bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in the Power Characteristics of the α-Rhythm in Students with Different Levels of Anxiety in Normal Sleep and Partial Deprivation Solving the Go/NoGo Problem
Authors: Cheremushkin E. A. , Petrenko N. E. , Alipov N. N. , Sergeeva O. V. 
Published: April 2022

Abstract
The effect of partial sleep deprivation on cognitive control was studied in 26 students with different levels of trait anxiety. The synchronization–desynchronization reactions of the EEG α-oscillations were evaluated during the Go/NoGo test. In less anxious students, a reduction in sleep time on the night before the study led to a decrease in the desynchronization response to a positive conditioning stimulus (Go) and thus smoothed out the differences with the response to a stimulus that inhibited the behavioral response (NoGo). The smoothing of the α-rhythm responses to stimuli of different signal significance after deprivation indicated deterioration of cognitive control in this group. In students with a high level of anxiety, there were no differences in responses to Go/No Go stimuli either after a night’s sleep of normal duration or after a single sharp reduction of it. They probably had a reduced level of cognitive control, and it did not depend on partial sleep deprivation.
Left Atrial Reservoir Strain-Based Left Ventricular Diastolic Function Grading and Incident Heart Failure in Hypertrophic Cardiomyopathy
Authors: Lee Hyun-Jung , Kim Hyung-Kwan , Rhee Tae-Min , Choi You-Jung , Hwang In-Chang , Yoon Yeonyee E. , Park Jun-Bean , Lee Seung-Pyo , Kim Yong-Jin , Cho Goo-Yeong 
Published: April 2022

Background:
The echocardiographic assessment of left ventricular (LV) diastolic dysfunction (LVDD) in patients with hypertrophic cardiomyopathy is complex and not well-established. We investigated whether the left atrial reservoir strain (LARS) could be used to categorize LVDD and whether this grading is predictive of heart failure (HF) events in hypertrophic cardiomyopathy.

Methods:
A total of 414 patients with hypertrophic cardiomyopathy (aged 58.3±12.8 years; 65.7% male) were categorized using LARS-defined LVDD (LARS-DD) grades: ≥35% (grade 0), ≥24% to <35%, ≥19% to <24%, and <19% (grade 3). Patients were followed for a median of 6.9 years to assess hospitalization for HF or HF-related death.

Results:

An increase in LARS-DD grade was associated with worse conventional echocardiographic parameters of LVDD, such as lower e′, higher E/e′ ratio, greater maximum tricuspid regurgitation velocity, and restrictive mitral inflow pattern. Higher LARS-DD grade was also associated with parameters reflecting increased LV filling pressure, such as greater LV wall thickness, greater extent of fibrosis, obstructive physiology, and decreased LV longitudinal strain. Furthermore, higher LARS-DD grade was associated with worse HF-free survival (log-rank
P
<0.001). Patients with LARS-DD grades 0, 1, 2, and 3 showed 10-year HF-free survival of 100%, 91.6%, 84.1%, and 67.5%, respectively. LARS-DD grade was an independent predictor of HF events after adjusting for clinical and echocardiographic variables (hazard ratio, 1.53 [95% CI, 1.03–2.28], per 1-grade increase). The LARS-DD grade also had incremental prognostic value for incident HF events over the traditional echocardiographic LVDD parameters and grading system. The prognostic value of advanced LARS-DD grade was consistent in sensitivity analyses and various patient subgroups.

Conclusions:
LARS can be used as a simple single or supplemental index to categorize LV diastolic function and predict HF events in hypertrophic cardiomyopathy.
Potential Influencers of COVID-19 Vaccine Acceptance Among Adults Living in the United States Who Have Accepted or Plan to Accept the Vaccine: An Online Survey
Authors: Duck Angela Allen , Hall Katie C. , Douglas Kimberly , Price Tara S. 
Published: April 2022

