bluuebunny/crossref_metadata_2025_split huggingface dataset:
Valued living among veterans in breath-based meditation treatment or cognitive processing therapy for posttraumatic stress disorder: Exploratory outcome of a randomized controlled trial
Authors: Schulz-Heik R Jay , Lazzeroni Laura C , Hernandez Beatriz , Avery Timothy J , Mathersul Danielle C , Tang Julia S , Hugo Emily , Bayley Peter J 
Published: June 2022

Background Valued living is the extent to which an individual’s behavior is consistent with what they believe is important or good. It is unknown whether many complementary and integrative treatments and psychotherapies for posttraumatic stress disorder enhance valued living, and for whom. Objectives Measure within- and between-group changes in valued living in Veterans who completed cognitive processing therapy (CPT) and sudarshan kriya yoga (SKY) for posttraumatic stress disorder (PTSD); evaluate moderators of improvement. Methods Participants with clinically significant symptoms of PTSD were assigned to CPT, a first line, evidence-based psychotherapy for PTSD or SKY, an emerging breath-based meditation with strong preliminary empirical support in a parallel-groups randomized controlled trial at a single Veterans Affairs healthcare center. The Valuing Questionnaire subscales for progress in valued living (VQ-P) and obstruction in valued living (VQ-O) were exploratory outcome measures. Assessors were blind to treatment assignment. Results 59 participants completed treatment (29 CPT, 30 SKY). Participants in the CPT group improved from baseline to end of treatment in both VQ-Progress ( d=0.55, p=0.02) and VQ–Obstruction ( d=-0.51, p=0.03), while the SKY group did not improve on either subscale ( d=0.08, p=0.69; d=0.00, p=1.00). However, differences between treatments were not statistically significant ( p=0.16, 0.11, respectively). Participants reporting less valued living and more depression symptoms at baseline reported greater improvements in valued living following treatment. Conclusion CPT may have a positive effect on valued living. Individuals lower in valued living and with more depression may derive relatively more benefit.
Nature and Composition of Earnings Reported by Health Economists and Related Professionals: Gender, Education, and job Characteristics Matter
Authors: Popovici Ioana , Carvajal Manuel J. , Peeples Patti , Rabionet Silvia E. 
Published: June 2022

Background Despite the fast growth of the workforce comprising health economics (HE), outcomes research (OR), and market access (MA) professionals, little is known about their earnings determination. Only three studies have examined their earnings and none has considered the number of hours worked, traditionally a critical component of income determination models. Objectives (i) Estimate an indicator of annual earnings of HE/OR/MA professionals, comparing male versus female and U.S. versus non-U.S. earnings levels, and (ii) assess the magnitude of the effect of selected human-capital and job-related covariates on their annual earnings determination. Methods The study used 2019 self-reported survey data from a sample of 304 HE/OR/MA professionals registered in the HealthEconomics.com global subscriber list. A two-way classification model with multiple replications was used to identify and test earnings variations of HE/OR/MA professionals across genders and locations. An earnings determination function using ordinary least squares was used to identify disparities in response to covariates including average workweek, human-capital stock, and job-related variables by gender and location. Results Substantial earning disparities were observed between HE/OR/MA professionals living in the U.S. and those living in other countries. Non-U.S. respondents exhibited earnings gaps of 44.7% in wages/salaries and 46.8% in total earnings relative to their U.S. counterparts with greater gaps for women than men. The female earnings gap outside the U.S. was considerably greater than in the U.S. Holding a graduate degree; working in a pharmaceutical or biotechnology firm; age, a proxy for experience; and working remotely impacted earnings differentials across different subgroups. Conclusions The findings of this paper shed light into the nature and composition of earnings of HE/OR/MA professionals across genders and locations. Exploring the dynamics of earning disparities by gender and location has increased in relevance given the rapidly-changing and uncertain job market environment driven by the COVID-19 pandemic.
Relationship Between Psychosocial Stress and Blood Pressure: The National Heart, Lung, and Blood Institute Family Heart Study
Authors: Nwanaji-Enwerem Uzoji , Onsomu Elijah O. , Roberts Dionne , Singh Abanish , Brummett Beverly H. , Williams Redford B. , Dungan Jennifer R. 
Published: June 2022

