bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interactive effect of ambient temperature and brood size manipulation on nestling body mass in blue tits: an exploratory analysis of a long-term study
Authors: Arct Aneta , Drobniak Szymon M. , Dubiec Anna , Martyka Rafał , Sudyka Joanna , Gustafsson Lars , Cichoń Mariusz 
Published: February 2022

Abstract
Background
Relatively few studies have examined the interactive effects of ecological factors on physiological responses in wild animals. Nearly all of them have been short-term investigations that did not include experimental manipulations, limiting our ability to understand how climate change will affect natural populations. Using a 10-year brood size manipulation experiment in wild blue tits (Cyanistes caeruleus), we quantified the impact of weather conditions and brood competition on the body mass and structural size (tarsus length) of nestlings just prior to leaving the nest.

Results
We found that variation in nestling body mass on day 14 after hatching was explained by an interactive effect between average ambient temperature experienced during nestling period and brood size treatment. Specifically, in control broods nestling body mass was correlated with temperature in a non-linear manner (concave) with the vertex point (maximum body mass) at ca. 13 °C. In contrast, in enlarged broods nestling body mass permanently increased (also non-linearly) as temperature advanced.

Conclusions
Our results highlight the importance of considering the effects of brood rearing conditions alongside other environmental factors experienced during growth while investigating early-life environmental effects on body condition.
Efficacy and mechanisms of traditional Chinese medicine for COVID-19: a systematic review
Authors: Kang Xiaomin , Jin De , Jiang Linlin , Zhang Yuqing , Zhang Yuehong , An Xuedong , Duan Liyun , Yang Cunqing , Zhou Rongrong , Duan Yingying , Sun Yuting , Lian Fengmei 
Published: February 2022

AbstractSince the outbreak of coronavirus disease 2019 (COVID-19), traditional Chinese medicine (TCM) has made an important contribution to the prevention and control of the epidemic. This review aimed to evaluate the efficacy and explore the mechanisms of TCM for COVID-19. We systematically searched 7 databases from their inception up to July 21, 2021, to distinguish randomized controlled trials (RCTs), cohort studies (CSs), and case–control studies (CCSs) of TCM for COVID-19. Two reviewers independently completed the screening of literature, extraction of data, and quality assessment of included studies. Meta-analysis was performed using Review Manager 5.4 software. Eventually, 29 RCTs involving 3060 patients and 28 retrospective studies (RSs) involving 12,460 patients were included. The meta-analysis demonstrated that TCM could decrease the proportion of patients progressing to severe cases by 55% and the mortality rate of severe or critical patients by 49%. Moreover, TCM could relieve clinical symptoms, curtail the length of hospital stay, improve laboratory indicators, and so on. In addition, we consulted the literature and obtained 149 components of Chinese medicinal herbs that could stably bind to antiviral targets or anti-inflammatory or immune-regulating targets by the prediction of molecular docking. It suggested that the mechanisms involved anti-virus, anti-inflammation, and regulation of immunity. Our study made a systematic review on the efficacy of TCM for COVID-19 and discussed the possible mechanisms, which provided clinical reference and theoretical basis for further research on the mechanism of TCM for COVID-19.
Systematic review and meta-analysis of the effects of exercise on depression in adolescents
Authors: Wang Xiang , Cai Zhi-dong , Jiang Wan-ting , Fang Yan-yan , Sun Wen-xin , Wang Xing 
Published: February 2022

AbstractBackgroundDepression is widespread among adolescents and seriously endangers their quality of life and academic performance. Developing strategies for adolescent depression has important public health implications. No systematic review on the effectiveness of physical exercise for adolescents aged 12–18 years with depression or depressive symptoms has previously been conducted. This study aims to systematically evaluate the effect of physical exercise on adolescent depression in the hope of developing optimum physical exercise programs.MethodsNine major databases at home and abroad were searched to retrieve randomized controlled trials (RCTs) on exercise interventions among adolescents with depression or depressive symptoms. The retrieval period started from the founding date of each database to May 1, 2021. The methodological quality of the included articles was evaluated using the modified PEDro scale. A meta-analysis, subgroup analysis, sensitivity analysis, and publication bias tests were then conducted.ResultsFifteen articles, involving 19 comparisons, with a sample size of 1331, were included. Physical exercise significantly reduced adolescent depression (standardized mean difference [SMD] = − 0.64, 95% CI − 0.89, − 0.39, p < 0.01), with a moderate effect size, in both adolescents with depression (SMD = -0.57, 95% CI − 0.90, − 0.23, p < 0.01) and adolescents with depressive symptoms (SMD = − 0.67, 95% CI − 1.00, − 0.33, p < 0.01). In subgroups of different depression categories (depression or depressive symptoms), aerobic exercise was the main form of exercise for the treatment of adolescents with depression. For adolescents with depression, interventions lasting 6 weeks, 30 min/time, and 4 times/week had optimum results. The effects of aerobic exercise and resistance + aerobic exercise in the subgroup of adolescents with depressive symptoms were significant, while the effect of physical and mental exercise (yoga) was not significant. For adolescents with depressive symptoms, aerobic exercise lasting 8 weeks, 75–120 min/time, and 3 times/week had optimum results. Physical exercise with moderate intensity is a better choice for adolescents with depression and depressive symptoms.ConclusionsPhysical exercise has a positive effect on the improvement of depression in adolescents.The protocol for this study was registered with INPLASY (202170013). DOI number is 10.37766/inplasy2021.7.0013. Registration Date:2021.7.06.
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
Authors: Du Yuxuan , Sun Fengzhu 
Published: February 2022

AbstractRecovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available athttps://github.com/dyxstat/HiCBin.
LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin
Authors: Bao Kaiwen , Zhang Qi , Liu Shuai , Song Nan , Guo Qiushi , Liu Ling , Tian Shanshan , Hao Jihui , Zhu Yi , Zhang Kai , Ai Ding , Yang Jie , Yao Zhi , Foisner Roland , Shi Lei 
Published: February 2022

Abstract
Background
Single-stranded DNA (ssDNA) coated with replication protein A (RPA) acts as a key platform for the recruitment and exchange of genome maintenance factors in DNA damage response. Yet, how the formation of the ssDNA-RPA intermediate is regulated remains elusive.

Results
Here, we report that the lamin-associated protein LAP2α is physically associated with RPA, and LAP2α preferentially facilitates RPA deposition on damaged chromatin via physical contacts between LAP2α and RPA1. Importantly, LAP2α-promoted RPA binding to ssDNA plays a critical role in protection of replication forks, activation of ATR, and repair of damaged DNA. We further demonstrate that the preference of LAP2α-promoted RPA loading on damaged chromatin depends on poly ADP-ribose polymerase PARP1, but not poly(ADP-ribosyl)ation.

Conclusions
Our study provides mechanistic insight into RPA deposition in response to DNA damage and reveals a genome protection role of LAP2α.
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome
Authors: Marwaha Shruti , Knowles Joshua W. , Ashley Euan A. 
Published: February 2022

AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
Clinical and genetic characterization of a large cohort of patients with Wilson’s disease in China
Authors: Zhang Shijie , Yang Wenming , Li Xiang , Pei Pei , Dong Ting , Yang Yue , Zhang Jing 
Published: February 2022

AbstractBackgroundWilson’s disease (WD) is an autosomal recessive disorder of copper metabolism caused byATP7B(encoding a copper-transporting P-type ATPase) variants that shows various characteristics according to race and geographical region. This study was aimed to provide a comprehensive analysis ofATP7Bvariants in China and to investigate a plausible role of common variants in WD manifestations.MethodsA total of 1366 patients (1302 index patients and 64 siblings) clinically diagnosed with WD (Leipzig score ≥ 4) were recruited. They underwentATP7Bgene sequencing and information of age and symptoms at onset was collected. The genotype–phenotype correlation was assessed in the index patients who were examined with two pathogenic variants and onset with hepatic (n = 276) or neurologic (n = 665) symptoms.ResultsWe identified 294 potentially pathogenicATP7Bvariants (112 truncating, 174 missense, 8 in-frame) in the 1302 index patients, including 116 novel variants. The most frequent variant was c.2333G>T (R778L, allele frequency: 28.96%), followed by c.2975C>T (P992L, 13.82%), c.2621C>T (A874V, 5.99%), c.2755C>G (R919G, 2.46%), and c.3646G>A (V1216M, 1.92%). In 1167 patients, both pathogentic variants were identified, of which 532 different variant combinations were found. By binary logistic regression analysis, the factor associated with neurological presentation was high age-at-onset, but not sex, protein-truncating variant (PTV), or the common missense variants (R778L, P992L, and A874V). In the neurological group, low age-at-onset was a factor associated with dystonia, gait abnormality, and salivation; high age-at-onset was a factor associated with tremor; and the sex, low age-at-onset and A874V were independent factors associated with dysarthria. In addition, PTV, R778L, and P992L were predominant in early-onset patients, whereas A874V was predominant in late-onset patients, and patients with R778L/A874V genotype displayed a higher age-at-onset than patients with R778L/R778L or R778L/P992L genotype.ConclusionsOur work expanded theATP7Bvariant spectrum and highlighted the differences among patients with WD in age-at-onset andATP7Bvariants, which may provide some valuable insights into the diagnosis, counseling, and treatment of patients with WD.
Successful administration of chimeric antigen receptor (CAR) T-cell therapy in patients requiring hemodialysis
Authors: Hunter Bradley D. , Hoda Daanish , Nguyen Andy , Gouw Launce , Huber Bryan , Jensen Ryan R. , Preedit Justine , Evens Andrew , Huang Esther , Park Jiyeon , Cooper Dennis L. 
Published: February 2022

AbstractChimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment of relapsed/refractory B-cell malignancies. However, there is no data on the safety and efficacy of CAR T-cell therapy in patients with end stage renal disease (ESRD) requiring dialysis. In this report, we present two patients with DLBCL and ESRD who were successfully treated with different CAR T-cell products. Patient #1 is a 66 year-old woman with a history of HIV who was treated to complete response with axicabtagene ciloleucel with treatment complicated by grade 1 cytokine release syndrome (CRS) and grade 2 immune effector cell-associated neurolotoxicity syndrome (ICANS). Patient #2 is 52 year old woman whose ESRD was caused by ifosphamide toxicity and was treated to complete response with lisocabtagene maraleucel and did not experience either CRS or ICANS. Both patients received lymphodepletion chemotherapy with fludarabine and cyclophosphamide, which was dose-adjusted for ESRD with scheduled dialysis 12 h after each dose of lymphodepletion chemotherapy. Patients with DLBCL and ESRD can be safely administered both lymphodepletion chemotherapy and CAR T-cell therapy. Additionally, the fact that both patients achieved complete response to therapy suggests that CAR T-cell therapy should be strongly considered in patients with ESRD. Long-term follow up is needed to determine if therapy in this setting is of curative intent.
University students’ views on the impact of Instagram on mental wellbeing: a qualitative study
Authors: Moreton Laura , Greenfield Sheila 
Published: February 2022

Abstract
Background
In the UK, undergraduate students are considered highly susceptible to mental ill-health, with current figures indicating a 94% increase in the demand for university counselling services in the last five years alone. Whilst the cause of this increase is currently undetermined, current evidence speculates that social media may be a contributing factor. Recent quantitative literature has determined that Instagram can negatively impact mental wellbeing. However, limited studies have been conducted among undergraduate student students, a population with the highest proportion of Instagram use by age, compared to the general public. Furthermore, no current research has qualitatively explored how and why Instagram has an impact on mental wellbeing. This study therefore aimed to identify UK university students’ understanding of the term ‘mental wellbeing’ and explore university students’ views on the impact of Instagram on their mental wellbeing.

Methods
16 undergraduate students (56.3% female, mean age 19.8 years, age range 18–23 years) who were fluent in English and used Instagram took part in semi-structured interviews. Participants were excluded if they no longer used Instagram or were unable to give written informed consent. Thematic analysis was utilised to identify codes and themes within the dataset.

Results
Five key themes were identified; knowledge of mental wellbeing, social connectivity, the Instagram ideal, social acceptance through quantitative data and cyberbullying. Students had a basic understanding of the term mental wellbeing and correctly associated productivity and accepting life’s adversities with the term. However, students often misinterpreted happiness and good mental health as a state of wellbeing. Whilst students perceived Instagram as positive for the development and maintenance of friendships, they also believed Instagram negatively impacted their wellbeing through the presentation of ideals, the presence of cyberbullying and the search for social acceptance.

Conclusions
This research reveals multiple implications for Instagram use on the mental wellbeing of undergraduate students. It is therefore essential for university counselling services to address Instagram use in consultations with students. Further research exploring the extent of cyberbullying on Instagram and the effects of presenting an idealistic life on wellbeing is necessary.
Hydraulic modeling of water flow in the thick vadose zone under precipitation
Authors: Wang Yu , Li Tonglu , Hou Xiaokun , Zhang Yaguo , Li Ping 
Published: February 2022

