bluuebunny/crossref_metadata_2025_split huggingface dataset:
An enriched biosignature of gut microbiota-dependent metabolites characterizes maternal plasma in a mouse model of fetal alcohol spectrum disorder
Authors: Virdee Manjot S. , Saini Nipun , Kay Colin D. , Neilson Andrew P. , Kwan Sze Ting Cecilia , Helfrich Kaylee K. , Mooney Sandra M. , Smith Susan M. 
Published: January 2021

AbstractPrenatal alcohol exposure (PAE) causes permanent cognitive disability. The enteric microbiome generates microbial-dependent products (MDPs) that may contribute to disorders including autism, depression, and anxiety; it is unknown whether similar alterations occur in PAE. Using a mouse PAE model, we performed untargeted metabolome analyses upon the maternal–fetal dyad at gestational day 17.5. Hierarchical clustering by principal component analysis and Pearson’s correlation of maternal plasma (813 metabolites) both identified MDPs as significant predictors for PAE. The majority were phenolic acids enriched in PAE. Correlational network analyses revealed that alcohol altered plasma MDP-metabolite relationships, and alcohol-exposed maternal plasma was characterized by a subnetwork dominated by phenolic acids. Twenty-nine MDPs were detected in fetal liver and sixteen in fetal brain, where their impact is unknown. Several of these, including 4-ethylphenylsulfate, oxindole, indolepropionate, p-cresol sulfate, catechol sulfate, and salicylate, are implicated in other neurological disorders. We conclude that MDPs constitute a characteristic biosignature that distinguishes PAE. These MDPs are abundant in human plasma, where they influence physiology and disease. Their altered abundance here may reflect alcohol’s known effects on microbiota composition and gut permeability. We propose that the maternal microbiome and its MDPs are a previously unrecognized influence upon the pathologies that typify PAE.
Validation and comparison of non-invasive prediction models based on liver stiffness measurement to identify patients who could avoid gastroscopy
Authors: Hu Youwen , Wen Zhili 
Published: January 2021

AbstractSeveral non‐invasive tests (NITs) based on liver stiffness measurement (LSM) have been developed to rule out varices needing treatment (VNT), including the Baveno VI criteria (B6C), the expanded Baveno VI criteria (EB6C), the LSM-spleen diameter to platelet ratio score (LSPS), and the VariScreen algorithm. We aimed to validate and compare those NITs in patients with compensated advanced chronic liver disease (cACLD). This retrospective study enrolled 354 patients with cACLD; LSM, platelet count (PLT), international normalized ratio (INR), gastroscopy and spleen diameter (SD) were collected. VNT prevalence was 28.5%. In comparison, patients with VNT included higher LSM, INR, and SD and lower PLT. Gastroscopies were spared for 27.7% of patients using the B6C with 1.0% VNT missed rate, 47.2% of patients using the EB6C with 5.9% VNT missed rate, 57.6% of patients using the LSPS with 9.9% VNT missed rate, and 45.5% of patients using the VariScreen algorithm with 3.0% VNT missed rate. Only the B6C and the VariScreen algorithm could safely avoid gastroscopies, and the VariScreen algorithm spared more gastroscopies than the B6C. The results were consistent with the previous when performed subgroup analysis. In conclusion, the VariScreen algorithm performed the best and can be used in clinical.
Causes of variations of trace and rare earth elements concentration in lakes bottom sediments in the Bory Tucholskie National Park, Poland
Authors: Sojka Mariusz , Choiński Adam , Ptak Mariusz , Siepak Marcin 
Published: January 2021

