bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in compensation claim contents following reorganization of emergency hospital care
Authors: Birkeland Søren , Brabrand Mikkel , Mikkelsen Kim Lyngby , Bie Bogh Søren 
Published: October 2020

Abstract

Objectives
To study the effects of the reorganization on patient compensation claim contents relating to health care quality and patient safety.

Design and settings
Danish emergency care has developed considerably over the past decades, including a major reorganization to improve health care quality and patient safety through ensuring easier access to specialist treatment. Analysis of compensation claim patterns is used to evaluate the effects of such health care system changes.

Participants, interventions and main outcome measures
A sample of 1613 compensation claims to the Danish Patient Assurance organization was reviewed using a standardized taxonomy (the Healthcare Complaints Analysis Tool [HCAT]). Using trend analysis, we compared the proportions of claims categorized under HCAT domains, problem categories and sub-categories before and after the reorganization, with particular emphasis on the ‘Clinical problems’ domain covering health care quality and patient safety issues.

Results
We observed a baseline increase in claims relating to clinical problems (P &lt; 0.01), but this increase was less pronounced following the reorganization. This appeared to be driven mainly by a decrease in claims about clinician skills (P = 0.03) and health care neglects (P = 0.01). However, claims about diagnostic errors and patient outcomes showed a tendency (insignificant) to increase.

Conclusions
Emergency care reorganization apparently has been followed by a shift in claim contents towards fewer claims about health care neglect and staff competencies, although claims about other matters may have become more common. Present analyses of compensation claim trends should be supplemented by effect studies using traditional outcome measures such as mortality and readmission rates.
Key genetic elements, single and in clusters, underlying geographically dependent SARS-CoV-2 genetic adaptation and their impact on binding affinity for drugs and immune control
Authors: Salpini Romina , Alkhatib Mohammad , Costa Giosuè , Piermatteo Lorenzo , Ambrosio Francesca Alessandra , Di Maio Velia Chiara , Scutari Rossana , Duca Leonardo , Berno Giulia , Fabeni Lavinia , Alcaro Stefano , Ceccherini-Silberstein Francesca , Artese Anna , Svicher Valentina 
Published: October 2020

Abstract

Objectives
To define key genetic elements, single or in clusters, underlying SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) evolutionary diversification across continents, and their impact on drug-binding affinity and viral antigenicity.

Methods
A total of 12 150 SARS-CoV-2 sequences (publicly available) from 69 countries were analysed. Mutational clusters were assessed by hierarchical clustering. Structure-based virtual screening (SBVS) was used to select the best inhibitors of 3-chymotrypsin-like protease (3CL-Pr) and RNA-dependent RNA polymerase (RdRp) among the FDA-approved drugs and to evaluate the impact of mutations on binding affinity of these drugs. The impact of mutations on epitope recognition was predicted following Grifoni et al. (Cell Host Microbe 2020;

27
671–80.)

Results
Thirty-five key mutations were identified (prevalence: ≥0.5%), residing in different viral proteins. Sixteen out of 35 formed tight clusters involving multiple SARS-CoV-2 proteins, highlighting intergenic co-evolution. Some clusters (including D614GSpike + P323LRdRp + R203KN + G204RN) occurred in all continents, while others showed a geographically restricted circulation (T1198KPL-Pr + P13LN + A97VRdRp in Asia, L84SORF-8 + S197LN in Europe, Y541CHel + H504CHel + L84SORF-8 in America and Oceania). SBVS identified 20 best RdRp inhibitors and 21 best 3CL-Pr inhibitors belonging to different drug classes. Notably, mutations in RdRp or 3CL-Pr modulate, positively or negatively, the binding affinity of these drugs. Among them, P323LRdRp (prevalence: 61.9%) reduced the binding affinity of specific compounds including remdesivir while it increased the binding affinity of the purine analogues penciclovir and tenofovir, suggesting potential hypersusceptibility. Finally, specific mutations (including Y541CHel + H504CHel) strongly hampered recognition of Class I/II epitopes, while D614GSpike profoundly altered the structural stability of a recently identified B cell epitope target of neutralizing antibodies (amino acids 592–620).

