bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dietary carbohydrates influence muscle texture of olive flounder Paralichthys olivaceus through impacting mitochondria function and metabolism of glycogen and protein
Authors: Liu Jiahuan , Deng Kangyu , Pan Mingzhu , Liu Guangxia , Wu Jing , Yang Mengxi , Huang Dong , Zhang Wenbing , Mai Kangsen 
Published: December 2020

AbstractThe present study was conducted to estimate the effects of dietary carbohydrates on muscle quality and the underlying mechanisms. Six isonitrogenous and isolipidic diets were formulated to contain graded levels of carbohydrates (0%, 8%, 12%, 16%, 20% and 24%, respectively). These diets were named as C0, C8, C12, C16, C20 and C24, respectively. After a 10-week feeding trial, results showed that the muscle pH, liquid holding capacity (LHC) and hardness were significantly decreased by the increasing dietary carbohydrate levels. Dietary carbohydrates significantly decreased the muscle fibre diameter, and the highest value was found in the C0 group. Accumulated glycogen and degenerated mitochondrial cristae were observed in the C24 group. Significantly higher contents of protein carbonyls were observed in the C20 group and C24 group (P < 0.05). There was a significant decrease of mtDNA copy number in the C24 group compared with that in the C0 and C8 groups. The AMP/ATP ratio in muscle decreased first and then increased with the increasing dietary carbohydrate levels. The dietary incorporation of carbohydrate significantly reduced the expression of opa1, pygm and genes involved in myogenesis (myf5 and myog). Meanwhile, proteolysis-related genes (murf-1, mafbx, capn2 and ctsl), pro-inflammatory cytokines (il-6 and tnf-α) and mstn were significantly up-regulated. In the C24 group, significant increase of phosphorylation of AMPK (Thr172), up-regulation of PGC-1α and GLUT4 were observed, while the phosphorylation level of S6 (Ser235/236) was significantly decreased. It was concluded that excessive dietary carbohydrate level (24%) had negative impacts on mitochondria function and promoted glycogen accumulation, and thereafter influenced the muscle quality of olive flounder. The activation of AMPK as well as the upregulation of PGC-1α and GLUT4 was the key mechanism.
Symmetry prediction and knowledge discovery from X-ray diffraction patterns using an interpretable machine learning approach
Authors: Suzuki Yuta , Hino Hideitsu , Hawai Takafumi , Saito Kotaro , Kotsugi Masato , Ono Kanta 
Published: December 2020

AbstractDetermination of crystal system and space group in the initial stages of crystal structure analysis forms a bottleneck in material science workflow that often requires manual tuning. Herein we propose a machine-learning (ML)-based approach for crystal system and space group classification based on powder X-ray diffraction (XRD) patterns as a proof of concept using simulated patterns. Our tree-ensemble-based ML model works with nearly or over 90% accuracy for crystal system classification, except for triclinic cases, and with 88% accuracy for space group classification with five candidates. We also succeeded in quantifying empirical knowledge vaguely shared among experts, showing the possibility for data-driven discovery of unrecognised characteristics embedded in experimental data by using an interpretable ML approach.
Shorebirds wintering in Southeast Asia demonstrate trans-Himalayan flights
Authors: Li David , Davison Geoffrey , Lisovski Simeon , Battley Phil F. , Ma Zhijun , Yang Shufen , How Choon Beng , Watkins Doug , Round Philip , Yee Alex , Srinivasan Vupasana , Teo Clarice , Teo Robert , Loo Adrian , Leong Chee Chiew , Er Kenneth 
Published: December 2020

AbstractMany birds wintering in the Indian subcontinent fly across the Himalayas during migration, including Bar-headed Geese (Anser indicus), Demoiselle Cranes (Anthropoides virgo) and Ruddy Shelducks (Tadorna ferruginea). However, little is known about whether shorebirds migrate across the Himalayas from wintering grounds beyond the Indian subcontinent. Using geolocators and satellite tracking devices, we demonstrate for the first time that Common Redshanks (Tringa totanus) and Whimbrels (Numenius phaeopus) wintering in Singapore can directly fly over the Himalayas to reach breeding grounds in the Qinghai-Tibet Plateau and north-central Russia respectively. The results also show that migratory shorebirds wintering in Southeast Asia can use both the Central Asian Flyway and the East Asian-Australasian Flyway. For Redshanks, westerly-breeding birds crossed the Himalayas while more easterly breeders on the Plateau migrated east of the Himalayas. For Whimbrels, an individual that crossed the Himalayas was probably from a breeding population that was different from the others that migrated along the coast up the East Asian-Australasian Flyway. The minimum required altitude of routes of trans-Himalayan Redshanks were no higher on average than those of eastern migrants, but geolocator temperature data indicate that birds departing Singapore flew at high elevations even when not required to by topography, suggesting that the Himalayan mountain range may be less of a barrier than assumed.
Defective membrane repair machinery impairs survival of invasive cancer cells
Authors: Bouvet F. , Ros M. , Bonedeau E. , Croissant C. , Frelin L. , Saltel F. , Moreau V. , Bouter A. 
Published: December 2020

