bluuebunny/crossref_metadata_2025_split huggingface dataset:
The iron-sulfur cluster is essential for DNA binding by human DNA polymerase ε
Authors: Lisova Alisa E. , Baranovskiy Andrey G. , Morstadt Lucia M. , Babayeva Nigar D. , Stepchenkova Elena I. , Tahirov Tahir H. 
Published: October 2022

AbstractDNA polymerase ε (Polε) is a key enzyme for DNA replication in eukaryotes. Recently it was shown that the catalytic domain of yeast Polε (PolεCD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we show that human PolεCD (hPolεCD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPolεCD produced in insect cells contains significantly lower level of iron. The iron content of purified hPolECD samples correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPolε interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding as well as DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. The binding studies demonstrated low affinity of hPolεCD to DNA and a strong effect of salt concentration on stability of the hPolεCD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s−1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 µM.
Salivary cortisol levels and stress in adults with profound intellectual and multiple disabilities participating in the Structured Water Dance Intervention: a randomised controlled crossover trial
Authors: Lundqvist Lars-Olov , Matérne Marie , Frank Andre , Mörelius Evalotte , Duberg Anna 
Published: October 2022

AbstractThe Structured Water Dance Intervention (SWAN) is a dance-oriented aquatic group activity directed to give opportunities for the joy of movement, relaxation, and reduced stress. This study aimed to evaluate the effects of SWAN on salivary cortisol and stress in adults with profound intellectual and multiple disabilities (PIMD). A total of 34 adults with PIMD at four habilitation centres in Sweden completed the SWAN intervention. The intervention was administered for 40 min once a week during a 12-week period. Saliva cortisol was collected in the morning and evening at baseline one week before the intervention, thrice during the intervention period, and one week after the intervention. Moreover, in connection with the SWAN sessions, the participants’ level of stress was also assessed by the accompanying assistants. The results showed that salivary cortisol and participants stress decreased significantly, directly after the SWAN sessions compared with measures directly before sessions. The study demonstrates that adults with PIMD have diurnal salivary cortisol patterns consistent with those observed in adults without disability and that the SWAN reduces salivary cortisol levels and stress in people with PIMD; this justifies that SWAN could be considered in the choice of interventions to reduce stress in adults with PIMD.Trial registration: This study is registered 09/04/2019 on ClinicalTrials.gov (ID: NCT03908801).
Magnetic properties of FeGa/Kapton for flexible electronics
Authors: Pradhan Gajanan , Celegato Federica , Barrera Gabriele , Olivetti Elena Sonia , Coisson Marco , Hajduček Jan , Arregi Jon Ander , Čelko Ladislav , Uhlíř Vojtěch , Rizzi Paola , Tiberto Paola 
Published: October 2022

AbstractFlexible materials have brought up a new era of application-based research in stretchable electronics and wearable devices in the last decade. Tuning of magnetic properties by changing the curvature of devices has significant impact in the new generation of sensor-based technologies. In this work, magnetostrictive FeGa thin films have been deposited on a flexible Kapton sheet to exploit the magneto-elastic coupling effect and modify the magnetic properties of the sample. The FeGa alloy has high magnetostriction constant and high tensile strength making its properties susceptible to external stress. Tensile or compressive strain generated by the convex or concave states influence the uniaxial magnetic anisotropy of the system. Low temperature measurements show a hard magnetic behavior and the presence of exchange-bias effect after field cooling to 2 K. The results obtained in this study prove essential for the development of flexible electronics.
Genome-wide association study reveals distinct genetic associations related to leaf hair density in two lineages of wheat-wild relative Aegilops tauschii
Authors: Mahjoob Mazin Mahjoob Mohamed , Kamal Nasrein Mohamed , Gorafi Yasir Serag Alnor , Tsujimoto Hisashi 
Published: October 2022

