bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giant linear magnetoresistance in half-metallic Sr2CrMoO6 thin films
Authors: Wang Zhao-Cai , Chen Lei , Li Shuang-Shuang , Ying Jing-Shi , Tang F. , Gao Guan-Yin , Fang Y. , Zhao Weiyao , Cortie David , Wang Xiaolin , Zheng Ren-Kui 
Published: May 2021

AbstractLinear magnetoresistance (LMR) is a special case of a magnetic-field induced resistivity response, which has been reported in highly disordered semiconductor systems and in topological materials. In this work, we observe LMR effect in half-metallic perovskite Sr2CrMoO6 thin films, of which the maximum MR value exceeds +1600% at 2 K and 14 T. It is an unusual behavior in ferrimagnetic double perovskite material like Sr2CrMoO6, which are known for intrinsic tunneling-type negative magnetoresistance. In the thin films, the high carriers’ density (~1022 cm−3) and ultrahigh mobility (~104 cm2 V−1 s−1) provide a low-resistivity (~10 nΩ·cm) platform for spin-polarized current. Our DFT calculations and magnetic measurements further support the half-metal band structure. The LMR effect in Sr2CrMoO6 could possibly originate from transport behavior that is governed by the guiding center motion of cyclotron orbitals, where the magnetic domain structure possibly provides disordered potential. The ultrahigh mobility and LMR in this system could broaden the applications of perovskites, and introduce more research on metallic oxide ferri-/ferro-magnetic materials.
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits
Authors: Azevedo Tiago , Dimitri Giovanna Maria , Lió Pietro , Gamazon Eric R. 
Published: May 2021

AbstractHere, we performed a comprehensive intra-tissue and inter-tissue multilayer network analysis of the human transcriptome. We generated an atlas of communities in gene co-expression networks in 49 tissues (GTEx v8), evaluated their tissue specificity, and investigated their methodological implications. UMAP embeddings of gene expression from the communities (representing nearly 18% of all genes) robustly identified biologically-meaningful clusters. Notably, new gene expression data can be embedded into our algorithmically derived models to accelerate discoveries in high-dimensional molecular datasets and downstream diagnostic or prognostic applications. We demonstrate the generalisability of our approach through systematic testing in external genomic and transcriptomic datasets. Methodologically, prioritisation of the communities in a transcriptome-wide association study of the biomarker C-reactive protein (CRP) in 361,194 individuals in the UK Biobank identified genetically-determined expression changes associated with CRP and led to considerably improved performance. Furthermore, a deep learning framework applied to the communities in nearly 11,000 tumors profiled by The Cancer Genome Atlas across 33 different cancer types learned biologically-meaningful latent spaces, representing metastasis (p < 2.2 × 10−16) and stemness (p < 2.2 × 10−16). Our study provides a rich genomic resource to catalyse research into inter-tissue regulatory mechanisms, and their downstream consequences on human disease.
In silico analysis of BRCA1 and BRCA2 missense variants and the relevance in molecular genetic testing
Authors: Poon Kok-Siong 
Published: May 2021

AbstractOver the years since the genetic testing of BRCA1 and BRCA2 has been conducted for research and later introduced into clinical practice, a high number of missense variants have been reported in the literature and deposited in public databases. Polymorphism Phenotyping v2 (PolyPhen-2) and Sorting Intolerant from Tolerant (SIFT) are two widely applied bioinformatics tools used to assess the functional impacts of missense variants. A total of 2605 BRCA1 and 4763 BRCA2 variants from the ClinVar database were analysed with PolyPhen2 and SIFT. When SIFT was evaluated alongside PolyPhen-2 HumDiv and HumVar, it had shown top performance in terms of negative predictive value (NPV) (100%) and sensitivity (100%) for ClinVar classified benign and pathogenic BRCA1 variants. Both SIFT and PolyPhen-2 HumDiv achieved 100% NPV and 100% sensitivity in prediction of pathogenicity of the BRCA2 variants. Agreement was achieved in prediction outcomes from the three tested approaches in 55.04% and 68.97% of the variants of unknown significance (VUS) for BRCA1 and BRCA2, respectively. The performances of PolyPhen-2 and SIFT in predicting functional impacts varied across the two genes. Due to lack of high concordance in prediction outcomes among the two tested algorithms, their usefulness in classifying the pathogenicity of VUS identified through molecular testing of BRCA1 and BRCA2 is hence limited in the clinical setting.
Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells
Authors: Kimura Kazumasa , Koizumi Takumi , Urasawa Takaya , Ohta Yuki , Takakura Daisuke , Kawasaki Nana 
Published: May 2021

