bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repression of a large number of genes requires interplay between homologous recombination and HIRA
Authors: Misova Ivana , Pitelova Alexandra , Budis Jaroslav , Gazdarica Juraj , Sedlackova Tatiana , Jordakova Anna , Benko Zsigmond , Smondrkova Maria , Mayerova Nina , Pichlerova Karoline , Strieskova Lucia , Prevorovsky Martin , Gregan Juraj , Cipak Lubos , Szemes Tomas , Polakova Silvia Bagelova 
Published: January 2021

AbstractDuring homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51–DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data
Authors: Norouzi-Beirami Mohammad H , Marashi Sayed-Amir , Banaei-Moghaddam Ali M , Kavousi Kaveh 
Published: January 2021

AbstractMetagenomics is the study of genomic DNA recovered from a microbial community. Both assembly-based and mapping-based methods have been used to analyze metagenomic data. When appropriate gene catalogs are available, mapping-based methods are preferred over assembly based approaches, especially for analyzing the data at the functional level. In this study, we introduce CAMAMED as a composition-aware mapping-based metagenomic data analysis pipeline. This pipeline can analyze metagenomic samples at both taxonomic and functional profiling levels. Using this pipeline, metagenome sequences can be mapped to non-redundant gene catalogs and the gene frequency in the samples are obtained. Due to the highly compositional nature of metagenomic data, the cumulative sum-scaling method is used at both taxa and gene levels for compositional data analysis in our pipeline. Additionally, by mapping the genes to the KEGG database, annotations related to each gene can be extracted at different functional levels such as KEGG ortholog groups, enzyme commission numbers and reactions. Furthermore, the pipeline enables the user to identify potential biomarkers in case-control metagenomic samples by investigating functional differences. The source code for this software is available from https://github.com/mhnb/camamed. Also, the ready to use Docker images are available at https://hub.docker.com.
Rapid discovery of novel prophages using biological feature engineering and machine learning
Authors: Sirén Kimmo , Millard Andrew , Petersen Bent , Gilbert M Thomas P , Clokie Martha R J , Sicheritz-Pontén Thomas 
Published: January 2021

Abstract
Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, yet this remains the paradigm and thus many phages remain unidentified. We present a novel, fast and generalizing machine learning method based on feature space to facilitate novel prophage discovery. To validate the approach, we reanalyzed publicly available marine viromes and single-cell genomes using our feature-based approaches and found consistently more phages than were detected using current state-of-the-art tools while being notably faster. This demonstrates that our approach significantly enhances bacteriophage discovery and thus provides a new starting point for exploring new biologies.
Shifting Coronavirus Disease 2019 Testing Policy and Research to Include the Full Translation Pipeline
Authors: Catania Joseph A , Martin Jeffrey , Dolcini M Margaret , Orellana E Roberto , Henne Jeffrey 
Published: January 2021

Abstract
The current severe acute respiratory syndrome coronavirus 2 testing policy and practice limits testing as a prevention tool. Radical shifts are required to increase the scale of rapid testing strategies and improve dissemination and implementation of venue-based and self-testing approaches. Attention to the full translation pipeline is required to reach high-risk segments of the population.
Evaluation of No-Touch Technologies for Decontamination of Toys in Pediatric Healthcare Settings
Authors: Haydar Hanan , Kumar Jessica A , Cadnum Jennifer L , Zangla Emily , Hoyen Claudia K , Donskey Curtis J 
Published: January 2021

Abstract
No-touch technologies could be useful to decontaminate shared toys in healthcare settings. A high-level disinfection cabinet and electrostatic sprayer were effective against methicillin-resistant Staphylococcus aureus (MRSA), bacteriophage MS2, and Clostridioides difficile spores on toys. An ultraviolet-C light box was less effective but reduced MRSA and bacteriophage MS2 by &gt;2 log10.
A Network Analysis of Clinical Variables in Chronic Pain: A Study from the Swedish Quality Registry for Pain Rehabilitation (SQRP)
Authors: Åkerblom Sophia , Cervin Matti , Perrin Sean , Rivano Fischer Marcelo , Gerdle Björn , McCracken Lance M 
Published: January 2021

Abstract

Background
Efforts to identify specific variables that impact most on outcomes from interdisciplinary pain rehabilitation are challenged by the complexity of chronic pain. Methods to manage this complexity are needed. The purpose of the study was to determine the network structure entailed in a set of self-reported variables, examine change, and look at potential predictors of outcome, from a network perspective.

