bluuebunny/crossref_metadata_2025_split huggingface dataset:
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data
Authors: de Torrenté Laurence , Zimmerman Samuel , Suzuki Masako , Christopeit Maximilian , Greally John M. , Mar Jessica C. 
Published: December 2020

Abstract
Background
In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly applicable it may be to all genes that are in the transcriptome. Our study investigated the prevalence of a range of gene expression distributions in three different tumor types from the Cancer Genome Atlas (TCGA).

Results
Surprisingly, the expression of less than 50% of all genes was Normally-distributed, with other distributions including Gamma, Bimodal, Cauchy, and Lognormal also represented. Most of the distribution categories contained genes that were significantly enriched for unique biological processes. Different assumptions based on the shape of the expression profile were used to identify genes that could discriminate between patients with good versus poor survival. The prognostic marker genes that were identified when the shape of the distribution was accounted for reflected functional insights into cancer biology that were not observed when standard assumptions were applied. We showed that when multiple types of distributions were permitted, i.e. the shape of the expression profile was used, the statistical classifiers had greater predictive accuracy for determining the prognosis of a patient versus those that assumed only one type of gene expression distribution.

Conclusions
Our results highlight the value of studying a gene’s distribution shape to model heterogeneity of transcriptomic data and the impact on using analyses that permit more than one type of gene expression distribution. These insights would have been overlooked when using standard approaches that assume all genes follow the same type of distribution in a patient cohort.
LDscaff: LD-based scaffolding of de novo genome assemblies
Authors: Zhao Zicheng , Zhou Yingxiao , Wang Shuai , Zhang Xiuqing , Wang Changfa , Li Shuaicheng 
Published: December 2020

AbstractBackgroundGenome assembly is fundamental forde novogenome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population data indicate non-random association among alleles at different loci, can provide physical distance signals to guide scaffolding.ResultsIn this paper, we proposeLDscafffor draft genome assembly incorporating linkage disequilibrium information in population data. We evaluated the performance of our method with both simulated data and real data. We simulated scaffolds by splitting the pig reference genome and reassembled them. Gaps between scaffolds were introduced ranging from 0 to 100 KB. The genome misassembly rate is 2.43% when there is no gap. Then we implemented our method to refine the Giant Panda genome and the donkey genome, which are purely assembled by NGS data. AfterLDscafftreatment, the resulting Panda assembly has scaffold N50 of 3.6 MB, 2.5 times larger than the original N50 (1.3 MB). The re-assembled donkey assembly has an improved N50 length of 32.1 MB from 23.8 MB.ConclusionsOur method effectively improves the assemblies with existed re-sequencing data, and is an potential alternative to the existing assemblers required for the collection of new data.
Compositional zero-inflated network estimation for microbiome data
Authors: Ha Min Jin , Kim Junghi , Galloway-Peña Jessica , Do Kim-Anh , Peterson Christine B. 
Published: December 2020

AbstractBackgroundThe estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challenges in the inference of such networks from high-throughput data. Since the abundances in each sample are constrained to have a fixed sum and there is incomplete overlap in microbial populations across subjects, the data are both compositional and zero-inflated.ResultsWe propose the COmpositional Zero-Inflated Network Estimation (COZINE) method for inference of microbial networks which addresses these critical aspects of the data while maintaining computational scalability. COZINE relies on the multivariate Hurdle model to infer a sparse set of conditional dependencies which reflect not only relationships among the continuous values, but also among binary indicators of presence or absence and between the binary and continuous representations of the data. Our simulation results show that the proposed method is better able to capture various types of microbial relationships than existing approaches. We demonstrate the utility of the method with an application to understanding the oral microbiome network in a cohort of leukemic patients.ConclusionsOur proposed method addresses important challenges in microbiome network estimation, and can be effectively applied to discover various types of dependence relationships in microbial communities. The procedure we have developed, which we refer to as COZINE, is available online athttps://github.com/MinJinHa/COZINE.
Blood loss from transverse versus longitudinal uterine incision in abdominal myomectomy: a randomized controlled trial
Authors: Elguindy Alaa , Hemeda Hosam , Shawky Mohamed Esmat , Elsenity Mohamed , Elsayed Medhat Adel , Fahim Ahmed , Afifi Khaled , Nawara Maii 
Published: December 2020

Abstract
Background
It is unclear whether transverse uterine incision is non-inferior to longitudinal incision during myomectomy with regard to bleeding. Our aim was to compare between transverse and longitudinal uterine incisions in myomectomy.

Methods
A parallel randomized controlled single-blinded study in a university affiliated hospital, in the period between January 2017 and April 2018, in which 52 women candidates for abdominal myomectomy were randomized into transverse uterine incision or longitudinal uterine incision groups (26 in each group). Intraoperative blood loss (estimated directly by blood volume in suction bottle and linen towels and indirectly by difference between preoperative and postoperative hematocrit), operative time and postoperative fever were analyzed.