Purpose The purpose of this study was to 1) determine the demographic differences between adults who have accepted, or plan to accept, the COVID-19 vaccine and those who will not accept the COVID-19 vaccine and 2) describe the potential influencers in deciding to accept the COVID-19 vaccine among adults living in the United States who have accepted or plan to accept the vaccine. Design A cross-sectional design utilizing an online survey was deployed using social media and a crowdsourcing platform. Setting United States. Subjects One thousand three hundred ninety-five (1395) adults completed the survey. The majority were white, male, between the ages of 25 and 45, and with representation from 50 states and Puerto Rico. Measures A two-branched survey was used to assess demographic information, vaccination intention, and 19 potential influencers of COVID-19 vaccine acceptance. Analysis Analysis included descriptive statistics and Chi-square tests to determine differences between groups. Results A higher proportion of male ( P < .001), married ( P < .001), and college-educated ( P < .001) participants reported acceptance of the vaccine. The factors with the highest mean score of reported level of influence were duty to protect the vulnerable and contribution to move society back to a sense of normalcy. Conclusion Understanding the potential influencers of vaccine acceptance may provide insight into strategies that could increase vaccination uptake.
MALVIRUS: an integrated application for viral variant analysis
Authors: Ciccolella Simone , Denti Luca , Bonizzoni Paola , Della Vedova Gianluca , Pirola Yuri , Previtali Marco 
Published: April 2022

Abstract
Background
Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe.

Results
We present , an easy-to-install and easy-to-use application that assists users in multiple tasks required for the analysis of a viral population, such as the SARS-CoV-2. allows to: (1) construct a variant catalog consisting in a set of variations (SNPs/indels) from the population sequences, (2) efficiently genotype and annotate variants of the catalog supported by a read sample, and (3) when the considered viral species is the SARS-CoV-2, assign the input sample to the most likely Pango lineages using the genotyped variations.

Conclusions
Tests on Illumina and Nanopore samples proved the efficiency and the effectiveness of in analyzing SARS-CoV-2 strain samples with respect to publicly available data provided by NCBI and the more complete dataset provided by GISAID. A comparison with state-of-the-art tools showed that is always more precise and often have a better recall.
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet
Authors: Winkler Sebastian , Winkler Ivana , Figaschewski Mirjam , Tiede Thorsten , Nordheim Alfred , Kohlbacher Oliver 
Published: April 2022

Abstract
Background
With a growing amount of (multi-)omics data being available, the extraction of knowledge from these datasets is still a difficult problem. Classical enrichment-style analyses require predefined pathways or gene sets that are tested for significant deregulation to assess whether the pathway is functionally involved in the biological process under study. De novo identification of these pathways can reduce the bias inherent in predefined pathways or gene sets. At the same time, the definition and efficient identification of these pathways de novo from large biological networks is a challenging problem.

Results
We present a novel algorithm, DeRegNet, for the identification of maximally deregulated subnetworks on directed graphs based on deregulation scores derived from (multi-)omics data. DeRegNet can be interpreted as maximum likelihood estimation given a certain probabilistic model for de-novo subgraph identification. We use fractional integer programming to solve the resulting combinatorial optimization problem. We can show that the approach outperforms related algorithms on simulated data with known ground truths. On a publicly available liver cancer dataset we can show that DeRegNet can identify biologically meaningful subgraphs suitable for patient stratification. DeRegNet can also be used to find explicitly multi-omics subgraphs which we demonstrate by presenting subgraphs with consistent methylation-transcription patterns. DeRegNet is freely available as open-source software.

Conclusion
The proposed algorithmic framework and its available implementation can serve as a valuable heuristic hypothesis generation tool contextualizing omics data within biomolecular networks.
Docosahexaenoic acid supplementation represses the early immune response against murine cytomegalovirus but enhances NK cell effector function
Authors: Wu Shuting , Wang Shanshan , Wang Lili , Peng Hongyan , Zhang Shuju , Yang Qinglan , Huang Minghui , Li Yana , Guan Shuzhen , Jiang Wenjuan , Zhang Zhaohui , Bi Qinghua , Li Liping , Gao Yuan , Xiong Peiwen , Zhong Zhaoyang , Xu Bo , Deng Yafei , Deng Youcai 
Published: April 2022