AbstractThe objective of this study was to analyse spatial variability of the trace elements (TEs) and rare earth elements (REEs) concentration in lake bottom sediments in Bory Tucholskie National Park (BTNP); Poland. The following research questions were posed: which factors have a fundamental impact on the concentration and spatial variability of elements in bottom sediments, which of the elements can be considered as indicators of natural processes and which are related to anthropogenic sources. The research material was sediments samples collected from 19 lakes. The concentrations of 24 TEs and 14 REEs were determined. The analyses were carried out using the inductively coupled plasma mass spectrometry (ICP-QQQ). Cluster analysis and principal component analysis were used to determine the spatial variability of the TEs and REEs concentrations, indicate the elements that are the indicators of natural processes and identify potential anthropogenic sources of pollution. The geochemical background value (GBV) calculations were made using 13 different statistical methods. However, the contamination of bottom sediments was evaluated by means of the index of geo-accumulation, the enrichment factor, the pollution load index, and the metal pollution index. The BTNP area is unique because of its isolation from the inflow of pollutants from anthropogenic sources and a very stable land use structure over the last 200 years. This study shows high variability of TE and REE concentrations in lake sediments. The values of geochemical indices suggest low pollution of lakes bottom sediments. It was found that TEs originated mainly from geogenic sources. However, the concentrations of Li, Ni, Sc, Se, Be, Se, Ag, Re, Tl, Cd, Sb and U may be related to the impact of point sources found mainly in the Ostrowite Lake. Almost all REEs concentrations were strongly correlated and their presence was linked to with geochemical processes. The elements allowing to identify natural processes and anthropogenic pollution sources were Cr, Co, Cu, Ag, Cd, Zn, Bi, Re, Ba, Al and Rb in TEs group and Nd, Gd, Yb, Lu, Eu, Dy and Ce in REEs group. The analysis shows high spatial variability of TE and REE concentrations in lake sediments. The values of geochemical indices point to low pollution of lakes sediments. The anthropogenic sources only for two lakes had an impact on concentrations of selected TEs and REEs. The analyses allowed to identify elements among TEs and REEs documenting geochemical processes and those indicating anthropogenic sources of pollution.
Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney
Authors: Matsui Isao , Matsumoto Ayumi , Inoue Kazunori , Katsuma Yusuke , Yasuda Seiichi , Shimada Karin , Sakaguchi Yusuke , Mizui Masayuki , Kaimori Jun-ya , Takabatake Yoshitsugu , Isaka Yoshitaka 
Published: January 2021

AbstractKidney development requires the coordinated growth and differentiation of multiple cells. Despite recent single cell profiles in nephrogenesis research, tools for data analysis are rapidly developing, and offer an opportunity to gain additional insight into kidney development. In this study, single-cell RNA sequencing data obtained from embryonic mouse kidney were re-analyzed. Manifold learning based on partition-based graph-abstraction coordinated cells, reflecting their expected lineage relationships. Consequently, the coordination in combination with ForceAtlas2 enabled the inference of parietal epithelial cells of Bowman’s capsule and the inference of cells involved in the developmental process from the S-shaped body to each nephron segment. RNA velocity suggested developmental sequences of proximal tubules and podocytes. In combination with a Markov chain algorithm, RNA velocity suggested the self-renewal processes of nephron progenitors. NicheNet analyses suggested that not only cells belonging to ureteric bud and stroma, but also endothelial cells, macrophages, and pericytes may contribute to the differentiation of cells from nephron progenitors. Organ culture of embryonic mouse kidney demonstrated that nerve growth factor, one of the nephrogenesis-related factors inferred by NicheNet, contributed to mitochondrial biogenesis in developing distal tubules. These approaches suggested previously unrecognized aspects of the underlying mechanisms for kidney development.
Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice
Authors: Schukken Klaske M. , Zhu Yinan , Bakker Petra L. , Koster Mirjam H. , Harkema Liesbeth , Youssef Sameh A. , de Bruin Alain , Foijer Floris 
Published: January 2021

AbstractChromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last 2 decades. These models have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of the epithelia of the jejunum and ileum, substantial weight loss, and death within 2–3 weeks after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the lower proliferation rate in these tissues. We conclude that high-grade CIN in vivo in adult mice is most toxic to the high cell turnover intestinal epithelia.
The effects of anticholinergic medications on cognition in children: a systematic review and meta-analysis
Authors: Ghezzi Erica , Chan Michelle , Kalisch Ellett Lisa M. , Ross Tyler J. , Richardson Kathryn , Ho Jun Ni , Copley Dayna , Steele Claire , Keage Hannah A. D. 
Published: January 2021

AbstractCognitive side effects of anticholinergic medications in older adults are well documented. Whether these poor cognitive outcomes are observed in children has not been systematically investigated. We aimed to conduct a systematic review and meta-analysis on the associations between anticholinergic medication use and cognitive performance in children. Systematic review was conducted using Medline, PsychInfo, and Embase, identifying studies testing cognitive performance relative to the presence versus absence of anticholinergic medication(s) in children. We assessed effects overall, as well as relative to drug class, potency (low and high), cognitive domain, and duration of administration. The systematic search identified 46 articles suitable for meta-analysis. For the most part, random effects meta-analyses did not identify statistically significant associations between anticholinergic exposure and cognitive performance in children; the one exception was a small effect of anticholinergic anti-depressants being associated with better cognitive function (Hedges’ g = 0.24, 95% CI 0.06–0.42, p = 0.01). Anticholinergic medications do not appear to be associated with poor cognitive outcomes in children, as they do in older adults. The discrepancy in findings with older adults may be due to shorter durations of exposure in children, differences in study design (predominantly experimental studies in children rather than predominantly epidemiological in older adults), biological ageing (e.g. blood brain barrier integrity), along with less residual confounding due to minimal polypharmacy and comorbidity in children.
Factors associated with measles resurgence in the United States in the post-elimination era
Authors: Dimala Christian Akem , Kadia Benjamin Momo , Nji Miriam Aiwokeh Mbong , Bechem Ndemazie Nkafu 
Published: January 2021

