bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relaxing environments make people with high neuroticism more concentrated: An EEG study of auditory steady-state response
Authors: Hashizume Ayana , Yamamoto Masataka , Nakadai Hisanao , Takemura Hiroshi 
Published: January 2024

Abstract

Considering that new ways of working are increasing in modern society, where people can choose their own workspace, workers must understand the most suitable environment for concentration. Personality is crucial for determining a suitable and focused environment for each individual. However, few studies have investigated the relationship between personality and the environment, in which it is easy to concentrate using objective methods. We explored whether differences exist in the environment in which people can concentrate easily, depending on their personalities. We measured concentration using the auditory steady-state response, a brain response to sound. For each of the Big Five personality factors, we compared concentration after presenting videos simulating both relaxed and tense environments and investigated the relationship with personality scores. The results indicated a negative correlation between neuroticism scores and concentration in a tense environment. People with lower neuroticism concentrated more in a tense environment, while those with higher neuroticism concentrated more in a relaxed environment. These findings not only assist employees in choosing their workspace but also may support educational settings such as schools and universities.
Endothelial tip-cell position, filopodia formation and biomechanics require BMPR2 expression and signaling
Authors: Knaus Petra , Hiepen Christian , Benamar Mounir , Barrasa-Fano Jorge , Cóndo Mar , Ilhan Mustafa , Münch Juliane , Hastar Nurcan , Kerkhoff Yannic , Harms Gregory , Mielke Thorsten , König Benjamin , Block Stephan , Seyfried Salim , Oosterwyck Hans Van 
Published: January 2024

Abstract

Blood vessel formation relies on biochemical and mechanical signals, particularly in sprouting angiogenesis where endothelial tip cells (TCs) guide sprouting through filopodia formation. The role of BMP receptors in defining endothelial tip-cell characteristics remains unclear. Our study elucidates the pivotal role of BMPR2 in actin-driven filopodia formation and mechanical properties of endothelial cells (ECs). Targeting bmpr2b in zebrafish impairs sprouting angiogenesis, while BMPR2-deficient human ECs diminished filopodia, impacting cell migration and actomyosin localization. Spheroid assays reveal reduced sprouting in fibrin gels, and in mosaic spheroids, BMPR2-deficient ECs fail to acquire tip-cell positions. Surprisingly, 3D traction force microscopy shows no significant differences in force-induced matrix deformations from BMPR2-deficient tip cells, which instead adopt a distinct cone-shaped morphology. BMPR2 localizes near filopodia interacting with BORG5 to regulate CDC42. Our findings unveil BMPR2 as a central hub integrating biochemical and biomechanical processes crucial for endothelial tip cells during angiogenesis.
Causal relationship between COVID-19 and membranous nephropathy: A bidirectional Mendelian randomization study
Authors: Zhou Tong , Zhang Heping , Zhao Jiayu , Ma Yimei , He Linqian , Ren Zhouting , Lin Fulian , Chen Zhihui , Yang Kun , Tang Jincheng , Liu Jiali , Deng Fei 
Published: January 2024

