bluuebunny/crossref_metadata_2025 huggingface dataset:
MAGUS: Multiple sequence Alignment using Graph clUStering
Authors: Smirnov Vladimir , Warnow Tandy
Published: November 2020

Motivation

The estimation of large multiple sequence alignments (MSAs) is a basic bioinformatics challenge. Divide-and-conquer is a useful approach that has been shown to improve the scalability and accuracy of MSA estimation in established methods such as SATé and PASTA. In these divide-and-conquer strategies, a sequence dataset is divided into disjoint subsets, alignments are computed on the subsets using base MSA methods (e.g. MAFFT), and then merged together into an alignment on the full dataset.

Results

We present MAGUS, Multiple sequence Alignment using Graph clUStering, a new technique for computing large-scale alignments. MAGUS is similar to PASTA in that it uses nearly the same initial steps (starting tree, similar decomposition strategy, and MAFFT to compute subset alignments), but then merges the subset alignments using the Graph Clustering Merger, a new method for combining disjoint alignments that we present in this study. Our study, on a heterogeneous collection of biological and simulated datasets, shows that MAGUS produces improved accuracy and is faster than PASTA on large datasets, and matches it on smaller datasets.

Availability and implementation

MAGUS: https://github.com/vlasmirnov/MAGUS

Supplementary information

Supplementary data are available at Bioinformatics online.
A span-graph neural model for overlapping entity relation extraction in biomedical texts
Authors: Fei Hao , Zhang Yue , Ren Yafeng , Ji Donghong
Published: November 2020

Motivation

Entity relation extraction is one of the fundamental tasks in biomedical text mining, which is usually solved by the models from natural language processing. Compared with traditional pipeline methods, joint methods can avoid the error propagation from entity to relation, giving better performances. However, the existing joint models are built upon sequential scheme, and fail to detect overlapping entity and relation, which are ubiquitous in biomedical texts. The main reason is that sequential models have relatively weaker power in capturing long-range dependencies, which results in lower performance in encoding longer sentences. In this article, we propose a novel span-graph neural model for jointly extracting overlapping entity relation in biomedical texts. Our model treats the task as relation triplets prediction, and builds the entity-graph by enumerating possible candidate entity spans. The proposed model captures the relationship between the correlated entities via a span scorer and a relation scorer, respectively, and finally outputs all valid relational triplets.

Results

Experimental results on two biomedical entity relation extraction tasks, including drug–drug interaction detection and protein–protein interaction detection, show that the proposed method outperforms previous models by a substantial margin, demonstrating the effectiveness of span-graph-based method for overlapping relation extraction in biomedical texts. Further in-depth analysis proves that our model is more effective in capturing the long-range dependencies for relation extraction compared with the sequential models.

Availability and implementation

Related codes are made publicly available at http://github.com/Baxelyne/SpanBioER.
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples
Authors: Ye Wenbin , Liu Tao , Fu Hongjuan , Ye Congting , Ji Guoli , Wu Xiaohui
Published: November 2020

Motivation

Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically. Studies based on 3′ end sequencing and/or RNA-seq have profiled poly(A) sites in various species with diverse pipelines, yet no unified and easy-to-use toolkit is available for comprehensive APA analyses.

Results

We developed an R package called movAPA for modeling and visualization of dynamics of alternative polyadenylation across biological samples. movAPA incorporates rich functions for preprocessing, annotation and statistical analyses of poly(A) sites, identification of poly(A) signals, profiling of APA dynamics and visualization. Particularly, seven metrics are provided for measuring the tissue-specificity or usages of APA sites across samples. Three methods are used for identifying 3′ UTR shortening/lengthening events between conditions. APA site switching involving non-3′ UTR polyadenylation can also be explored. Using poly(A) site data from rice and mouse sperm cells, we demonstrated the high scalability and flexibility of movAPA in profiling APA dynamics across tissues and single cells.

Availability and implementation

https://github.com/BMILAB/movAPA.

Supplementary information

Supplementary data are available at Bioinformatics online.
FinaleDB: a browser and database of cell-free DNA fragmentation patterns
Authors: Zheng Haizi , Zhu Michelle S , Liu Yaping
Published: November 2020

Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.

Availability and implementation

FinaleDB service: http://finaledb.research.cchmc.org/. FinaleDB source code: https://github.com/epifluidlab/finaledb_portal, https://github.com/epifluidlab/finaledb_workflow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Spatial-temporal patterns of childhood immunization in New Zealand (2006–2017): an improving pattern but not for all?
Authors: Marek Lukas , Hobbs Matthew , Wiki Jesse , McCarthy John , Tomintz Melanie , Campbell Malcolm , Kingham Simon
Published: November 2020

Background

Declining childhood immunization represents a serious public health problem globally and in New Zealand. To guide efforts to increase immunization coverage, this study monitors nationwide change in immunization coverage since the introduction of the National Immunisation Register (NIR) in 2005 and spatiotemporal patterns of immunization coverage from 2006 to 2017.

