bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust penalized-regression-based method for multivariable Mendelian randomization using GWAS summary statistics
Authors: Zhao Hongyu , Jiang Wei , Song Shuang , Lyu Liangbo , Chang Changgee , Zhao Yize , Wu Baolin , Wang Lan , Girgenti Matthew 
Published: October 2023

Abstract
Mendelian randomization (MR) is a statistical approach to inferring the causal relationships from genome-wide association studies (GWAS) by using genetic variants as instrumental variables (IVs). As IVs, the selected genetic variants should be solely associated with the exposure of interest, and have no associations with confounders and the studied outcome except through the exposure. Sometimes the selected genetic variants have effects on the outcome through other pathways, a phenomenon known as horizontal pleiotropy, which makes the selected variants violate IV assumptions. Two different approaches have been proposed to address this issue: one is to improve robustness to pleiotropic effects, and the other one is to generalize univariate exposure to multivariate cases so that we can incorporate possible pathways into MR analysis. Compared to pleiotropy-robust methods, multivariable Mendelian randomization (MVMR) can uncover the exposures having direct effects on the outcome. However, measuring all possible pathways from genetic variants to the outcome in MVMR analysis is difficult. Although MVMR methods with robustness to unmeasured pleiotropy have been proposed recently, they are statistically inefficient as a result of ignoring correlations among exposures and distributions of effect sizes.

Given the limitations from both directions, we propose a novel method named MVMR-PRESS that can infer causal relationships between multivariate exposures and the outcome with robustness to horizontal pleiotropic effects from unconsidered pathways. MVMR-PRESS estimates causal effects by using a Penalized Regression on Summary Statistics from GWAS considering both correlations among exposures and distributions of effect sizes. One merit of MVMR-PRESS is that samples in GWAS of different exposures can have overlaps, which allows us to include GWAS summary statistics from the same cohort or consortium. Simulation experiments showed that our method achieved the smallest bias and highest power compared to existing pleiotropy-robust MR and MVMR methods while the type 1 error rate was well-controlled. Applying MVMR-PRESS to publicly available GWAS summary statistics demonstrated that body mass index (BMI), height (HT), and low-density lipoprotein cholesterol (LDL) have significant causal effects on coronary artery disease (CAD), and BMI and high-density lipoprotein cholesterol (HDL) were causally related to type 2 diabetes (T2D). On the contrary, the causal estimates of triglycerides (TG), HDL, and total cholesterol (TC) on CAD, and the estimates of HT, LDL, TG, and TC on T2D were non-significant. In addition, we found no evidence suggesting BMI, HT, and lipid levels have causal effects on inflammatory bowel disease (IBD) and schizophrenia (SCZ).
Long-term outcomes of physical activity counseling in in-patients with major depressive disorder: Results from the PACINPAT randomized controlled trial
Authors: Kreppke Jan-Niklas , Cody Robyn , Beck Johannes , Brand Serge , Donath Lars , Eckert Anne , Faude Oliver , Hatzinger Martin , Imboden Christian , Lang Undine , Ludyga Sebastian , Mans Sarah , Mikoteit Thorsten , Oswald Anja , Schweinfurt Nina , Holsboer-Trachsler Edith , Zahner Lukas , Gerber Markus 
Published: October 2023