Abstract
Recent studies have suggested a potential link between COVID-19 and the initiation or exacerbation of membranous nephropathy (MN) caused by the SARS-CoV-2 virus. However, a causal relationship between COVID-19 and MN remains unconfirmed. Here, we used the Mendelian randomization (MR) approach to investigate whether this causal relationship exists. We utilized data from the COVID-19 Host Genetics Initiative, comprising the largest available genome-wide association study (GWAS) datasets from European and East Asian populations. For MN, we used the largest literature-reported GWAS dataset. We selected single nucleotide polymorphisms as instrumental variables and used the inverse variance weighted (IVW) method, supplemented with MR Egger, weighted median, and mode methods. The MR-Egger intercept test and the MR-PRESSO global test were applied to assess horizontal pleiotropy. The robustness of the MR findings was evaluated using Cochran’s Q test and leave-one-out analysis. In both cohorts, MR methods showed SARS-CoV-2 infection, hospitalization, and severe COVID-19 did not increase the risk of MN. Conversely, MN potentially increased the risk of COVID-19-related hospitalization in Europeans, supported by the IVW and other methods. In East Asians, MR Egger suggested an increased risk of severe COVID-19 associated with MN, but other MR methods did not support this. No significant evidence of horizontal pleiotropy was detected. Cochran’s Q test showed no heterogeneity, and leave-one-out analysis confirmed the MR findings' reliability. The bidirectional MR analysis confirmed that COVID-19 did not increase MN risk, but MN might increase the risk of COVID-19-related hospitalization in Europeans, indicating a potential causal relationship.
Mechanism of SETX-BRCA1-BARD1 complex in resolution of R-loops and transcription-replication conflicts
Authors: Sung Patrick , Dutta Arijit , Ji Jae-Hoon , Fang Qingming , Zhou Shuo , Liang Fengshan , Nyalwidhe Julius , Dray Eloise , Verway-Cohen Amy , McDonald Drew , Avalos Bárbara de la Peña , Li Wenjing , Herrero Ane , Fitzgerald O’Taveon , Taylor Alexander , Kwon Youngho , Semmes Oliver , Tsai Miaw-Sheue , Hromas Robert , Burma Sandeep , Bishop Alexander , Mazin Alexander , Wasmuth Elizabeth , Olsen Shaun , Zhou Daohong , Zhao Weixing , Kupfer Gary 
Published: January 2024

Abstract
Senataxin (SETX), a putative RNA-DNA helicase, is recruited to transcription pause sites via the tumor suppressor BRCA1. Here, we define the mechanism by which SETX-BRCA1 resolves transcription-associated R-loops to prevent deleterious outcomes. Specifically, we show that SETX unwinds R-loops, and that the complex of BRCA1 and its obligatory partner BARD1 binds R-loops and stimulates R-loop unwinding by SETX. Importantly, BRCA1-BARD1 alleviates the inhibitory effect of RAD52 on SETX-mediated R-loop unwinding. We also demonstrate that phosphorylation of Ser642 in SETX promotes its interaction with BRCA1 via the tandem BRCT domain of the latter. Accordingly, mutations in the catalytic domain or Ser642 in SETX lead to R-loop accumulation, transcription-replication conflicts, replication fork stalling, and DNA double strand breaks in human cells. Our results thus establish the molecular basis for functional synergy between SETX and BRCA1-BARD1 in R-loop resolution and the mitigation of transcription-replication conflicts to preserve genome integrity.
A Study on the Unstable Evolution Characteristics of Loose Particle Slopes under Dynamic Supply of Material Sources
Authors: Wang Jianhu , Xie Liangfu , Xie YongTian , Wu Liming 
Published: January 2024

Abstract
The instability of granular slopes is one of the typical natural disasters in the cold mountainous areas of Xinjiang, posing significant threats to transportation facilities and pedestrian safety. Dynamic source supply is a major factor inducing the instability and destruction of these slopes. This paper investigates the instability evolution process, morphological changes, and destruction characteristics of granular slopes under continuous and periodic dynamic source supply conditions through physical model experiments and numerical simulations. The results demonstrate that: (i) granular slopes exhibit a "accumulation-instability-accumulation" cyclic evolutionary process with the continuous increase in supply; (ii) the surface slope angle at the middle position of the slope increases with each increase in supply until a steep decline of about 5° occurs after each overall instability event; (iii) under continuous supply, the slope experiences several local instabilities before an overall collapse, and the scale of the overall instability increases with the number of occurrences.
The association between celiac disease and digestive system cancers: A Mendelian randomization study.
Authors: Yuan Chang , Feng cuncheng 
Published: January 2024