Results
No statistically significant difference was found between transverse and longitudinal incisions regarding intraoperative blood loss (389.7 ± 98.56 ml vs 485.04 ± 230.6 ml respectively, p value = 0.07), operative time (59.96 ± 16.78 min vs 66.58 ± 17.33 min respectively, p value = 0.18), and postoperative fever (4% vs 8.33%, p value = 0.6).

Conclusion
Transverse uterine incision does not cause more blood loss than longitudinal incision and is a reasonable option during abdominal myomectomy.
Trial registration: NCT03009812 at clinicaltrials.gov, registered January 2017
Beliefs, knowledge and the impact of COVID19 on menopause therapies in Spanish women: COMEM-treatment study
Authors:   The COMEM Study Spanish investigators, Baquedano Laura , Espiau Andrea , Fasero María , Ortega Silvia , Ramirez Isabel , Mendoza Nicolás 
Published: December 2020

Abstract
Objective
To study what women think about menopause treatments and assess their knowledge about them. To analyze adherence to treatment during COVID-19 confinement as a secondary objective.

Methods
A multi-center cross-sectional observational study was conducted using a survey of 2500 women between January and June 2019. This was administered following a non-probability sampling procedure including women between 35 and 75 years. An extension study was conducted during the coronavirus pandemic, between March and June 2020.

Results
The responses of 2355 surveyed women were analyzed. Of this sample, 42% knew about menopause hormone therapy (MHT). The most frequently identified indication was the treatment of hot flashes (65.6%). The MHT risks most frequently perceived were weight gain (24.2%) and breast cancer (21.7%); the main reason for rejecting MHT was a lack of information (96.1%). Comparative analyses were conducted according to age, menopausal status, type of menopause, place of residence, type of health care and level of education. During the coronavirus confinement period, 85 women using MHT were located, of which 84.7% continued it.

Conclusions
Women hold certain false beliefs about menopause, and their knowledge of the available treatments is somewhat limited. Adherence to MHT during the COVID-19 confinement in Spain has been high.
The impact of death and dying on the personhood of medical students: a systematic scoping review
Authors: Ho Chong Yao , Kow Cheryl Shumin , Chia Chin Howe Joshua , Low Jia Ying , Lai Yong Hao Melvin , Lauw Sarah-Kei , How Ashley Ern Hui , Tan Lorraine Hui En , Ngiam Xin Ling Lisa , Chan Natalie Pei Xin , Kuek Tze Yin Joshua , Kamal Nur Haidah Ahmad , Chia Jeng Long , Abdurrahman Ahmad Bin Hanifah Marican , Chiam Min , Ong Yun Ting , Chin Annelissa Mien Chew , Toh Ying Pin , Mason Stephen , Krishna Lalit Kumar Radha 
Published: December 2020

AbstractBackgroundThe re-introduction of medical students into healthcare systems struggling with the COVID-19 pandemic raises concerns as to whether they will be supported when confronted with death and dying patients in resource-limited settings and with reduced support from senior clinicians. Better understanding of how medical students respond to death and dying will inform educationalists and clinicians on how to best support them.MethodsWe adopt Krishna’s Systematic Evidence Based Approach to carry out a Systematic Scoping Review (SSR in SEBA) on the impact of death and dying on medical students. This structured search process and concurrent use of thematic and directed content analysis of data from six databases (Split Approach) enhances the transparency and reproducibility of this review.ResultsSeven thousand six hundred nineteen were identified, 149 articles reviewed and 52 articles included. The Split Approach revealed similar themes and categories that correspond to the Innate, Individual, Relational and Societal domains in the Ring Theory of Personhood.ConclusionFacing death and dying amongst their patients affect how medical students envisage their personhood. This underlines the need for timely, holistic and longitudinal support systems to ensure that problems faced are addressed early. To do so, there must be effective training and a structured support mechanism.
Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies
Authors: Li Binze , Dong Julian , Yu Jiaqi , Fan Yuqi , Shang Lulu , Zhou Xiang , Bai Yongsheng 
Published: December 2020

Abstract
Background
Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein–protein interaction, transcription factor and gene binding, and post-transcriptional regulation (e.g., miRNA targeting) information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3′ untranslated regions (3′UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3′UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues.

Methods
By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3′UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network.

Results
Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3′UTR regions of genes (SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme.

