bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America
Authors: Delgado Elena , Fernández-García Aurora , Pérez-Losada Marcos , Moreno-Lorenzo María , Fernández-Miranda Ismael , Benito Sonia , Montero Vanessa , Gil Horacio , Hernáez Silvia , Muñoz Josefa , Zubero-Sulibarria Miren Z. , García-Bodas Elena , Sánchez Mónica , del Romero Jorge , Rodríguez Carmen , Elorduy Luis , Bereciartua Elena , Culebras Esther , Rodríguez-Avial Icíar , Giménez-Alarcón María Luisa , Martín-Salas Carmen , Gómez-González Carmen , García-Irure José J. , Cenzual Gema , Martínez-Sapiña Ana , Maiques-Camarero María , Pérez-Álvarez Lucía , Thomson Michael M. 
Published: June 2021

AbstractCirculating recombinant forms (CRFs) contribute substantially to the HIV-1 pandemic. Among 105 CRFs described in the literature, 16 are BF intersubtype recombinants, most of South American origin, of which CRF12_BF is the most widely spread. A BF recombinant cluster identified in Bolivia was suggested to represent a new CRF_BF. Here we find that it belongs to a larger cluster incorporating 39 viruses collected in 7 countries from 3 continents, 22 of them in Spain, most from Bolivian or Peruvian individuals, and 12 in South America (Bolivia, Argentina, and Peru). This BF cluster comprises three major subclusters, two associated with Bolivian and one with Peruvian individuals. Near full-length genome sequence analyses of nine viruses, collected in Spain, Bolivia, and Peru, revealed coincident BF mosaic structures, with 13 breakpoints, 6 and 7 of which coincided with CRF12_BF and CRF17_BF, respectively. In a phylogenetic tree, they grouped in a clade closely related to these CRFs, and more distantly to CRF38_BF and CRF44_BF, all circulating in South America. These results allowed to identify a new HIV-1 CRF, designated CRF89_BF. Through phylodynamic analyses, CRF89_BF emergence was estimated in Bolivia around 1986. CRF89_BF is the fifth CRF member of the HIV-1 recombinant family related to CRF12_BF.
Citizen science and niche modeling to track and forecast the expansion of the brown marmorated stinkbug Halyomorpha halys (Stål, 1855)
Authors: Streito Jean-Claude , Chartois Marguerite , Pierre Éric , Dusoulier François , Armand Jean-Marc , Gaudin Jonathan , Rossi Jean-Pierre 
Published: June 2021

AbstractHalyomorpha halys (Stål, 1855), the Brown Marmorated StinkBug (BMSB) is a highly successful invasive species native to eastern Asia that managed to spread into North America and Europe in recent decades. We set up a citizen science survey to monitor BMSB expansion in France in 2012 and analyzed the data it yielded between 2012 and 2019 to examine the local expansion of the insect. These data were gathered with occurrences form various sources (GBIF, literature) to calibrate a species niche model and assess potential current BMSB range. We evaluated the potential changes to the BMSB range due to climate change by projecting the model according to 6 global circulation models (GCM) and the shared socio-economic pathways SSP245 in two time periods 2021–2040 and 2041–2060. Citizen science allowed to track BMSB expansion in France and provided information about its phenology and its habitat preferences. The model highlighted the potential for further range expansion in Europe and illustrated the impact of climate change. These results could help managing the current BMSB invasion and the framework of this survey could contribute to a better preparedness of phytosanitary authorities either for the BMSB or other invasive pests.
Immunological and hematological outcomes following protracted low dose/low dose rate ionizing radiation and simulated microgravity
Authors: Paul Amber M. , Overbey Eliah G. , da Silveira Willian A. , Szewczyk Nathaniel , Nishiyama Nina C. , Pecaut Michael J. , Anand Sulekha , Galazka Jonathan M. , Mao Xiao Wen 
Published: June 2021