Abstract

Background Relevant studies have shown a causal relationship between celiac disease and digestive system cancers risk. However, the causal relationship is controversial. Therefore, we aimed to investigate whether CD is causally associated digestive system cancers, including colorectal cancer, Gastric cancer, Oesophageal Cancer, Small intestine cancer, Hepatic cancer, Pancreatic cancer, and Gallbladder cancer using an mendelian randomization (MR) approach.Methods We conducted analyses using two sets of instrumental variables in a two-sample MR design. Summary-level data for colorectal cancer, gastric cancer, oesophageal cancer, Small intestine cancer, Hepatic cancer, Pancreatic cancer, and Gallbladder cancer were obtained from genome-wide association analyses of the UK Biobank study. Summary-level data for celiac disease was derived from a genome-wide association study conducted in the UK Biobank population. We calculated the causal effect using the inverse variance weighted method. Sensitivity analyses and leave-one-out analyses were performed to ensure the consistency and robustness of causal estimates.Results IVW analysis showed a positive causal relationship between CD and CRC risk (OR = 1.106, 95%CI: 1.043–1.173, p < 0.001). In reverse Mendelian randomization, we found that: colorectal cancer is not causally related to celiac disease(OR = 0.968, 95%CI: 0.913–1.027, p = 0.276). IVW analysis demonstrated that CD didn’t have causal association with the other digestive tract cancers (Gastric cancer :OR = 0.220, 95%CI:4.12E-5-1.180E + 3, p = 0.730; Oesophageal cancer: OR = 0.997, 95%CI: 0.986–1.007, p = 0.089; Small intestine cancer: OR = 1.017, 95%CI: 0.998–1.036, p = 0.547; Hepatic cancer: OR = 0.053c, 95%CI: 2.28E-10-1.236E + 7, p = 0.770; pancreatic cancer: OR = 40.763, 95%CI: 0.011-1.492E + 5, p = 0.376; Gallbladder cancer: OR = 169.240, 95%CI: 1.90E-68-1.51E + 72, p = 0.950). No evidence of horizontal pleiotropy was identified (MR Pleiotropy Residual Sum and Outlier global test and MR-Egger intercept with P > 0.05). The leave-one-out sensitivity analyses revealed that the causal estimates were not disproportionately influenced by any individual SNP.Conclusion Our findings suggest that coeliac disease was positively associated with the risk of colorectal and colon cancer, but not causally associated with Gastric cancer, Oesophageal Cancer, Small intestine cancer, Hepatic cancer, Pancreatic cancer, and Gallbladder cancer.
An Evaluation of High-Risk HPV in Squamous Cell Carcinomas of the Lip in a South African Cohort
Authors: Harbor Sharon N. , Schneider Johann W. , Solomons Nadine , Sanderson Micheline , Afrogheh Amir H. 
Published: January 2024

Abstract

Background
To determine the prevalence of HR-HPV in a series of lip SCC from South African patients, using currently accepted HPV-testing methodologies and to define the clinical and histomorphologic features of HPV-associated lip SCC.
Methods
Fifty SCC of lip and 50 control cases were tested for HR-HPV using p16 and HR-HPV DNA PCR. p16-equivocal/positive and HPV DNA PCR-positive SCC were further evaluated for the expression of HPV-16 and HPV-18 mRNA transcripts using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to confirm transcriptionally active HPV.
Results
p16 was positive in 22% (n = 11) and equivocal in 4% (n = 2) of the SCC. One p16-positive case showed positivity for both HPV-16 DNA and HPV-16 E6/E7 mRNA transcripts (HPV prevalence rate of 2%). The HPV-positive case was non-keratinizing and occurred in an 80-year-old female. The two p16-equivocal cases were HR-HPV DNA positive and mRNA PCR negative. p16 was found to have a positive predictive value of 52%.
Conclusions
Findings from our cohort of lip SCC suggest that HR-HPV may have an insignificant role in the pathogenesis of SCC at this site. Due to its low ppv, p16 is insufficient to establish HR-HPV infection in SCC of the lip. The combination of p16 and DNA PCR, appears to correlate with the presence of transcriptionally active virus. HPV E6/E7 mRNA detection is the gold standard for identifying HR-HPV. mRNA testing is not widely available in sub-Saharan Africa due to technical and financial constraints, however, the test appears to be of great value in p16-equivocal lip SCC.
Pilot study suggests cellular immunity changes in bats from urban landscapes
Authors: Tovstukha Ihor , Fritze Marcus , Kravchenko Kseniia , Kovalov Victor , Vlaschenko Anton 
Published: January 2024