AbstractWild relatives of modern crops represent a promising source of genetic variation that can be mined for adaptations to climate change. Aegilops tauschii, the D-sub-genome progenitor of bread wheat (Triticum aestivum), constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Leaf hairiness plays an essential biological role in plant defense against biotic and abiotic stress. We investigated the natural variation in leaf hair density (LHD) among 293 Ae. tauschii accessions. Genome-wide association studies were performed for LHD with 2430 and 3880 DArTseq derived single nucleotide polymorphism (SNP) markers in two lineages of this species, TauL1 and TauL2, respectively. In TauL1, three marker-trait associations (MTAs) were located on chromosome 2D, whereas in TauL2, eight MTAs were identified, two associations were localized on each of the chromosomes 2D, 3D, 5D, and 7D. The markers explained phenotypic variation (R2) from 9 to 13% in TauL1 and 11 to 36% in TauL2. The QTLs identified in chromosomes 2D and 5D might be novel. Our results revealed more rapid and independent evolution of LHD in TauL2 compared to TauL1. The majority of LHD candidate genes identified are associated with biotic and abiotic stress responses. This study highlights the significance of intraspecific diversity of Ae. tauschii to enhance cultivated wheat germplasm.
3D multi-physics uncertainty quantification using physics-based machine learning
Authors: Degen Denise , Cacace Mauro , Wellmann Florian 
Published: October 2022

AbstractQuantitative predictions of the physical state of the Earth’s subsurface are routinely based on numerical solutions of complex coupled partial differential equations together with estimates of the uncertainties in the material parameters. The resulting high-dimensional problems are computationally prohibitive even for state-of-the-art solver solutions. In this study, we introduce a hybrid physics-based machine learning technique, the non-intrusive reduced basis method, to construct reliable, scalable, and interpretable surrogate models. Our approach, to combine physical process models with data-driven machine learning techniques, allows us to overcome limitations specific to each individual component, and it enables us to carry out probabilistic analyses, such as global sensitivity studies and uncertainty quantification for real-case non-linearly coupled physical problems. It additionally provides orders of magnitude computational gain, while maintaining an accuracy higher than measurement errors. Although in this study we use a thermo-hydro-mechanical reservoir application to illustrate these features, all the theory described is equally valid and applicable to a wider range of geoscientific applications.
Alignment-invariant signal reality reconstruction in hyperspectral imaging using a deep convolutional neural network architecture
Authors: Mousavi M. S. Shayan , Pofelski Alexandre , Teimoori Hassan , Botton Gianluigi A. 
Published: October 2022

AbstractThe energy resolution in hyperspectral imaging techniques has always been an important matter in data interpretation. In many cases, spectral information is distorted by elements such as instruments’ broad optical transfer function, and electronic high frequency noises. In the past decades, advances in artificial intelligence methods have provided robust tools to better study sophisticated system artifacts in spectral data and take steps towards removing these artifacts from the experimentally obtained data. This study evaluates the capability of a recently developed deep convolutional neural network script, EELSpecNet, in restoring the reality of a spectral data. The particular strength of the deep neural networks is to remove multiple instrumental artifacts such as random energy jitters of the source, signal convolution by the optical transfer function and high frequency noise at once using a single training data set. Here, EELSpecNet performance in reducing noise, and restoring the original reality of the spectra is evaluated for near zero-loss electron energy loss spectroscopy signals in Scanning Transmission Electron Microscopy. EELSpecNet demonstrates to be more efficient and more robust than the currently widely used Bayesian statistical method, even in harsh conditions (e.g. high signal broadening, intense high frequency noise).
Epidemiology of acute gastroenteritis in France from November 2019–August 2021, in light of reported adherence to COVID-19 barrier measures
Authors: Nisavanh Athinna , Horrigue Imene , Debin Marion , Turbelin Clément , Kengne-Kuetche Charly , Nassany Oriane , Ambert-Balay Katia , Jourdan-Da Silva Nathalie , Pontais Isabelle , de Valk Henriette , Jones Gabrielle 
Published: October 2022