AbstractUsing a ground-based model to simulate spaceflight [21-days of single-housed, hindlimb unloading (HLU) combined with continuous low-dose gamma irradiation (LDR, total dose of 0.04 Gy)], an in-depth survey of the immune and hematological systems of mice at 7-days post-exposure was performed. Collected blood was profiled with a hematology analyzer and spleens were analyzed by whole transcriptome shotgun sequencing (RNA-sequencing). The results revealed negligible differences in immune differentials. However, hematological system analyses of whole blood indicated large disparities in red blood cell differentials and morphology, suggestive of anemia. Murine Reactome networks indicated majority of spleen cells displayed differentially expressed genes (DEG) involved in signal transduction, metabolism, cell cycle, chromatin organization, and DNA repair. Although immune differentials were not changed, DEG analysis of the spleen revealed expression profiles associated with inflammation and dysregulated immune function persist to 1-week post-simulated spaceflight. Additionally, specific regulation pathways associated with human blood disease gene orthologs, such as blood pressure regulation, transforming growth factor-β receptor signaling, and B cell differentiation were noted. Collectively, this study revealed differential immune and hematological outcomes 1-week post-simulated spaceflight conditions, suggesting recovery from spaceflight is an unremitting process.
Genome-wide analysis of RING-type E3 ligase family identifies potential candidates regulating high amylose starch biosynthesis in wheat (Triticum aestivum L.)
Authors: Parveen Afsana , Rahim Mohammed Saba , Sharma Ankita , Mishra Ankita , Kumar Prashant , Fandade Vikas , Kumar Pankaj , Bhandawat Abhishek , Verma Shailender Kumar , Roy Joy 
Published: June 2021

AbstractIn ubiquitin-mediated post-translational modifications, RING finger families are emerged as important E3 ligases in regulating biological processes. Amylose and amylopectin are two major constituents of starch in wheat seed endosperm. Studies have been found the beneficial effects of high amylose or resistant starch on health. The ubiquitin-mediated post-translational regulation of key enzymes for amylose/amylopectin biosynthesis (GBSSI and SBEII) is still unknown. In this study, the genome-wide analysis identified 1272 RING domains in 1255 proteins in wheat, which is not reported earlier. The identified RING domains classified into four groups—RING-H2, RING-HC, RING-v, RING-G, based on the amino acid residues (Cys, His) at metal ligand positions and the number of residues between them with the predominance of RING-H2 type. A total of 1238 RING protein genes were found to be distributed across all 21 wheat chromosomes. Among them, 1080 RING protein genes were identified to show whole genome/segmental duplication within the hexaploid wheat genome. In silico expression analysis using transcriptome data revealed 698 RING protein genes, having a possible role in seed development. Based on differential gene expression and correlation analysis of 36 RING protein genes in diverse (high and low) amylose mutants and parent, 10 potential RING protein genes found to be involved in high amylose biosynthesis and significantly associated with two starch biosynthesis genes; GBSSI and SBEIIa. Characterization of mutant lines using next-generation sequencing method identified unique mutations in 698 RING protein genes. This study signifies the putative role of RING-type E3 ligases in amylose biosynthesis and this information will be helpful for further functional validation and its role in other biological processes in wheat.
p62 overexpression induces TDP-43 cytoplasmic mislocalisation, aggregation and cleavage and neuronal death
Authors: Foster A. D. , Flynn L. L. , Cluning C. , Cheng F. , Davidson J. M. , Lee A. , Polain N. , Mejzini R. , Farrawell N. , Yerbury J. J. , Layfield R. , Akkari P. A. , Rea S. L. 
Published: June 2021

AbstractAmyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) that exist on a spectrum of neurodegenerative disease. A hallmark of pathology is cytoplasmic TDP-43 aggregates within neurons, observed in 97% of ALS cases and ~ 50% of FTLD cases. This mislocalisation from the nucleus into the cytoplasm and TDP-43 cleavage are associated with pathology, however, the drivers of these changes are unknown. p62 is invariably also present within these aggregates. We show that p62 overexpression causes TDP-43 mislocalisation into cytoplasmic aggregates, and aberrant TDP-43 cleavage that was dependent on both the PB1 and ubiquitin-associated (UBA) domains of p62. We further show that p62 overexpression induces neuron death. We found that stressors (proteasome inhibition and arsenic) increased p62 expression and that this shifted the nuclear:cytoplasmic TDP-43 ratio. Overall, our study suggests that environmental factors that increase p62 may thereby contribute to TDP-43 pathology in ALS and FTLD.
Percolation and tortuosity in heart-like cells
Authors: Rabinovitch R. , Biton Y. , Braunstein D. , Aviram I. , Thieberger R. , Rabinovitch A. 
Published: June 2021

