bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the COPD alveolar niche using single-cell RNA sequencing
Authors: Sauler Maor , McDonough John E. , Adams Taylor S. , Kothapalli Neeharika , Barnthaler Thomas , Werder Rhiannon B. , Schupp Jonas C. , Nouws Jessica , Robertson Matthew J. , Coarfa Cristian , Yang Tao , Chioccioli Maurizio , Omote Norihito , Cosme Carlos , Poli Sergio , Ayaub Ehab A. , Chu Sarah G. , Jensen Klaus H. , Gomez Jose L. , Britto Clemente J. , Raredon Micha Sam B. , Niklason Laura E. , Wilson Andrew A. , Timshel Pascal N. , Kaminski Naftali , Rosas Ivan O. 
Published: January 2022

AbstractChronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, however our understanding of cell specific mechanisms underlying COPD pathobiology remains incomplete. Here, we analyze single-cell RNA sequencing profiles of explanted lung tissue from subjects with advanced COPD or control lungs, and we validate findings using single-cell RNA sequencing of lungs from mice exposed to 10 months of cigarette smoke, RNA sequencing of isolated human alveolar epithelial cells, functional in vitro models, and in situ hybridization and immunostaining of human lung tissue samples. We identify a subpopulation of alveolar epithelial type II cells with transcriptional evidence for aberrant cellular metabolism and reduced cellular stress tolerance in COPD. Using transcriptomic network analyses, we predict capillary endothelial cells are inflamed in COPD, particularly through increased CXCL-motif chemokine signaling. Finally, we detect a high-metallothionein expressing macrophage subpopulation enriched in advanced COPD. Collectively, these findings highlight cell-specific mechanisms involved in the pathobiology of advanced COPD.
Modular assembly of the principal microtubule nucleator γ-TuRC
Authors: Würtz Martin , Zupa Erik , Atorino Enrico S. , Neuner Annett , Böhler Anna , Rahadian Ariani S. , Vermeulen Bram J. A. , Tonon Giulia , Eustermann Sebastian , Schiebel Elmar , Pfeffer Stefan 
Published: January 2022

AbstractThe gamma-tubulin ring complex (γ-TuRC) is the principal microtubule nucleation template in vertebrates. Recent cryo-EM reconstructions visualized the intricate quaternary structure of the γ-TuRC, containing more than thirty subunits, raising fundamental questions about γ-TuRC assembly and the role of actin as an integral part of the complex. Here, we reveal the structural mechanism underlying modular γ-TuRC assembly and identify a functional role of actin in microtubule nucleation. During γ-TuRC assembly, a GCP6-stabilized core comprising GCP2-3-4-5-4-6 is expanded by stepwise recruitment, selective stabilization and conformational locking of four pre-formed GCP2-GCP3 units. Formation of the lumenal bridge specifies incorporation of the terminal GCP2-GCP3 unit and thereby leads to closure of the γ-TuRC ring in a left-handed spiral configuration. Actin incorporation into the complex is not relevant for γ-TuRC assembly and structural integrity, but determines γ-TuRC geometry and is required for efficient microtubule nucleation and mitotic chromosome alignment in vivo.
Magnetic Moment Tensor Potentials for collinear spin-polarized materials reproduce different magnetic states of bcc Fe
Authors: Novikov Ivan , Grabowski Blazej , Körmann Fritz , Shapeev Alexander 
Published: January 2022

AbstractWe present the magnetic Moment Tensor Potentials (mMTPs), a class of machine-learning interatomic potentials, accurately reproducing both vibrational and magnetic degrees of freedom as provided, e.g., from first-principles calculations. The accuracy is achieved by a two-step minimization scheme that coarse-grains the atomic and the spin space. The performance of the mMTPs is demonstrated for the prototype magnetic system bcc iron, with applications to phonon calculations for different magnetic states, and molecular-dynamics simulations with fluctuating magnetic moments.
A review of plant extracts as green corrosion inhibitors for CO2 corrosion of carbon steel
Authors: Fazal Basit Raza , Becker Thomas , Kinsella Brian , Lepkova Katerina 
Published: January 2022