Methods
In this study we apply network analysis to a large sample of people seeking interdisciplinary pain treatment (N = 2,241). Variables analyzed include pain intensity, pain interference, extent of pain, depression, anxiety, insomnia, and psychological variables from cognitive behavioral models of chronic pain.

Results
We found that Acceptance, Pain Interference, and Depression were key, “central,” variables in the pretreatment network. Interestingly, there were few changes in the overall network configuration following treatment, specifically with respect to which variables appear most central relative to each other. On the other hand, Catastrophizing, Depression, Anxiety, and Pain Interference each became less central over time. Changes in Life Control, Acceptance, and Anxiety were most strongly related to changes in the remainder of the network as a whole. Finally, no network differences were found between treatment responders and non-responders.

Conclusions
This study highlights potential future targets for pain treatment. Further application of a network approach to interdisciplinary pain rehabilitation data is recommended. Going forward, it may be better to next do this in a more comprehensive theoretically guided fashion, and ideographically, to detect unique individual differences in potential treatment processes.
Is Neck Posture Subgroup in Late Adolescence a Risk Factor for Persistent Neck Pain in Young Adults? A Prospective Study
Authors: Richards Karen V , Beales Darren J , Smith Anne L , O’Sullivan Peter B , Straker Leon M 
Published: January 2021

Abstract

Objective
The purpose of this study was to determine whether sagittal neck sitting posture subgroup membership in late adolescence was a risk factor for persistent neck pain (PNP) in young adults.

Methods
There were 686 participants enrolled in the Raine Study at the 17- and 22-year follow-ups. At 17 years of age, posture was measured by photographs, and 4 subgroups of sitting neck posture were determined by cluster analysis. Height and weight were measured, and exercise frequency, depression, and PNP were assessed by questionnaire. At 22 years of age, participants answered questions about neck pain and occupation type. Logistic regression examined if neck posture subgroups at 17 years of age were a risk factor for PNP at 22 years of age, taking into account other factors.

Results
Female sex (odds ratio [OR] = 1.75, 95% CI = 1.16–2.65) and PNP at 17 years of age (OR = 3.78, 95% CI = 2.57–5.57) were associated with PNP at 22 years of age. In females, neck posture subgroup at 17 years of age was a risk factor for PNP at 22 years of age. Compared with the upright subgroup, both the slumped thorax/forward head subgroup groups and the intermediate subgroup had decreased odds for PNP at 22 years of age (OR = 0.24, 95% CI = 0.08–0.76; OR = 0.38, 95% CI = 0.15–0.99, respectively). No association was found in males.

Conclusion
After taking into account PNP at 17 years, sitting neck posture at 17 was not a risk factor for PNP at 22 years of age in males, whereas in females, more relaxed postures (slumped thorax/forward head and Intermediate postures) were protective of neck pain compared with upright posture.

Impact
Females in late adolescence who sat in slumped thorax/forward head or intermediate posture rather than upright sitting posture had a lower risk of PNP as a young adult. The practice of generic public health messages to sit up straight to prevent neck pain needs rethinking.
Implementation and Evaluation of the Graded Repetitive Arm Supplementary Program (GRASP) for People With Stroke in a Real World Community Setting: Case Report
Authors: Yang Chieh-Ling , Bird Marie-Louise , Eng Janice J 
Published: January 2021

Abstract

Objective
Exercise programs to improve upper extremity function following stroke in the community setting are needed as the length of hospital stay continues to decrease. However, little has been done to increase understanding of how to translate an evidence-based rehabilitation intervention to real-world programs. The purpose of this case report was to describe a process evaluation of the implementation of an evidence-based upper extremity rehabilitation intervention for stroke, the Graded Repetitive Arm Supplementary Program, in a community setting.

Methods (Case Description)
A partnership between a nonprofit support organization and a local community center was established to deliver the program in the community. The Reach, Effectiveness, Adoption, Implementation, Maintenance (RE-AIM) framework with mixed methods was used to evaluate the implementation.

Results
Reach: Twenty people were screened, 14 people met eligibility requirements, and 13 consented to participate. The program reached approximately 1.25% of the potential target population. Effectiveness: Participants with stroke demonstrated significant improvement in upper extremity function and quality of life as measured by the Fugl-Meyer Assessment for upper extremity, Action Research Arm Test, Rating of Everyday Arm-use in the Community and Home Scale, and Stroke Impact Scale. Adoption: Factors that facilitated program uptake were the well-planned implementation and the workplace coaching based on the audit results. Factors contributing to ongoing participation were the social support within the group environment and the instructor’s capability of engaging the group. Implementation: A partnership between a nonprofit organization and a local community center was successfully established. The program was implemented as intended as verified by a fidelity checklist. Participant adherence was high as confirmed by the average attendance and practice time. Maintenance: Both the partner organization and community center continued to offer the program.