Methods

The study population consisted of 4 482 499 individual immunization records that were obtained from the NIR (2005–2017). Data on yearly and average immunization coverage in census area units (CAUs) in New Zealand were calculated by milestone age (6/8/12/18/24/60/144 months). Data for 2005 were excluded due to missing records in the introductory period of the NIR. We analyzed spatial and spatiotemporal patterns using Gi* and SaTScan methods.

Results

Immunization coverage improved since the introduction of the NIR in 2005, reaching a peak in 2014 and 2015 with a slight decrease in 2016 and 2017. Well and insufficiently immunized areas were identified with spatial autocorrelation analyses highlighting several hot- and cold-spots. Comparison of CAUs with neighbouring CAUs allowed for the identification of places where immunization coverage was significantly higher or lower than expected, over both time and space.

Conclusion

We provide the first spatiotemporal analysis of childhood immunization in New Zealand that utilizes a large sample of over 4.4 million individual immunization records. Our spatial analyses enable policymakers to understand the development of childhood immunization coverage and make more effective prevention strategies in New Zealand.
Demographic and public health characteristics explain large part of variability in COVID-19 mortality across countries
Authors: Hradsky Ondrej , Komarek Arnost
Published: November 2020

Background

The numbers of coronavirus disease 2019 (COVID-19) deaths per million people differ widely across countries. Often, the causal effects of interventions taken by authorities are unjustifiably concluded based on the comparison of pure mortalities in countries where interventions consisting different strategies have been taken. Moreover, the possible effects of other factors are only rarely considered.

Methods

We used data from open databases (European Centre for Disease Prevention and Control, World Bank Open Data, The BCG World Atlas) and publications to develop a model that could largely explain the differences in cumulative mortality between countries using non-interventional (mostly socio-demographic) factors.

Results

Statistically significant associations with the logarithmic COVID-19 mortality were found with the following: proportion of people aged 80 years and above, population density, proportion of urban population, gross domestic product, number of hospital beds per population, average temperature in March and incidence of tuberculosis. The final model could explain 67% of the variability. This finding could also be interpreted as follows: less than a third of the variability in logarithmic mortality differences could be modified by diverse non-pharmaceutical interventions ranging from case isolation to comprehensive measures, constituting case isolation, social distancing of the entire population and closure of schools and borders.

Conclusions

In particular countries, the number of people who will die from COVID-19 is largely given by factors that cannot be drastically changed as an immediate reaction to the pandemic and authorities should focus on modifiable variables, e.g. the number of hospital beds.
Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing
Authors: Kasimatis Katja R , Sánchez-Ramírez Santiago , Stevenson Zachary C
Published: November 2020

Sexual reproduction often leads to selection that favors the evolution of sex-limited traits or sex-specific variation for shared traits. These sexual dimorphisms manifest due to sex-specific genetic architectures and sex-biased gene expression across development, yet the molecular mechanisms underlying these patterns are largely unknown. The first step is to understand how sexual dimorphisms arise across the genotype–phenotype–fitness map. The emergence of “4D genome technologies” allows for efficient, high-throughput, and cost-effective manipulation and observations of this process. Studies of sexual dimorphism will benefit from combining these technological advances (e.g., precision genome editing, inducible transgenic systems, and single-cell RNA sequencing) with clever experiments inspired by classic designs (e.g., bulked segregant analysis, experimental evolution, and pedigree tracing). This perspective poses a synthetic view of how manipulative approaches coupled with cutting-edge observational methods and evolutionary theory are poised to uncover the molecular genetic basis of sexual dimorphism with unprecedented resolution. We outline hypothesis-driven experimental paradigms for identifying genetic mechanisms of sexual dimorphism among tissues, across development, and over evolutionary time.
Neuroligin dependence of social behaviour inCaenorhabditis elegansprovides a model to investigate an autism-associated gene
Authors: Rawsthorne Helena , Calahorro Fernando , Feist Emily , Holden-Dye Lindy , O’Connor Vincent , Dillon James
Published: November 2020

Autism spectrum disorder (ASD) is characterized by a triad of behavioural impairments including social behaviour. Neuroligin, a trans-synaptic adhesion molecule, has emerged as a penetrant genetic determinant of behavioural traits that signature the neuroatypical behaviours of autism. However, the function of neuroligin in social circuitry and the impact of genetic variation to this gene is not fully understood. Indeed, in animal studies designed to model autism, there remains controversy regarding the role of neuroligin dysfunction in the expression of disrupted social behaviours. The model organism, Caenorhabditis elegans, offers an informative experimental platform to investigate the impact of genetic variants on social behaviour. In a number of paradigms, it has been shown that inter-organismal communication by chemical cues regulates C. elegans social behaviour. We utilize this social behaviour to investigate the effect of autism-associated genetic variants within the social domain of the research domain criteria. We have identified neuroligin as an important regulator of social behaviour and segregate the importance of this gene to the recognition and/or processing of social cues. We also use CRISPR/Cas9 to edit an R-C mutation that mimics a highly penetrant human mutation associated with autism. C. elegans carrying this mutation phenocopy the behavioural dysfunction of a C. elegans neuroligin null mutant, thus confirming its significance in the regulation of animal social biology. This highlights that quantitative behaviour and precision genetic intervention can be used to manipulate discrete social circuits of the worm to provide further insight into complex social behaviour.
On the Fully Nonlinear Alt–Phillips Equation
Authors: Wu Yijing , Yu Hui
Published: November 2020

