bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators
Authors: Pérez-Pulido Antonio J , Asencio-Cortés Gualberto , Brokate-Llanos Ana M , Brea-Calvo Gloria , Rodríguez-Griñolo Rosario , Garzón Andrés , Muñoz Manuel J 
Published: December 2020

Abstract
The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of heterogeneous and normalized transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and common transcriptional regulators in any biological model. The present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an opportunity to test this novel approach due to the wealth of data that are being generated, which could be used for validating results. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV viruses and searched for genes tightly co-expressed with them. We have found 1899 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlaps with those identified by former laboratory high-throughput screenings (with P-value near 0). Our results reveal a series of common regulators, involved in immune and inflammatory responses that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors.
Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing
Authors: Kumar Das Jayanta , Tradigo Giuseppe , Veltri Pierangelo , H Guzzi Pietro , Roy Swarup 
Published: December 2020

AbstractMotivationThe outbreak of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, also known as COVID-19) in Wuhan has attracted worldwide attention. SARS-CoV-2 causes severe inflammation, which can be fatal. Consequently, there has been a massive and rapid growth in research aimed at throwing light on the mechanisms of infection and the progression of the disease. With regard to this data science is playing a pivotal role in in silico analysis to gain insights into SARS-CoV-2 and the outbreak of COVID-19 in order to forecast, diagnose and come up with a drug to tackle the virus. The availability of large multiomics, radiological, bio-molecular and medical datasets requires the development of novel exploratory and predictive models, or the customisation of existing ones in order to fit the current problem. The high number of approaches generates the need for surveys to guide data scientists and medical practitioners in selecting the right tools to manage their clinical data.ResultsFocusing on data science methodologies, we conduct a detailed study on the state-of-the-art of works tackling the current pandemic scenario. We consider various current COVID-19 data analytic domains such as phylogenetic analysis, SARS-CoV-2 genome identification, protein structure prediction, host–viral protein interactomics, clinical imaging, epidemiological research and drug discovery. We highlight data types and instances, their generation pipelines and the data science models currently in use. The current study should give a detailed sketch of the road map towards handling COVID-19 like situations by leveraging data science experts in choosing the right tools. We also summarise our review focusing on prime challenges and possible future research directions.Contacthguzzi@unicz.it, sroy01@cus.ac.in
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19
Authors: Yang Yanqing , Zhu Zhengdan , Wang Xiaoyu , Zhang Xinben , Mu Kaijie , Shi Yulong , Peng Cheng , Xu Zhijian , Zhu Weiliang 
Published: December 2020

Abstract
Discovering efficient drugs and identifying target proteins are still an unmet but urgent need for curing coronavirus disease 2019 (COVID-19). Protein structure-based docking is a widely applied approach for discovering active compounds against drug targets and for predicting potential targets of active compounds. However, this approach has its inherent deficiency caused by e.g. various different conformations with largely varied binding pockets adopted by proteins, or the lack of true target proteins in the database. This deficiency may result in false negative results. As a complementary approach to the protein structure-based platform for COVID-19, termed as D3Docking in our previous work, we developed in this study a ligand-based method, named D3Similarity, which is based on the molecular similarity evaluation between the submitted molecule(s) and those in an active compound database. The database is constituted by all the reported bioactive molecules against the coronaviruses, viz., severe acute respiratory syndrome coronavirus (SARS), Middle East respiratory syndrome coronavirus (MERS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human betacoronavirus 2c EMC/2012 (HCoV-EMC), human CoV 229E (HCoV-229E) and feline infectious peritonitis virus (FIPV), some of which have target or mechanism information but some do not. Based on the two-dimensional (2D) and three-dimensional (3D) similarity evaluation of molecular structures, virtual screening and target prediction could be performed according to similarity ranking results. With two examples, we demonstrated the reliability and efficiency of D3Similarity by using 2D × 3D value as score for drug discovery and target prediction against COVID-19. The database, which will be updated regularly, is available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php.
‘Suppression on top of oppression’: A symbolic interactionist perspective on the affective experience of incarceration
Authors: Umamaheswar Janani 
Published: December 2020

AbstractPenological research has extensively documented how incarcerated men’s identities are shaped by the prison setting, highlighting how these men cope with and adapt to the ‘pains of imprisonment’ through careful emotion management. Significantly less research has focused explicitly on the role of emotion in incarcerated men’s constructions of their selves. In this article, I draw on 24 in-depth interviews with incarcerated men to reveal how the prison setting generates negative emotions (such as sadness, shame, humiliation, and anger) that in turn perpetuate the isolation that these men face. Emotions thus constitute an overlooked source of these men’s social marginalization. Additionally, I draw on theoretical literature derived from symbolic interactionism (and identity theory in particular) to explore how participants cope with, and make efforts to overcome, their negative emotions by engaging in active emotion and identity work centred on constructing morality narratives of pride, self-worth, and superiority.
The Guiding Principles on Shared Responsibility in International Law: Too Much or Too Little?
Authors: Lanovoy Vladyslav 
Published: December 2020