AbstractData from field monitoring and artificial rainfall experiments suggest that the thick vadose zone can be divided into two sub-zones based on soil water variation, namely the active and steady zones. The soil water content of the top active zone (2–5 m depth) is sensitive to precipitation and evaporation and dominated by transient water flow. Soil water content of the underlying steady zone remains constant over time and there is a steady flow under the force of gravity. However, since the transition from transient flow to steady flow is difficult to observe in nature, the physical mechanism of this transition remains poorly understood. This study establishes a hydraulic model to visually demonstrate water flow in the entire vadose zone under multiple infiltration events. The model comprises of a series vertically aligned water tanks, each with a small outlet at the bottom, and each representing a soil unit. The water level in a tank represents the water content and the related permeability of the soil unit. The results of an experiment conducted with the model clearly show that transient flow in the upper active zone will transfer to steady flow. A zoomed out data with an annual rainfall record at a site in the central Chinese Loess Plateau is applied in the model to simulate the water content and the flow state of the vertical profile, and the results are in accordance with in-situ monitoring data. The outcomes of this study suggest that although water content in the steady zone remains unchanged, there is a constant steady flow seeping downward through the zone, acting as a typical source of groundwater recharge in the loess region.
The challenge of equipoise: qualitative interviews exploring the views of health professionals and women with multiple ipsilateral breast cancer on recruitment to a surgical randomised controlled feasibility trial
Authors: Ingram Jenny , Beasant Lucy , Benson John , Brunt Adrian Murray , Maxwell Anthony , Harvey James Richard , Greenwood Rosemary , Roberts Nicholas , Williams Norman , Johnson Debbie , Winters Zoe 
Published: February 2022

Abstract
Background
A multicentre feasibility trial (MIAMI), comparing outcomes and quality of life of women with multiple ipsilateral breast cancer randomised to therapeutic mammoplasty or mastectomy, was conducted from September 2018 to March 2020. The MIAMI surgical trial aimed to investigate recruitment of sufficient numbers of women. Multidisciplinary teams at 10 breast care centres in the UK identified 190 with MIBC diagnosis; 20 were eligible for trial participation but after being approached only four patients were recruited. A nested qualitative study sought to understand the reasons for this lack of recruitment.

Methods
Interviews were conducted from November 2019 to September 2020 with 17 staff from eight hospital-based breast care centres that recruited and attempted to recruit to MIAMI; and seven patients from four centres, comprising all patients who were recruited to the trial and some who declined to take part. Interviews were audio-recorded, anonymised and analysed using thematic methods of building codes into themes and sub-themes using the process of constant comparison.

Results
Overarching themes of (1) influences on equipoise and recruitment and (2) effects of a lack of equipoise were generated. Within these themes, health professional themes described the barriers to recruitment as ‘the treatment landscape has changed’, ‘staff preferences and beliefs’ which influenced equipoise and patient advice; and how different the treatments were for patients. Patient themes of ‘altruism and timing of trial approach’, ‘influences from consultants and others’ and ‘diagnostic journey doubts’ all played a part in whether patients agreed to take part in the trial.

Conclusions
Barriers to recruiting to breast cancer surgical trials can be significant, especially where there are substantial differences between the treatments being offered and a lack of equipoise communicated by healthcare professionals to patients. Patients can become overwhelmed by numerous requests for participation in research trials and inappropriate timing of trial discussions. Alternative study designs to the gold standard randomised control trial for surgical interventions may be required to provide the high-quality evidence on which to base practice.

Trial registration
ISRCTN (ISRCTN17987569) registered on April 20, 2018, and ClinicalTrials.gov (NCT03514654).
To what extent are patients involved in researching safety in acute mental healthcare?
Authors: Brierley-Jones Lyn , Ramsey Lauren , Canvin Krysia , Kendal Sarah , Baker John 
Published: February 2022

Abstract
Background
There is a growing need to involve patients in the development of patient safety interventions. Mental health services, despite their strong history of patient involvement, have been slow to develop patient safety interventions, particularly in inpatient settings.

Methods
A systematic search was undertaken of both academic and grey literature. Whilst no lay member of the team worked directly on the review, they were part of the project steering group which provided oversight throughout the review process. This included people with lived experience of mental health services. From a research perspective the main focus for lay members was in co-producing the digital technology, the key project output. Smits et al.’s (Res Involv Engagem 6:1–30, 2020) Involvement Matrix was used to taxonomise levels of patient involvement. Studies were included if they were set in any inpatient mental health care context regardless of design. The quality of all selected studies was appraised using Mixed Methods Appraisal Methodology (MMAT).

Results
Fifty-two studies were classified, synthesised and their levels of patient involvement in the research and development of patient safety interventions were taxonomised. Almost two-thirds of studies (n = 33) researched reducing restrictive practices. Only four studies reported engaging patients in the research process as decision-makers, with the remaining studies divided almost equally between engaging patients in the research process as partners, advisors and co-thinkers. Just under half of all studies engaged patients in just one stage of the research process.

Conclusion
Involvement of patients in researching patient safety and developing interventions in an inpatient mental health context seems diverse in its nature. Researchers need to both more fully consider and better describe their approaches to involving patients in safety research in inpatient mental health. Doing so will likely lead to the development of higher quality safety interventions.