AbstractN-glycosylation of glycoproteins, a major post-translational modification, plays a crucial role in various biological phenomena. In central nervous systems, N-glycosylation is thought to be associated with differentiation and regeneration; however, the state and role of N-glycosylation in neuronal differentiation remain unclear. Here, we conducted sequential LC/MS/MS analyses of tryptic digest, enriched glycopeptides, and deglycosylated peptides of proteins derived from human-induced pluripotent stem cells (iPSCs) and iPSC-derived neuronal cells, which were used as a model of neuronal differentiation. We demonstrate that the production profiles of many glycoproteins and their glycoforms were altered during neuronal differentiation. Particularly, the levels of glycoproteins modified with an N-glycan, consisting of five N-acetylhexosamines, three hexoses, and a fucose (HN5H3F), increased in dopaminergic neuron-rich cells (DAs). The N-glycan was deduced to be a fucosylated and bisected biantennary glycan based on product ion spectra. Interestingly, the HN5H3F-modified proteins were predicted to be functionally involved in neural cell adhesion, axon guidance, and the semaphorin-plexin signaling pathway, and protein modifications were site-selective and DA-selective regardless of protein production levels. Our integrated method for glycoproteome analysis and resultant profiles of glycoproteins and their glycoforms provide valuable information for further understanding the role of N-glycosylation in neuronal differentiation and neural regeneration.
Tipping points induced by parameter drift in an excitable ocean model
Authors: Pierini Stefano , Ghil Michael 
Published: May 2021

AbstractNumerous systems in the climate sciences and elsewhere are excitable, exhibiting coexistence of and transitions between a basic and an excited state. We examine the role of tipping between two such states in an excitable low-order ocean model. Ensemble simulations are used to obtain the model’s pullback attractor (PBA) and its properties, as a function of a forcing parameter $$\gamma$$
γ
and of the steepness $$\delta$$
δ
of a climatological drift in the forcing. The tipping time $$t_{\mathrm{{tp}}}$$

t
tp

is defined as the time at which the transition to relaxation oscillations (ROs) arises: at constant forcing this occurs at $$\gamma =\gamma _{\mathrm{c}}$$

γ
=

γ
c

. As the steepness $$\delta$$
δ
decreases, $$t_{\mathrm{{tp}}}$$

t
tp

is delayed and the corresponding forcing amplitude decreases, while remaining always above $$\gamma _{\mathrm{c}}$$

γ
c

. With periodic perturbations, that amplitude depends solely on $$\delta$$
δ
over a significant range of parameters: this provides an example of rate-induced tipping in an excitable system. Nonlinear resonance occurs for periods comparable to the RO time scale. Coexisting PBAs and total independence from initial states are found for subsets of parameter space. In the broader context of climate dynamics, the parameter drift herein stands for the role of anthropogenic forcing.
Type and magnitude of non-compliance and adulteration in neroli, mandarin and bergamot essential oils purchased on-line: potential consumer vulnerability
Authors: Pierson Marissa , Fernandez Xavier , Antoniotti Sylvain 
Published: May 2021

AbstractThirty-one samples of essential oils used both in perfumery and aromatherapy were purchased to business-to-consumers suppliers and submitted to standard gas chromatography-based analysis of their chemical composition. Their compliance with ISO AFNOR standards was checked and revealed, although ISO AFNOR ranges are relatively loose, that more than 45% of the samples analyzed failed to pass the test and more than 19% were diluted with solvents such as propylene and dipropylene glycol, triethyl citrate, or vegetal oil. Cases of non-compliance could be due to substitution or dilution with a cheaper essential oil, such as sweet orange oil, blending with selected compounds (linalool and linalyl acetate, maybe of synthetic origin), or issues of aging, harvest, or manufacturing that should be either deliberate or accidental. In some cases, natural variability could be invoked. These products are made available to the market without control and liability by resellers and could expose the public to safety issues, in addition to commercial prejudice, in sharp contrast with the ever-increasing regulations applying to the sector and the high demand of consumers for safe, controlled and traceable products in fragrances and cosmetic products.
Leucine-rich alpha-2 glycoprotein as a marker of mucosal healing in inflammatory bowel disease
Authors: Yasutomi Eriko , Inokuchi Toshihiro , Hiraoka Sakiko , Takei Kensuke , Igawa Shoko , Yamamoto Shumpei , Ohmori Masayasu , Oka Shohei , Yamasaki Yasushi , Kinugasa Hideaki , Takahara Masahiro , Harada Keita , Furukawa Masaki , Itoshima Kouichi , Okada Ken , Otsuka Fumio , Tanaka Takehiro , Mitsuhashi Toshiharu , Kato Jun , Okada Hiroyuki 
Published: May 2021