Conclusion
The Graded Repetitive Arm Supplementary Program had good fidelity of the critical principles and core components and was effective in improving upper extremity function and quality of life.

Impact
This partnership model may serve as the first step for future larger-scale implementation and could be used to move other stroke rehabilitation interventions into community settings.
Measurement Properties of Assessments of Freezing of Gait Severity in People With Parkinson Disease: A COSMIN Review
Authors: Scully Aileen E , Hill Keith D , Tan Dawn , Clark Ross , Pua Yong-Hao , de Oliveira Beatriz I R 
Published: January 2021

Abstract

Objective
Parkinson disease (PD) is the second-most common neurodegenerative condition worldwide. Approximately 50% of people with PD experience freezing of gait, a motor symptom associated with falls, disability, and poorer quality of life. Accurate assessment of freezing of gait severity is important for guiding management. The aim of this systematic review was to determine the measurement properties of subjective and objective clinical assessments of freezing of gait severity using the COSMIN methodology to facilitate better outcome measure selection.

Methods
Three databases (MEDLINE, EMBASE, and CINAHL) were searched. The COSMIN Risk of Bias checklist was used for evaluating quality of included studies. Data on measurement properties were extracted. Where possible, meta-analysis was performed.

Results
Nineteen studies investigating measurement properties of 7 outcome measures (patient-reported outcome measures, n = 3; objective assessment tools, n = 4) were included. Ten studies evaluated the Freezing of Gait Questionnaire. Based on COSMIN criteria, the best performing outcome measures were the Freezing of Gait Questionnaire and the Dynamic Parkinson Gait Scale. Both outcome measures demonstrated sufficient structural validity, internal consistency, reliability, construct validity, and responsiveness. The Freezing of Gait Questionnaire was supported with mostly moderate to high quality of evidence, but the evidence for the Dynamic Parkinson Gait Scale was of low quality due to inadequate sample size.

Conclusions
Content validity and measurement invariance remain unknown for all outcome measures. The Freezing of Gait Questionnaire is the best measure currently available. Further external validation and reliability studies would strengthen the evidence to support the use of the Dynamic Parkinson Gait Scale.

Impact
Awareness of limitations of outcome measures facilitates better selection. Without evidence for content validity and measurement invariance, clinicians should consider if their chosen test accurately measures freezing of gait severity and whether it can be applied in populations different to the original study’s population.

Lay Summary
Accurately assessing freezing of gait severity is important for guiding management of this disabling symptom. The best clinical assessment currently available is one that relies on the self-report of patients.
The effect of facilitating interdisciplinary cooperation on the research productivity of university research teams: The moderating role of government assistance
Authors: Chen Aihua , Wang Xiaoting 
Published: January 2021

AbstractInterdisciplinary research is vital to research productivity. However, the existing research has not given a reasonable explanation on how and under what condition facilitating interdisciplinary research cooperation promotes research productivity. This article aims to contribute to the existing literature by examining the link between facilitating interdisciplinary cooperation and research productivity as well as the role of government assistance in this link. Using a sample of 314 members of Chinese university research teams, we show that management, operations, evaluation, team building, and collaborating with industry to facilitate interdisciplinary cooperation all have significantly positive effects on the research productivity of university research teams. Among them, evaluation has the most significant impact on research productivity. Moreover, government assistance weakens the relationship between evaluation and research productivity but strengthens the relationship between management and research productivity. However, the moderating effects of government assistance on the links among team building, operations, collaborating with industry, and team research productivity are not statistically significant. Overall, our study has important implications for governments and universities seeking to facilitate interdisciplinary cooperation.
A FEASIBILITY TEST FOR QUICK RADON RISK ASSESSMENT BY MEASURING AN IN SITU RADIATION DOSE RATE
Authors: M Hassan Nabil , Kim Y J 
Published: January 2021