Abstract
The Guiding Principles on Shared Responsibility aim to ‘substantiate the existing rules of the law of international responsibility’ as they are codified in the International Law Commission’s 2001 Articles on the Responsibility of States for Internationally Wrongful Acts and the 2011 Articles on the Responsibility of International Organizations. This article examines the contribution of the Guiding Principles to the law of international responsibility and analyses some of their more controversial features, where the Guiding Principles seek to significantly expand the scope of the existing rules and, conversely, where they could have been much more ambitious.
Comparative analysis of secondary metabolite gene clusters in different strains of Magnaporthe oryzae
Authors: Saha Pallabi , Sarkar Atrayee , Sabnam Nazmiara , Shirke Meghana D , Mahesh H B , Nikhil Aman , Rajamani Anantharamanan , Gowda Malali , Roy-Barman Subhankar 
Published: December 2020

ABSTRACT
Rice blast caused by Magnaporthe oryzae continues to be a major constraint in rice production worldwide. Rice is one of the staple crops in India and rice blast causes huge economic losses. Interestingly, the Indian subcontinent is the centre for origin and diversity of rice as well as the Magnaporthe species complex. Secondary metabolites are known to play important role in pathogenesis and M. oryzae has high potential of genes involved in secondary metabolism but, unfortunately most of them remain uncharacterized. In the present study, we analysed the draft genome assemblies of M. oryzae strains isolated from different parts of India, for putative secondary metabolite key gene (SMKG) clusters encoding polyketide synthases, non-ribosomal peptide synthetases, diterpene cyclases and dimethylallyl tryptophan synthase. Based on the complete genome sequence of 70–15 strain and its previous reports of identified SMKGs, we have identified the key genes for the interrogated strains. Expression analysis of these genes amongst different strains indicates how they have evolved depending on the host and environmental conditions. To our knowledge, this study is first of its kind where the secondary metabolism genes and their role in functional adaptation were studied across several strains of M. oryzae.
A systematic review of contributing factors of and solutions to electronic health record–related impacts on physician well-being
Authors: Nguyen Oliver T , Jenkins Nyasia J , Khanna Neel , Shah Shivani , Gartland Alexander J , Turner Kea , Merlo Lisa J 
Published: December 2020

Abstract

Objective
Physicians often describe the electronic health record (EHR) as a cumbersome impediment to meaningful work, which has important implications for physician well-being. This systematic review (1) assesses organizational, physician, and information technology factors associated with EHR-related impacts on physician well-being; and (2) highlights potential improvements to EHR form and function, as recommended by frontline physicians.

Materials and methods
The MEDLINE, Embase, CINAHL, PsycINFO, ProQuest, and Web of Science databases were searched for literature describing EHR use by physicians and markers of well-being.

Results
After reviewing 7388 article, 35 ultimately met the inclusion criteria. Multiple factors across all levels were associated with EHR-related well-being among physicians. Notable predictors amenable to interventions include (1) total EHR time, (2) after-hours EHR time, (3) on-site EHR support, (4) perceived EHR usability, (5) in-basket burden, and (6) documentation burden. Physician recommendations also echoed these themes.

Conclusions
There are multiple complex factors involved in EHR-related well-being among physicians. Our review shows physicians have recommendations that span from federal regulations to organizational policies to EHR modifications. Future research should assess multipronged interventions that address these factors. As primary stakeholders, physicians should be included in the planning and implementation of such modifications to ensure compatibility with physician needs and clinical workflows.
Replacing fish oil and astaxanthin by microalgal sources produced different metabolic responses in juvenile rainbow trout fed 2 types of practical diets
Authors: Zhu Shanli , Portman Mark , Cleveland Beth M , Magnuson Andrew D , Wu Kun , Sealey Wendy , Lei Xin Gen 
Published: December 2020