Abstract
Background: Major depressive disorder (MDD) is an increasingly common psychiatric illness associated with a high risk of insufficient physical activity, which in turn is associated with negative mental and physical health outcomes. Theory-based, individually tailored, in-person and remote physical activity counseling has the potential to increase physical activity levels in various populations. Given this, the present study investigated the effect of such a physical activity intervention on the physical activity behavior of in-patients with MDD.
Methods: This was a multi-center, two-arm randomized controlled trial including initially insufficiently physically active adult in-patients with MDD from four study sites in Switzerland. The sample consisted of 220 participants (Mage = 41 ± 12.6 years, 52% women), 113 of whom were randomized to the intervention group and 107 to the control group. The main outcome, moderate-to-vigorous physical activity (MVPA), was assessed at three time points via hip-worn accelerometer.
Results: According to accelerometer measures, there was no significant difference in minutes spent in MVPA over a 12-month intervention period when comparing the intervention with the control group (β = -1.02, 95% CI = -10.68 to 8.64). Higher baseline physical activity significantly predicted physical activity at post and follow-up.
Conclusion: This study showed that it is feasible to deliver an individually tailored, theory-based physical activity counseling intervention to in-patients with MDD, however yielding no significant effects on accelerometer-based MVPA levels. Further efforts are warranted to identify efficacious approaches.
Trial registration: ISRCTN, ISRCTN10469580, registered on 3rd September 2018, https://www.isrctn.com/ISRCTN10469580
A modular framework for FAIR shallow landslide susceptibility mapping based on machine learning
Authors: Edrich Ann-Kathrin , Yildiz Anil , Roscher Ribana , Kowalski Julia 
Published: October 2023

Abstract
Machine learning (ML) has become increasingly popular in recent years for susceptibility and hazard mapping tasks. Necessary steps of ML-based workflows for various purposes in the context of geohazards are implemented repeatedly for new studies. To facilitate an effective, modular and extensible application of ML for susceptibility and hazard mapping, a generic framework based on a Random Forest (RF) classifier is presented herein. It supports especially data pre-processing and RF input dataset generation, as well as the susceptibility or hazard map generation adapted to an individual research question. The FAIR data principles were adopted as a guideline during the design and implementation of the framework. In addition to the reproducibility of the resulting binary maps, the implementation enables extensibility and scalability. The framework is applied to the test case of rainfall triggered shallow landslide susceptibility in canton Grisons, Switzerland. Computational experiments investigating the influence of the composition of the training dataset on the mapping result are conducted. Thereby the combination of features, sampling strategies for absence (non-landslide) locations, and transferability from local to regional scale were of interest. The results emphasise the importance of considering the composition of training data for the quality of the model and as a result also the reliability of the generated map.
Oral Health Related Quality Of Life In Head And Neck Cancer Patients Visiting A Tertiary Center In Central Nepal
Authors: Koirala Resham , shrestha ashish , bhagat tarakant , agrawal santosh kumari , rimal jyotsna , gautam dejkumar 
Published: October 2023

Abstract
Background: Head and Neck Cancer (HNC) cases are rising every year. It is associated with various manifestations in oral cavity and leads to a compromise in Oral Health Related Quality of Life of the pateints.
Objectives: This study was conducted to assess Oral Health Related Quality of Life (OHRQoL) in Head and Neck cancer patients and compare it with their apparently normal counterparts.
Methods: A comparative cross–sectional study was conducted among 65 cases of HNC and their apparently normal counterparts visiting a tertiary cancer center in central Nepal. Diagnosed cases of HNC who were 18 years or more, providing consent and willing to participate in the study were taken as cases and 65 apparently healthy attendants after matching of age, sex and socio-economic status were taken as controls. Terminally ill, pregnant and those not providing consent were excluded from the study. Translated and validated OHIP-14 questionnaire was used to assess the Oral Health Related Quality of Life. Stage of cancer, site of cancer and time since diagnosed was assessed from the patient’s record file. Response to OHIP-14 items were recorded on a likert scale and the mean score was calculated. The results were statistically analysed using Mann-Whitney U test and Kruskal Wallis test.
Results: Majority of the participants belonged to upper lower socio-economic class. Mean OHIP -14 score in case group and control group were 23.91±9.71 and 6.54±4.86 respectively and the difference was statistically significant (p<0.001). The highest affected domain in case group was psychological discomfort (6.10±1.49) and that in control group was physical pain (2.50±1.70). In salivary gland tumor, the highest affected domain was handicap. In all other tumors, psychological discomfort was the highest affected domain and the values were not statistically significant.
Conclusion: There is an impairment of the OHRQoL in HNC patients which is higher than their normal counterparts.
TREM2+ macrophages regulate suppressive tumor microenvironment in TNBC
Authors: Sun Xiaohu , Yu Zhihao , Wang Kenie , Yu Yue , Wang Xin , Kang Ning , Cao Xu-Chen 
Published: October 2023