AbstractCancer cells are able to reach distant tissues by migration and invasion processes. Enhanced ability to cope with physical stresses leading to cell membrane damages may offer to cancer cells high survival rate during metastasis. Consequently, down-regulation of the membrane repair machinery may lead to metastasis inhibition. We show that migration of MDA-MB-231 cells on collagen I fibrils induces disruptions of plasma membrane and pullout of membrane fragments in the wake of cells. These cells are able to reseal membrane damages thanks to annexins (Anx) that are highly expressed in invasive cancer cells. In vitro membrane repair assays reveal that MDA-MB-231 cells respond heterogeneously to membrane injury and some of them possess a very efficient repair machinery. Finally, we show that silencing of AnxA5 and AnxA6 leads to the death of migrating MDA-MB-231 cells due to major defect of the membrane repair machinery. Disturbance of the membrane repair process may therefore provide a new avenue for inhibiting cancer metastasis.
Segregation distortion: high genetic load suggested by a Chinese shrimp family under high-intensity selection
Authors: Fu Qiang , Meng Xianhong , Luan Sheng , Chen Baolong , Cao Jiawang , Li Xupeng , Kong Jie 
Published: December 2020

AbstractSegregation distortion is a common phenomenon found in most genetic mapping studies and is an important resource to dissect the mechanism of action in gene loci that cause deviation. Marine animals possess high genetic diversity and genomic heterozygosity, they therefore are ideal model organisms to study segregation distortion induced by selection. In the present study, we constructed a full-sib family of Fenneropenaeus chinensis and exerted high-intensity selection on 10,000 incipient progenies. 2b-RAD method was employed in remaining 273 individuals to develop genome-wide SNPs for segregating analysis and 41,612 SNPs were developed. 50.77% of 32,229 high-quality representative markers deviated from the expected Mendelian ratio. Results showed that most of these distorted markers (91.57%) were influenced at zygotic level. Heterozygote excess (53.07%) and homozygous deletions (41.96%) may both play an important role, sum of which explained 95.03% of distortion after fertilization. However, further results identified highly probable linkage among deleterious alleles, which may account for a considerable portion of heterozygote excess rather than single locus with heterozygote advantage. Results of this study support a major role of deleterious alleles in genetic load, thus in favor of partial dominance hypothesis. It would also offer necessary recommendations for the formulation of breeding strategy in shrimps.
The inhibitory effect of word neighborhood size when reading with central field loss is modulated by word predictability and reading proficiency
Authors: Sauvan Lauren , Stolowy Natacha , Aguilar Carlos , François Thomas , Gala Núria , Matonti Frédéric , Castet Eric , Calabrèse Aurélie 
Published: December 2020