AbstractIn the last several years, quite a few papers on the joint question of transport, tortuosity and percolation have appeared in the literature, dealing with passage of miscellaneous liquids or electrical currents in different media. However, these methods have not been applied to the passage of action potential in heart fibrosis (HF), which is crucial for problems of heart arrhythmia, especially of atrial tachycardia and fibrillation. In this work we address the HF problem from these aspects. A cellular automaton model is used to analyze percolation and transport of a distributed-fibrosis inflicted heart-like tissue. Although based on a rather simple mathematical model, it leads to several important outcomes: (1) It is shown that, for a single wave front (as the one emanated by the heart's sinus node), the percolation of heart-like matrices is exactly similar to the forest fire case. (2) It is shown that, on the average, the shape of the transport (a question not dealt with in relation to forest fire, and deals with the delay of action potential when passing a fibrotic tissue) behaves like a Gaussian. (3) Moreover, it is shown that close to the percolation threshold the parameters of this Gaussian behave in a critical way. From the physical point of view, these three results are an important contribution to the general percolation investigation. The relevance of our results to cardiological issues, specifically to the question of reentry initiation, are discussed and it is shown that: (A) Without an ectopic source and under a mere sinus node operation, no arrhythmia is generated, and (B) A sufficiently high refractory period could prevent some reentry mechanisms, even in partially fibrotic heart tissue.
Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method
Authors: Su Chia-Hao , Chen Hui-Lung , Ju Shin-Pon , You Tai-Ding , Lin Yu-Sheng , Tseng Ta-Feng 
Published: June 2021

AbstractThe stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpAadsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpAbinds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpAnucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.
Enhanced thin-film transistor driven high-aperture in-plane switching liquid crystal displays without common line and black matrix
Authors: Ando Masahiko , Yoneya Makoto 
Published: June 2021

AbstractWe developed active-matrix in-plane switching liquid crystal displays (IPS-LCDs) with a new vertical structure composed of thin-film transistors (TFTs) that have an aperture ratio of 60% to reduce energy consumption. The novel TFT has a channel and a back channel made of a hydrogenated amorphous-silicon semiconductor layer sandwiched by thin silicon oxide insulating layers. The transfer characteristics are enhanced by uniformly shifting the threshold voltage to be higher than the maximum LC driving voltage (typically > 5 V). The enhanced TFT characteristics provided with a new driving scheme and shielding electrodes enables both the common line and black matrix to be eliminated. We fabricated an IPS TFT-LCD panel with aperture and contrast ratios that are 160% those of the conventional pixel structure.
A selective cytotoxic adenovirus vector for concentration of pluripotent stem cells in human pluripotent stem cell-derived neural progenitor cells
Authors: Hirai Takamasa , Kono Ken , Sawada Rumi , Kuroda Takuya , Yasuda Satoshi , Matsuyama Satoko , Matsuyama Akifumi , Koizumi Naoya , Utoguchi Naoki , Mizuguchi Hiroyuki , Sato Yoji 
Published: June 2021

AbstractHighly sensitive detection of residual undifferentiated pluripotent stem cells is essential for the quality and safety of cell-processed therapeutic products derived from human induced pluripotent stem cells (hiPSCs). We previously reported the generation of an adenovirus (Ad) vector and adeno-associated virus vectors that possess a suicide gene, inducible Caspase 9 (iCasp9), which makes it possible to sensitively detect undifferentiated hiPSCs in cultures of hiPSC-derived cardiomyocytes. In this study, we investigated whether these vectors also allow for detection of undifferentiated hiPSCs in preparations of hiPSC-derived neural progenitor cells (hiPSC-NPCs), which have been expected to treat neurological disorders. To detect undifferentiated hiPSCs, the expression of pluripotent stem cell markers was determined by immunostaining and flow cytometry. Using immortalized NPCs as a model, the Ad vector was identified to be the most efficient among the vectors tested in detecting undifferentiated hiPSCs. Moreover, we found that the Ad vector killed most hiPSC-NPCs in an iCasp9-dependent manner, enabling flow cytometry to detect undifferentiated hiPSCs intermingled at a lower concentration (0.002%) than reported previously (0.1%). These data indicate that the Ad vector selectively eliminates hiPSC-NPCs, thus allowing for sensitive detection of hiPSCs. This cytotoxic viral vector could contribute to ensuring the quality and safety of hiPSCs-NPCs for therapeutic use.
Association between sleep habits/disorders and emotional/behavioral problems among Japanese children
Authors: Takeshima Masahiro , Ohta Hidenobu , Hosoya Tomoko , Okada Masakazu , Iida Yukako , Moriwaki Aiko , Takahashi Hidetoshi , Kamio Yoko , Mishima Kazuo 
Published: June 2021