For a parameter $\gamma \in (1,2)$, we study the fully nonlinear version of the Alt–Phillips equation, $F(D^2u)=u^{\gamma -1}$, for $u\ge 0.$ We establish the optimal regularity of the solution, as well as the $C^1$ regularity of the regular part of the free boundary.
Monocyte CD169 Expression as a Biomarker in the Early Diagnosis of Coronavirus Disease 2019
Authors: Bedin Anne-Sophie , Makinson Alain , Picot Marie-Christine , Mennechet Frank , Malergue Fabrice , Pisoni Amandine , Nyiramigisha Esperance , Montagnier Lise , Bollore Karine , Debiesse Ségolène , Morquin David , Bourgoin Pénélope , Veyrenche Nicolas , Renault Constance , Foulongne Vincent , Bret Caroline , Bourdin Arnaud , Le Moing Vincent , Van de Perre Philippe , Tuaillon Edouard
Published: November 2020

We assessed the expression of CD169, a type I interferon-inducible receptor, on monocytes (monocyte CD169 [mCD169]) in 53 adult patients admitted to the hospital during the coronavirus disease 2019 (COVID-19) outbreak for a suspicion of severe acute respiratory syndrome coronavirus 2 infection. Monocyte CD169 was strongly overexpressed in 30 of 32 (93.7%) confirmed COVID-19 cases, compared with 3 of 21 (14.3%) patients in whom the diagnosis of COVID-19 was finally ruled out. Monocyte CD169 was associated with the plasma interferon-alpha level and thrombocytopenia. Monocyte CD169 testing may be helpful for the rapid triage of suspected COVID-19 patients during an outbreak.
The validity and reliability of self-reported satisfaction with healthcare as a measure of quality: a systematic literature review
Authors: ANUFRIYEVA Valentyna , PAVLOVA Milena , STEPURKO Tetiana , GROOT Wim
Published: November 2020

Purpose

The aim of this paper is to systematize the evidence on the validity and reliability of subjective measurements of satisfaction with healthcare.

Data sources

In this qualitative systematic literature review, we searched for relevant publications in PubMed and JSTOR databases.

Study selection

The key inclusion criteria included (i) original research articles in peer-reviewed journals, (ii) year of publication from 2008 onward and (iii) English language publications.

Data extraction

We applied directed qualitative content analysis to the publications included in the review.

Results of data synthesis

Overall, 1167 publications are found and screened. Of these, 39 publications that focus on the psychometric properties of the measurement of patient satisfaction are included. The majority of the studies validate the already existing instruments adapted to different contexts; the rest describe psychometric properties of self-developed tools. Psychometric properties are assessed by means of reliability and validity assessment. Reliability assessment is performed via Cronbach alpha and test–retest reliability. Overall, 94.9% of studies find that the satisfaction measures are reliable. Validation is performed by a variety of different methods, among which the most applicable are face validity and factor analysis. Overall, 71.8% of studies find that the satisfaction measures are valid.

Conclusion

Because of the complexity of the studies, we cannot make strong recommendations on the application of self-reported satisfaction measures. We recommend the following key strategies: (i) developing of a unified standard toward satisfaction measurement and (ii) identifying a combination of tools to routinely measure satisfaction. We also suggest to further research the issue of subjectivity reduction.
Bringing evidence from press release to the clinic in the era of COVID-19
Authors: McMahon James H , Lydeamore Michael J , Stewardson Andrew J
Published: November 2020

The urgent need to develop effective therapeutics and disseminate information from clinical studies has led to data from clinical trials being made available by alternate methods prior to peer-reviewed publication, including press releases, social media and pre-print papers. While this allows clinicians more open access to these data, a trust has to be placed with the investigators releasing these data without the availability of scientifically rigorous peer review. The examples of results from trials studying dexamethasone and hydroxychloroquine for treatment of COVID-19 have had contrasting outcomes, including the potential for significant numbers of lives saved with the early release of results from the RECOVERY trial studying dexamethasone contrasting with unsubstantiated data being presented from trials studying hydroxychloroquine. Clinicians and researchers must maintain a healthy scepticism when reviewing results prior to peer-reviewed publication, but also consider when these opportunities may allow for early implementation of potentially lifesaving interventions for people infected with COVID-19.
The burden of the digital environment: a systematic review on organization-directed workplace interventions to mitigate physician burnout
Authors: Thomas Craig Kelly J , Willis Van C , Gruen David , Rhee Kyu , Jackson Gretchen P
Published: November 2020

Objective

To conduct a systematic review identifying workplace interventions that mitigate physician burnout related to the digital environment including health information technologies (eg, electronic health records) and decision support systems) with or without the application of advanced analytics for clinical care.

Materials and Methods

Literature published from January 1, 2007 to June 3, 2020 was systematically reviewed from multiple databases and hand searches. Subgroup analysis identified relevant physician burnout studies with interventions examining digital tool burden, related workflow inefficiencies, and measures of burnout, stress, or job satisfaction in all practice settings.