AbstractFor normally sighted readers, word neighborhood size (i.e., the total number of words that can be formed from a single word by changing only one letter) has a facilitator effect on word recognition. When reading with central field loss (CFL) however, individual letters may not be correctly identified, leading to possible misidentifications and a reverse neighborhood size effect. Here we investigate this inhibitory effect of word neighborhood size on reading performance and whether it is modulated by word predictability and reading proficiency. Nineteen patients with binocular CFL from 32 to 89 years old (mean ± SD = 75 ± 15) read short sentences presented with the self-paced reading paradigm. Accuracy and reading time were measured for each target word read, along with its predictability, i.e., its probability of occurrence following the two preceding words in the sentence using a trigram analysis. Linear mixed effects models were then fit to estimate the individual contributions of word neighborhood size, predictability, frequency and length on accuracy and reading time, while taking patients’ reading proficiency into account. For the less proficient readers, who have given up daily reading as a consequence of their visual impairment, we found that the effect of neighborhood size was reversed compared to normally sighted readers and of higher amplitude than the effect of frequency. Furthermore, this inhibitory effect is of greater amplitude (up to 50% decrease in reading speed) when a word is not easily predictable because its chances to occur after the two preceding words in a specific sentence are rather low. Severely impaired patients with CFL often quit reading on a daily basis because this task becomes simply too exhausting. Based on our results, we envision lexical text simplification as a new alternative to promote effective rehabilitation in these patients. By increasing reading accessibility for those who struggle the most, text simplification might be used as an efficient rehabilitation tool and daily reading assistive technology, fostering overall reading ability and fluency through increased practice.
Structural and functional comparison of SARS-CoV-2-spike receptor binding domain produced in Pichia pastoris and mammalian cells
Authors:   Argentinian AntiCovid Consortium, Arbeitman Claudia R. , Auge Gabriela , Blaustein Matías , Bredeston Luis , Corapi Enrique S. , Craig Patricio O. , Cossio Leandro A. , Dain Liliana , D’Alessio Cecilia , Elias Fernanda , Fernández Natalia B. , Gándola Yamila B. , Gasulla Javier , Gorojovsky Natalia , Gudesblat Gustavo E. , Herrera María G. , Ibañez Lorena I. , Idrovo Tommy , Rando Matías Iglesias , Kamenetzky Laura , Nadra Alejandro D. , Noseda Diego G. , Paván Carlos H. , Pavan María F. , Pignataro María F. , Roman Ernesto , Ruberto Lucas A. M. , Rubinstein Natalia , Santos Javier , Velazquez Francisco , Zelada Alicia M. 
Published: December 2020

AbstractThe yeast Pichia pastoris is a cost-effective and easily scalable system for recombinant protein production. In this work we compared the conformation of the receptor binding domain (RBD) from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Spike protein expressed in P. pastoris and in the well established HEK-293T mammalian cell system. RBD obtained from both yeast and mammalian cells was properly folded, as indicated by UV-absorption, circular dichroism and tryptophan fluorescence. They also had similar stability, as indicated by temperature-induced unfolding (observed Tm were 50 °C and 52 °C for RBD produced in P. pastoris and HEK-293T cells, respectively). Moreover, the stability of both variants was similarly reduced when the ionic strength was increased, in agreement with a computational analysis predicting that a set of ionic interactions may stabilize RBD structure. Further characterization by high-performance liquid chromatography, size-exclusion chromatography and mass spectrometry revealed a higher heterogeneity of RBD expressed in P. pastoris relative to that produced in HEK-293T cells, which disappeared after enzymatic removal of glycans. The production of RBD in P. pastoris was scaled-up in a bioreactor, with yields above 45 mg/L of 90% pure protein, thus potentially allowing large scale immunizations to produce neutralizing antibodies, as well as the large scale production of serological tests for SARS-CoV-2.
Model-size reduction for reservoir computing by concatenating internal states through time
Authors: Sakemi Yusuke , Morino Kai , Leleu Timothée , Aihara Kazuyuki 
Published: December 2020

AbstractReservoir computing (RC) is a machine learning algorithm that can learn complex time series from data very rapidly based on the use of high-dimensional dynamical systems, such as random networks of neurons, called “reservoirs.” To implement RC in edge computing, it is highly important to reduce the amount of computational resources that RC requires. In this study, we propose methods that reduce the size of the reservoir by inputting the past or drifting states of the reservoir to the output layer at the current time step. To elucidate the mechanism of model-size reduction, the proposed methods are analyzed based on information processing capacity proposed by Dambre et al. (Sci Rep 2:514, 2012). In addition, we evaluate the effectiveness of the proposed methods on time-series prediction tasks: the generalized Hénon-map and NARMA. On these tasks, we found that the proposed methods were able to reduce the size of the reservoir up to one tenth without a substantial increase in regression error.
Synthesis, characterization and catalytic testing of MCM-22 derived catalysts for n-hexane cracking
Authors: Ahmad Ali , Naqvi Salman Raza , Rafique Muhammad , Nasir Habib , Sarosh Ali 
Published: December 2020

