bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomic analysis of Illumina and MGI next generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells
Authors: Póliska Szilárd , Fareh Chahra , Lengyel Adél , Göczi Loránd , Tőzsér József , Szatmari Istvan 
Published: March 2023

Abstract
We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-Seq testing two next generation sequencing (NGS) technologies. We compared the DNA nanoball (DNB) based MGI DNBSEQ G400 sequencer with the bridge-PCR based Illumina NextSeq 500 instrument. Moreover, we also compared two types of MGI sequencing reagents (Standard- versus Hot-MPS) with the DNBSEQ G400. Importantly, very similar gene expression profile and greatly overlapping RUNX3 and ZBTB46 regulated gene sets were detected with both platforms. Moreover, almost identical gene expression pattern was obtained with the Hot-MPS reagent compared to the Standard-MPS chemistry. This transcriptomic analysis also facilitated the identification of RUNX3 and ZBTB46 regulated genes. For example, we found that Gzmd, Gdf6 and Ccr7 genes were robustly upregulated upon the forced expression of Runx3, on the other hand, Gpx2, Tdpoz4 and Arg2 were induced upon the ectopic expression of Zbtb46. Together these findings demonstrate that the DNBSEQ G400 system is also suitable for global transcript profiling and target gene selection with lower cost.
A coupled hydro-chemo-mechanical approach to model the degradation and appearance of cracks in cementitious materials subject to carbonation
Authors: Seigneur Nicolas , Socié Adrien , Bary Benoit , Poyet Stéphane , Touzé Gaëtan 
Published: March 2023

Abstract
Coupled Thermal-Hydraulic-Mechanical-Chemical (THMC) approaches are crucial for assessing the durability of cementitious materials. We present a novel approach to overcome past limitations of THMC modelling and validate it based on experimental results of accelerated carbonation tests. Our numerical approach rests on a sequential coupling between Hytec and Cast3M. Hytec computes the evolution of hydraulic and mineralogical fields allowing to compute the micromechanical properties (e.g. Young modulus). The mineral reactions generate tensile stresses and Cast3M computes the associated strain tensors and the damage evolution represented by the opening or sealing of cracks, impacting subsequent reactive transport processes. Our approach manages to reproduce the crack patterns and non-uniform degradation depths observed on microtomographic images of carbonated cement samples, which can only be explained by the coupled dynamics of chemical and mechanical processes. Our approach can be extended to a wide range of cement-concrete pathologies and contexts.
Causal associations of brain structure with bone mineral density: a large-scale genetic correlation study
Authors: Zhao Shu-Shan , Guo Bin , Wang Chao , Zhu Yong , Liu Zhi , Long Haitao , Ruan Zhe , Lin Zhang , Fan Zhi , Li Yusheng 
Published: March 2023

Abstract
This study aimed to investigate the causal associations of brain structure with bone mineral density (BMD). Based on the genome-wide association studies (GWAS) summary statistics of 1325 brain imaging-derived phenotypes (BIDPs) of brain structure from the UK Biobank, and GWAS summary datasets of 5 BMD locations, including total body, femoral neck, lumbar spine, forearm, and heel from GEFOS Consortium, linkage disequilibrium score regression (LDSC) was conducted to determine the genetic correlations and Mendelian randomization (MR) was then performed to explore the causal relationship between the BIDPs and BMD. Several sensitivity analyses were performed to verify the strength and stability of the present MR outcomes. To increase confidence in our findings, we also performed a confirmatory MR between BIDPs and osteoporosis. LDSC revealed that 1.93% of BIDPs, with a false discovery rate (FDR) < 0.01, genetically correlated with BMD. Additionally, we observed that 1.31% of BIDPs exhibited a significant causal relationship with BMD (FDR < 0.01) through MR. Both the LDSC and MR results demonstrated that the BIDPs “Volume of normalized brain”, “Volume of grey matter in Left Inferior Frontal Gyrus, pars opercularis”, “Volume of Estimated Total Intra Cranial” and “Volume-ratio of brain segmentation/estimated total intracranial” had strong associations with BMD. Interestingly, our results showed that more left BIDPs were causally associated with BMD, especially within and around the left frontal region. In conclusion, a part of brain structure causally influences BMD, which may provide important perspectives for the prevention of osteoporosis and offer valuable insights for further research of the brain-bone axis.
Empirical comparison of assembly complexity assessment approaches in manufacturing
Authors: Capponi Matteo , Mastrogiacomo Luca , Franceschini Fiorenzo 
Published: March 2023