Results

The search strategy identified 4806 citations of which 81 met inclusion criteria. Thirty-eight studies reported interventions to decrease digital tool burden. Sixty-eight percent of these studies reported improvement in burnout and/or its proxy measures. Burnout was decreased by interventions that optimized technologies (primarily electronic health records), provided training, reduced documentation and task time, expanded the care team, and leveraged quality improvement processes in workflows.

Discussion

The contribution of digital tools to physician burnout can be mitigated by careful examination of usability, introducing technologies to save or optimize time, and applying quality improvement to workflows.

Conclusion

Physician burnout is not reduced by technology implementation but can be mitigated by technology and workflow optimization, training, team expansion, and careful consideration of factors affecting burnout, including specialty, practice setting, regulatory pressures, and how physicians spend their time.
Comprehensiveness of Breast Radiology Fellowship Online Content
Authors: Beck Spencer , Khurana Aditya , Lourenco Ana P , Eltorai Adam E M
Published: November 2020

Objective

The content of websites for fellowship programs is an important source of information for residents applying to breast imaging fellowship programs (BIFPs). The purpose of this study is to evaluate the comprehensiveness of online content of BIFPs.

Methods

A list of BIFPs was obtained from the Society of Breast Imaging website. Each program’s website was evaluated for the presence of 19 training-relevant content variables. Impact of program characteristics on comprehensiveness scores was determined. For statistical analysis, Kruskal–Wallis tests were used to assess differences in comprehensiveness scores based upon region, and two-tailed t-tests were used to compare based upon program size.

Results

A total of 79 BIFP websites were analyzed. The mean comprehensiveness score of BIFP websites based on meeting the 19 criteria was 44.1% (8.4 ± 2.7/19). Program coordinator contact information (72/79, 91.1%), application requirements (71/79, 89.9%), and faculty information (56/79, 70.9%) appeared on >70% of websites. The majority of fellowships had a dedicated webpage for their program (71/79, 89.9%). Information regarding 12 of the 19 criteria appeared on fewer than 50% of websites. Program region (P = 0.32) and size (P = 0.16) were not associated with any differences in mean comprehensiveness score. Additionally, there was no significant difference in scores associated with filling all available positions for the 2020 match cycle (P = 0.77).

Conclusion

There is a paucity of information commonly sought out by applicants on the websites of most BIFPs. Both programs and applicants may mutually benefit from increasing comprehensive online content.
Evolutionary Interpretation and International Law
Authors: Vidigal Geraldo
Published: November 2020

Debates about the meaning of ‘evolutionary interpretation’ reveal the existence of two conflicting views. Some see evolutionary interpretation as an inevitable step in the ordinary process of applying fixed written language to changing reality. Others see it as a means for interpreters—and, crucially, adjudicators—to update the agreement being applied, infusing into the text the interpreter’s view of what would be a desirable development of the relevant provisions. Benefitting from the views expounded and decisions collected by the authors of Evolutionary Interpretation and International Law, edited by Georges Abi-Saab, Kenneth Keith, Gabrielle Marceau, and Clément Marquet (Hart 2020), this piece investigates two core questions that run through debates regarding evolutionary interpretation. First is the question of what is meant by evolutionary interpretation, whether an unavoidable step in the norm application process or a decision to develop obligations beyond their original scope. Second is the question of the distinctive role of adjudicators, i.e. of whether evolutionary interpretation is a tool used by adjudicators to exercise authority over the legal framework being applied, bypassing the constraints of the consent-based international rule-making system.
Parallels Between the Antiviral State and the Irradiated State
Authors: McGee Heather M , Marciscano Ariel E , Campbell Allison M , Monjazeb Arta M , Kaech Susan M , Teijaro John R
Published: November 2020

Improved understanding of host antiviral defense and antitumor immunity have elucidated molecular pathways important to both processes. During viral infection, RNA or DNA in the host cell serves as a danger signal that initiates the antiviral response. Recent studies have elucidated similarities in the signaling pathways activated by viruses and the signaling pathways induced by tumor DNA that is released into the cytoplasm of irradiated tumor cells. Both the host defense to viral infection and the sterile inflammation provoked by radiotherapy induce a type I interferon response that is necessary for pathogen control and immune-mediated tumor control, respectively. These findings have led to the hypothesis that radiotherapy employs a form of viral mimicry.
Short-Term Outcomes After Multisystem Inflammatory Syndrome in Children Treatment
Authors: Clouser Katharine N , Gadhavi Jasmine , Bhavsar Sejal M , Lewis Rachel , Ballance Cathleen , Michalak Zuzanna , Baer Aryeh , Kriegel Marni , Pall Harpreet , Piwoz Julia , Slavin Kevin , Siegel Mark E , Tozzi Meghan E , Tozzi Robert , Walker David M , Lapidus Sivia , Aschner Judy
Published: November 2020

This is a retrospective chart review of 20 patients treated with a consensus-driven treatment algorithm in multisystem inflammatory syndrome in children patients across a wide clinical spectrum. Their treatments and clinical status are described as well as their favorable return to functional baseline by 30 days post presentation.
Syndactyly
Authors: Geoghegan Luke , Knowles Billie Georgina , Nikkhah Dariush
Published: November 2020