Conclusions
Key genetic elements reflect geographically dependent SARS-CoV-2 genetic adaptation, and may play a potential role in modulating drug susceptibility and hampering viral antigenicity. Thus, a close monitoring of SARS-CoV-2 mutational patterns is crucial to ensure the effectiveness of treatments and vaccines worldwide.
SynTEG: a framework for temporal structured electronic health data simulation
Authors: Zhang Ziqi , Yan Chao , Lasko Thomas A , Sun Jimeng , Malin Bradley A 
Published: October 2020

Abstract

Objective
Simulating electronic health record data offers an opportunity to resolve the tension between data sharing and patient privacy. Recent techniques based on generative adversarial networks have shown promise but neglect the temporal aspect of healthcare. We introduce a generative framework for simulating the trajectory of patients’ diagnoses and measures to evaluate utility and privacy.

Materials and Methods
The framework simulates date-stamped diagnosis sequences based on a 2-stage process that 1) sequentially extracts temporal patterns from clinical visits and 2) generates synthetic data conditioned on the learned patterns. We designed 3 utility measures to characterize the extent to which the framework maintains feature correlations and temporal patterns in clinical events. We evaluated the framework with billing codes, represented as phenome-wide association study codes (phecodes), from over 500 000 Vanderbilt University Medical Center electronic health records. We further assessed the privacy risks based on membership inference and attribute disclosure attacks.

Results
The simulated temporal sequences exhibited similar characteristics to real sequences on the utility measures. Notably, diagnosis prediction models based on real versus synthetic temporal data exhibited an average relative difference in area under the ROC curve of 1.6% with standard deviation of 3.8% for 1276 phecodes. Additionally, the relative difference in the mean occurrence age and time between visits were 4.9% and 4.2%, respectively. The privacy risks in synthetic data, with respect to the membership and attribute inference were negligible.

Conclusion
This investigation indicates that temporal diagnosis code sequences can be simulated in a manner that provides utility and respects privacy.
Quantification of Classic, Prescription and Synthetic Opioids in Hair by LC–MS-MS
Authors: Platosz Natalia A , Binz Tina M , Baumgartner Markus R , Lendoiro Elena , de Castro Ana , Concheiro Marta 
Published: October 2020

Abstract
The current use and misuse of synthetic and prescription opioids in the USA has reached epidemic status. According to the US Department of Health and Human Services, every day more than 130 people in the USA die after overdosing on opioids, and 2.1 million had an opioid use disorder in 2018. Hair is becoming an alternative matrix of increasing interest in forensic toxicology to investigate drug use and abuse patterns due to its long window of detection. The focus of this project was to develop and validate a method that simultaneously detects and quantifies 27 classic, prescription and synthetic opioids in hair by liquid chromatography–tandem mass spectrometry (LC–MS-MS). Hair samples were decontaminated and pulverized in a bead mill. Twenty-five milligrams of hair powder were incubated in a buffer overnight. Mixed mode cation exchange solid phase extraction was carried out before undergoing reversed-phase chromatographic separation, successfully resolving isobaric opioids. We used two multiple reaction monitoring transitions in positive mode to identify each analyte. The linearity range was 1–500 pg/mg for fentanyl and synthetic opioids and 10–500 pg/mg for prescription and classic opioids. Imprecision was &lt;17.5% and bias ranged from −13.6 to 12.0%. Majority of compounds showed extraction efficiency &gt;50%, and ion suppression from −89.2 to −26.6% (CV &lt; 19%, n = 10). This method was applied to 64 authentic cases, identifying 13 compounds from our panel. A sensitive and specific method was developed for the identification and quantification of 27 classic, prescription and synthetic opioids in hair by LC–MS-MS.
Feasibility of Patient-Created Orff Chant as a Music-Based Intervention in Supportive Cancer Care
Authors: Colwell Cynthia M , Fiore Jennifer 
Published: October 2020