Abstract
Investigating assembly complexity is a continuing concern within manufacturing field, as it may impact quality and costs of products. There is a growing body of literature aimed at developing novel and reliable methods to assess assembly complexity. The first aim of this paper is to provide an extensive literature review, identifying the main approaches to this problem. Three main approaches emerged: product-centred approach, information-centred approach and system-centred approach. A second goal is to carry out a comparative analysis of these approaches highlighting their advantages, limitations and providing guidance for process and product designers seeking to control assembly complexity. For each approach, a representative method was chosen, analysed in detail, and applied to three different real products.
Factors influencing HIV Testing among young women aged 15-24 in the 2015-2016 Malawi Demographic and Health Survey
Authors: Koroma Mark Momoh , Chigoneka Kuleza , Kabba John Alimamy , Yu Jing-Rong , Senabye Pauline Kerapetse , Dai Ying-Chun , Wang Lu , Xie Dong-Jie , Wanda Jessicah 
Published: March 2023

Abstract
Purpose
Adolescent girls and young women exhibit two of three global new HIV infections every day, yet they perceived little risk of acquiring it, thus neglecting their status. HIV Testing is fundamental to its prevention and achieving the UNAIDS three 90s.
Methods
We obtained data from the 2015–2016 Malawi Demographic and Health Survey on women to establish the HIV testing factors. We employed SPSS bivariate and multivariate logistic regression to determine HIV testing factors among young women aged 15–24.
Results
Of all 10422 young women, 69.5% have done the test, and most were rural dwellers. Ages 20–24 were more than 2.6 times (AOR = 2.69; 95% CI = 2.11–3.43) more likely to do HIV testing than those aged 15–19. Reading newspapers or magazines less than once a week and listening to the radio at least once a week increased HIV testing by 1.9 and 1.5 times, respectively. A visit to a health facility in the past 12 months influenced HIV testing by 3 (AOR = 3.06; 95% CI = 2.41–3.89) times. Contraceptives and condoms used influenced HIV testing 4.4 (AOR = 4.40; 95% CI = 3.24–5.96) and 2.1 (AOR = 2.17; 95% CI = 1.09–4.30) times. Employed and wealthy young women were 1.6 times more likely to be tested. Husbands’ education positively influenced HIV testing while living in rural areas negatively influenced it.
Conclusions
Our findings highlight potential factors in improving HIV testing and indicate that robust strategies need to be implemented to increase HIV testing among young women in Malawi. Future research should focus on motivating factors that will enhance HIV testing uptake in Malawi young women.
Spatial modelling of both extra zeros and extreme values in ecological counts: an example with sardine eggs in Portugal
Authors: Pereira Soraia , Moreira Guido , Menezes Raquel , Angélico Maria Manuel , Marques Tiago 
Published: March 2023