AbstractThe use of corrosion inhibitors is a cost-effective corrosion mitigation strategy for carbon steel. There is an increased focus on developing and using low-cost, biodegradable and environmentally friendly inhibitor formulations. Plant-based extracts have been evaluated in many studies using a multitude of electrochemical methods and characterisation techniques. Although plant extracts appear as promising alternatives for commercially synthesised inhibitor formulations, a significant amount of optimisation is required. The majority of the research on plant extracts does not elucidate the effect of other synergistic combinations in commercial inhibitor formulations. Therefore, further development of plant extracts as corrosion inhibitors is of significant interest.
Recognition of NiCrAlY coating based on convolutional neural network
Authors: Liu Rui , Wang Minghao , Wang Huan , Chi Jianning , Meng Fandi , Liu Li , Wang Fuhui 
Published: January 2022

AbstractThis paper established an eight-layer convolu-tional neural network to automatically recognize the characteristic phases of the NiCrAlY coating, the coating/substrate interface, and the oxide layer. Using this neural network, the Cr-rich phase, the coating/substrate interface, and the oxide layer, as the features of the NiCrAlY coating, were successfully identified and retrieved at different constant oxidation temperatures. Based on this achievement, the variations of the Cr-rich phase distribution and the changes of the oxide layer thickness calculated by the network were obtained, which are all consistent with the trend of the oxidation kinetic curves at different temperatures; the preliminary intelligent calculation of oxidation kinetics of the coating was carried out through the thickness of the oxide layer from the SEM images.
GWAS identifies candidate susceptibility loci and microRNA biomarkers for acute encephalopathy with biphasic seizures and late reduced diffusion
Authors: Kasai Mariko , Omae Yosuke , Kawai Yosuke , Shibata Akiko , Hoshino Ai , Mizuguchi Masashi , Tokunaga Katsushi 
Published: January 2022

AbstractAcute encephalopathy with biphasic seizures and late reduced diffusion (AESD) is a severe encephalopathy preceded by viral infections with high fever. AESD is a multifactorial disease, however, few disease susceptibility genes have previously been identified. Here, we conducted a genome-wide association study (GWAS) and assessed functional variants in non-coding regions to study genetic susceptibility in AESD using 254 Japanese children with AESD and 799 adult healthy controls. We also performed a microRNA enrichment analysis using GWAS statistics to search for candidate biomarkers in AESD. The variant with the lowest p-value, rs1850440, was located in the intron of serine/threonine kinase 39 gene (STK39) on chromosome 2q24.3 (p = 2.44 × 10−7, odds ratio = 1.71). The minor allele T of rs1850440 correlated with the stronger expression of STK39 in peripheral blood. This variant possessed enhancer histone modification marks in STK39, the encoded protein of which activates the p38 mitogen-activated protein kinase (MAPK) pathway. In the replication study, the odds ratios of three SNPs, including rs1850440, showed the same direction of association with that in the discovery stage GWAS. One of the candidate microRNAs identified by the microRNA enrichment analysis was associated with inflammatory responses regulated by the MAPK pathway. This study identified STK39 as a novel susceptibility locus of AESD, found microRNAs as potential biomarkers, and implicated immune responses and the MAPK cascade in its pathogenesis.
NLRP3 inflammasome in rosmarinic acid-afforded attenuation of acute kidney injury in mice
Authors: Akhter Juheb , Khan Jasim , Baghel Madhu , Beg Mirza Masroor Ali , Goswami Poonam , Afjal Mohd Amir , Ahmad Shahzad , Habib Haroon , Najmi Abul Kalam , Raisuddin Sheikh 
Published: January 2022