Here we present an interesting case of simple syndactyly and provide a narrative review of its incidence, associations and management.
Narratives as a coordinating device for reversing regional disequilibrium
Authors: Collier Paul , Tuckett David
Published: November 2020

Substantial differences in productivity, accompanied by growing social and political discontent, have widened across UK regions in the last 40 years, creating a dysfunctional spatial equilibrium; a coordination failure that has so far proved resistant to change. In this paper, we link such persistent regional disequilibria with current socio-psychological theories about the role of narrative in decision-making under radical uncertainty to explore how and why ideas held collectively within a social network can become the coordinating device for a range of decisions within networked communities that have extra-market effects (externalities), analogous to the role that prices play within markets. Drawing on findings from a pilot interview study in two UK regions, we show the potential for local leadership to use well-constructed narratives to coordinate fragmented agents to cooperate on a common purpose and more generally propose a framework to understand how low-income equilibria become stable but might be re-set. In this way we bring new insights into the need for an expanded economic theory of knowledge applicable to expectation and preference formation in conditions of radical uncertainty.
Overproduction of Chloroplast Glyceraldehyde-3-Phosphate Dehydrogenase Improves Photosynthesis Slightly under Elevated [CO2] Conditions in Rice
Authors: Suzuki Yuji , Ishiyama Keiki , Sugawara Misaki , Suzuki Yuka , Kondo Eri , Takegahara-Tamakawa Yuki , Yoon Dong-Kyung , Suganami Mao , Wada Shinya , Miyake Chikahiro , Makino Amane
Published: November 2020

Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) limits the regeneration of ribulose 1,5-bisphosphate (RuBP) in the Calvin–Benson cycle. However, it does not always limit the rate of CO2 assimilation. In the present study, the effects of overproduction of GAPDH on the rate of CO2 assimilation under elevated [CO2] conditions, where the capacity for RuBP regeneration limits photosynthesis, were examined in transgenic rice (Oryza sativa). GAPDH activity was increased to 3.2- and 4.5-fold of the wild-type levels by co-overexpression of the GAPDH genes, GAPA and GAPB, respectively. In the transgenic rice plants, the rate of CO2 assimilation under elevated [CO2] conditions increased by approximately 10%, whereas that under normal and low [CO2] conditions was not affected. These results indicate that overproduction of GAPDH is effective in improving photosynthesis under elevated [CO2] conditions, although its magnitude is relatively small. By contrast, biomass production of the transgenic rice plants was not greater than that of wild-type plants under elevated [CO2] conditions, although starch content tended to increase marginally.
Annual phytoplankton succession results from niche-environment interaction
Authors: Caracciolo Mariarita , Beaugrand Grégory , Hélaouët Pierre , Gevaert Francois , Edwards Martin , Lizon Fabrice , Kléparski Loïck , Goberville Eric
Published: November 2020

Annual plankton succession has been investigated for many decades with hypotheses ranging from abiotic to biotic mechanisms being proposed to explain these recurrent patterns. Here, using data collected by the Continuous Plankton Recorder (CPR) survey and models originating from the MacroEcological Theory on the Arrangement of Life, we investigate Annual Phytoplankton Succession (APS) in the North Sea at a species level. Our results show that this phenomenon can be predicted well by models combining photosynthetically active radiation, temperature and macro-nutrients. Our findings suggest that APS originates from the interaction between species’ ecological niches and the annual environmental fluctuations at a community level. We discuss our results in the context of traditional hypotheses formulated to explain this recurrent pattern in the marine field.
Building Resilient Health Systems: Experimental Evidence from Sierra Leone and The 2014 Ebola Outbreak*
Authors: Christensen Darin , Dube Oeindrila , Haushofer Johannes , Siddiqi Bilal , Voors Maarten
Published: November 2020

Skepticism about the quality of health systems and their consequent underuse are thought to contribute to high rates of mortality in the developing world. The perceived quality of health services may be especially critical during epidemics, when people choose whether to cooperate with response efforts and frontline health workers. Can improving the perceived quality of health care promote community health and ultimately help to contain epidemics? We leverage a field experiment in Sierra Leone to answer this question in the context of the 2014 West African Ebola crisis. Two years before the outbreak, we randomly assigned two interventions to government-run health clinics—one focused on community monitoring, and the other conferred nonfinancial awards to clinic staff. Prior to the Ebola crisis, both interventions increased clinic utilization and patient satisfaction. Community monitoring additionally improved child health, leading to 38% fewer deaths of children under age five. Later, during the crisis, the interventions also increased reporting of Ebola cases by 62%, and community monitoring significantly reduced Ebola-related deaths. Evidence on mechanisms suggests that both interventions improved the perceived quality of health care, encouraging patients to report Ebola symptoms and receive medical care. Improvements in health outcomes under community monitoring suggest that these changes partly reflect a rise in the underlying quality of administered care. Overall, our results indicate that promoting accountability not only has the power to improve health systems during normal times, but can also make them more resilient to emergent crises.
ESTIMATION OF ACTUAL DOSE BASED ON BAYESIAN PROBABILISTIC APPROACH USING PERSONNEL MONITORING DOSE RECORDS
Authors: Pathan Munir S , Pradhan S M , Selvam T Palani
Published: November 2020