Abstract
Understanding the spatial distribution of animals, as well as how the distributions are influenced by environmental covariates, is a fundamental requirement for the effective management of animal populations. The sardine is one of the most important fisheries species in Portugal, for its economic, sociologic, anthropologic and cultural values. Here we intend to understand the spatial distribution of the sardine eggs density ($eggs/m^3$). The data structure presents an excess of zeros and extreme values relative to the commonly chosen distributions to fit this data. To deal with this, we propose a geostatistical Gamma - Generalized Pareto hurdle model to jointly model the probability of presence, the positive sardine eggs density, and the corresponding exceedances. We have followed a Bayesian hierarchical approach and the inference was made through Markov Chain Monte Carlo methods. The results show that presence of sardine eggs is associated with depth, salinity and fluorescence; whereas positive density of sardine eggs is mainly associated with depth and fluorescence. The variable that most explains the extreme values is fluorescence.
Loci Associated with Postpartum Depression: A Genome-Wide Association Study
Authors: Tomita Hiroaki , Li Xue , Takahashi Nagahide , Narita Akira , Nakamura Yukako , Sakurai-Yageta Mika , Murakami Keiko , Ishikuro Mami , Obara Taku , Kikuya Masahiro , Ueno Fumihiko , Metoki Hirohito , Ohseto Hisashi , Takahashi Ippei , Nakamura Tomohiro , Warita Noriko , Shoji Tomoka , Yu Zhiqian , Ono Chiaki , Kobayashi Natsuko , Kikuchi Saya , Nagami Fuji , Ogishima Soichi , Sugawara Junichi , Hoshiai Tetsuro , Saito Masatoshi , Fuse Nobuo , Kinoshita Kengo , Yamamoto Masayuki , Yaegashi Nobuo , Ozaki Norio , Tamiya Gen , Kuriyama Shinichi 
Published: March 2023

Abstract
Although postpartum depression (PPD) has been identified as a severe public health problem, its genetic basis has yet to be elucidated. Therefore, we conducted a genome-wide association study (GWAS) to identify the loci significantly associated with PPD. The first and second cohorts (n = 9,260 and n = 8,582 perinatal women enrolled in the Tohoku Medical Megabank Project [TMM]), and the third cohort (n = 997), recruited at Nagoya University, were subjected to genotyping. PPD was defined based on the Edinburgh Postnatal Depression Scale one month after delivery. Logistic regression analyses were performed to evaluate genetic associations with PPD after adjusting for the most influential confounders, including the number of deliveries and the number of family members living together. A meta-analysis of GWAS results from the three cohorts indicated the following loci as significantly associated with PPD (P < 5´10–8): rs377546683 at DAB1 (1p32.2), rs11940752 near UGT8 (4q26), rs141172317, rs117928019, rs76631412, rs118131805 at DOCK2 (5q35.1), rs188907279 near ZNF572 (8q24.13), rs504378, rs690150, rs491868, rs689917, rs474978, rs690118, rs690253 near DIRAS2 (9q22.2), rs1435984417 at ZNF618 (9q31.3), rs57705782 near PTPRM (18p11.23), and rs185293917 near PDGFB (22q13.1). Pathway analyses indicated that SNPs suggestively associated with PPD were mostly over-represented in categories including long-term depression, GnRH signaling, Glutamatergic synapse, Oxytocin signaling, and Rap1 signaling. Thus, the current GWAS study identified eight loci significantly associated with PPD, which may enlighten the genetic structure underlying the pathogenesis of PPD.
Respiratory Function at 3 Months After Hospital Discharge in Critically Ill Patients With Covid-19
Authors: Filho Joaquim Henrique de Carvalho Lobato , Tavares Guilherme Bruarca , Neto Francisco de Souza Trindade , Souza Suellen Christine de Carvalho , Freitas Hugo Leonardo , Cruz Adlyene Muniz da Silva , Silva Ana Chaves , de Azevedo Jose Raimundo Araujo 
Published: March 2023