Introduction Various domains of psychosocial stress have been significantly related to blood pressure. However, ambiguity is present in how these relationships are defined in the literature. Objective To add to the existing literature and examine the relationship between psychosocial stress (financial strain and job strain) and other cofactors on blood pressure. Methods This secondary analysis is designed to analyze the relationship between levels of job and financial stress and blood pressure outcomes among participants in the National Heart, Lung, and Blood Institute (NHLBI) Family Heart Study 2004–2008. The descriptive, cross-sectional design uses data from a subset of study participants, 350 White and 195 Black (n = 545), 338 female (62%), and all aged 18–56 years. Psychosocial stress was measured using the Singh Stress Scale. Resting systolic (SBP) and diastolic (DBP) blood pressure values obtained on a stress reactivity protocol day in the primary study, as well as calculated mean arterial pressure (MAP) were used for this analysis. Multivariate linear regression analyses were used to explore the relationship between psychosocial stress and blood pressure. Results In this young cohort, self-report of either financial strain or job strain was associated with lower blood pressure levels than those of participants who reported neither stressor. Differential sex and race effects appear to contribute to these results. Blood pressure levels were not significantly associated with self-report of both stressors. Conclusion Understanding the effects of various forms of stress on blood pressure may inform more precise HTN risk-factor screening and interventions to improve BP management.
American Society of Hematology living guidelines on the use of anticoagulation for thromboprophylaxis for patients with COVID-19: March 2022 update on the use of anticoagulation in critically ill patients
Authors: Cuker Adam , Tseng Eric K. , Schünemann Holger J. , Angchaisuksiri Pantep , Blair Clifton , Dane Kathryn , DeSancho Maria T. , Diuguid David , Griffin Daniel O. , Kahn Susan R. , Klok Frederikus A. , Lee Alfred Ian , Neumann Ignacio , Pai Ashok , Righini Marc , Sanfilippo Kristen M. , Siegal Deborah M. , Skara Mike , Terrell Deirdra R. , Touri Kamshad , Akl Elie A. , Al Jabiri Reyad , Al Jabiri Yazan , Boulos Mary , Brignardello-Petersen Romina , Charide Rana , Colunga-Lozano Luis E. , Dearness Karin , Darzi Andrea J. , Karam Samer G. , Morgano Gian Paolo , Morsi Rami Z. , Philip Binu A. , Benitez Yetiani Roldan , Stevens Adrienne , Solo Karla , Wiercioch Wojtek , Mustafa Reem A. , Nieuwlaat Robby 
Published: June 2022

AbstractBackground:COVID-19–related critical illness is associated with an increased risk of venous thromboembolism (VTE).Objective:These evidence-based guidelines of the American Society of Hematology (ASH) are intended to support patients, clinicians, and other health care professionals in decisions about the use of anticoagulation for patients with COVID-19.Methods:ASH formed a multidisciplinary guideline panel, including 3 patient representatives, and applied strategies to minimize potential bias from conflicts of interest. The McMaster University Grading of Recommendations Assessment, Development and Evaluation (GRADE) Centre supported the guideline development process, including performing systematic evidence reviews (up to January 2022). The panel prioritized clinical questions and outcomes according to their importance for clinicians and patients. The panel used the GRADE approach to assess evidence and make recommendations, which were subject to public comment. This is an update to guidelines published in February 2021 and May 2021 as part of the living phase of these guidelines.Results:The panel made 1 additional recommendation: a conditional recommendation for the use of prophylactic-intensity over therapeutic-intensity anticoagulation for patients with COVID-19–related critical illness who do not have suspected or confirmed VTE. The panel emphasized the need for an individualized assessment of thrombotic and bleeding risk.Conclusions:This conditional recommendation was based on very low certainty in the evidence, underscoring the need for additional, high-quality, randomized controlled trials comparing different intensities of anticoagulation for patients with COVID-19–related critical illness.
Robust Resistive Switching Constancy and Quantum Conductance in High-k Dielectric-Based Memristor for Neuromorphic Engineering
Authors: Ismail Muhammad , Mahata Chandreswar , Kang Myounggon , Kim Sungjun 
Published: June 2022

AbstractFor neuromorphic computing and high-density data storage memory, memristive devices have recently gained a lot of interest. So far, memristive devices have suffered from switching parameter instability, such as distortions in resistance values of low- and high-resistance states (LRSs and HRSs), dispersion in working voltage (set and reset voltages), and a small ratio of high and low resistance, among other issues. In this context, interface engineering is a critical technique for addressing the variation issues that obstruct the use of memristive devices. Herein, we engineered a high band gap, low Gibbs free energy Al2O3interlayer between the HfO2switching layer and the tantalum oxy-nitride electrode (TaN) bottom electrode to operate as an oxygen reservoir, increasing the resistance ratio between HRS and LRS and enabling multilayer data storage. The Pt/HfO2/Al2O3/TaN memristive device demonstrates analog bipolar resistive switching behavior with a potential ratio of HRS and LRS of > 105and the ability to store multi-level data with consistent retention and uniformity. On set and reset voltages, statistical analysis is used; the mean values (µ) of set and reset voltages are determined to be − 2.7 V and + 1.9 V, respectively. There is a repeatable durability over DC 1000 cycles, 105AC cycles, and a retention time of 104 s at room temperature. Quantum conductance was obtained by increasing the reset voltage with step of 0.005 V with delay time of 0.1 s. Memristive device has also displayed synaptic properties like as potentiation/depression and paired-pulse facilitation (PPF). Results show that engineering of interlayer is an effective approach to improve the uniformity, ratio of high and low resistance, and multiple conductance quantization states and paves the way for research into neuromorphic synapses.
Predicting the pathogenicity of bacterial genomes using widely spread protein families
Authors: Naor-Hoffmann Shaked , Svetlitsky Dina , Sal-Man Neta , Orenstein Yaron , Ziv-Ukelson Michal 
Published: June 2022