AbstractLeucine-rich alpha-2 glycoprotein (LRG) may be a novel serum biomarker for patients with inflammatory bowel disease. The association of LRG with the endoscopic activity and predictability of mucosal healing (MH) was determined and compared with those of C-reactive protein (CRP) and fecal markers (fecal immunochemical test [FIT] and fecal calprotectin [Fcal]) in 166 ulcerative colitis (UC) and 56 Crohn’s disease (CD) patients. In UC, LRG was correlated with the endoscopic activity and could predict MH, but the performance was not superior to that of fecal markers (areas under the curve [AUCs] for predicting MH: LRG: 0.61, CRP: 0.59, FIT: 0.75, and Fcal: 0.72). In CD, the performance of LRG was equivalent to that of CRP and Fcal (AUCs for predicting MH: LRG: 0.82, CRP: 0.82, FIT: 0.70, and Fcal: 0.88). LRG was able to discriminate patients with MH from those with endoscopic activity among UC and CD patients with normal CRP levels. LRG was associated with endoscopic activity and could predict MH in both UC and CD patients. It may be particularly useful in CD.
Chemical analysis and computed tomography of metallic inclusions in Roman glass to unveil ancient coloring methods
Authors: Di Turo Francesca , Moro Giulia , Artesani Alessia , Albertin Fauzia , Bettuzzi Matteo , Cristofori Davide , Moretto Ligia Maria , Traviglia Arianna 
Published: May 2021

AbstractThis paper describes the analysis of two near-spherical metallic inclusions partially incorporated within two Roman raw glass slags in order to elucidate the process that induced their formation and to determine whether their presence was related to ancient glass colouring processes. The theory of metallic scraps or powder being used in Roman times for glass-making and colouring purposes is widely accepted by the archaeological scientific community, although the assumption has been mainly based on oral traditions and documented medieval practices of glass processing. The analysis of the two inclusions, carried out by X-ray computed tomography, electrochemical analyses, and scanning electron microscopy, revealed their material composition, corrosion and internal structure. Results indicate that the two metallic bodies originated when, during the melting phase of glass, metal scraps were added to colour the material: the colloidal metal–glass system reached then a supersaturation condition and the latter ultimately induced metal expulsion and agglomeration. According to the authors’ knowledge, these two inclusions represent the first documented and studied finds directly associated with the ancient practise of adding metallic agents to colour glass, and their analysis provides clear insights into the use of metallic waste in the glass colouring process.
Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection
Authors: Tanaka Yoshihisa , Higashihara Kako , Nakazawa Mai Adachi , Yamashita Fumiyoshi , Tamada Yoshinori , Okuno Yasushi 
Published: May 2021

AbstractThe current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by researchers globally with the aim of resolving this disruptive crisis. This investigation process is indispensable to understand how SARS-CoV-2 behaves in human host cells. However, little is known about the systematic molecular mechanisms involved in the effects of SARS-CoV-2 infection on human host cells. Here, we present gene-to-gene regulatory networks in response to SARS-CoV-2 using a Bayesian network. We examined the dynamic changes in the SARS-CoV-2-purturbated networks established by our proposed framework for gene network analysis, thus revealing that interferon signaling gradually switched to the subsequent inflammatory cytokine signaling cascades. Furthermore, we succeeded in capturing a COVID-19 patient-specific network in which transduction of these signals was concurrently induced. This enabled us to explore the local regulatory systems influenced by SARS-CoV-2 in host cells more precisely at an individual level. Our panel of network analyses has provided new insights into SARS-CoV-2 research from the perspective of cellular systems.
The importance of the urinary output criterion for the detection and prognostic meaning of AKI
Authors: Vanmassenhove Jill , Steen Johan , Vansteelandt Stijn , Morzywolek Pawel , Hoste Eric , Decruyenaere Johan , Benoit Dominique , Van Biesen Wim 
Published: May 2021