AbstractThere have been growing concerns of a potential re-establishment of measles transmission in the United States (US) in the years to come. This study aims to explore potential factors underlying the resurgence of measles in the US by objectively assessing the associations between annual incidence rates (AIR), case importation, vaccination status and disease outbreaks. Data on measles transmission between January 1st, 2001 and December 31st, 2019 were obtained from the national centres for disease control and prevention (CDC) surveillance databases and other published reports. Changes in incidence rates over time were assessed by binomial regression models. Of the 3874 cases of measles in the US over the study period, 3506 (90.5%, 95% CI: 89.5–91.4) occurred in US residents. The AIR per million population in US residents over this period was 0.60 (95% CI: 0.59–0.61), with an overall significant increase over time (p = 0.011). The median percentage of imported and vaccinated cases were 36% [17.9–46.6] and 15% [12.1–23.2] respectively. There was a significant decrease in the percentage of imported cases (p < 0.001) but not of vaccinated cases (p = 0.159) over time. There was a moderate and weak negative correlation between the AIR and the percentage of imported and vaccinated cases respectively (r = –0.59 and r = –0.27 respectively). On multiple linear regression there was a significant linear association between the AIR and the number of outbreaks (p = 0.003) but not with the percentage of imported cases (p = 0.436) and vaccinated cases (p = 0.692), R2 = 0.73. Strong negative and positive correlations were seen between the number of outbreaks and the percentage of imported cases (r = –0.61) and the of number states affected (r = 0.88) respectively. Despite the overall reduction in the percentage of imported cases of measles over the past two decades, pockets of internal transmission of the disease following importation via increasing number of outbreaks in unvaccinated subpopulations, reinforced by vaccine hesitancy, account for the sustained increase in measles incidence rates in the US. Controlling indigenous transmission through efficient vaccination coverage in at-risk subpopulations and among international US travellers, improved disease surveillance and rapid outbreak containment are essential in curbing the measles resurgence.
Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes
Authors: Verma Rahul K. , Kalyakulina Alena , Giuliani Cristina , Shinde Pramod , Kachhvah Ajay Deep , Ivanchenko Mikhail , Jalan Sarika 
Published: January 2021

AbstractNetworks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral ‘RSRS50’ variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.
Substrate induced electronic phase transitions of CrI$$_{3}$$ based van der Waals heterostructures
Authors: Chakraborty Shamik , Ravikumar Abhilash 
Published: January 2021

AbstractWe perform first principle density functional theory calculations to predict the substrate induced electronic phase transitions of CrI$$_{3}$$

3

based 2-D heterostructures. We adsorb graphene and MoS$$_{2}$$

2

on novel 2-D ferromagnetic semiconductor—CrI$$_{3}$$

3

and investigate the electronic and magnetic properties of these heterostructures with and without spin orbit coupling (SOC). We find that when strained MoS$$_{2}$$

2

is adsorbed on CrI$$_{3}$$

3

, the spin dependent band gap which is a characteristic of CrI$$_{3}$$

3

, ceases to remain. The bandgap of the heterostructure reduces drastically ($$\sim$$
∼
70%) and the heterostructure shows an indirect, spin-independent bandgap of $$\sim$$
∼
0.5 eV. The heterostructure remains magnetic (with and without SOC) with the magnetic moment localized primarily on CrI$$_{3}$$

3

. Adsorption of graphene on CrI$$_{3}$$

3

induces an electronic phase transition of the subsequent heterostructure to a ferromagnetic metal in both the spin configurations with magnetic moment localized on CrI$$_{3}$$

3

. The SOC induced interaction opens a bandgap of $$\sim$$
∼
30 meV in the Dirac cone of graphene, which allows us to visualize Chern insulating states without reducing van der Waals gap.
Hypoxia-induced amniotic fluid stem cell secretome augments cardiomyocyte proliferation and enhances cardioprotective effects under hypoxic-ischemic conditions
Authors: Kukumberg Marek , Phermthai Tatsanee , Wichitwiengrat Suparat , Wang Xiaoyuan , Arjunan Subramanian , Chong Suet Yen , Fong Chui-Yee , Wang Jiong-Wei , Rufaihah Abdul Jalil , Mattar Citra Nurfarah Zaini 
Published: January 2021