AbstractCisplatin (CP) is a well-known anticancer drug used to effectively treat various kinds of solid tumors. CP causes acute kidney injury (AKI) and unfortunately, there is no therapeutic approach in hand to prevent AKI. Several signaling pathways are responsible for inducing AKI which leads to inflammation in proximal convoluted tubule cells in the kidney. Furthermore, the nucleotide-binding oligomerization domain (NOD)-like receptor containing pyrin domain 3 (NLRP3) inflammasome is involved in the CP-induced AKI. In this study, we investigated therapeutic effects of rosmarinic acid (RA) against inflammation-induced AKI. RA was orally administered at the dose of 100 mg/kg for two consecutive days after 24 h of a single injection of CP at the dose of 20 mg/kg administered intraperitoneally in Swiss albino male mice. Treatment of RA inhibited the activation of NLRP3 signaling pathway by blocking the activated caspase-1 and downstream signal molecules such as IL-1β and IL18. CP activated HMGB1-TLR4/MyD88 axis was also found to be downregulated with the RA treatment. Activation of nuclear factor-κB and elevated protein expression of cyclooxygenase-2 (COX-2) were also found to be downregulated in RA-treated animals. Alteration of early tubular injury biomarker, kidney injury molecule-1 (KIM-1), was found to be subsided in RA-treated mice. RA has been earlier reported for antioxidant and anti-inflammatory properties. Our findings show that blocking a critical step of inflammasome signaling pathway by RA treatment can be a novel and beneficial approach to prevent the CP-induced AKI.
Parvalbumin expressing interneurons control spike-phase coupling of hippocampal cells to theta oscillations
Authors: Strüber Michael , Sauer Jonas-Frederic , Bartos Marlene 
Published: January 2022

AbstractEncoding of information by hippocampal neurons is defined by the number and the timing of action potentials generated relative to ongoing network oscillations in the theta (5–14 Hz), gamma (30–80 Hz) and ripple frequency range (150–200 Hz). The exact mechanisms underlying the temporal coupling of action potentials of hippocampal cells to the phase of rhythmic network activity are not fully understood. One critical determinant of action potential timing is synaptic inhibition provided by a complex network of Gamma-amino-hydroxy-butyric acid releasing (GABAergic) interneurons. Among the various GABAergic cell types, particularly Parvalbumin-expressing cells are powerful regulators of neuronal activity. Here we silenced Parvalbumin-expressing interneurons in hippocampal areas CA1 and the dentate gyrus in freely moving mice using the optogenetic silencing tool eNpHR to determine their influence on spike timing in principal cells. During optogenetic inhibition of Parvalbumin-expressing cells, local field potential recordings revealed no change in power or frequency of CA1 or dentate gyrus network oscillations. However, CA1 pyramidal neurons exhibited significantly reduced spike-phase coupling to CA1 theta, but not gamma or ripple oscillations. These data suggest that hippocampal Parvalbumin-expressing interneurons are particularly important for an intact theta-based temporal coding scheme of hippocampal principal cell populations.
Sensitive asprosin detection in clinical samples reveals serum/saliva correlation and indicates cartilage as source for serum asprosin
Authors: Morcos Yousef A. T. , Lütke Steffen , Tenbieg Antje , Hanisch Franz-Georg , Pryymachuk Galyna , Piekarek Nadin , Hoffmann Thorben , Keller Titus , Janoschek Ruth , Niehoff Anja , Zaucke Frank , Dötsch Jörg , Hucklenbruch-Rother Eva , Sengle Gerhard 
Published: January 2022

AbstractThe C-terminal pro-fibrillin-1 propeptide asprosin is described as white adipose tissue derived hormone that stimulates rapid hepatic glucose release and activates hunger-promoting hypothalamic neurons. Numerous studies proposed correlations of asprosin levels with clinical parameters. However, the enormous variability of reported serum and plasma asprosin levels illustrates the need for sensitive and reliable detection methods in clinical samples. Here we report on newly developed biochemical methods for asprosin concentration and detection in several body fluids including serum, plasma, saliva, breast milk, and urine. Since we found that glycosylation impacts human asprosin detection we analyzed its glycosylation profile. Employing a new sandwich ELISA revealed that serum and saliva asprosin correlate strongly, depend on biological sex, and feeding status. To investigate the contribution of connective tissue-derived asprosin to serum levels we screened two cohorts with described cartilage turnover. Serum asprosin correlated with COMP, a marker for cartilage degradation upon running exercise and after total hip replacement surgery. This together with our finding that asprosin is produced by primary human chondrocytes and expressed in human cartilage suggests a contribution of cartilage to serum asprosin. Furthermore, we determined asprosin levels in breast milk, and urine, for the first time, and propose saliva asprosin as an accessible clinical marker for future studies.
Effect of delayed entry of blood culture bottles in BACTEC automated blood culture system in the context of laboratory consolidation
Authors: Deslandes Vincent , Rafipour Darya , Gorn Ivan , Sabri Elham , Sant Nadia , Desjardins Marc 
Published: January 2022