Abstract
Environmental pollution and habitat loss and are influencing the health status of wild animals and increase the risk of zoonosis outbreaks. For example, the ongoing urbanisation leads to significant habitat changes and burden of anthropogenic stressors. Bats are a diverse mammalian order occurring in urban areas. In a pilot study, we investigated the general immunity status of two common bat species along urban-natural gradients. We used haematological parameters as cellular immunity indicators and intensity of light pollution as a proxy for urbanisation level (i.e. anthropogenic stress) at the sampling points. We found higher total white blood cell, lymphocytes and neutrophil proportions in Nyctalus noctula from suburban and urban habitats in comparison to those from natural ones. At the same time Eptesicus serotinus, a species commonly living in cities, had a lower neutrophil level and a trend towards lower neutrophil-to-lymphocyte ratio and intoxication index compared to N. noctula which only uses the suburban-urban area seasonally. Our study suggests that the cellular immunity in bats is altered by urban stressors, yet depends on species-specific tolerance. We call for more research in this area and, as precaution principle, conservation of habitats in urban areas in order to mitigate the negative impact of urban stressors on the health of wildlife.
ESDP: An Emotion-Sensitive Dialogue Policy for Task-Oriented Dialogue System
Authors: Zhu Hui , Wang Xv , Wang Zhenyu , Xv Kai 
Published: January 2024

Abstract

Reinforcement learning (RL) is an effective method in training dialogue policies to steer the conversation towards successful task completion. However, most RL-based methods only rely on semantic inputs that lack empathy as they ignore the user emotional information. Moreover, these methods suffer from delayed rewards caused by the user simulator returning valuable results only at dialogue end. Recently, some methods have been proposed to learn the reward function together with user emotions, but they missing to consider user emotion in each dialogue turn. In this paper, we proposed an emotion-sensitive dialogue policy model (ESDP), it incorporates user emotions information into dialogue policy and selects the optimal action by the combination of top-k actions with the user emotions. The user emotion information in each turn is used as an immediate reward for the current dialogue state to solve sparse rewards and termination dependency. Extensive experiments validate that our method outperforms the baseline approaches when combined with different Q-Learning algorithms, and also surpasses other popular existing dialog policies' performance.
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Authors: Nikoloski Zoran , Hsieh Yunli , Tandon Kshitij , Verbruggen Heroen 
Published: January 2024

Abstract

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing metagenomics data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of microbial communities.
Normothermic ex vivo kidney perfusion preserves mitochondrial and graft function after warm ischemia and is further enhanced by AP39
Authors: Robinson Lisa , Kawamura Masataka , Parmentier Catherine , Ray Samrat , Clotet-Freixas Sergi , Leung Sharon , John Rohan , Mazilescu Laura , Nogueira Emmanuel , Noguchi Yuki , Goto Toru , Arulratnam Bhranavi , Ganesh Sujani , Tamang Tomas , Lees Kaitlin , Reichman Trevor , Andreazza Ana , Kim Peter K. , Konvalinka Ana , Selzner Markus 
Published: January 2024

Abstract

We previously reported that normothermic ex vivo machine perfusion (NEVKP) is superior in terms of organ protection compared to static cold storage (SCS), which is still the standard method of organ preservation, but the detailed mechanism is unclear. We used a large animal kidney autotransplant model to evaluate mitochondrial function during organ preservation and after kidney transplantation utilizing live cells extracted from renal tissue. Porcine kidneys stored under normothermic perfusion showed preserved mitochondrial function and higher ATP levels compared to kidneys stored at 4°C (SCS). Mitochondrial respiration and ATP levels were further enhanced when AP39, a mitochondria-targeted hydrogen sulfide donor, was administered during warm perfusion. Correspondingly, the combination of NEVKP and AP39 was associated with decreased oxidative stress and inflammation, and with improved graft function after transplantation. In conclusion, our findings suggest that the organ-protective effects of normothermic perfusion are mediated by maintenance of mitochondrial function and enhanced by AP39 administration. AP39, in combination with warm perfusion, has the potential to become the new standard of care for long-term renal preservation.
Association between psoriasis and risk of malignancy: observational and genetic investigations
Authors: Chen Aijun , Li Ruolin , Chen Xiangjun , Zeng Qinglian , Luo Wenjin , Yang Shumin , Wang Ping , Hu Jinbo 
Published: January 2024