In this study, the Bayesian probabilistic approach is applied for the estimation of the actual dose using personnel monitoring dose records of occupational workers. To implement the Bayesian approach, the probability distribution of the uncertainty in the reported dose as a function of the actual dose is derived. Using the uncertainty distribution function of reported dose and prior knowledge of dose levels generally observed in a monitoring period, the posterior probability distribution of the actual dose is estimated. The posterior distributions of each monitoring period in a year are convoluted to arrive at actual annual dose distribution. The estimated actual doses distributions show a significant deviation from reported annual doses particularly for low annual doses.
Auditory-Based Cognitive Training Drives Short- and Long-Term Plasticity in Cortical Networks in Schizophrenia
Authors: Koshiyama Daisuke , Miyakoshi Makoto , Thomas Michael L , Joshi Yash B , Molina Juan L , Tanaka-Koshiyama Kumiko , Nungaray John A , Sprock Joyce , Braff David L , Swerdlow Neal R , Light Gregory A
Published: November 2020

Schizophrenia patients have widespread deficits in neurocognitive functioning linked to underlying abnormalities in gamma oscillations that are readily measured by the 40 Hz auditory steady-state response (ASSR). Emerging interventions such as auditory-based targeted cognitive training (TCT) improve neurocognitive function in patients. While acute ASSR changes after 1 hour of TCT predict clinical and cognitive gains after a 30-hour course of TCT, the neural substrates of underlying short- and long-term TCT interventions are unknown. To determine the neural substrates underlying TCT-associated ASSR changes, a novel data analysis method was applied to assess the effective connectivity of gamma-band ASSR among estimated cortical sources. In this study, schizophrenia patients (N = 52) were randomized to receive either a treatment as usual (TAU; N = 22) or TAU augmented with TCT (N = 30). EEG recordings were obtained immediately before (T0) and after 1 hour of either computer games (TAU) or cognitive training (TCT; T1), and at 65 ± 15 days (mean ± SD) post-randomization (T2). Results showed increased connectivity from the left ventral middle cingulate gyrus to the left posterior cingulate gyrus, accompanied by decreased connectivity from the left Rolandic operculum (a region that includes auditory cortex) to the right ventral middle cingulate gyrus after 1 hour of TCT. After 30 hours, decreased connectivity from the frontal cortex to a region near the calcarine sulcus were detected. Auditory-based cognitive training drives short- and long-term plasticity in cortical network functioning in schizophrenia patients. These findings may help us understand the mechanisms underlying cognitive training effects in schizophrenia patients and enhance the development of pro-cognitive therapeutics.
Nocturnal hypoxemia severity influences the effect of CPAP therapy on renal renin–angiotensin–aldosterone system activity in humans with obstructive sleep apnea
Authors: Nicholl David D M , Hanly Patrick J , Zalucky Ann A , Handley George B , Sola Darlene Y , Ahmed Sofia B
Published: November 2020

Study Objectives

Nocturnal hypoxemia (NH) in obstructive sleep apnea (OSA) is associated with renal renin–angiotensin–aldosterone system (RAAS) up-regulation and loss of kidney function. Continuous positive airway pressure (CPAP) therapy is associated with RAAS down-regulation, though the impact of NH severity remains unknown. We sought to determine whether NH severity alters the effect of CPAP on renal hemodynamics and RAAS activity in humans.

Methods

Thirty sodium-replete, otherwise healthy, OSA participants (oxygen desaturation index ≥ 15 h−1) with NH (SpO2 < 90% ≥ 12%/night) were studied pre- and post-CPAP (>4 h/night∙4 weeks). NH severity was characterized as moderate (mean SpO2[MSpO2] ≥ 90%; N = 15) or severe (MSpO2 < 90%; N = 15). Glomerular filtration rate (GFR), renal plasma flow (RPF), and filtration fraction (FF) were measured at baseline and in response to angiotensin-II (3 ng/kg/min∙30 min, 6 ng/kg/min∙30 min), a marker of RAAS activity.

Results

Pre-CPAP, baseline renal hemodynamics did not differ by NH severity. Pre-CPAP, severe NH participants demonstrated blunted GFR (Δ30 min, −9 ± 4 vs 1 ± 3 mL/min, p = 0.021; Δ60 min, −5 ± 5 vs 8 ± 5 mL/min, p = 0.017) and RPF (Δ30 min, −165 ± 13 vs −93 ± 19 mL/min, p = 0.003; Δ60 min, −208 ± 18 vs −112 ± 22 mL/min, p = 0.001; moderate vs severe) responses to angiotensin-II. Post-CPAP, severe NH participants demonstrated maintained GFR (112 ± 5 vs 108 ± 3 mL/min, p = 0.9), increased RPF (664 ± 35 vs 745 ± 34 mL/min, p = 0.009), reduced FF (17.6 ± 1.4 vs 14.9 ± 0.6%, p = 0.009), and augmented RPF responses to Angiotensin-II (Δ30 min, −93 ± 19 vs −138 ± 16 mL/min, p = 0.009; Δ60 min, −112 ± 22 vs −175 ± 20 mL/min, p = 0.001; pre- vs post-CPAP), while moderate participants were unchanged.