Conclusions
The non-coding variants identified from GWAS studies are casually assumed to be not critical to translated protein product. However, 3′ untranslated regions (3′UTRs) of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies.
Calcium mediated functional interplay between myocardial cells upon laser-induced single-cell injury: an in vitro study of cardiac cell death signaling mechanisms
Authors: Sridhar Krishna Chander , Hersch Nils , Dreissen Georg , Merkel Rudolf , Hoffmann Bernd 
Published: December 2020

AbstractBackgroundThe electromechanical function of myocardial tissue depends on the intercellular communication between cardiomyocytes (CMs) as well as their crosstalk with other cell types. Cell injury, and subsequent death trigger inflammation as in myocardial infarction (MI) resulting in myocardial remodeling. Although mechanisms underlying myocardial cell death have been studied so far, the signaling events following single cell death and spontaneous response of connected cells in the myocardial tissue is still barely understood.MethodsHere, we investigated the effect of laser-induced single cell death on Calcium (Ca2+) concentrations and transport in myocardial cell clusters in vitro. Spatial and temporal changes in intracellular Ca2+concentrations [Ca2+]iwere studied using a fluorescent calcium indicator, Fluo-4AM. Spontaneous signaling events following cell death were studied in rat embryonic cardiomyocytes and non-myocytes using separate cell culture systems.ResultsCell death triggered spontaneous increase in intracellular Ca2+levels ([Ca2+]i) of surrounding cells. The spread of the observed propagating Ca2+signal was slow and sustained in myocytes while it was rapid and transient in fibroblasts (Fbs). Further, sustained high Ca2+levels temporarily impaired the contractility in CMs. The cell-type specific effect of ablation was confirmed using separate cultures of CMs and Fbs. Comparing Ca2+propagation speed in myocytes and fibroblasts, we argue for a diffusion-driven Ca2+propagation in myocytes, but not in fibroblasts. Radial and sequential Ca2+diffusion across the CMs through cell–cell contacts and presence of Cx43-based intercellular junctions indicated a gap junction flow of Ca2+.ConclusionsThese findings illustrate the spontaneous Ca2+-mediated functional interplay in myocardial cell clusters upon mechanical injury and, further, the difference in Ca2+signaling in cardiomyocytes and fibroblasts.
Genetic variation in the Middle East—an opportunity to advance the human genetics field
Authors: Abou Tayoun Ahmad N. , Rehm Heidi L. 
Published: December 2020

AbstractWe highlight the current lack of representation of the Middle East from large genomic studies and emphasize the expected high impact of cataloging its variation. We discuss the limiting factors and possible solutions to generating and accessing research and clinical sequencing data from this part of the world.
Sustaining primary care teams in the midst of a pandemic
Authors: Sullivan Erin E. , Phillips Russell S. 
Published: December 2020

AbstractThe challenges wrought by the COVID-19 pandemic on health systems have tested primary care clinicians, who are on the front lines of care delivery. To ensure the longevity of the primary care workforce, strong interprofessional teams are one important solution to alleviating burnout and increasing clinician and patient satisfaction, but the pandemic has demonstrated that the operating manual needs to be adapted for virtual work. Essential principles of primary care, including preventative care, communication and collaboration, and building strong relationships, can be applied to strengthen virtual primary care teams.
New fractional inequalities of Hermite–Hadamard type involving the incomplete gamma functions
Authors: Mohammed Pshtiwan Othman , Abdeljawad Thabet , Baleanu Dumitru , Kashuri Artion , Hamasalh Faraidun , Agarwal Praveen 
Published: December 2020

AbstractA specific type of convex functions is discussed. By examining this, we investigate new Hermite–Hadamard type integral inequalities for the Riemann–Liouville fractional operators involving the generalized incomplete gamma functions. Finally, we expose some examples of special functions to support the usefulness and effectiveness of our results.
Investigating the relationship between COVID-19-related and distress and ICD-11 adjustment disorder: two cross-sectional studies
Authors: Ben-Ezra Menachem , Hou Wai Kai , Goodwin Robin 
Published: December 2020

Background
To assess the prevalence of elevated risk of serious mental illness and probable ICD-11 adjustment disorder in the UK population at two time points during COVID-19, and their association with COVID-19-related stressful events.

Aims
To check the dose–response model for stress between the number of COVID-19-related stressful events and mental health indices.

Method
We conducted two cross-sectional studies, using internet survey samples across the UK (N = 1293 for study 1; N = 1073 for study 2). Samples used internet panel surveys during March–April 2020 and 3 months later (June 2020), and used random stratified samples. Studies assessed prevalence of serious risk of mental illness and probable ICD-11 adjustment disorder.