AbstractBackgroundDocosahexaenoic acid (DHA) supplementation is beneficial for several chronic diseases; however, its effect on immune regulation is still debated. Given the prevalence of cytomegalovirus (CMV) infection and because natural killer (NK) cells are a component of innate immunity critical for controlling CMV infection, the current study explored the effect of a DHA-enriched diet on susceptibility to murine (M) CMV infection and the NK cell effector response to MCMV infection.ResultsMale C57BL/6 mice fed a control or DHA-enriched diet for 3 weeks were infected with MCMV and sacrificed at the indicated time points postinfection. Compared with control mice, DHA-fed mice had higher liver and spleen viral loads at day 7 postinfection, but final MCMV clearance was not affected. The total numbers of NK cells and their terminal mature cell subset (KLRG1+and Ly49H+NK cells) were reduced compared with those in control mice at day 7 postinfection but not day 21. DHA feeding resulted in higher IFN-γ and granzyme B expression in splenic NK cells at day 7 postinfection. A mechanistic analysis showed that the splenic NK cells of DHA-fed mice had enhanced glucose uptake, increased CD71 and CD98 expression, and higher mitochondrial mass than control mice. In addition, DHA-fed mice showed reductions in the total numbers and activation levels of CD4+and CD8+T cells.ConclusionsThese results suggest that DHA supplementation represses the early response to CMV infection but preserves NK cell effector functions by improving mitochondrial activity, which may play critical roles in subsequent MCMV clearance.
Tea plant roots respond to aluminum-induced mineral nutrient imbalances by transcriptional regulation of multiple cation and anion transporters
Authors: Hao Jing , Peng Anqi , Li Yingying , Zuo Hao , Li Ping , Wang Jinsong , Yu Keke , Liu Chun , Zhao Shancen , Wan Xiaochun , Pittman Jon K. , Zhao Jian 
Published: April 2022

Abstract
Background
Tea is one of the most popular non-alcoholic beverages in the world for its flavors and numerous health benefits. The tea tree (Camellia sinensis L.) is a well-known aluminum (Al) hyperaccumulator. However, it is not fully understood how tea plants have adapted to tolerate high concentrations of Al, which causes an imbalance of mineral nutrition in the roots.

Results
Here, we combined ionomic and transcriptomic profiling alongside biochemical characterization, to probe the changes of metal nutrients and Al responsive genes in tea roots grown under increasing concentrations of Al. It was found that a low level of Al (~ 0.4 mM) maintains proper nutrient balance, whereas a higher Al concentration (2.5 mM) compromised tea plants by altering micro- and macro-nutrient accumulation into roots, including a decrease in calcium (Ca), manganese (Mn), and magnesium (Mg) and an increase in iron (Fe), which corresponded with oxidative stress, cellular damage, and retarded root growth. Transcriptome analysis revealed more than 1000 transporter genes that were significantly changed in expression upon Al exposure compared to control (no Al) treatments. These included transporters related to Ca and Fe uptake and translocation, while genes required for N, P, and S nutrition in roots did not significantly alter. Transporters related to organic acid secretion, together with other putative Al-tolerance genes also significantly changed in response to Al. Two of these transporters, CsALMT1 and CsALS8, were functionally tested by yeast heterologous expression and confirmed to provide Al tolerance.

Conclusion
This study shows that tea plant roots respond to high Al-induced mineral nutrient imbalances by transcriptional regulation of both cation and anion transporters, and therefore provides new insights into Al tolerance mechanism of tea plants. The altered transporter gene expression profiles partly explain the imbalanced metal ion accumulation that occurred in the Al-stressed roots, while increases to organic acid and Al tolerance gene expression partly explains the ability of tea plants to be able to grow in high Al containing soils. The improved transcriptomic understanding of Al exposure gained here has highlighted potential gene targets for breeding or genetic engineering approaches to develop safer tea products.
Activated TAZ induces liver cancer in collaboration with EGFR/HER2 signaling pathways
Authors: Moon Hyuk , Park Hyunjung , Chae Min Jee , Choi Hye Jin , Kim Do Young , Ro Simon Weonsang 
Published: April 2022

Abstract
Background
Liver cancer is a major global health concern due to the steady increases in its incidence and mortality. Transcription factors, yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1, also known as TAZ) have emerged as critical regulators in human hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC), the two major types of primary liver cancer. However, our study as well as other previous reports have shown that activation of YAP and TAZ (YAP/TAZ) in adult murine livers is insufficient for the development of liver cancer, suggesting a requirement for an additional oncogenic collaborator for liver carcinogenesis in adulthood. Therefore, we sought to identify the oncogenic partners of YAP/TAZ that promote hepatocarcinogenesis in adults.