Abstract
A cancer diagnosis and subsequent treatment can produce distress symptoms, including pain, anxiety, fatigue, and altered mood. These symptoms can have a negative psychological and physiological impact on patients. Patients may need to engage in supportive care with opportunities for emotional responses associated with the disease and chemotherapy treatment to ameliorate distress symptoms. The purpose of the current study was to assess the feasibility of 2 music-based interventions, 1 traditional and 1 novel, and explore the preliminary efficacy of these interventions as supportive care of cancer patients in outpatient treatment rooms. Supportive care options were: standard care (control), patient-selected singing with accompaniment (traditional), and patient-created chant using the Orff process (novel). Distress outcomes measured were: pain and fatigue using a 0–10 numerical rating scale, the State-Trait Anxiety Inventory (state form), and the Profile of Mood States 2 Short Form (for mood and fatigue). After obtaining consent, participants engaged in a single-session of 1 of 3 conditions lasting approximately 30 min. Feasibility measures indicated that the traditional and novel interventions were appropriate for the setting. Results indicated that although not always statistically significant, there were positive changes in pain, fatigue, anxiety, and mood for the 2 music-based conditions over standard care. Conclusions indicate the patient-selected condition was more impactful for pain, anxiety, and mood, while the patient-created chant using the Orff process was more impactful for fatigue. These conclusions might be clinically relevant for therapists pending cancer-related symptoms present during the assessment.
Decision-Making in Collaborative Governance Networks: Pathways to Input and Throughput Legitimacy
Authors: Mosley Jennifer E , Wong Jade 
Published: October 2020

AbstractParticipants may lose faith in collaborative governance processes if they do not perceive internal decision-making processes to be legitimate. Yet, understanding how to assess internal legitimacy and what network characteristics are associated with it has been an enduring challenge. In this article, we propose conceptualizing internal legitimacy as multi-vectored, contrasting input legitimacy—the degree of openness and access that participants experience in their attempt to offer voice—with throughput legitimacy—the quality of the decision-making process itself. Using data from a comparative case study of 18 different US Department of Housing and Urban Development (HUD)-mandated Continuums of Care, we assess this framework with a mixed-methods approach, combining thematic analysis of interview data (n = 145) with Qualitative Comparative Analysis (QCA) to show (1) differences in how participants experience input and throughput legitimacy, (2) the nature of the relationship between input and throughput legitimacy, and (3) what specific network characteristics are associated with positive assessments of each. Our findings indicate that input and throughput legitimacy are distinct but related—throughput legitimacy is harder to achieve and dependent on positive assessments of input legitimacy. Some network characteristics, particularly large size and commissioner-style network management, pose challenges, but a focus on in-person engagement can help ameliorate them. We conclude that distinguishing between input and throughput legitimacy can help managers identify where and how to intervene in order to improve the legitimacy of decision-making processes in collaborative governance networks.
A new branch of understanding for barley inflorescence development
Authors: Levin Kara A , Boden Scott A 
Published: October 2020

This article comments on:Shang Y, Yuan L, Di Y, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. 2020. A CYC/TB1 type TCP transcription factor controls spikelet meristem identity in barley. Journal of Experimental Botany 71, 7118–7131.
Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis
Authors: Ben-Assa Nadav , Coyne Michael J , Fomenkov Alexey , Livny Jonathan , Robins William P , Muniesa Maite , Carey Vincent , Carasso Shaqed , Gefen Tal , Jofre Juan , Roberts Richard J , Comstock Laurie E , Geva-Zatorsky Naama 
Published: October 2020

Abstract
The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.
SMART: recent updates, new developments and status in 2020
Authors: Letunic Ivica , Khedkar Supriya , Bork Peer 
Published: October 2020

AbstractSMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART’s vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.
How to tackle health literacy problems in chronic kidney disease patients? A systematic review to identify promising intervention targets and strategies
Authors: Boonstra Marco D , Reijneveld Sijmen A , Foitzik Elisabeth M , Westerhuis Ralf , Navis Gerjan , de Winter Andrea F 
Published: October 2020

Abstract

Background
Limited health literacy (LHL) is associated with multiple adverse health outcomes in chronic kidney disease (CKD). Interventions are needed to improve this situation, but evidence on intervention targets and strategies is lacking. This systematic review aims to identify potential targets and strategies by summarizing the evidence on: (i) patient- and system-level factors potentially mediating the relation between LHL and health outcomes; and (ii) the effectiveness of health literacy interventions customized to CKD patients.