AbstractBackgroundThe human body is inhabited by a diverse community of commensal non-pathogenic bacteria, many of which are essential for our health. By contrast, pathogenic bacteria have the ability to invade their hosts and cause a disease. Characterizing the differences between pathogenic and commensal non-pathogenic bacteria is important for the detection of emerging pathogens and for the development of new treatments. Previous methods for classification of bacteria as pathogenic or non-pathogenic used either raw genomic reads or protein families as features. Using protein families instead of reads provided a better interpretability of the resulting model. However, the accuracy of protein-families-based classifiers can still be improved.ResultsWe developed a wide scope pathogenicity classifier (WSPC), a new protein-content-based machine-learning classification model. We trained WSPC on a newly curated dataset of 641 bacterial genomes, where each genome belongs to a different species. A comparative analysis we conducted shows that WSPC outperforms existing models on two benchmark test sets. We observed that the most discriminative protein-family features in WSPC are widely spread among bacterial species. These features correspond to proteins that are involved in the ability of bacteria to survive and replicate during an infection, rather than proteins that are directly involved in damaging or invading the host.
Moment estimators of relatedness from low-depth whole-genome sequencing data
Authors: Herzig Anthony F. , Ciullo M. ,   FranceGenRef Consortium, Deleuze Jean-François , Génin Emmanuelle , Redon Richard , Adjou Chantal , Chatel Stéphanie , Férec Claude , Goldberg Marcel , Halbout Philippe-Antoine , Le Marec Hervé , L’Helgouach David , Rouault Karen , Schott Jean-Jacques , Vogelsperger Anne , Zins Marie , Bacq Delphine , Blanchet Hélène , Boland Anne , Lindenbaum Pierre , Ludwig Thomas , Meyer Vincent , Olaso Robert , Velo-Suárez Lourdes , Alves Isabel , Bocher Ozvan , Dina Christian , Herzig Anthony F. , Karakachoff Matilde , Marenne Gaëlle , Pierre Aude Saint , Leutenegger A-L. , Perdry H. 
Published: June 2022

AbstractBackgroundEstimating relatedness is an important step for many genetic study designs. A variety of methods for estimating coefficients of pairwise relatedness from genotype data have been proposed. Both the kinship coefficient$$\varphi$$φand the fraternity coefficient$$\psi$$ψfor all pairs of individuals are of interest. However, when dealing with low-depth sequencing or imputation data, individual level genotypes cannot be confidently called. To ignore such uncertainty is known to result in biased estimates. Accordingly, methods have recently been developed to estimate kinship from uncertain genotypes.ResultsWe present new method-of-moment estimators of both the coefficients$$\varphi$$φand$$\psi$$ψcalculated directly from genotype likelihoods. We have simulated low-depth genetic data for a sample of individuals with extensive relatedness by using the complex pedigree of the known genetic isolates of Cilento in South Italy. Through this simulation, we explore the behaviour of our estimators, demonstrate their properties, and show advantages over alternative methods. A demonstration of our method is given for a sample of 150 French individuals with down-sampled sequencing data.ConclusionsWe find that our method can provide accurate relatedness estimates whilst holding advantages over existing methods in terms of robustness, independence from external software, and required computation time. The method presented in this paper is referred to as LowKi (Low-depthKinship) and has been made available in an R package (https://github.com/genostats/LowKi).
SAPFIR: A webserver for the identification of alternative protein features
Authors: Zhou Delong , Tran Yvan , Abou Elela Sherif , Scott Michelle S. 
Published: June 2022

Abstract
Background
Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, the extent to which splicing events have functional consequences remains unclear and predicting the impact of splicing events on protein activity is limited to gene-specific analysis.

Results
To accelerate the identification of functionally relevant alternative splicing events we created SAPFIR, a predictor of protein features associated with alternative splicing events. This webserver tool uses InterProScan to predict protein features such as functional domains, motifs and sites in the human and mouse genomes and link them to alternative splicing events. Alternative protein features are displayed as functions of the transcripts and splice sites. SAPFIR could be used to analyze proteins generated from a single gene or a group of genes and can directly identify alternative protein features in large sequence data sets. The accuracy and utility of SAPFIR was validated by its ability to rediscover previously validated alternative protein domains. In addition, our de novo analysis of public datasets using SAPFIR indicated that only a small portion of alternative protein domains was conserved between human and mouse, and that in human, genes involved in nervous system process, regulation of DNA-templated transcription and aging are more likely to produce isoforms missing functional domains due to alternative splicing.

