: Regimes of Relevance in Russia and Beyond; three studies that theorize on the history of theory, John E. Drabinski’s Glissant and the Middle Passage: Philosophy, Beginning, Abyss, John Frow’s On Interpretive Conflict, and Anne Anlin Cheng’s Ornamentalism; and five texts indicative of a surge of interest in the linguisticity of ‘death’, David Wills’s Killing Times: The Temporal Technology of the Death Penalty, Michael Rothberg’s The Implicated Subject: Beyond Victims and Perpetrators, David Simpson’s States of Terror: History, Theory, Literature, and Marc Crépon’s Murderous Consent: On the Accommodation of Violent Death and The Vocation of Writing: Literature, Philosophy, and the Test of Violence.
Subgroups of Pediatric Patients With Functional Abdominal Pain
Authors: Stone Amanda L. , Han Gloria T. , Bruehl Stephen , Garber Judy , Smith Craig A. , Anderson Julia , Palermo Tonya M. , Walker Lynn S. 
Published: September 2020

Objectives:
Prior work in a cohort of youth with functional abdominal pain (FAP) identified patient subgroups (High Pain Dysfunctional, High Pain Adaptive, Low Pain Adaptive) that predicted differences in the course of FAP from childhood into young adulthood. We aimed to replicate these subgroups in a new sample of adolescents with FAP using the original classification algorithm and to extend subgroup characteristics to include parental characteristics and health service use.

Methods:
Adolescents (n=278; ages 11 to 17 y, 66% females) presenting to a gastroenterology clinic for abdominal pain, and their parents (92% mothers) completed self-report measures; adolescents also completed a 7-day pain diary.

Results:
The replicated patient subgroups exhibited distress and impairment similar to subgroups in the original sample. Moreover, in novel findings, the High Pain Dysfunctional subgroup differed from other subgroups by the predominance of mother-daughter dyads jointly characterized by high levels of anxiety, depressive symptoms, pain behavior, and pain catastrophizing. The High Pain Dysfunctional subgroup used more health care services than Low Pain Adaptive but did not differ from High Pain Adaptive.

Discussion:
Findings replicate and extend the original FAP classification and suggest that the subgroups have unique patient and parent features that may reflect distinct illness mechanisms requiring different treatments.
Digitalization and Physician Learning
Authors: Vallo Hult Helena , Hansson Anders , Gellerstedt Martin 
Published: September 2020

Introduction:
The emerging context of online platforms and digitally engaged patients demands new competencies of health care professionals. Although information and communication technologies (ICTs) can strengthen continuous professional development (CPD) and learning at work, more research is needed on ICT for experiential and collegial learning.

Methods:
The study builds on prior qualitative research to identify issues and comprises a quantitative assessment of ICT usage for learning in health care. A survey was administered to Swedish physicians participating in a CPD program as part of specialist medical training. Conclusions focused specifically on learning dimensions are drawn from correlation analyses complemented with multiple regression.

Results:
The findings show that physicians' actual use of ICT is related to perceived performance, social influence, and organizational context. Social norm was the most important variable for measured general usage, whereas performance expectancy (perceived usefulness of ICT) was important for ICT usage for learning. The degree of individual digitalization affects performance and, in turn, actual use.

Discussion:
The study highlights the need to incorporate ICT effectively into CPD and clinical work. Besides formal training and support for specific systems, there is a need to understand the usefulness of digitalization integrated into practice. Moving beyond instrumentalist views of technology, the model in this study includes contextualized dimensions of ICT and learning in health care. Findings confirm that medical communities are influencers of use, which suggests that an emphasis on collegial expectations for digital collaboration will enhance practitioner adaptation.
Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital
Authors: Li Dai-Xi , Zhai Yao , Zhang Zhao , Guo Ya-Tao , Wang Zhan-Wei , He Zi-Long , Hu Song-Nian , Chen Yu-Sheng , Kang Yu , Gao Zhan-Cheng 
Published: September 2020

Abstract

Background
Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant bla
KPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital.

Methods
Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing. The six ST11 XDR CP-Kp, as well as three multi-drug resistant (MDR) and four susceptible strains, were sequenced using single-molecule real-time method. Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains.

Results
We found that ST11 XDR bla
KPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital. Functionally, genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains, especially genes correlative with mobile genetic elements (MGEs) such as transposons and prophages. Structurally, eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons, integrons, prophages, genomic islands, and integrative and conjugative elements. Three of them were located on plasmids and eight on chromosomes; five of them were with antimicrobial resistance genes and eight with adaptation associated genes. Notably, a new bla
KPC-2-bearing ΔΔTn1721-bla
KPC-2 transposon, probably transposed and truncated from ΔTn1721-bla
KPC-2 by IS903D and ISKpn8, was identified in all six ST11 XDR CP-Kp strains.