Methods
Data analysis of the transcriptome of patients with liver cancer was performed using the national center for biotechnology information (NCBI) gene expression omnibus (GEO) database and the cancer genome atlas (TCGA). The cancer therapeutics response portal (CTRP) was used to investigate the correlation between sensitivity to chemicals and the copy number of TAZ in human cancer cell lines. Transposons encoding constitutively activated forms of TAZ (TAZS89A), BRAF (BRAFV600E), and PIK3CA (PI3KE545K) were used for hydrodynamic tail vein injection. Mice were monitored at least twice per week and sacrificed when moribund. Tumor-bearing livers were formalin fixed for hematoxylin–eosin staining and immunohistochemistry.

Results
Through database analyses, we identified EGFR/HER2 signaling to be essential in human cancers with high TAZ activity. Furthermore, immunohistochemical analyses showed that human HCC and CC tissues with high YAP/TAZ activities exhibited concomitant activation of EGFR/HER2 signaling pathways. To demonstrate that EGFR/HER2 signaling promotes YAP/TAZ-mediated hepatocarcinogenesis, TAZS89A was simultaneously expressed in murine adult livers with BRAFV600E or PI3KE545K, activated forms of effector molecules downstream of EGFR/HER2 signaling pathways. Expression of TAZS89A plus BRAFV600E induced HCC, whereas TAZS89A and PI3KE545K led to the development of CC-like cancer.

Conclusions
Our study demonstrates that TAZ collaborates with EGFR/HER2 signaling pathways to induce both HCC and CC.
CT-707 overcomes hypoxia-mediated sorafenib resistance in Hepatocellular carcinoma by inhibiting YAP signaling
Authors: Chen Zibo , Yuan Tao , Yan Fangjie , Ye Song , Xie Qin , Zhang Bo , Lin Nengmin , He Qiaojun , Yang Bo , Zhu Hong 
Published: April 2022

Abstract
Background
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Sorafenib is the first-line treatment for advanced HCC, but the anti-cancer effects remain to be improved as indicated by its low response rates and failure to prolong the progression-free survival (PFS). Thus, it is urgent to explore approaches to improve the clinical outcome.

Materials and methods
The effect of Sorafenib in HCC was analyzed by SRB (sulforhodamine B) assay in normoxia and hypoxia, respectively. The different dose combination effect of CT707 and sorafenib was analyzed by SRB assay in hypoxia. Flow cytometry assay was used to detect the cell apoptosis rate with CT707 and sorafenib treatment in hypoxia. Western blotting was used to detect the expression levels of apoptosis -related proteins and the mechanism of CT707 overcome the resistance of sorafenib in hypoxia.

Results
Our study showed that the characteristic intratumor hypoxia of advanced HCC is one of the major factors which mediated the drug resistance towards sorafenib in HCC. And CT-707, a novel multi-kinase inhibitor, could sensitize the hypoxic HCC cells towards sorafenib. Further studies showed that CT-707 abolished the nuclear translocation of Yes Associate-Protein (YAP), which has been demonstrated as one of mechanism of hypoxia-mediated sorafenib-resistance in HCC.

Conclusions
Overall, this study not only favors the development of this novel multi-kinase inhibitor CT-707 as a therapeutic agent against HCC, but also provides a potential strategy to overcome the hypoxia-mediated resistance to sorafenib in HCC patients.
Individual and residency program factors related to depression, anxiety and burnout in physician residents – a Brazilian survey
Authors: de Mélo Silva Júnior Mário Luciano , Valença Marcelo Moraes , Rocha-Filho Pedro Augusto Sampaio 
Published: April 2022

Abstract
Background
Psychological distress is common among medical trainees. This study aimed to assess the frequency of depression, anxiety and burnout among physician residents and their association with both individual and residency program-related factors.

Methods
This was a cross-sectional study applying an online survey in a national-wide sample of medical residents from Brazil. Depression, anxiety, burnout and diurnal somnolence were assessed with validated tools (Patient Health Questionnaire-4, 2 items version of Maslach Burnout Inventory, and Epworth Sleepiness Scale). Socio-demographic and residency program-related factors were measured with internally validated instruments. We performed multivariate binary logistic regression analysis for each of the main outcomes.