AbstractDelayed entry of blood culture bottles is frequent in consolidated laboratories. A retrospective study evaluated time from insertion to detection and total detection time as a function of preincubation time, and we prospectively looked for false negative results. 69,604 blood culture bottles were reviewed for preincubation time, incubation time and total detection time. Positive cultures for specific bacterial subtypes were reviewed to assess the effect of preincubation time on likelihood of detection. 492 negative blood cultures were prospectively tested by 16S RNA PCR and Staphylococcus-specific PCR for the presence of bacterial DNA. Mean preincubation time for samples collected within the city-limits was 3.94 h versus 9.49–18.89 h for other client sites. Higher preincubation times were partially mitigated by a lower incubation time, with an overall increase in total detection time. A lower odds ratio of recovery of Staphylococcus spp was identified, but not confirmed by terminal subcultures and molecular assays. Prolonged preincubation of blood cultures affects total detection time despite a reduction in incubation time. Successful centralization of microbiological services may depend upon optimization of courier routes for inoculated blood culture bottles. Our data supports consideration for an increase in suggested maximum preincubation times.
Population transcriptomics reveals the effect of gene flow on the evolution of range limits
Authors: Tamagawa Katsunori , Yoshida Kotone , Ohrui Shiori , Takahashi Yuma 
Published: January 2022

AbstractOne of the most important questions in evolutionary biology is how the spatial distribution of species is limited. Asymmetric gene flow from core populations is suggested to increase the number of poorly adapted immigrants in the populations at the range edge. Genetic load due to migration, i.e., migration load, should prevent adaptation to the local habitat, leading to decreases in distribution range via local extinction or the limiting range expansion. However, few experimental studies have examined the effects of immigration on fitness and natural selection within recipient populations. To investigate the influence of migration load on the evolution of distribution range, we performed field and laboratory observations as well as population transcriptomics for the common river snail, Semisulcospira reiniana. This species meets the conditions that migration from source populations can prevent local adaptation in a sink population because they inhabit the broader range of environments, including middle/upper reaches of a river and estuaries within a single river and they may be more vulnerable to being swept away by water currents due to lowered spontaneous (upward) locomotion activity. We found that river steepness was related to the lower distribution limit of S. reiniana, with a narrower distribution range in the steeper river. Population transcriptomic analysis showed that gene flow was heavily asymmetric from the upstream populations to downstream ones in the steep river, suggesting a greater migration load in the steep river. The number of genes putatively involved in adaptation to the local habitat was lower in the steep river than in the gentle river. Gene expression profiles suggested that individuals achieve better local adaptation in the gentle river. Laboratory experiments suggested that evolutionary differences in salinity tolerance among local populations were only found in the gentle river. Our results consistent with the hypothesis that migration load owing to asymmetric gene flow disturbs local adaptation and restricts the distribution range of river snails.
Protective effects of gallocatechin gallate against ultraviolet B induced skin damages in hairless mice
Authors: Sheng Yue-Yue , Xiang Jing , Lu Jian-Liang , Ye Jian-Hui , Chen Zi-Jiu , Zhao Jian-Wen , Liang Yue-Rong , Zheng Xin-Qiang 
Published: January 2022

AbstractEpigallocatechin gallate (EGCG) has the effect to protect skin from ultraviolet B (UVB) induced damages, but it is unstable under ambient conditions, being susceptible to become brown in color. Gallocatechin gallate (GCG), an epimer counterpart of EGCG, is more stable chemically than EGCG. The potential effects of GCG against UVB-induced skin damages has not been available. The objective of this study was to investigate the protective effects of GCG against UVB-induced skin photodamages. GCG was topically applied on the skin of hairless mice at three dosage levels (LL, 12.5 mg/mL; ML 25 mg/mL; HL, 50 mg/mL), with EGCG and a commercially available baby sunscreen lotion SPF50 PA+++ as control. The mice were then irradiated by UVB (fluence rate 1.7 µmol/m2 s) for 45 min. The treatments were carried out once a day for 6 consecutive days. Skin measurements and histological studies were performed at the end of experiment. The results show that GCG treatments at ML and HL levels inhibited the increase in levels of skin oil and pigmentation induced by UVB irradiation, and improved the skin elasticity and collagen fibers. GCG at ML and HL levels inhibited the formation of melanosomes and aberrations in mitochondria of UVB-irradiated skin in hairless mice. It is concluded that GCG protected skin from UVB-induced photodamages by improving skin elasticity and collagen fibers, and inhibiting aberrations in mitochondria and formation of melanosomes.
Scalable reaction network modeling with automatic validation of consistency in Event-B
Authors: Sanwal Usman , Hoang Thai Son , Petre Luigia , Petre Ion 
Published: January 2022