Methods
We performed a systematic review of peer-reviewed research articles in Medline, Embase and Web of Science, 2009–19. We assessed the quality of the studies and conducted a best-evidence synthesis.

Results
We identified 860 publications and included 48 studies. Most studies were of low quality (n = 26) and focused on dialysis and transplantation (n = 38). We found strong evidence for an association of LHL with smoking and having a suboptimal transplantation process. Evidence was weak for associations between LHL and a variety of factors related to self-care management (n = 25), utilization of care (n = 23), patient–provider interaction (n = 8) and social context (n = 5). Six interventions were aimed at improving knowledge, decision-making and health behaviours, but evidence for their effectiveness was weak.

Conclusions
Study heterogeneity, low quality and focus on kidney failure largely impede the identification of intervention targets and strategies for LHL. More and higher quality studies in earlier CKD stages are needed to unravel how LHL leads to worse health outcomes, and to identify targets and strategies to prevent disease deterioration. Healthcare organizations need to develop and evaluate efforts to support LHL patients.
PCB126 Exposure Revealed Alterations in m6A RNA Modifications in Transcripts Associated With AHR Activation
Authors: Aluru Neelakanteswar , Karchner Sibel I 
Published: October 2020

Abstract
Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Authors: Moura Mariana Neves , Cardoso Danon Clemes , Cristiano Maykon Passos 
Published: October 2020

AbstractThe mechanisms and processes driving change and variation in the genome size (GS) are not well known, and only a small set of ant species has been studied. Ants are an ecologically successful insect group present in most distinct ecosystems worldwide. Considering their wide distribution and ecological plasticity in different environmental contexts, we aimed to expand GS estimation within Formicidae to examine distribution patterns and variation in GS and base composition and to reconstruct the ancestral state of this character in an attempt to elucidate the generalized pattern of genomic expansions. Genome size estimates were generated for 99 ant species, including new GS estimates for 91 species of ants, and the mean GS of Formicidae was found to be 0.38 pg. The AT/GC ratio was 62.40/37.60. The phylogenetic reconstruction suggested an ancestral GS of 0.38 pg according to the Bayesian inference/Markov chain Monte Carlo method and 0.37 pg according to maximum likelihood and parsimony methods; significant differences in GS were observed between the subfamilies sampled. Our results suggest that the evolution of GS in Formicidae occurred through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication. However, further studies are needed to verify whether these changes in DNA content are related to colonization processes, as suggested at the intraspecific level.
Evaluation of Dried Amniotic Membrane on Wound Healing at Split-Thickness Skin Graft Donor Sites: A Randomized, Placebo-Controlled, Double-blind Trial
Authors: Vaheb Mojtaba , Kohestani Bahareh Mohajer , Karrabi Maryam , Khosrojerdi Maryam , Khajeh Mahtab , Shahrestanaki Ehsan , Sahebkar Mohammad 
Published: October 2020

ABSTRACT

OBJECTIVE
To evaluate the effect of amniotic membrane (AM) at split-thickness skin graft (STSG) donor sites.

METHODS
This double-blind randomized controlled trial was conducted on 35 eligible participants referred to the burn unit of Vasei Hospital of Sabzevar, Iran, during 2017 and 2018. Each STSG donor site was divided into two sides, and the respective halves were covered with either a dried AM or petrolatum gauze (control). Outcomes were evaluated on postprocedure days 10, 20, and 30 using the Vancouver Scar Scale.

RESULTS
The mean age of the patients was 39.4 ± 13.97 years, and 62.8% (n = 22) were male. There was no statistically significant difference in wound healing rate on day 10 (P = .261), 20 (P = .214), or 30 (P = .187) between groups. The intervention group had significantly better epithelialization than the control group on day 10 (investigator 1, 1.62 ± 0.59 vs 1.40 ± 0.88 [P = .009); investigator 2, 1.22 ± 0.84 vs 0.91 ± 0.85 [P = .003]), as well as pain reduction (P < .001 during the follow-up period). However, there was no statistically significant difference between groups in terms of pigmentation or vascularization (P > .05).

CONCLUSIONS
Findings suggest that the use of AM is not superior to petrolatum gauze in terms of STSG healing rate; however, AM achieved better pain reduction and epithelialization on day 10.