Abstract
Triple negative breast cancer (TNBC) possesses the poorest prognosis among the major breast cancer subtypes due to the limited treatment options. Nevertheless, TNBC is more immune-activated than other subtypes due to the higher mutation load, implicating that TNBC patients might benefit from immunotherapy. Previous studies have reported that the presence of tumor infiltrating lymphocytes in TNBC might create a suppressive immune microenvironment, which is associated with worse prognosis. Therefore, our work aims to compare the tumor microenvironment (TME) differences among breast cancer subtypes and discover the targetable Achilles’ heel of TNBC. We utilized public single-cell RNA-Seq (scRNA-Seq) dataset to analyze the cell composition and cell-cell communication network differences between TNBC and other subtypes. Further differential gene analysis and enrichment analysis was performed to define the transcriptomic variation. Our data showed that TREM2+ macrophages were elevated in TNBC and centrally located in the communication network. Finally, survival analysis was conducted in large cohort data to assess the involvement of TREM2+ macrophages in the progression of TNBC. Notably, the advanced TREM2+ macrophage signature was implicated with the survival outcomes of TNBC patients but not all breast cancer patients. Accordingly, this study uncovered a highly suppressive TME in TNBC, highlighted the essential role of TREM2+ macrophages in regulating the TME in TNBC, and revealed TREM2+ macrophages as a promising target for generating more favorable therapies in TNBC treatment.
Novel Compound Heterozygous MYO15A Splicing Variants in Autosomal Recessive Non-syndromic Hearing Loss
Authors: Zheng Kaifeng , Lin Sheng , Gao Jian , Chen Shiguo , Su Jindi , Liu Zhiqiang , Duan Shan 
Published: October 2023

Abstract
Background:Hereditary hearing loss is ahighly heterogeneous disorder both genetically and clinically. In this study, we aimed to identify the genetic cause of a Chinese family with autosomal recessive nonsyndromic sensorineural hearing loss (ARNSHL).
Methods:Clinical information and peripheral blood samples were collected from the proband and its parents. Two-stephigh-throughput next-generation sequencing on theIon Torrent platform was applied to detect mutations as follows. First, long-range PCR was performed to amplify the entire regions of the GJB2, GJB3, SLC26A4 and MT-RNR1 genes, and the products were submitted to next-generation sequencing. Targeted exon sequencing with AmpliSeq technology was further performed to examine another 64 deafness-associated genes. The identified variants and the cosegregationwith disease phenotypes in the family were validated by Sanger sequencing. We then assessed the effect of the mutation on the splicing of the MYO15A gene by bioinformatics prediction and minigene assays.
Results:Two candidate MYO15A gene heterozygous splicing mutations, c.6177+1G>T and c.9690+1G>A, were identified in the proband, and these two variants were both annotated as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Further bioinformatic analysis predicted that thec.6177+1G>T mutation might cause exon skipping and that the c.9690+1G>A mutation might activate a cryptic splicing donor site in the downstream intronic region. An in vitro minigene assay confirmed the above predictions.
Conclusions:We identified a compound heterozygous splicing mutation in the MYO15A gene in a Han Chinese family with ARNSHL. Our results broaden the spectrum of MYO15A mutations, potentially benefiting the early diagnosis, prevention and treatment of the disease.
Heracleum sosnowskyi or Heracleum mantegazzianum? DNA-based identification of invasive hogweeds (Apiaceae) in two key regions of the species' invasion history in the territory of the former Soviet Union
Authors: Shadrin Dmitry , Dalke Igor , Zakhozhiy Ilya , Shilnikov Dmitry , Kozhin Mikhail , Chadin Ivan 
Published: October 2023