AbstractSince the start of the COVID-19 pandemic, French health authorities have encouraged barrier measures and implemented three lockdowns to slow SARS-CoV-2 transmission. We aimed to examine the impact of these measures on the epidemiology of acute gastroenteritis (AGE) in France, from November 2019 to August 2021. We describe trends in AGE indicators from syndromic surveillance and a sentinel surveillance network. Additionally, we describe reported AGE illness data from a community based cohort, and frequencies of adherence to COVID-19 barrier measures from repeated quantitative surveys. From week 7 in 2020, all AGE indicators reached the lowest levels observed since the last decade. During the first lockdown, the median incidence rate reported by the sentinel network was 32 per 100,000 inhabitants, 1.9 times lower than the minimum registered during the 2010–2019 period. Low activity persisted until April 2021. Reported illness from the community cohort mirrored these trends. Adherence to COVID-19 barrier measures was highest during the first lockdown, coinciding with the steep decrease in AGE incidence. Among children under 5 years, AGE incidence increased after the third lockdown in June and July 2021, but remained lower than previous winter-season peaks. Our study indicates that a reduction in adherence to COVID-19 barrier measures, and the end of the lockdowns, coincided with an increase in AGE incidence, particularly among young children. We therefore strongly recommend maintaining adherence to barrier measures in order to in order to limit the transmission of AGE related pathogens.
Peripheral T cell cytotoxicity predicts the efficacy of anti-PD-1 therapy for advanced non-small cell lung cancer patients
Authors: Iwahori Kota , Uenami Takeshi , Yano Yukihiro , Ueda Toshihiko , Tone Mari , Naito Yujiro , Suga Yasuhiko , Fukushima Kiyoharu , Shiroyama Takayuki , Miyake Kotaro , Koyama Shohei , Hirata Haruhiko , Nagatomo Izumi , Kida Hiroshi , Mori Masahide , Takeda Yoshito , Kumanogoh Atsushi , Wada Hisashi 
Published: October 2022

AbstractAnti-programmed cell death-1 (PD-1) therapy exerts beneficial effects in a limited population of cancer patients. Therefore, more accurate diagnostics to predict the efficacy of anti-PD-1 therapy are desired. The present study investigated whether peripheral T cell cytotoxicity predicts the efficacy of anti-PD-1 therapy for advanced non-small cell lung cancer (NSCLC) patients. Advanced NSCLC patients treated with anti-PD-1 monotherapy (nivolumab or pembrolizumab) were consecutively enrolled in the present study. Peripheral blood samples were subjected to an analysis of peripheral T cell cytotoxicity and flow cytometry prior to the initiation of anti-PD-1 therapy. Peripheral T cell cytotoxicity was assessed using bispecific T-cell engager (BiTE) technology. We found that progression-free survival was significantly longer in patients with high peripheral T cell cytotoxicity (p = 0.0094). In the multivariate analysis, treatment line and peripheral T cell cytotoxicity were independent prognostic factors for progression-free survival. The analysis of T cell profiles revealed that peripheral T cell cytotoxicity correlated with the ratio of the effector memory population in CD4+ or CD8+ T cells. Furthermore, the results of flow cytometry showed that the peripheral CD45RA+CD25+/CD4+ T cell ratio was higher in patients with than in those without severe adverse events (p = 0.0076). These results indicated that the peripheral T cell cytotoxicity predicted the efficacy of anti-PD-1 therapy for advanced NSCLC patients.
Classification of breast cancer histology images using MSMV-PFENet
Authors: Liu Linxian , Feng Wenxiang , Chen Cheng , Liu Manhua , Qu Yuan , Yang Jiamiao 
Published: October 2022