Conclusion
Our findings suggested that together with clonal spread, MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability, which facilitated their widespread dissemination in hospital.
Mechanisms of resistance to immune checkpoint inhibitors and strategies to reverse drug resistance in lung cancer
Authors: Qian Fang-Fei , Han Bao-Hui 
Published: September 2020

Abstract
In recent years, the research of immune checkpoint inhibitors has made a great breakthrough in lung cancer treatment. Currently, a variety of immune checkpoint inhibitors have been applied into clinical practice, including antibodies targeting the programmed cell death-1, programmed cell death-ligand 1, and cytotoxic T-lymphocyte antigen 4, and so on. However, not all patients can benefit from the treatment. Abnormal antigen presentation, functional gene mutation, tumor microenvironment, and other factors can lead to primary or secondary resistance. In this paper, we reviewed the molecular mechanism of immune checkpoint inhibitor resistance and various combination strategies to overcome resistance, in order to expand the beneficial population and enable precision medicine.
The Coronavirus Disease 2019 pandemic: how does it spread and how do we stop it?
Authors: Li Xin , Sridhar Siddharth , Chan Jasper Fuk-Woo 
Published: September 2020

Purpose of review
The Coronavirus Disease 2019 (COVID-19) pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat associated with major socioeconomic disruptions. Understanding on the transmission characteristics of SARS-CoV-2 is crucial for optimizing preventive strategies.

Recent findings
SARS-CoV-2 can be transmitted efficiently between persons through respiratory droplets and direct and indirect contact. The significance of airborne droplet nuclei in SARS-CoV-2 transmission in the community setting is less clear. SARS-CoV-2 RNA and live viral particles may also be detected in other bodily fluids. Outbreaks have been reported in families, nursing homes, markets, restaurants, churches, shipping vessels, gyms, and healthcare facilities. Nonpharmaceutical preventive measures at both the community and individual levels are essential for reducing the transmission of SARS-CoV-2.

Summary
Because well tolerated and effective vaccines for SARS-CoV-2 are unlikely to be widely available in the near future, there is an urgent need for finding other measures to reduce the spread of the COVID-19 pandemic. With better understanding of its transmission characteristics, practical nonpharmaceutical preventive measures remain essential to reduce SARS-CoV-2 transmission and its associated health and socioeconomic burdens.
HIV care during the coronavirus disease-2019 pandemic in Shenzhen, China
Authors: Wang Hui 
Published: September 2020

Purpose of review
Due to the stringent measures including quarantine of infected individuals and social distancing, the COVID-19 pandemic has posted great challenges for HIV-1 care in China. In this mini-review, I will discuss the situation in Shenzhen city as a window of China to reflect our strategies in fighting the concurrent HIV/AIDS and COVID-19 pandemics.

Recent findings
Prevention of nosocomial infection, minimizing the follow-up visits to the hospital, maintaining the delivery of PreP/PEP services and testing for SARS-Cov-2 and HIV when someone have fever or respiratory symptoms were the four major approaches to maintain uninterrupted HIV care in Shenzhen. None of 15 000 PLWH seeking HIV care at Shenzhen were diagnosed with COVID-19 during this pandemic.

Summary
This article share the experience unprecedented from Shenzhen. We have to adapt our care and service to continue to engage PLWH to avoid poor outcomes. More research is needed to know the long-term implications of pandemic for the health of PLWH.
Advances in contraception research and development
Authors: Cahill Erica P. , Kaur Simranvir 
Published: September 2020

Purpose of review
In the past few years, there have been great advances in contraceptive technology and development. Here we review advances in contraception over the past two years including new medications, and technologies.

Recent findings
Contraception must be discussed within the context of individual goals and context. New contraceptive options approved by the FDA in the past two years include a year-long vaginal ring, a progestin-only pill that is as effective as combined oral contraceptive pills, a new hormonal patch and a vaginal gel that may also help prevent sexually transmitted infections.
There are still areas of contraceptive research that are very much unknown including biomarkers of contraceptive efficacy or side effects, how individuals or groups metabolize contraception, initiation around reproductive life events or the discontinuation of other methods.

Summary
There have been many new contraceptives developed over the past few years to address challenges of existing contraception and create new methods; yet, there remain many unanswered questions in contraceptive research. Contraceptive technology has far-reaching consequences, and independent of technology itself, represents a great opportunity for truly personalized medicine.
NONARTERITIC ANTERIOR ISCHEMIC OPTIC NEUROPATHY AFTER INTRAVITREAL AFLIBERCEPT FOR AGE-RELATED MACULAR DEGENERATION
Authors: Paxton Andrew B. , Christakis Panos G. , Micieli Jonathan A. 
Published: September 2020

Purpose:
To report a case of nonarteritic anterior ischemic optic neuropathy (NAION) after intravitreal injection in a patient with a history of fellow-eye NAION.

Methods:
Observational case report.

Results:
An 82-year-old woman with a history of fellow eye NAION developed an inferior visual field defect 1 day after an intravitreal aflibercept injection for neovascular age-related macular degeneration. She was found to have optic disk edema and an inferior altitudinal defect, consistent with NAION. The mechanism may have involved compromised perfusion to the optic nerve head related to elevated intraocular pressure or vasoconstriction because of antivascular endothelial growth factor activity.

Conclusion:
Nonarteritic anterior ischemic optic neuropathy is a rare complication of intravitreal injection and may be related to postinjection elevation in intraocular pressure. Monitoring of intraocular pressure postinjection with low-threshold for preinjection aqueous suppression or postinjection anterior chamber paracentesis for persistently elevated intraocular pressure is recommended in patients with a history of NAION.