Abstract
Radon concentration was estimated using an accumulation chamber equipped with AlphaGUARD radon monitor. It varies from 12.6 ± 1.20 to 363 ± 19.3 Bq m−3 with a mean value of 180 ± 11.2 Bq m−3. A good correlation between radium content and radon concentrations was obtained of R = 0.754, which suggests that radium is the main reason of releasing radon to the atmosphere. Radon emanation coefficient and exhalation rate were also calculated. Furthermore, the radiation dose rate was measured with a high-pressure ionization chamber detector. The radiation dose rate was strongly correlated with the radon concentration and exhalation rate of R = 0.85 and 0.63. The obtained results support our idea that the radiation dose rate can be a good indicator to the radon level in the atmosphere. In addition, the dependence of radon concentration on the water content was discussed.
N-methyl-D-aspartate Receptor Antibody and White Matter Deficits in Schizophrenia Treatment-Resistance
Authors: Tong Jinghui , Zhou Yanfang , Huang Junchao , Zhang Ping , Fan Fengmei , Chen Song , Tian Baopeng , Cui Yimin , Tian Li , Tan Shuping , Wang Zhiren , Feng Wei , Yang Fude , Hare Stephanie , Goldwaser Eric L , Bruce Heather A , Kvarta Mark , Chen Shuo , Kochunov Peter , Tan Yunlong , Hong L Elliot 
Published: January 2021

Abstract
Insufficient or lack of response to antipsychotic medications in some patients with schizophrenia is a major challenge in psychiatry, but the underlying mechanisms remain unclear. Two seemingly unrelated observations, cerebral white matter and N-methyl-D-aspartate receptor (NMDAR) hypofunction, have been linked to treatment-resistant schizophrenia (TRS). As NMDARs are critical to axonal myelination and signal transduction, we hypothesized that NMDAR antibody (Ab), when present in schizophrenia, may impair NMDAR functions and white matter microstructures, contributing to TRS. In this study, 50 patients with TRS, 45 patients with nontreatment-resistant schizophrenia (NTRS), 53 patients with schizophrenia at treatment initiation schizophrenia (TIS), and 90 healthy controls were enrolled. Serum NMDAR Ab levels and white matter diffusion tensor imaging fractional anisotropy (FA) were assessed. The white matter specificity effects by NMDAR Ab were assessed by comparing with effects on cortical and subcortical gray matter. Serum NMDAR Ab levels of the TRS were significantly higher than those of the NTRS (P = .035). In patients with TRS, higher NMDAR Ab levels were significantly associated with reduced whole-brain average FA (r = −.37; P = .026), with the strongest effect at the genu of corpus callosum (r = −.50; P = .0021, significant after correction for multiple comparisons). Conversely, there was no significant correlation between whole-brain or regional cortical thickness or any subcortical gray matter structural volume and NMDAR Ab levels in TRS. Our finding highlights a potential NMDAR mechanism on white matter microstructure impairment in schizophrenia that may contribute to their treatment resistance to antipsychotic medications.
Neoliberal governance, evaluations, and the rise of win–win ideology in corporate responsibility discourse, 1960–2010
Authors: Brandtner Christof , Bromley Patricia 
Published: January 2021

AbstractDespite conflicts between social and economic goals, contemporary US firms routinely depict such aims as synergistic. Analyzing 300 annual reports from a sample of 80 large US public firms between 1960 and 2010, we examine the rise of ‘win–win’ conceptions of corporate responsibility (CR), which include both the social benefits of economic activities and economic gains from social responsibility. Our findings support arguments that the rise of win–win ideology in large corporations is tied to the emergence of neoliberal governance in society. Indicators of firms’ changing institutional context include financialization, numbers of non-profit organizations and voluntary regulation schemes. However, the macroeffect is mediated by firm attention to these institutional changes; mentions of external evaluations in annual reports are associated with higher levels of win–win ideology. The study contributes to institutional theories of the historical development of CR and to understanding heterogeneous organizational responses to societal-level institutional change.
Sleep is more than rest for plasticity in the human cortex
Authors: Nissen Christoph , Piosczyk Hannah , Holz Johannes , Maier Jonathan G , Frase Lukas , Sterr Annette , Riemann Dieter , Feige Bernd 
Published: January 2021

Abstract
Sleep promotes adaptation of behavior and underlying neural plasticity in comparison to active wakefulness. However, the contribution of its two main characteristics, sleep-specific brain activity and reduced stimulus interference, remains unclear. We tested healthy humans on a texture discrimination task, a proxy for neural plasticity in primary visual cortex, in the morning and retested them in the afternoon after a period of daytime sleep, passive waking with maximally reduced interference, or active waking. Sleep restored performance in direct comparison to both passive and active waking, in which deterioration of performance across repeated within-day testing has been linked to synaptic saturation in the primary visual cortex. No difference between passive and active waking was observed. Control experiments indicated that deterioration across wakefulness was retinotopically specific to the trained visual field and not due to unspecific performance differences. The restorative effect of sleep correlated with time spent in NREM sleep and with electroencephalographic slow wave energy, which is thought to reflect renormalization of synaptic strength. The results indicate that sleep is more than a state of reduced stimulus interference, but that sleep-specific brain activity restores performance by actively refining cortical plasticity.