AbstractMost reports on AKI claim to use KDIGO guidelines but fail to include the urinary output (UO) criterion in their definition of AKI. We postulated that ignoring UO alters the incidence of AKI, may delay diagnosis of AKI, and leads to underestimation of the association between AKI and ICU mortality. Using routinely collected data of adult patients admitted to an intensive care unit (ICU), we retrospectively classified patients according to whether and when they would be diagnosed with KDIGO AKI stage ≥ 2 based on baseline serum creatinine (Screa) and/or urinary output (UO) criterion. As outcomes, we assessed incidence of AKI and association with ICU mortality. In 13,403 ICU admissions (62.2% male, 60.8 ± 16.8 years, SOFA 7.0 ± 4.1), incidence of KDIGO AKI stage ≥ 2 was 13.2% when based only the SCrea criterion, 34.3% when based only the UO criterion, and 38.7% when based on both criteria. By ignoring the UO criterion, 66% of AKI cases were missed and 13% had a delayed diagnosis. The cause-specific hazard ratios of ICU mortality associated with KDIGO AKI stage ≥ 2 diagnosis based on only the SCrea criterion, only the UO criterion and based on both criteria were 2.11 (95% CI 1.85–2.42), 3.21 (2.79–3.69) and 2.85 (95% CI 2.43–3.34), respectively. Ignoring UO in the diagnosis of KDIGO AKI stage ≥ 2 decreases sensitivity, may lead to delayed diagnosis and results in underestimation of KDIGO AKI stage ≥ 2 associated mortality.
Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers
Authors: Halleran J. L. , Callahan B. J. , Jacob M. E. , Sylvester H. J. , Prange T. , Papich M. G. , Foster D. M. 
Published: May 2021

AbstractFluoroquinolones are a class of antimicrobial commonly used in human medicine, and deemed critical by the World Health Organization. Nonetheless, two formulations are approved for the treatment of respiratory disease in beef cattle. The objective of this study was to determine the gastrointestinal pharmacokinetics and impact on enteric bacteria of cattle when receiving one of the two dosing regimens (high: 40 mg/kg SC once or low: 20 mg/kg IM q48hr) of danofloxacin, a commonly utilized synthetic fluoroquinolone in veterinary medicine. Danofloxacin was administered to 12 steers (age 7 months) fitted with intestinal ultrafiltration devices at two different dosing regimens to assess the gastrointestinal pharmacokinetics, the shifts in the gastrointestinal microbiome and the development of resistant bacterial isolates. Our results demonstrated high intestinal penetration of danofloxacin for both dosing groups, as well as, significant differences in MIC values for E. coli and Enterococcus between dosing groups at selected time points over a 38 day period. Danofloxacin treatment consistently resulted in the Euryarchaeota phyla decreasing over time, specifically due to a decrease in Methanobrevibacter. Although microbiome differences were minor between dosing groups, the low dose group had a higher number of isolates with MIC values high enough to cause clinically relevant resistance. This information would help guide veterinarians as to appropriate dosing schemes to minimize the spread of antimicrobial resistance.
Kernel weighted least square approach for imputing missing values of metabolomics data
Authors: Kumar Nishith , Hoque Md. Aminul , Sugimoto Masahiro 
Published: May 2021

AbstractMass spectrometry is a modern and sophisticated high-throughput analytical technique that enables large-scale metabolomic analyses. It yields a high-dimensional large-scale matrix (samples × metabolites) of quantified data that often contain missing cells in the data matrix as well as outliers that originate for several reasons, including technical and biological sources. Although several missing data imputation techniques are described in the literature, all conventional existing techniques only solve the missing value problems. They do not relieve the problems of outliers. Therefore, outliers in the dataset decrease the accuracy of the imputation. We developed a new kernel weight function-based proposed missing data imputation technique that resolves the problems of missing values and outliers. We evaluated the performance of the proposed method and other conventional and recently developed missing imputation techniques using both artificially generated data and experimentally measured data analysis in both the absence and presence of different rates of outliers. Performances based on both artificial data and real metabolomics data indicate the superiority of our proposed kernel weight-based missing data imputation technique to the existing alternatives. For user convenience, an R package of the proposed kernel weight-based missing value imputation technique was developed, which is available at https://github.com/NishithPaul/tWLSA.
Poor prey quality is compensated by higher provisioning effort in passerine birds
Authors: Senécal Sarah , Riva Julie-Camille , O’Connor Ryan S. , Hallot Fanny , Nozais Christian , Vézina François 
Published: May 2021