Results
Screening for depression, anxiety and burnout was positive respectively in 46.9%, 56.6% and 37.0% of our sample (n = 1,419). Depression was independently related to female sex, longer duty hours, absence of day off, poor learning perception, poor feeling about the residency program, overall occurrence of psychological abuse, anxiety, diurnal somnolence and burnout (AUROC = .859 [95%CI = .840-.878], p < .001). Anxiety was independently associated with female sex, higher age and duty hours, work-personal life conflicts, few classroom activities, providing assistance without supervision, depression and diurnal somnolence (837 [.816-.857], p < .001). Burnout was related to lower age and leisure time, male sex, longer duty hours, absence of day off, provision of care without supervision, choice of the wrong specialty, poor learning, psychological abuse, depression and diurnal somnolence (.780 [.753-.806], p < .001).

Conclusion
Frequency of psychological distress in residency training is high and related to both individuals and environmental factors, namely high workloads, occurrence of psychological abuse, poor faculty supervision, poor learning experience and work-personal life conflicts.
Administrative data deficiencies plague understanding of the magnitude of rape-related crimes in Indian women and girls
Authors: Dandona Rakhi , Gupta Aradhita , George Sibin , Kishan Somy , Kumar G. Anil 
Published: April 2022

Abstract
Background
This paper investigates trends in rape-related crimes against women and girls reported in the Indian administrative data from 2001 to 2018 to assess the burden of crime, describe sub-national variations, and highlight data gaps to address sexual violence effectively in India.

Methods
Data on five rape-related crimes were extracted from the annual reports of National Crimes Record Bureau (NCRB), and included assault with the intent to outrage modesty of woman, rape, insult to the modesty of women, attempt to commit rape, and murder with rape/gang-rape. Rates for all categories combined, and for each crime were estimated for women and girls for India and its states. Trends for type of offender for rape, mean number of people arrested, and legal status of the cases was also assessed.

Results
The rate of all rape-related crime increased from 11.6 in 2001 to 19.8 in 2018 per 100,000 women and girls. Most of the 70.7% increase in rate between 2001 and 2018 was post 2012 following a gang-rape and murder case in India’s capital. The largest proportion of crimes was recorded as assault with the intent to outrage modesty of the woman, followed by rape. The cited offender in rape cases was for the majority a close known person (44·3%) or other known person (43·1%). By the end of 2018, only 9·6% of the cases had completed trials, with acquittals in 73% cases.

Conclusions
The wide variations in the yearly crime rates at state-level highlighted significant issues in data quality including under-reporting, non-comparability, possible bias in data reporting in NCRB, definition of rape-related crime in India, and access in reporting of crimes. Addressing barriers to reporting, improving quality and scope of administrative data recorded on sexual violence is urgently needed for India to meet SDG targets of eliminating all forms of violence against women and girls.
Maximal inspiratory and expiratory flow at moderate altitude: a study of a Latin American population
Authors: Gochicoa-Rangel Laura , Rodríguez-Peralta Keylin Yaoska , Gutiérrez-Bautista Ana Karen , Guzmán-Valderrábano Carlos , Fernández-Plata Rosario , Torre-Bouscoulet Luis , Martínez-Briseño David 
Published: April 2022

Abstract
Background
Peak inspiratory and expiratory flows (PIF, PEF) are parameters used to evaluate the mechanics of the respiratory system. These parameters can vary based on whether they are measured using mechanical devices vs. spirometry and based on the barometric pressure at which the measurements are obtained. Our objectives were (1) to report the normal values and variability of PEF and PIF of a Latin American population living at a moderate altitude (2240 m above sea level), (2) to analyze the adjustment of reference values obtained at sea level with those obtained in healthy subjects living at a moderate altitude, and (3) to assess the correlation between PEF obtained by spirometry (PEFs) and PEF obtained by mechanical devices (PEFm).

Methods
In this prospective and transversal study, men and women with good respiratory health aged between 2.8 and 68 years old were invited to participate. Randomly, they underwent spirometry (to measure PEFs and PIFs) and mechanical flowmetry (to measure PEFm).

Results
A total of 314 subjects participated, with an average age of 24.3 ± 16.4 years; 59% were Women. The main determinants for the reference equations were age, weight, height and sex at birth. The agreement of the PEFm, PEFs and PIFs values was inconsistent with that reported by other authors, even at the same barometric pressure. The association between PEFm and PEFs was r = 0.91 (p < 0.001), and the correlation coefficient of concordance was 0.84.

Conclusions
The PEFm, PEFs, and PIFs measurements in individuals living at moderate altitudes are different from those found by other authors in cities with different barometric pressures and ethnicities.