Abstract
Background: Up to 20% of patients with COVID-19 get critically ill and require intensive care unit (ICU)admission. At hospital discharge, most patients still have physical and mental limitations, which affect their quality of life. Pulmonaryfunctional alterations in patients with COVID-19 vary from the absence of functional abnormalities to restrictive and diffusion impairments. We aimed to describe pulmonary function abnormalities as well as their impact on the 6-minute walk test (6 MWT) and SF-36 physical component summary (PCS) score in patients with COVID-19 at ≥ 3 months after hospital discharge.
Methods: Weincluded 65 patients aged ≥ 18 years with severe COVID-19 confirmed throughreal-time reverse transcriptase-polymerase chain reaction andadmitted to the ICU between April 2020 and October 2021. Patients were evaluated at ≥ 3 months after hospital discharge using the 6 MWT, pulmonary function tests (PFTs), and the PCS score.
Results: Among the included patients, 27patients had abnormal PFT findings, 21 (32.3%) had forced vital capacity < 80%, 17 (26.1%) had forced expiratory volume in 1 s< 80%, and 4 (6.1%) had a maximal mid-expiratory flow< 65%. Compared with patients without abnormal PFT findings, patientswith abnormal PFT findings were older and had significantlyhigher ferritin levels. There were no significant between-group differences ininvasive and noninvasive respiratory support, mechanical ventilation duration, vasopressor use,and renal replacement therapy. However, compared with patients with normalPFT findings, patients with abnormal PFT findings showed asignificantly lower 6-MWT score [78% (0.0–92) vs.95% (75–100), p = 0.01] and worse PCS scores [39.4 (32.1–51.3) vs. 52.0 (47.4–57.3), p = 0.007]. There was an independent association between the PCS scores and PFT findings.
Conclusions: We found that a significant proportion of patients present pulmonary functional alterations ≥ 3 months after discharge from the hospital after treatment forsevere COVID-19; further, these alterations affectphysical functional capacity and quality of life.
Trial registration: The trial protocol was approved by the Research Ethics Committee of the Hospital Sao Domingos (Number 5.403.663) in May 12, 2022 and registered in clinical trials. Gov(NCT05249842), February 22, 2022.
Comparison of Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus viral load in peripheral blood mononuclear cells and oral fluids of HIV-negative individuals aged 3 to 89 years from Uganda
Authors: Nalwoga Angela , Marshall Vickie , Miley Wendell , Labo Nazzarena , Whitby Denise , Newton Robert , Rochford Rosemary 
Published: March 2023

Abstract
We previously found that age, sex, and malaria were associated with KSHV viral load in individuals from Uganda. In this study, we have evaluated factors associated with presence of EBV DNA in blood and oral fluids among the same individuals, using the same biological samples. Overall, 74% of oral fluids samples and 46% of PBMCs had detectable EBV, compared to 24% and 11% for KSHV respectively Individuals with EBV in PBMCs were more likely to have KSHV in PBMCs (P=0.016). The peak age for detection of EBV in oral fluids was 3-5 years while that of KSHV was 6-12 years. In PBMCs, the peak age for detection of EBV was 66+ years and KSHV was 3-5 years. Individuals with malaria had higher levels of EBV in PBMCs compared to malaria-negative individuals (P=0.002). In summary, our results show that younger age and malaria are associated with higher levels of EBV and KSHV in PBMCs suggesting malaria impacts immunity to EBV and KSHV.
From tropical forest to agroecosystems: Changes in lizard functional diversity and species diversity in southeastern Mexico
Authors: Badillo-Saldaña Luis M. , Pineda Eduardo , Ramírez-Bautista Aurelio 
Published: March 2023

Abstract

The transformation of tropical forests to agricultural systems modifies the diversity of species. Species respond differentially to disturbance depending on how they interact with their environment; therefore, the diversity of species that results following the transformation of a tropical forest could depend on the type of agricultural system that is established and the traits and functions of the species that make up the native communities. In this study, the effect of establishing two agricultural systems on an assemblage of tropical forest lizards was evaluated. To do so, the functional diversity and species diversity of lizards in tropical forest, a citrus crop and a coconut crop in southeastern Mexico were analyzed. The results showed that both the functional diversity and the diversity of species decrease when the tropical forest was transformed into either of these agricultural systems. However, this decrease differs in magnitude depending on the type of crop, since in the citrus crop (less heterogeneous) there was a greater reduction in richness of species, of functional groups, and of the members of the functional groups than in the coconut crop (more heterogeneous). The agricultural systems studied are not capable of maintaining the diversity of native species or the functional diversity of tropical forest lizards. Therefore, in landscapes modified by humans, it is essential to maintain fragments of native forest between agricultural plots to conserve those species highly susceptible to tropical forest transformation, as well as assemblages of species with a wide variety of functional traits.
Deep-sea benthic foraminiferal response to the early Oligocene cooling: A study from the Southern Ocean ODP Hole 1138A
Authors: Kumar Rakesh , Singh Dharmendra Pratap , Maurya Abhayanand Singh 
Published: March 2023