Conclusions

Correction of severe, but not moderate, NH with CPAP therapy was associated with improved renal hemodynamics and decreased renal RAAS activity in humans with OSA.
A special issue addressing healthful food access and food insecurity: risk factors, behavioral variables, interventions, and measurement
Authors: Calloway Eric E , Parks Courtney A , Byker Shanks Carmen , Bowen Deborah J , Yaroch Amy L
Published: November 2020

This article introduces a special issue in Translational Behavioral Medicine that focuses on translational aspects of food insecurity research. The purpose of this special issue was to add to the evidence base to inform short- and intermediate-term intervention development and implementation and to spark additional future discourse around these important topics. The special issue included 12 articles and 2 commentaries roughly evenly split across four topic areas, including subpopulation food insecurity risk factors; food behaviors and psychosocial variables; implementation and/or evaluation of food insecurity interventions; and food insecurity-related measurement issues. The articles in this special issue offer a number of contributions to the translational literature specific to food insecurity. They add to our understanding that depression, stress, and social isolation (sometimes related to language barriers) may play a large role in individuals’ food insecurity experience. The articles explored the differences between food insecure and food secure households in relation to food and grocery shopping behaviors, and nutritional self-efficacy. In addition, authors described the implementation and/or efficacy of interventions meant to promote healthful diets and food access among food insecure populations. And finally, several studies explored current measurement issues such as intra-household subjectivity, disconnect between perceived and objective measures of food access, and a need for more holistic and nutrition-focused measurement approaches. While there are deeper systemic factors driving food insecurity, the findings provided in this special issue can help guide those addressing the current challenges faced by food insecure households that struggle to achieve healthful diets.
Drug-resistant Mycobacterium tuberculosis and its genotypes isolated from an outbreak in western Thailand
Authors: Rudeeaneksin Janisara , Phetsuksiri Benjawan , Nakajima Chie , Bunchoo Supranee , Suthum Krairerk , Tipkrua Nattakan , Fukushima Yukari , Suzuki Yasuhiko
Published: November 2020

Background

Multidrug-resistant TB (MDR-TB) outbreaks have occurred in the Thamaka district, Kanchanaburi province in Thailand.

Methods

Seventy-two isolates, which included 7% mono-, 30.6% MDR and extensively drug-resistant TB (XDR-TB), were genotyped by spoligotyping, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) and single nucleotide polymorphism genotyping, and their drug resistance was analysed.

Results

The spoligotyping results showed that Beijing spoligo-international type (SIT)1 was predominant (n=38; 52.8%) while the remaining were non-Beijing sublineages (n=34). The MIRU-VNTR analysis showed that Beijing isolates, most of which belonged to the modern type (n=37), formed 5 clusters and 13 individual patterns. In katG, only mutation Ser315Thr was identified. In rpoB, Ser531Leu was predominant, except for His526Arg and Leu533Pro, which were found in two isolates. A cluster of 14 Beijing strains contained these common mutations and shared the MIRU-VNTR genotype with isolates in the Thamaka district that had spread previously. Two U SIT523 isolates contained the mutations A1400G in rrs and Asp94Gly in gyrA genes, indicating a spread of XDR-TB.

Conclusions

Most mutations were associated with drug resistance and the specific MDR Beijing and XDR-TB in U SIT523 isolates remain. This genotyping is a key tool for tracking TB transmission in the Thamaka district of Thailand.
Genome Resources of Two Pathotypes of the Potato Cyst NematodeGlobodera rostochiensisfrom New York
Authors: Wang Xiaohong , Yang Huijun , Véronneau Pierre-Yves , Thurston David , Mimee Benjamin
Published: November 2020

The potato cyst nematode Globodera rostochiensis is a regulated pest posing a serious threat to potato production worldwide. Although the endemic pathotype (Ro1) of G. rostochiensis has been confined to New York State for several decades as a result of quarantine regulations and management with resistant potato cultivars, a virulent pathotype, Ro2, has emerged, for which control measures are scarce. The ability to detect Ro2 early in fields is necessary to sustain the success of G. rostochiensis quarantine in the United States. Here, we report the comparative analysis of whole-genome sequences of multiple single-cyst-derived Ro1 and Ro2 lines, propagated from original field populations. The identified discriminant variants are good targets for developing molecular diagnostic tools for differentiating G. rostochiensis pathotypes in New York.
Nursing Homes in the Crosshairs
Authors: Nelson Roxanne
Published: November 2020

COVID-19 exposes ongoing risks to residents.
Hydrochlorothiazide Associated with Risk of Skin Cancer
Authors: Aschenbrenner Diane S.
Published: November 2020

The Food and Drug Administration has added a risk of skin cancer to the list of potential adverse effects of hydrochlorothiazide, a common diuretic used in hypertension treatment.
New Treatment Option for Adult Growth Hormone Deficiency
Authors: Aschenbrenner Diane S.
Published: November 2020