Abstract
Dietary fish oil supplementation provides n-3 long-chained polyunsaturated fatty acids for supporting fish growth and metabolism and enriching fillet with eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; c22:6n-3). Two experiments were performed as a 3 × 2 factorial arrangement of dietary treatments for 16 wk to determine effects and mechanisms of replacing 0%, 50%, and 100% fish oil with DHA-rich microalgae in combination with synthetic vs. microalgal source of astaxanthin in plant protein meal (PM)- or fishmeal (FM)- based diets for juvenile rainbow trout (Oncorhynchus mykiss). Fish (22 ± 0.26 g) were stocked at 17/tank and 3 tanks/diet. The 100% fish oil replacement impaired (P &lt; 0.0001) growth performance, dietary protein and energy utilization, body indices, and tissue accumulation of DHA and EPA in both diet series. The impairments were associated (P &lt; 0.05) with upregulation of hepatic gene expression related to growth (ghr1and igf1) and biosynthesis of DHA and EPA (fads6 and evol5) that was more dramatic in the FM than PM diet-fed fish, and more pronounced on tissue EPA than DHA concentrations. The source of astaxanthin exerted interaction effects with the fish oil replacement on several measures including muscle total cholesterol concentrations. In conclusion, replacing fish oil by the DHA-rich microalgae produced more negative metabolic responses than the substitution of synthetic astaxanthin by the microalgal source in juvenile rainbow trout fed 2 types of practical diets.
Identification of Lice Stored in Alcohol Using MALDI-TOF MS
Authors: Benyahia Hanene , Ouarti Basma , Diarra Adama Zan , Boucheikhchoukh Mehdi , Meguini Mohamed Nadir , Behidji Makhlouf , Benakhla Ahmed , Parola Philippe , Almeras Lionel 
Published: December 2020

Abstract
Lice pose major public and veterinary health problems with economic consequences. Their identification is essential and requires the development of an innovative strategy. MALDI-TOF MS has recently been proposed as a quick, inexpensive, and accurate tool for the identification of arthropods. Alcohol is one of the most frequently used storage methods and makes it possible to store samples for long periods at room temperature. Several recent studies have reported that alcohol alters protein profiles resulting from MS analysis. After preliminary studies on frozen lice, the purpose of this research was to evaluate the influence of alcohol preservation on the accuracy of lice identification by MALDI-TOF MS. To this end, lice stored in alcohol for variable periods were submitted for MS analysis and sample preparation protocols were optimized. The reproducibility and specificity of the MS spectra obtained on both these arthropod families allowed us to implement the reference MS spectra database (DB) with protein profiles of seven lice species stored in alcohol. Blind tests revealed a correct identification of 93.9% of Pediculus humanus corporis (Linnaeus, 1758) and 98.4% of the other lice species collected in the field. This study demonstrated that MALDI-TOF MS could be successfully used for the identification of lice stored in alcohol for different lengths of time.
Neoadjuvant Immunotherapy for High-Risk, Resectable Malignancies: Scientific Rationale and Clinical Challenges
Authors: Krishnamoorthy Mithunah , Lenehan John G , Maleki Vareki Saman 
Published: December 2020

Abstract
Neoadjuvant immunotherapy involves administering immune checkpoint inhibitors before surgical resection in high-risk resectable disease. This strategy was shown to have a high pathological response rate and prolonged relapse-free survival in randomized trials in melanoma, glioblastoma, and colon cancer with small numbers of patients. In resectable cancers, immune checkpoint inhibitors such as anti-programmed cell death-1 (PD1) and anti-cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) can enhance antitumor immunity by activating antigen-specific T cells found in the primary tumor. These tumor-reactive T cells continue to exert antitumor effects on remaining neoplastic cells after the resection of the primary tumor, potentially preventing relapses from occurring. Based on the scientific rationale and early clinical observations with surrogate survival endpoints, neoadjuvant immunotherapy may provide an effective alternative to other therapeutic strategies such as adjuvant treatment. However, this can be determined only by conducting randomized controlled trials comparing neoadjuvant immunotherapy with the current standard of care for each tumor site. This review discusses the cellular mechanisms that occur during successful neoadjuvant immunotherapy and highlights the clinical data from the available human studies that support the preclinical mechanistic data. Here we also discuss strategies required for successful neoadjuvant immunotherapy, including combination treatment strategies and resistance mechanisms to neoadjuvant treatment.
Understanding Shoulder Pain: A Qualitative Evidence Synthesis Exploring the Patient Experience
Authors: Maxwell Christina , Robinson Katie , McCreesh Karen 
Published: December 2020