Abstract

The relationship between psoriasis and site-specific cancers remains unclear. We aimed to investigate whether psoriasis is causally associated with site-specific cancers. We used observational and genetic data from UK Biobank. We obtained genome-wide association study (GWAS) summary data, expression quantitative trait locus (eQTL) analysis data, The Cancer Genome Atlas (TCGA) data and genotype-tissue expression (GTEx) data from public datasets. We used a phenome-wide association study (PheWAS), PRS analysis, and one-sample and two-sample Mendelian randomization (MR) analysis to investigate potential causal associations between psoriasis and cancers. We added gene annotation for potential molecular associations. A total of 13463 patients with psoriasis and 463136 participants without psoriasis were included. In unselected PheWAS analysis, psoriasis was associated with higher risks of 14 types of cancer. In one-sample MR analyses, genetically predicted psoriasis was associated with higher risks of anal canal cancer (hazard ratio [HR] 1.61, 95% CI 1.12–2.32), breast cancer (HR 1.06, 95% CI 1.02–1.11) and nonmelanoma skin cancer (HR 1.07, 95% CI 1.01–1.14) in women and lung cancer (HR 1.17, 95% CI 1.04–1.32) and kidney cancer (HR 1.34, 95% CI 1.13–1.58) in men. Two-sample MR analysis indicated that psoriasis was causally associated with breast cancer (inverse variance weighted [IVW] odds ratio 1.02, 95% CI 1.01–1.03) and lung cancer (IVW odds ratio 1.12, 95% CI 1.02–1.22). Gene annotation revealed that psoriasis-related genes (such as ERAP1 and C6orf3) were significantly changed in lung and breast cancer tissues. Our findings demonstrate psoriasis is causally associated with lung cancer and breast cancer. Regular screening for lung and breast cancer might be relevant for patients with psoriasis.
GIS and Cellular Automata based slope rainwater movement process model and its application
Authors: Liu Lei , Chen Yu , Zhang Yanjun , Liu Yalei , Lian Zhipeng , Pei Laizheng 
Published: January 2024

Abstract

Rainfall is an important cause of slope stability issues in mountainous areas, and simulating the process of slope rainwater movement is an important method for analyzing the stability of rainfall induced slopes. By combining computer numerical simulation technology with traditional hydraulic and hydrological calculation theories, an efficient and accurate rainwater movement model can be constructed for simulating and analyzing the rainwater movement process on slopes. Taking natural slopes as the research object, the cellular automaton method was applied to simulate rainfall runoff on slopes, and a Cellular Automata (CA) based model for rainwater movement process was developed. The model modified the Green-Ampt (G-A) infiltration model, adopted an elliptical water content curve, and introduced a coefficient to describe the ratio of saturated to unsaturated depth; At the same time, improvements were made to the rules of runoff generation and convergence within the slope and on the slope surface to simulate the entire rainwater movement process on the slope. Furthermore, the effectiveness of the model was validated through analytical solutions under simplified conditions, laboratory experiments on rainfall and runoff in the flume, and calculation results from on-site monitoring data at the slope scale. The results show that the infiltration calculation results of the rainwater movement model are closer to the experimental values, and their overall values are slightly higher than the measured values, which are basically consistent with the model test results; The runoff calculation results show a phenomenon of initially increasing and gradually approaching the measured values compared to the measured values. Using the model established in this paper for the on-site slope, it was found that the model can fully consider the influence of slope inner diameter flow and unsaturated layer infiltration process, simulate slope infiltration and runoff processes more reasonably, and dynamically output results at different times.