Results
Elevated risk of serious mental illness was found among those with COVID-19-related social life or occupationally stressful events (study 1). Elevated risk of serious mental illness and probable ICD-11 adjustment disorder was evident among those reporting COVID-19-related stressful events (personal health problems and caregiving; study 2). Cumulative COVID-19-related stressful events were associated with elevated risk of serious mental illness in study 1 (odds ratio 1.65; 95% CI 1.03–2.64; P = 0.037), and with both elevated risk of serious mental illness (odds ratio 2.19; 95% CI 1.15–4.15; P = 0.017) and probable ICD-11 adjustment disorder (odds ratio 2.45; 95% CI 1.27–4.72; P = 0.007) in study 2.

Conclusions
Psychiatrists should be aware that COVID-19-related stressful events can lead to serious psychological problems. Mental health professionals need to pay particular attention to patients who report cumulative COVID-19-related stressful events, and consider them for mental health assessment and treatment.
The role of psychiatry in championing positive life outcomes for children and adults with neurodevelopmental disorders and their families
Authors: Newbold Yvonne , Busk Mary 
Published: December 2020

SummaryChildren and adults with neurodevelopmental disorders make up an estimated 10% of the population. Addressing health inequalities and poorer life outcomes is essential to deliver better quality care. Two parent-carers working in national roles in England suggest ways to increase understanding and work together in coproduction to achieve this.
No Longer Home: The Smellscape of Mexico City, 1500–1600
Authors: Mundy Barbara E. 
Published: December 2020

AbstractDuring the course of the sixteenth century, the Aztec (or Mexica) city of Tenochtitlan-Tlatelolco (present-day Mexico City) was transformed from a sweet-smelling lacustrine city into a foul one, the direct result of the Spanish invasion (1519–21). This article reconstructs both the sources of odors and culturally situated ideas about smell among the city’s Nahuatl-speaking residents. They are opposed to the ideas about smell held by settler colonists, derived from the framework of Hippocratic medicine. These imported ideas about acceptable smells (like those of urban slaughterhouses) and dangerous smells (swamps) came to have disastrous consequences as they played out in the unique environment of the Basin of Mexico.
Synthesis of Chloroauric Acid from Gold Electrodes in Alkali Halide Salt Solution by AC Electrolysis and the Sequential Formation of Gold Nanoparticles by Turkevich Method
Authors: Oya Kei , Aoshika Kei , Ageishi Masaki , Magara Hideyuki , Ogawa Shuichi , Takakuwa Yuji , Takami Tomohide 
Published: December 2020

Abstract
Gold nanoparticles have been commonly made by a wet process from chloroauric acid or dry process using vacuum evaporation to solid surfaces. Here, we have shown a method to make gold particle from gold electrodes in potassium chloride solution by AC electrolysis and the following Turkevich method. The developed AC electrolysis method provides an environment-friendly process to produce gold particles from gold electrodes without using any strong acids such as aqua regia or hydrochloric acid.
Bone Microarchitecture and Strength Adaptation to Physical Activity: A Within-Subject Controlled HRpQCT Study
Authors: WARDEN STUART J. , WRIGHT CHRISTIAN S. , FUCHS ROBYN K. 
Published: December 2020

ABSTRACT

Purpose
Physical activity benefits bone mass and cortical bone size. The current study assessed the impact of chronic (≥10 yr) physical activity on trabecular microarchitectural properties and microfinite element analyses of estimated bone strength.

Methods
Female collegiate-level tennis players (n = 15; age = 20.3 ± 0.9 yr) were used as a within-subject controlled model of chronic unilateral upper-extremity physical activity. Racquet-to-nonracquet arm differences at the distal radius and radial diaphysis were assessed using high-resolution peripheral quantitative computed tomography. The distal tibia and the tibial diaphysis in both legs were also assessed, and cross-country runners (n = 15; age = 20.8 ± 1.2 yr) included as controls.

Results
The distal radius of the racquet arm had 11.8% (95% confidence interval [CI] = 7.9% to 15.7%) greater trabecular bone volume/tissue volume, with trabeculae that were greater in number, thickness, connectivity, and proximity to each other than that in the nonracquet arm (all P < 0.01). Combined with enhanced cortical bone properties, the microarchitectural advantages at the distal radius contributed a 18.7% (95% CI = 13.0% to 24.4%) racquet-to-nonracquet arm difference in predicted load before failure. At the radial diaphysis, predicted load to failure was 9.6% (95% CI = 6.7% to 12.6%) greater in the racquet versus nonracquet arm. There were fewer and smaller side-to-side differences at the distal tibia; however, the tibial diaphysis in the leg opposite the racquet arm was larger with a thicker cortex and had 4.4% (95% CI = 1.7% to 7.1%) greater strength than the contralateral leg.

Conclusion
Chronically elevated physical activity enhances trabecular microarchitecture and microfinite element estimated strength, furthering observations from short-term longitudinal studies. The data also demonstrate that tennis players exhibit crossed symmetry wherein the leg opposite the racquet arm possesses enhanced tibial properties compared with in the contralateral leg.