AbstractConstructing a large biological model is a difficult, error-prone process. Small errors in writing a part of the model cascade to the system level and their sources are difficult to trace back. In this paper we extend a recent approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to validate for model consistency step-by-step in an automated way. We demonstrate this approach on a model of the heat shock response in eukaryotes and its scalability on a model of the $$\mathsf {ErbB}$$
ErbB
signaling pathway. All consistency properties of the model were proved automatically with computer support.
Carbohydrate antigen 125 and risk of heart failure readmissions in patients with heart failure and preserved ejection fraction
Authors: Miñana Gema , de la Espriella Rafael , Palau Patricia , Llácer Pau , Núñez Eduardo , Santas Enrique , Valero Ernesto , Lorenzo Miguel , Núñez Gonzalo , Bodí Vicente , Heredia Raquel , Sanchis Juan , Bayés-Genís Antoni , Chorro Francisco J. , Núñez Julio 
Published: January 2022

AbstractWe aimed to assess the association between CA125 and the long-term risk of total acute heart failure (AHF) admissions in patients with an index hospitalization with AHF and preserved ejection fraction (HFpEF). We prospectively included 2369 patients between 2008 and 2019 in three centers. CA125 and NT-proBNP were measured during early hospitalization and evaluated as continuous and categorized in quartiles (Q). Negative binomial regressions were used to assess the association with the risk of recurrent AHF admission. The mean age of the sample patients was 76.7 ± 9.5 years and 1443 (60.9%) were women. Median values of CA125 and NT-proBNP were 38.3 (19.0–90.0) U/mL, and 2924 (1590–5447) pg/mL, respectively. During a median follow-up of 2.2 (0.8–4.6) years, 1200 (50.6%) patients died, and 2084 AHF admissions occurred in 1029 (43.4%) patients. After a multivariate adjustment, CA125, but not NT-proBNP, was positively and non-linearly associated with the risk of cumulative AHF-readmission (p < 0.001). Compared to Q1, patients belonging to Q2, Q3, and Q4 showed a stepwise risk increase (IRR = 1.29, 95% CI 1.08–1.55, p = 0.006; IRR = 1.35, 95% CI 1.12–1.63, p = 0.002; and IRR = 1.62, 95% CI 01.34–1.96, p < 0.001, respectively). In conclusion, CA125 predicted the risk of long-term AHF-readmission burden in patients with HFpEF and a recent admission for AHF.
FOXO1 forkhead domain mutants in B-cell lymphoma lack transcriptional activity
Authors: Sablon Ariane , Bollaert Emeline , Pirson Constance , Velghe Amélie I. , Demoulin Jean-Baptiste 
Published: January 2022

AbstractSomatic point mutations of the FOXO1 transcription factor were reported in non-Hodgkin lymphoma including diffuse large B-cell lymphoma, follicular lymphoma and Burkitt lymphoma. These alterations were associated with a poor prognosis and resistance to therapy. Nearly all amino acid substitutions are localized in two major clusters, affecting either the N-terminal region (Nt mutations) or the forkhead DNA-binding domain (DBD mutations). While recent studies have focused on Nt mutations, we characterized FOXO1 DBD mutants. We analyzed their transcriptional activity, DNA binding, phosphorylation and protein–protein interaction. The majority of DBD mutants showed a decrease in activity and DNA binding, while preserving AKT phosphorylation and interaction with the cytoplasmic ATG7 protein. In addition, we investigated the importance of conserved residues of the α-helix 3 of the DBD. Amino acids I213, R214, H215 and L217 appeared to be crucial for FOXO1 activity. Our data underlined the key role of multiple amino-acid residues of the forkhead domain in FOXO1 transcriptional activity and revealed a new type of FOXO1 loss-of-function mutations in B-cell lymphoma.