AbstractLayered zeolites and their delaminated structures are novel materials that enhance the catalytic performance of catalysts by addressing diffusion limitations of the reactant molecules. n-Hexane catalytic cracking was observed over MCM-22 layered zeolite and its derivative structures over the temperature range of 450–650 °C for the production of olefins. MCM-22, H-MCM-22, and ITQ-2 zeolites were prepared by the hydrothermal method. Oxalic acid was used as a dealuminating reagent to obtain H-MCM-22 with various Si/Al ratios ranging from 09–65. The prepared samples were characterized by XRD, SEM, TGA, and BET. The cracking of n-hexane was carried out by Pyro/GC–MS. It was observed that the selectivity for olefins was improved by increasing the Si/Al ratio. H-MCM-22–10% produced the highest relative olefinic concentration of 68% as compared to other dealuminated structures. Moreover, the product distribution showed that higher reaction temperature is favorable to produce more olefins. Furthermore, a comparison between ITQ-2 and MCM-22 derived structures showed that ITQ-2 is more favorable for olefins production at high temperatures. The concentration of relative olefins was increased up to 80% over ITQ-2 at 650 °C.
Large global variations in measured airborne metal concentrations driven by anthropogenic sources
Authors: McNeill Jacob , Snider Graydon , Weagle Crystal L. , Walsh Brenna , Bissonnette Paul , Stone Emily , Abboud Ihab , Akoshile Clement , Anh Nguyen Xuan , Balasubramanian Rajasekhar , Brook Jeffrey R. , Coburn Craig , Cohen Aaron , Dong Jinlu , Gagnon Graham , Garland Rebecca M. , He Kebin , Holben Brent N. , Kahn Ralph , Kim Jong Sung , Lagrosas Nofel , Lestari Puji , Liu Yang , Jeba Farah , Joy Khaled Shaifullah , Martins J. Vanderlei , Misra Amit , Norford Leslie K. , Quel Eduardo J. , Salam Abdus , Schichtel Bret , Tripathi S. N. , Wang Chien , Zhang Qiang , Brauer Michael , Gibson Mark D. , Rudich Yinon , Martin Randall V. 
Published: December 2020

AbstractGlobally consistent measurements of airborne metal concentrations in fine particulate matter (PM2.5) are important for understanding potential health impacts, prioritizing air pollution mitigation strategies, and enabling global chemical transport model development. PM2.5 filter samples (N ~ 800 from 19 locations) collected from a globally distributed surface particulate matter sampling network (SPARTAN) between January 2013 and April 2019 were analyzed for particulate mass and trace metals content. Metal concentrations exhibited pronounced spatial variation, primarily driven by anthropogenic activities. PM2.5 levels of lead, arsenic, chromium, and zinc were significantly enriched at some locations by factors of 100–3000 compared to crustal concentrations. Levels of metals in PM2.5 and PM10 exceeded health guidelines at multiple sites. For example, Dhaka and Kanpur sites exceeded the US National Ambient Air 3-month Quality Standard for lead (150 ng m−3). Kanpur, Hanoi, Beijing and Dhaka sites had annual mean arsenic concentrations that approached or exceeded the World Health Organization’s risk level for arsenic (6.6 ng m−3). The high concentrations of several potentially harmful metals in densely populated cites worldwide motivates expanded measurements and analyses.
Difference of ecological half-life and transfer coefficient in aquatic invertebrates between high and low radiocesium contaminated streams
Authors: Yoshimura Mayumi , Akama Akio 
Published: December 2020

AbstractThe Fukushima accident emitted radioactive substances into the environment, contaminating litter, algae, sand substrate, aquatic invertebrates, and fish in freshwater streams. Because these substances have substantial effects on stream ecology over many years, it is necessary to clarify the diffusion and decay mechanisms of radiocesium. The transfer coefficient differed among aquatic invertebrate groups, likely due to the differences in habitat. The ecological half-life of cesium was longer where the air dose rate was lower. The transfer coefficient was also higher in areas with lower air dose rate. The radiocesium concentration in algae was inversely related to stream current velocity in the radiocesium-contaminated area. However, this relationship was not observed in the lower air dose rate area: the radiocesium concentration in algae in the rapid-velocity areas tended to be higher than that in the slow-velocity areas. This reverse trend would lead to a longer period of freshwater contamination. The radiocesium concentration would continue to decrease in highly contaminated areas, but it would be difficult to reduce the radiocesium concentration in less-contaminated areas because different contamination mechanisms are at work. Controlling the water flow is key to regulating radiocesium concentration in freshwater ecosystems.
Tree rings reveal signs of Europe’s sustainable forest management long before the first historical evidence
Authors: Muigg Bernhard , Skiadaresis Georgios , Tegel Willy , Herzig Franz , Krusic Paul J. , Schmidt Uwe E. , Büntgen Ulf 
Published: December 2020