Abstract
Ongoing rapid climate change has a major effect on marine fauna, and understanding these faunal changes analogous to future climatic periods is crucial. The Oligocene is commonly considered a critical transition period, linking the archaic world of the tropical Eocene and the more modern ecosystems of the Miocene. Here, we show the response of marine benthic foraminifera to the early Oligocene climatic changes at Ocean Discovery Program (ODP) Hole 1138A of the Southern Ocean (Indian Sector). We made use of the diversity parameters, the relative abundance of dominant benthic foraminifera and isotopic data to understand past oceanographic changes. Our results suggest that the early Oligocene was an interval of unstable conditions dominated by the species of high oxygen, intermediate food supply, and well-ventilated, cold, corrosive bottom water conditions. The high value of diversity parameters coincides with the Oligocene events (Oi events). The species richness abruptly decreases at the end of the studied interval, which shows the major Southern hemisphere glaciation. During this time, species were characterized by relatively cold and carbonate corrosive bottom water. Additionally, the present study of the benthic foraminiferal abundance and diversity indices reveals the cooling of the Southern Ocean at the early and late stages of the studied interval interrupted by a short-lived warming event. The study further enhances the understanding of paleo-marine ecology by evaluating the response of deep-sea benthic foraminifera to global climate change.
Epigenome-wide analysis identifies methylome profiles linked to obsessive-compulsive disorder, disease severity, and treatment response
Authors: Ramirez Alfredo , Campos-Martin Rafael , Bey Katharina , Elsner Bjoern , Reuter Benedikt , Klawohn Julia , Philipsen Alexandra , Kathmann Norbert , Wagner Michael 
Published: March 2023

Abstract
Obsessive-compulsive disorder (OCD) is a mental disorder affecting 2-3% of the general population. The dynamic nature of epigenetics provides a unique opportunity to find biomarkers of OCD symptoms, clinical progression, and treatment response. Consequently, we analyzed a case-control study on Illumina Methylation EPIC BeadChip from 185 OCD patients and 199 controls. Patients and controls were assessed by trained therapists using the Structured Clinical Interview for DSM-IV. We identified 12 CpGs capable of classifying OCD patients and predicting symptom severity. These CpGs are enriched with the sweet-compulsive brain hypothesis, which proposes that OCD patients may have impaired insulin signaling sensitivity due to abnormal dopaminergic transmission in the striatum. Three of the twelve CpG signals were replicated in an independent study reported in the Han Chinese population. Our findings support the role of epigenetic mechanisms in OCD and may help pave the way for biologically-informed and individualized treatment options.
Investigation of the dynamics of a coating flow on a vertical fiber immersed in surrounding liquid phase
Authors: Zhang Yufeng , Liu Rong , Chen Xue 
Published: March 2023

Abstract
In the present paper, we investigated experimentally the dynamics of coating flow on a vertical fiber immersed in a liquid phase environment. This flow exhibits rich dynamics which is different from the coating flow in air. In the experiments, it is found that the dynamics of immersed coating flow at different flow rates exhibited three flow regimes, i.e., highly regular beads chain, bound state and beads-like flow with irregular coalescence. The regular and irregular beads-like flows correspond to absolute instability and convective instability, respectively. The bound state flow occurs at the boundary of absolute instability and convective instability. The behavior of immersed coating flow is examined by analyzing the spatiotemporal diagram. In addition, we quantitatively investigated three important characteristic parameters of the immersed coating flow, i.e., wave thickness, wave spacing and wave speed in different flow regimes.