Conclusion
Overall SAPFIR represents a new tool for the rapid identification of functional alternative splicing events and enables the identification of cellular functions affected by a defined splicing program. SAPFIR is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/, a website implemented in Python, with all major browsers supported. The source code is available at https://github.com/DelongZHOU/SAPFIR.
Ectopic expression of a combination of 5 genes detects high risk forms of T-cell acute lymphoblastic leukemia
Authors: Peng Li-Jun , Zhou Yue-Bo , Geng Mei , Bourova-Flin Ekaterina , Chuffart Florent , Zhang Wei-Na , Wang Tao , Gao Meng-Qing , Xi Meng-Ping , Cheng Zhong-Yi , Zhang Jiao-Jiao , Liu Yuan-Fang , Chen Bing , Khochbin Saadi , Wang Jin , Rousseaux Sophie , Mi Jian-Qing 
Published: June 2022

Abstract
Background
T cell acute lymphoblastic leukemia (T-ALL) defines a group of hematological malignancies with heterogeneous aggressiveness and highly variable outcome, making therapeutic decisions a challenging task. We tried to discover new predictive model for T-ALL before treatment by using a specific pipeline designed to discover aberrantly active gene.

Results
The expression of 18 genes was significantly associated with shorter survival, including ACTRT2, GOT1L1, SPATA45, TOPAZ1 and ZPBP (5-GEC), which were used as a basis to design a prognostic classifier for T-ALL patients. The molecular characterization of the 5-GEC positive T-ALL unveiled specific characteristics inherent to the most aggressive T leukemic cells, including a drastic shut-down of genes located on the mitochondrial genome and an upregulation of histone genes, the latter characterizing high risk forms in adult patients. These cases fail to respond to the induction treatment, since 5-GEC either predicted positive minimal residual disease (MRD) or a short-term relapse in MRD negative patients.

Conclusion
Overall, our investigations led to the discovery of a homogenous group of leukemic cells with profound alterations of their biology. It also resulted in an accurate predictive tool that could significantly improve the management of T-ALL patients.
Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains
Authors: Chen Ning , Zhang Hao , Zang En , Liu Zhi-Xia , Lan Ya-Fei , Hao Wei-Li , He Shan , Fan Xing , Sun Gen-Lou , Wang Yi-Ling 
Published: June 2022

AbstractOpisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.
Whole genome sequencing analysis to evaluate the influence of T2DM on polymorphisms associated with drug resistance in M. tuberculosis
Authors: Bermudez-Hernández Gustavo Adolfo , Pérez-Martínez Damián Eduardo , Madrazo-Moya Carlos Francisco , Cancino-Muñoz Irving , Comas Iñaki , Zenteno-Cuevas Roberto 
Published: June 2022

Abstract
Background
Type 2 diabetes mellitus (T2DM) has been associated with treatment failure, and the development of drug resistance in tuberculosis (TB). Also, whole-genome sequencing has provided a better understanding and allowed the growth of knowledge about polymorphisms in genes associated with drug resistance. Considering the above, this study analyzes genome sequences to evaluate the influence of type 2 diabetes mellitus in the development of mutations related to tuberculosis drug resistance. M. tuberculosis isolates from individuals with (n = 74), and without (n = 74) type 2 diabetes mellitus was recovered from online repositories, and further analyzed.

Results
The results showed the presence of 431 SNPs with similar proportions between diabetics, and non-diabetics individuals (48% vs. 52%), but with no significant relationship. A greater number of mutations associated with rifampicin resistance was observed in the T2DM-TB individuals (23.2% vs. 16%), and the exclusive presence of rpoBQ432L, rpoBQ432P, rpoBS441L, and rpoBH445L variants. While these variants are not private to T2DM-TB cases they are globally rare highlighting a potential role of T2DM. The phylogenetic analysis showed 12 sublineages, being 4.1.1.3, and 4.1.2.1 the most prevalent in T2DM-TB individuals but not differing from those most prevalent in their geographic location. Four clonal complexes were found, however, no significant relationship with T2DM was observed. Samples size and potential sampling biases prevented us to look for significant associations.

Conclusions
The occurrence of globally rare rifampicin variants identified only in isolates from individuals with T2DM could be due to the hyperglycemic environment within the host. Therefore, further studies about the dynamics of SNPs’ generation associated with antibiotic resistance in patients with diabetes mellitus are necessary.