Abstract
Heracleum mantegazzianum Sommier & Levier and Heracleum sosnowskyi Manden. are two species that belong to the giant invasive hogweed complex. H. mantegazzianum is predominantly found in Western European countries, while H. sosnowskyi is invasive in the European part of Russia and Eastern European countries. The taxonomy of the Heracleum genus is quite complex, and identifying these species requires extensive expertise. Surprisingly, although H. mantegazzianum and H. sosnowskyi are considered separate species, their morphological and ecological-physiological properties, as well as their ontogeny and population structure, exhibit remarkable similarities, making them ecological twins. The intentional introduction of this invasive species was initially conducted in the cities of Kirovsk city (Murmansk region, Russia) and Syktyvkar city (Komi Republic, Russia). Plant materials sourced from these two regions were subsequently distributed to all regions encompassing the modern hogweed invasion range across the former USSR countries. The objective of this study was to test the hypothesis that the plants initially introduced in Kirovsk and Syktyvkar actually belong to H. mantegazzianum. To accomplish this, herbarium material was collected, and DNA barcoding was performed on 16 samples of giant invasive hogweed from the vicinity of the cities of Kirovsk and Syktyvkar, as well as on 30 H. mantegazzianum samples collected within its native range in the Western Caucasus. The results of morphological identification combined with DNA barcoding demonstrate that H. mantegazzianum and the plants growing in Kirovsk and Syktyvkar belong to the same species – H. mantegazzianum, rather than H. sosnowskyi as previously believed.
Parametric effects on the behavior of the center and wall modes in viscoelastic channel flow of FENE-P fluid
Authors: Cheng Haotian , Zhang Hongna , Wang Suming , Zhang Wenhua , Li Xiaobin , Li Fengchen 
Published: October 2023

Abstract
The stability analysis plays an important role in comprehending the origin of elasto-inertial turbulence (EIT) of viscoelastic fluid. Currently, there is still a debate on whether it is the center mode or the wall mode that is the origin of EIT. The present paper conducts the linear stability analysis of viscoelastic fluid channel flows with the finitely extensible non-linear elastic Peterlin (FENE-P) model and focuses on the parametric effects, especially the nonlinear extension effect, on the characteristics of the center mode and wall mode. The effects of increasing Weissenberg number (Wi) and Reynolds number (Re) on the center mode and the wall mode are completely different, and the ranges of perturbation wavenumber α inducing the center mode and the wall mode instability vary greatly. The perturbation wavenumber causing the wall mode instability is around 1, whereas the range of wavenumber for the center mode instability can extend about from 1 to tens or even hundreds under the parameters concerned in this study. Moreover, with the increase of the maximum extension length L2, the wall mode and the center mode show the evolution trends of U-shaped and inverted U-shaped, respectively, and these two non-monotonic evolution trends are linked to the effective elasticity of FENE-P fluid. Additionally, we obtained a scaling correlation corresponding to the most unstable center mode with the largest growth rate. It indicates that the combination of effective elasticity and elasticity number (E=Wi/Re) can better reflect the elasticity strength felt by viscoelastic fluid flows.
Physical, nutritional, functional and rehydration properties of palm beetle (Oryctes rhynoceros) larvae as affected by drying and roasting
Authors: Falade Kolawole , Vigbe David 
Published: October 2023