AbstractIn altricial avian species, nutrition can significantly impact nestling fitness by increasing their survival and recruitment chances after fledging. Therefore, the effort invested by parents towards provisioning nestlings is crucial and represents a critical link between habitat resources and reproductive success. Recent studies suggest that the provisioning rate has little or no effect on the nestling growth rate. However, these studies do not consider prey quality, which may force breeding pairs to adjust provisioning rates to account for variation in prey nutritional value. In this 8-year study using black-capped (Poecile atricapillus) and boreal (Poecile hudsonicus) chickadees, we hypothesized that provisioning rates would negatively correlate with prey quality (i.e., energy content) across years if parents adjust their effort to maintain nestling growth rates. The mean daily growth rate was consistent across years in both species. However, prey energy content differed among years, and our results showed that parents brought more food to the nest and fed at a higher rate in years of low prey quality. This compensatory effect likely explains the lack of relationship between provisioning rate and growth rate reported in this and other studies. Therefore, our data support the hypothesis that parents increase provisioning efforts to compensate for poor prey quality and maintain offspring growth rates.
One-step peracetic acid pretreatment of hardwood and softwood biomass for platform chemicals production
Authors: Kundu Chandan , Samudrala Shanthi Priya , Kibria Mahmud Arman , Bhattacharya Sankar 
Published: May 2021

AbstractLignocellulosic biomass is an attractive renewable resource to produce biofuel or platform chemicals. Efficient and cost-effective conversion systems of lignocellulosic biomass depend on their appropriate pretreatment processes. Alkali or dilute acid pretreatment of biomass requires a high temperature (> 150 °C) to remove xylan (hemicellulosic sugar) and lignin partially. In this study, peracetic acid was used to pretreat biomass feedstocks, including hardwood and softwood species. It was found that the thermally-assisted dilute acid pretreatment of biomass conducted under the mild temperature of 90 °C up to 5 h resulted in the effective removal of lignin from the biomass with a negligible loss of carbohydrates. This thermally-assisted pretreatment achieved 90% of delignification, and this result was compared with the microwave-assisted pretreatment method. In addition, the crystallinity index (CrI), surface morphology, and chemical structure were significantly changed after the acid pretreatment. The biomass digestibility increased significantly with increased reaction time, by 32% and 23% for hardwood and softwood, respectively. From this study, it is clear that peracetic acid pretreatment is an effective method to enrich glucan content in biomass by delignification.
Dietary and Plasmodium challenge effects on the cuticular hydrocarbon profile of Anopheles albimanus
Authors: Claudio-Piedras Fabiola , Recio-Tótoro Benito , Cime-Castillo Jorge , Condé Renaud , Maffei Massimo , Lanz-Mendoza Humberto 
Published: May 2021

AbstractThe cuticular hydrocarbon (CHC) profile reflects the insects’ physiological states. These include age, sex, reproductive stage, and gravidity. Environmental factors such as diet, relative humidity or exposure to insecticides also affect the CHC composition in mosquitoes. In this work, the CHC profile was analyzed in two Anopheles albimanus phenotypes with different degrees of susceptibility to Plasmodium, the susceptible-White and resistant-Brown phenotypes, in response to the two dietary regimes of mosquitoes: a carbon-rich diet (sugar) and a protein-rich diet (blood) alone or containing Plasmodium ookinetes. The CHCs were analyzed by gas chromatography coupled to mass spectrometry or flame ionization detection, identifying 19 CHCs with chain lengths ranging from 20 to 37 carbons. Qualitative and quantitative changes in CHCs composition were dependent on diet, a parasite challenge, and, to a lesser extent, the phenotype. Blood-feeding caused up to a 40% reduction in the total CHC content compared to sugar-feeding. If blood contained ookinetes, further changes in the CHC profile were observed depending on the Plasmodium susceptibility of the phenotypes. Higher infection prevalence caused greater changes in the CHC profile. These dietary and infection-associated modifications in the CHCs could have multiple effects on mosquito fitness, impacts on disease transmission, and tolerance to insecticides.