AbstractTo satisfy the increasing demand for wood in central Europe during medieval times, a new system of forest management was developed, one far superior to simple coppicing. The adoption of a sophisticated, Coppice-with-Standards (CWS) management practice created a two-storey forest structure that could provide fuelwood as well as construction timber. Here we present a dendrochronological study of actively managed CWS forests in northern Bavaria to detect the radial growth response to cyclical understorey harvesting in overstorey oaks (Quercussp.), so-calledstandards. All modernstandardsexhibit rapid growth releases every circa 30 years, most likely caused by regular understorey management. We further analyse tree-ring width patterns in 2120 oak timbers from historical buildings and archaeological excavations in southern Germany and north-eastern France, dating between 300 and 2015 CE, and succeeded in identifying CWS growth patterns throughout the medieval period. Several potential CWSstandardseven date to the first millennium CE, suggesting CWS management has been in practice long before its first mention in historical documents. Our dendrochronological approach should be expanded routinely to indentify the signature of past forest management practices in archaeological and historical oak wood.
Fine-mapping and cell-specific enrichment at corneal resistance factor loci prioritize candidate causal regulatory variants
Authors: Jiang Xinyi , Dellepiane Nefeli , Pairo-Castineira Erola , Boutin Thibaud , Kumar Yatendra , Bickmore Wendy A. , Vitart Veronique 
Published: December 2020

AbstractCorneal resistance factor (CRF) is altered during corneal diseases progression. Genome-wide-association studies (GWAS) indicated potential CRF and disease genetics overlap. Here, we characterise 135 CRF loci following GWAS in 76029 UK Biobank participants. Enrichment of extra-cellular matrix gene-sets, genetic correlation with corneal thickness (70% (SE = 5%)), reported keratoconus risk variants at 13 loci, all support relevance to corneal stroma biology. Fine-mapping identifies a subset of 55 highly likely causal variants, 91% of which are non-coding. Genomic features enrichments, using all associated variants, also indicate prominent regulatory causal role. We newly established open chromatin landscapes in two widely-used human cornea immortalised cell lines using ATAC-seq. Variants associated with CRF were significantly enriched in regulatory regions from the corneal stroma-derived cell line and enrichment increases to over 5 fold for variants prioritised by fine-mapping-including atGAS7, SMAD3andCOL6A1loci. Our analysis generates many hypotheses for future functional validation of aetiological mechanisms.
Signatures of a liquid-crystal transition in spin-wave excitations of skyrmions
Authors: Mohanta Narayan , Christianson Andrew D. , Okamoto Satoshi , Dagotto Elbio 
Published: December 2020

AbstractUnderstanding the spin-wave excitations of chiral magnetic order, such as the skyrmion crystal (SkX), is of fundamental interest to confirm such exotic magnetic order. The SkX is realized by competing Dzyaloshinskii-Moriya and ferromagnetic-exchange interactions with a magnetic field or anisotropy. Here, we compute the dynamical spin structure factor, using Monte Carlo and spin dynamics simulations, extracting the spin-wave spectrum in the SkX, in the vicinity of the paramagnet to SkX transition. Inside the SkX, we find six spin-wave modes, which are supplemented by another mode originating from the ferromagnetic background. Above the critical temperature Ts for the skyrmion crystallization, we find a diffusive regime, reminiscent of the liquid-to-crystal transition, revealing that topological spin texture of skyrmionic character starts to develop above Ts as the precursor of the SkX. We discuss the opportunities for the detection of the spin waves of the SkX using inelastic-neutron-scattering experiments in manganite-iridate heterostructures.
Hierarchically interconnected ZnO nanowires for low-temperature-operated reducing gas sensors: experimental and DFT studies
Authors: Chikate Parameshwar R. , Sharma Alfa , Rondiya Sachin R. , Cross Russell W. , Dzade Nelson Y. , Shirage Parasharam M. , Devan Rupesh S. 
Published: December 2020

The larger surface area and increased point contacts of hierarchically arranged ZnO nanowires (upper panel) offered more potential barriers for the gas molecule exhibiting binding strength CO < C2H5OH < NH3 (lower panel) and provided excellent gas-sensing performance at 100 °C for NH3 gas.