Abstract
The effects of sun-drying, oven-drying and roasting on physical, chemical, functional and rehydration properties of palm beetle (Oryctes rhinoceros L.) larvae were investigated. Average weight (18.64g), length (67.74mm), breadth (22.56mm), and thickness (19.12mm) of live larvae reduced to 2.85-3.86mm, 36.78-38.24mm, 20.10-21.05mm and 16.50-18.88mm, respectively, with degutting, drying and roasting. Generally, lightness (49.93) and yellowness (11.68) of live larvae reduced to 28.89 and 5.60, when sun-dried. Crude protein, ash, fat and crude fibre contents of processed larvae varied from 65.46–69.99, 9.75–10.27. 13.79–21.01 and 0.55-1.23g/100g, respectively. Potassium, magnesium and sodium contents of processed larvae varied from 212.6–379.1, 58.76–184.6, and 104.65–170.75mg/100g, respectively. Sun-dried larvae showed higher amino acids contents than oven-dried and roasted larvae. However, the processed beetle larvae were rich in leucine, lysine, phenylalanine, aspartic acid, glutamic acid, isoleucine, leucine, threonine, valine, arginine, histidine and tyrosine. The water and absorption, OAC, loose and packed bulk density and dispersibility varied between 1.77–2.03, 1.20–1.33, 0.38-0.41g/mL, 0.56-0.60g/mL, 15.15-24.67sec and 18.77-26.00sec, respectively. Moisture contents of rehydrated sun-dried larvae were higher than oven-dried and roasted larvae between 15-45oC.
The moderating effect of social participation on the relationship between health status and depressive symptoms in older adults
Authors: Ow Yvonne Su Yong , Wei Chia-Shine , Li Yang-Tzu 
Published: October 2023

Abstract
Background
Depression is a common mental health problem among older adults and a leading cause of disability worldwide. Health status and social participation has been found significantly associated with depression in older adults. However, the role of social participation in the relationship between health status and depression remains unclear. This study aims to investigate the relationship between health status and depressive symptoms in older adults and the moderating effect of social participation in the relationship.
Methods
A cross-sectional study with data from the National Health Interview Survey (NHIS) in 2013. Older adults aged 65 years or older were included in the study. Multiple regression analysis was performed to examine the relationship between health status and depressive symptoms and assess the moderating effect of social participation.
Results
Of the 2731 participants, higher depressive symptoms were observed among older women, older adults who were single, living alone and having lower satisfaction on financial status. Regression analyses showed that ADL and IADL disability were positively associated with higher depressive symptoms. Perceived health status, cognitive functions and social participation were found negatively associated with depressive symptoms. A significant moderating effect of social participation between perceived health status and depressive symptoms was observed in this study.
Conclusions
The findings highlight the role of social participation in moderating the effect of perceived health status on depressive symptoms and suggest that promoting social participation among older adults may be helpful for reducing depressive symptoms.
CHIP Drives Proteasomal Degradation of Nur77 to Alleviate Oxidative Stress and Intrinsic Apoptosis in Cisplatin-induced Nephropathy
Authors: Zhang Hao , Deng Zebin , Wang Yilong , Zheng Xiaoping , Zhou Lizhi , Yan Shu , Wang Yinhuai , Dai Yingbo , Kanwar Yashpal. S , Deng Fei 
Published: October 2023

Abstract
Carboxy-terminus of Hsc70-interacting protein (CHIP), an E3 ligase, modulates the stability of its targeted proteins to alleviate various pathological perturbations in various organ systems. Cisplatin is a widely used chemotherapeutic agent, but it is also known for its alarming renal toxicity. The role of CHIP in the pathogenesis of cisplatin-induced acute kidney injury (AKI) has not been adequately investigated. Herein, we demonstrate that CHIP is abundantly expressed in the renal proximal tubular epithelia, and its expression is downregulated in cisplatin-induced AKI. Further investigation revealed that CHIP overexpression or activation alleviated, while its gene disruption promoted, oxidative stress and apoptosis in renal proximal tubular epithelia induced by cisplatin. In terms of mechanism, CHIP interacted with and ubiquitinated Nur77 to promote its degradation, which consequently shielded Bcl2 to maintain mitochondrial permeability of renal proximal tubular cells in the presence of cisplatin. Also, we demonstrate that CHIP interacts with Nur77 via its central coiled-coil (CC) domain, a non-canonical interactive pattern. In conclusion, these findings indicate that CHIP ubiquitinates and degrades its substrate Nur77 to attenuate intrinsic apoptosis in cisplatin-treated renal proximal tubular epithelia, thus providing a novel insight for the pathogenesis of cisplatin-induced AKI.