AbstractSecretome derived from human amniotic fluid stem cells (AFSC-S) is rich in soluble bioactive factors (SBF) and offers untapped therapeutic potential for regenerative medicine while avoiding putative cell-related complications. Characterization and optimal generation of AFSC-S remains challenging. We hypothesized that modulation of oxygen conditions during AFSC-S generation enriches SBF and confers enhanced regenerative and cardioprotective effects on cardiovascular cells. We collected secretome at 6-hourly intervals up to 30 h following incubation of AFSC in normoxic (21%O2, nAFSC-S) and hypoxic (1%O2, hAFSC-S) conditions. Proliferation of human adult cardiomyocytes (hCM) and umbilical cord endothelial cells (HUVEC) incubated with nAFSC-S or hAFSC-S were examined following culture in normoxia or hypoxia. Lower AFSC counts and richer protein content in AFSC-S were observed in hypoxia. Characterization of AFSC-S by multiplex immunoassay showed higher concentrations of pro-angiogenic and anti-inflammatory SBF. hCM demonstrated highest proliferation with 30h-hAFSC-S in hypoxic culture. The cardioprotective potential of concentrated 30h-hAFSC-S treatment was demonstrated in a myocardial ischemia–reperfusion injury mouse model by infarct size and cell apoptosis reduction and cell proliferation increase when compared to saline treatment controls. Thus, we project that hypoxic-generated AFSC-S, with higher pro-angiogenic and anti-inflammatory SBF, can be harnessed and refined for tailored regenerative applications in ischemic cardiovascular disease.
Particle size-related limitations of persistent phosphors based on the doped Y3Al2Ga3O12 system
Authors: Boiko Vitalii , Dai Zhengfa , Markowska Marta , Leonelli Cristina , Mortalò Cecilia , Armetta Francesco , Ursi Federica , Nasillo Giorgio , Saladino Maria Luisa , Hreniak Dariusz 
Published: January 2021

AbstractCo-doped Ce3+, Cr3+and Pr3+yttrium–aluminium–gallium garnet powders of various sizes were obtained by co-precipitation method. The microstructure and morphology were investigated by XRPD, TEM and gas porosimetry. The luminescence properties were studied by excitation and emission spectra, quantum yield and decay times. Thermoluminescence measurements were performed to evaluate the activation energy, traps redistribution and frequency factor. Limitation in the energy transfer between dopant ions in the small particles, traps depth and surface defects were considered and investigated as responsible for the quenching of persistent luminescence. The phosphors annealed at 1100 °C show the optimal persistent luminescence and nano-particle size.
Ion tracks in silicon formed by much lower energy deposition than the track formation threshold
Authors: Amekura H. , Toulemonde M. , Narumi K. , Li R. , Chiba A. , Hirano Y. , Yamada K. , Yamamoto S. , Ishikawa N. , Okubo N. , Saitoh Y. 
Published: January 2021

AbstractDamaged regions of cylindrical shapes called ion tracks, typically in nano-meters wide and tens micro-meters long, are formed along the ion trajectories in many insulators, when high energy ions in the electronic stopping regime are injected. In most cases, the ion tracks were assumed as consequences of dense electronic energy deposition from the high energy ions, except some cases where the synergy effect with the nuclear energy deposition plays an important role. In crystalline Si (c-Si), no tracks have been observed with any monomer ions up to GeV. Tracks are formed in c-Si under 40 MeV fullerene (C60) cluster ion irradiation, which provides much higher energy deposition than monomer ions. The track diameter decreases with decreasing the ion energy until they disappear at an extrapolated value of ~ 17 MeV. However, here we report the track formation of 10 nm in diameter under C60 ion irradiation of 6 MeV, i.e., much lower than the extrapolated threshold. The diameters of 10 nm were comparable to those under 40 MeV C60 irradiation. Furthermore, the tracks formed by 6 MeV C60 irradiation consisted of damaged crystalline, while those formed by 40 MeV C60 irradiation were amorphous. The track formation was observed down to 1 MeV and probably lower with decreasing the track diameters. The track lengths were much shorter than those expected from the drop of Se below the threshold. These track formations at such low energies cannot be explained by the conventional purely electronic energy deposition mechanism, indicating another origin, e.g., the synergy effect between the electronic and nuclear energy depositions, or dual transitions of transient melting and boiling.