AbstractDeep learning has been used extensively in histopathological image classification, but people in this field are still exploring new neural network architectures for more effective and efficient cancer diagnosis. Here, we propose multi-scale, multi-view progressive feature encoding network (MSMV-PFENet) for effective classification. With respect to the density of cell nuclei, we selected the regions potentially related to carcinogenesis at multiple scales from each view. The progressive feature encoding network then extracted the global and local features from these regions. A bidirectional long short-term memory analyzed the encoding vectors to get a category score, and finally the majority voting method integrated different views to classify the histopathological images. We tested our method on the breast cancer histology dataset from the ICIAR 2018 grand challenge. The proposed MSMV-PFENet achieved 93.0$$\%$$
%
and 94.8$$\%$$
%
accuracies at the patch and image levels, respectively. This method can potentially benefit the clinical cancer diagnosis.
Early onset of sleep/wake disturbances in a progressive macaque model of Parkinson’s disease
Authors: Davin Aurélie , Chabardès Stéphan , Belaid Hayat , Fagret Daniel , Djaileb Loic , Dauvilliers Yves , David Olivier , Torres-Martinez Napoléon , Piallat Brigitte 
Published: October 2022

AbstractParkinsonian patients often experience sleep/wake disturbances, which may appear at an early stage of the disease; however, these disturbances have not been fully described. To better understand the evolution of these disturbances with respect to disease progression, we aimed to characterize these clinical signs in a progressive nonhuman primate model of Parkinson's disease. Three adult macaques (Macaca fascicularis) were equipped with a polysomnographic telemetry system allowing the characterization of sleep/wake behavior via long-term neurophysiological recordings and underwent a modified multiple sleep latency test. Experiments were first performed in a healthy state and then during the progressive induction of a parkinsonian syndrome by intramuscular injections of low doses of MPTP. We observed an early onset of significant sleep/wake disturbances (i.e., before the appearance of motor symptoms). These disturbances resulted in (i) a disorganization of nighttime sleep with reduced deep sleep quality and (ii) an excessive daytime sleepiness characterized by sleep episodes occurring more rapidly in the morning and spreading through the middle of the day. The present study suggests that nighttime and daytime sleep/wake disturbances may appear early in the disease and should be considered in the development of biomarkers in further studies.
Fractional anisotropy and peripheral cytokine concentrations in outpatients with depressive episode: a diffusion tensor imaging observational study
Authors: Sammer Gebhard , Neumann Elena , Blecker Carlo , Pedraz-Petrozzi Bruno 
Published: October 2022

AbstractOver the past few years, evidence of a positive relationship between inflammation and depression has grown steadily. The aim of the current study was to investigate whether such depression-related inflammation could also be associated with altered microstructural changes in the white matter. FA and serum cytokines (IL-1β, IL-6, TNF-α, and IFN-γ) were measured in 25 patients with depression (DE) and 24 healthy controls (HC). Diffusion tensor imaging was performed. Fractional anisotropy (FA) was calculated using the FSL pipeline for Tract-Based Spatial Statistics (TBSS). Both voxelwise and mean whole-brain FA were analyzed using general linear models (GLM). Higher concentrations of IL-1β were associated with lower whole-brain fractional anisotropy, particularly in people with depression (ρ = − 0.67; p < 0.001). TNF-α shared some variance with IL-1β and also showed a negative relationship between TNF-α concentrations and FA in depression (F1,46 = 11.13, p = 0.002, η2p = 0.21). In detail, the voxelwise analysis showed that the regression slopes of IL-1β on FA were more negative in the DE group than in the HC group, mainly in the corpus callosum (cluster statistics: genu corpus callosum, p = 0.022; splenium of corpus callosum, p = 0.047). Similar effects were not found for the other remaining cytokines. This study clearly demonstrated an association between peripherally measured IL-1β and white matter integrity in depression as assessed by DTI. The results suggest that microstructural changes in the corpus callosum are associated with increased peripheral IL-1β concentrations in depression.
Peripheral mononuclear cells composition in platelet-rich fibrin in canines with chronic conditions
Authors: Jasineviciute Indre , Grigas Juozas , Ziukaite Gintare , Pautienius Arnoldas , Razukevicius Dainius , Zymantiene Judita , Stankevicius Arunas 
Published: October 2022