AbstractObjectiveThe objective of this study was to review and synthesize qualitative research studies exploring the experiences of individuals living with shoulder pain to enhance understanding of the experiences of these individuals as well as facilitate health care developments.MethodsA meta-ethnographic approach was adopted to review and synthesize eligible published qualitative research studies. The findings from each included study were translated into one another using the Noblit and Hares 7-stage process. A systematic search of 11 electronic databases was conducted in March 2020. Methodological quality was assessed using the Critical Appraisal Skills Programme appraisal tool.ResultsNineteen studies were included in the meta-synthesis. Included articles explored the lived experiences as well as treatment-related experiences of participants. All of the included articles were deemed to be of high methodological quality. Three themes were identified: (1) negative emotional, social, and activity impact (“It has been a big upheaval”); (2) developing an understanding (“Why is it hurting so much?”); and (3) exercise (“Am I going to go through a lot of pain in moving it…?”). Across the included studies, the severe emotional and physical impact of shoulder pain was a core finding. Many people sought a “permanent” solution involving surgery. Openness to other treatment options was influenced by factors including understanding of pain, prior experiences, and treatment expectations.ConclusionThese findings deepen our understanding of the impact of shoulder pain on peoples’ lives and provide novel insight into the experience of treatment. Enhanced awareness of people’s experiences of shoulder pain and treatment is crucial for clinicians when planning and implementing evidence-based recommendation.ImpactTo the knowledge of the authors, this is the first qualitative evidence synthesis to explore the treatment-related experiences of individuals with shoulder pain. Shoulder surgery was considered by many as the only means to achieve a more permeant resolution of symptoms.Lay SummaryShoulder pain causes emotional and physical turmoil that can permeate every facet of life. People’s understanding of their shoulder pain appears to be deeply rooted in a biomechanical view of pain, which influences their expectations relating to diagnosis and treatment.
Using peer instruction in an analysis course: a report from the field
Authors: Kempen Leander 
Published: December 2020

Abstract
This paper is meant to give some kind of manual instruction for the use of audience response systems for performing peer instruction in class. The different aspects one has to take into account when trying to implement this method are presented. In all of the sections, additional links and references are provided. The author reports on and reflects on his individual decisions when conducting peer teaching in an analysis course at the university. Finally, the results of the corresponding evaluation are presented and discussed.
Academic Grade Inflation in Nursing Education: A Scoping Review of the Qualitative and Quantitative Literature
Authors: Del Prato Darlene M. , Bankert Esther G. 
Published: December 2020

Abstract

AIM
The aim of the study was to answer the research question: What is known from the literature about academic grading practices and grade inflation in nursing education?

BACKGROUND
Nursing students require authentic assessment that supports their professional formation. For teachers and students, integrity is fundamental to professional nursing excellence.

METHOD
Arskey and O′Malley’s framework was used to integrate and reinterpret findings from qualitative, quantitative, and mixed-method studies.

RESULTS
Twelve studies were reviewed. Contributing factors are described as institutional constraints, external standards, team teaching, lack of faculty confidence, and student incivility. Strategies that may mitigate grade inflation include establishing grading expectations and increasing pedagogical rigor with precise rubrics, valid and reliable examinations, interrater reliability, and faculty development.

CONCLUSION
Academic grading is a complex faculty responsibility grounded in ethical and relational competencies that can support or hinder students’ professional formation. Evaluation of strategies to mitigate grade inflation in nursing education is urgently needed.
Idiopathic pulmonary fibrosis
Authors: Pruitt Bill 
Published: December 2020

Abstract:
Idiopathic pulmonary fibrosis (IPF) is a restrictive lung disease in which the cause cannot be determined. This article discusses restrictive lung diseases that fall under the general category of interstitial lung disease with a focus on IPF—a fatal disease characterized by progressive fibrosis and interstitial pneumonia, dyspnea, and decreasing pulmonary function.
Unmasking misunderstandings
Authors: Kilgore Bradley , Harriger Cassandra , Gaeta Laura , Sharpp Tara J. 
Published: December 2020

Abstract:
Positive patient outcomes depend on successful communication. Increased use of personal protective equipment such as face masks during the COVID-19 pandemic can exacerbate communication difficulties. This article describes situations in which miscommunications may occur, identifies sources of communication breakdowns, and offers strategies to prevent them in real-life scenarios.
Use of toilet alarms in inpatient settings
Authors: Jones Lorrie , Hessler Karen , Winter Becky , Kupzyk Kevin 
Published: December 2020

Abstract

Purpose:
To investigate the use of toilet alarms among patients at an increased risk for falls in inpatient settings while allowing for privacy and maintaining safety.

Methods:
Pre- and postsurvey data were collected among patients in the intervention and control groups, as well as among the healthcare staff, to determine perceptions of privacy and safety.

Results:
Each participant group was compared according to the participants' responses to the pre- and postsurveys. On average, the intervention group perceived increased levels of privacy and safety compared with the control group. Staff also indicated increased privacy and safety.

Conclusion:
Additional research is necessary, but patient satisfaction, privacy, and dignity may be augmented by using toilet alarms in hospital settings.