Somapacitan (Sogroya), the first once-weekly injection to treat adult growth hormone deficiency, is now approved by the Food and Drug Administration. It should not be given to those with active malignancy, any stage of diabetic eye disease, acute critical illness, or acute respiratory failure.
Special Report: Frontline Nurses Say ‘Never Again’
Authors: Brown Theresa
Published: November 2020

Nurses share experiences from the pandemic and strategies to successfully manage future health care crises.
Advocating for Equality: The Backbone of the Sustainable Development Goals
Authors: Oerther Sarah E. , Rosa William E.
Published: November 2020

This article is one in a series in which contributing authors discuss how the United Nations (UN) Sustainable Development Goals (SDGs) are linked to everyday clinical issues; national public health emergencies; and other nursing issues, such as leadership, shared governance, and advocacy. The 2030 Agenda for Sustainable Development, a 15-year plan of action to achieve the goals, was unanimously adopted by all UN member states in September 2015 and took effect on January 1, 2016. The Agenda consists of 17 SDGs addressing social, economic, and environmental determinants of health and 169 associated targets focused on five themes: people, planet, peace, prosperity, and partnership. The SDGs build on the work of the UN Millennium Development Goals, which were in effect from 2000 to 2015. The current article describes the interdependent relationship between SDGs 3 and 10. In addition, the authors focus on nurses' varied and increasingly essential roles in addressing health care inequities through such practices as care coordination and preventive care and education—work which will indirectly play a role in supporting other SDGs related to social and financial equity. For information on all 17 SDGs, go to https://sustainabledevelopment.un.org/sdgs.
Keeping Calm in the Buffer Zone
Authors: Finifrock Monica M.
Published: November 2020

A community health nurse's perspective on COVID-19.
Honey is Useful in Treating Upper Respiratory Tract Infections
Authors: Rosenberg Karen
Published: November 2020

According to this study:

Honey is more effective and less harmful than usual care for symptomatic relief of upper respiratory tract infections and may provide an alternative to antibiotics.
Coronavirus disease 2019 and asthma, allergic rhinitis: molecular mechanisms and host–environmental interactions
Authors: Wakabayashi Mako , Pawankar Ruby , Narazaki Hidehiko , Ueda Takahiro , Itabashi Toshikazu
Published: November 2020

Purpose of review

Coronavirus disease 2019 (COVID-19), a respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus), is a pandemic in over 120 countries worldwide. Risk factors for severe COVID-19 include older age, ethnicity, sex, comorbidities, and living conditions. Although asthmatics and those with allergies are susceptible to more severe outcomes to viral infections, interestingly, asthma has not been reported to be a major comorbidity of COVID-19. However, there are some conflicting reports on the impact of asthma on COVID-19. The underlying immunological and molecular mechanisms may explain at least in part these observations. Furthermore, environmental factors like air pollution that have detrimental effects on asthma and respiratory illnesses also have an impact on COVID-19.

Recent findings

Angiotensin-converting enzyme 2 (ACE2) is the receptor for the attachment and entry of SARS-CoV-2 into the host cells that is upregulated by Th1-mediated responses. In asthmatics, ACE2 gene expression is generally reduced and recent studies have shown a negative correlation between the levels of Th2 cytokines including IL-4, IL-5, and IL-13 in airway epithelial cells and other type 2 biomarkers with ACE2 expression. This may explain in part the potential protective role of asthma on COVID-19. Here, we review the relation of respiratory viral illnesses and asthma, the immune-molecular mechanisms of SARS-CoV-2 infection, the impact of asthma on COVID-19 and that of SARS-CoV-2 on asthma and allergic rhinitis, and the impact of environmental factors like air pollution on COVID-19.

Expression of ACE2 in airway epithelial cells in SARS-COV-2 is influenced by inflammatory profile. Respiratory allergic diseases like asthma appear to have a protective effect against SARS-COV-2 infection. However, the clinical association between asthma and SARS-COV-2 is not fully established and the underlying immune-molecular mechanisms may explain these observations.
Cryoglobulinemic vasculitis: pathophysiological mechanisms and diagnosis
Authors: Kolopp-Sarda Marie N. , Miossec Pierre
Published: November 2020

Purpose of review

Cryoglobulins (CG) are immunoglobulins that precipitate in the cold, and dissolve at 37°C. In vivo, in cold exposed tissues and organs, they can induce vasculitis and occlusive vasculopathy after deposition on vascular endothelium under low temperature and high concentration conditions. Clinical manifestations are cutaneous (purpura, ulcers, vasomotor symptoms, and livedo reticularis), rheumatological (arthralgia and arthritis), and peripheral neuropathy (paresthesia and pain in the lower limbs). In profound organs such as the kidneys, CG deposition is less temperature-dependent, favored by local protein and anion concentrations, and can lead to glomerulonephritis. This review will focus on cryoglobulinemic vasculitis and vascular lesion, and their diagnosis.

Recent findings

The mechanisms of vascular lesions of pathogenic CG in function of CG type and their characteristics are better defined. Optimal conditions for CG detection are critical. The importance of looking for underlying diseases, especially hepatitis C virus status in mixed CG, is reminded.

A decision diagram for CG vasculitis diagnosis based on clinical and biological parameters is proposed.