AbstractPlatelet-rich fibrin (PRF) is a hot research topic because of its regenerative effect in humans. However, data reporting about its application in companion animals is lacking. The study aimed to supplement currently available data on PRF cell composition in canine patients by isolating peripheral blood mononuclear cells (PBMC), namely T cells, matured B cells, monocytes and macrophages, and adapting current protocols of cell flow cytometry for PRF analysis. The canine patient population was divided into three subgroups: animals with periodontitis only, animals with neoplasia and periodontitis, and healthy controls. Individual clinical parameters of the patients and evaluation of the wound healing quality were included in the research. In the present study, canine PRF cell composition was analyzed for the first-time using cell flow cytometry protocol. A higher proportion of PBMC cells related to wound healing (CD3+, CD3+ CD4+ CD8−, CD14+) were found in the PRF of control, periodontitis and neoplasia groups compared to the respective blood samples, which implies a positive outcome associated with clinical PRF usage in canine patients. Proportions of monocytes and macrophages were higher in PRF samples compared to the blood of healthy patients and periodontitis-affected patients. However, inflammatory and neoplastic processes do not affect the distribution of PBMC.
Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes
Authors: Lam Tony J. , Ye Yuzhen 
Published: October 2022

AbstractThe human gut microbiome is composed of a diverse and dynamic population of microbial species which play key roles in modulating host health and physiology. While individual microbial species have been found to be associated with certain disease states, increasing evidence suggests that higher-order microbial interactions may have an equal or greater contribution to host fitness. To better understand microbial community dynamics, we utilize networks to study interactions through a meta-analysis of microbial association networks between healthy and disease gut microbiomes. Taking advantage of the large number of metagenomes derived from healthy individuals and patients with various diseases, together with recent advances in network inference that can deal with sparse compositional data, we inferred microbial association networks based on co-occurrence of gut microbial species and made the networks publicly available as a resource (GitHub repository named GutNet). Through our meta-analysis of inferred networks, we were able to identify network-associated features that help stratify between healthy and disease states such as the differentiation of various bacterial phyla and enrichment of Proteobacteria interactions in diseased networks. Additionally, our findings show that the contributions of taxa in microbial associations are disproportionate to their abundances and that rarer taxa of microbial species play an integral part in shaping dynamics of microbial community interactions. Network-based meta-analysis revealed valuable insights into microbial community dynamics between healthy and disease phenotypes. We anticipate that the healthy and diseased microbiome association networks we inferred will become an important resource for human-related microbiome research.
Combination venetoclax and selinexor effective in relapsed refractory multiple myeloma with translocation t(11;14)
Authors: Nguyen Nina , Chaudhry Sana , Totiger Tulasigeri M. , Diaz Robert , Roberts Evan , Montoya Skye , Pardo Gabriel , Pardo Alejandro , Afaghani Jumana , Affer Maurizio , Jahn Jacob , Bradley Terrence , Maura Francesco , Kazandjian Dickran , Bilbao Daniel , Chapman Jennifer , Landgren Ola , Hoffman James , Taylor Justin 
Published: October 2022

AbstractPatients with multiple myeloma-bearing translocation t(11;14) have recently been shown to benefit from the apoptosis-inducing drug venetoclax; however, the drug lacks FDA approval in multiple myeloma thus far due to a potential safety signal in the overall patient population. Selinexor is an inhibitor of nuclear export that is FDA-approved for patients with multiple myeloma refractory to multiple lines of therapy. Here, we report that in four patients with multiple myeloma with t(11;14), the concomitant administration of venetoclax and selinexor was safe and associated with disease response. Moreover, the combination was synergistic in t(11;14) multiple myeloma cell lines and caused decreased levels of Cyclin D1 (which is overexpressed due to the CCND1-IGH fusion) when given in combination as compared to single agents. These data suggest that the combination of venetoclax and selinexor is effective and t(11;14) may serve as a therapeutic marker for response and target for future clinical trials.