AbstractActual sleep status and the association between sleep habits/disorders and emotional/behavioral problems among children in the development stage have not been fully clarified. A questionnaire survey was conducted on the sleep habits/disorders (Brief Child Sleep Questionnaire; BCSQ) and emotional/behavioral problems (Strengths and Difficulties Questionnaire; SDQ) of 87,548 children enrolled in ordinary classes in nine grade levels from the first grade of elementary school to the third grade of junior high school from December 2009 to April 2010. As school grade increased, children’s bedtimes were delayed and sleep duration was reduced by 2.0 h over the nine grade levels. Based on the BCSQ, 18.3% of children were judged to have some type of sleep disorder, and about 30% to 40% of children had sleep symptoms at bedtime, during sleep, and at wake time. Multiple regression analysis showed that emotional and behavioral problems were associated with presence of any sleep symptom, longer sleep latency, and longer awake time after sleep onset, whereas total sleep time was not. Sleep symptoms at wake time were most strongly associated with emotional and behavioral problems. Status of sleep habits/disorders should be considered when interpreting emotional/behavioral problems in school-age children.
Effect of age and body mass index on vitamin D level in children with asthma in Riyadh
Authors: Bindayel Iman Abdullah 
Published: June 2021

AbstractVitamin D deficiency prevalence in children has been rising. Low 25-hydroxyvitamin D3 (25(OH)D3) levels contribute to poor asthma control in children. This study assessed 25(OH)D3 levels in children with asthma from Riyadh with respect to anthropometrics, dietary, and lifestyle variables. Children with asthma (n, 60; 2–17 years) were assessed for serum 25-hydroxy vitamin D3 (25(OH)D3) level and body anthropometrics (weight, height, and body mass index [BMI]). Vitamin D dietary intake, sun exposure, and sociodemographic data were collected using a structured questionnaire. Thirty-one children (52%) had a 25(OH)D3 level < 50 nmol/L, 15 of whom (25%) had a level < 30 nmol/L. 25(OH)D3 level was significantly negatively correlated with age (P < 0.05), weight (P < 0.02), and height (P < 0.05). Children with a 25(OH)D3 level < 30 nmol/L had a significantly higher BMI than children with insufficient and sufficient vitamin D levels (P < 0.01). There was no significant effect of sex on 25(OH)D3 level. Higher 25(OH)D3 level was associated with a greater body area exposure to the sun. This study found that > 50% of the children with asthma had below sufficiency vitamin D levels. The vitamin D screening and supplementation of older and overweight children with asthma is recommended.
Reliability and efficacy of maximum fluorescein tear break-up time in diagnosing dry eye disease
Authors: Mou Yujie , Xiang Huan , Lin Lin , Yuan Kelan , Wang Xin , Wu Yaying , Min Jinjin , Jin Xiuming 
Published: June 2021

AbstractThis study aims to investigate the reliability and efficacy of maximum fluorescein tear break-up time (FTBUTmax) in diagnosing dry eye disease (DED). 147 participants were enrolled in this study. Ocular symptoms were assessed by Ocular Surface Disease Index (OSDI). The fluorescein tear break-up time (FTBUT) examination, corneal fluorescein staining (CFS), and Schirmer I test were performed on both eyes. Each participant underwent 3 consecutive FTBUT tests, and five types of FTBUT values including FTBUTmax, the minimum FTBUT (FTBUTmin), the first FTBUT (FTBUT1), the average of three FTBUTs (FTBUT123) and the average of the first and second FTBUT (FTBUT12) were recorded. FTBUTmax was larger than the other FTBUT values, but no differences were found among the values of FTBUT1, FTBUT123, FTBUT12 and FTBUTmin. In the ROC analysis, FTBUTmax had the largest or the second largest area under the ROC (AUROC) in all three DED diagnostic criteria, while FTBUTmin had the least AUROC of them. ROC efficacy of FTBUTmax was significantly higher than that of FTBUT123, FTBUT12, FTBUT1 and FTBUTmin in the OSDI criteria and higher than that of FTBUT1 and FTBUTmin in Schirmer I test and CFS tests. FTBUTmax has a close correlation with OSDI, Schirmer I test and CFS, and is an effective tool for the DED diagnosis.
Systems biology approach highlights mechanistic differences between Crohn’s disease and ulcerative colitis
Authors: Ruiz Castro Pedro A. , Yepiskoposyan Hasmik , Gubian Sylvain , Calvino-Martin Florian , Kogel Ulrike , Renggli Kasper , Peitsch Manuel C. , Hoeng Julia , Talikka Marja 
Published: June 2021

AbstractThe molecular mechanisms of IBD have been the subject of intensive exploration. We, therefore, assembled the available information into a suite of causal biological network models, which offer comprehensive visualization of the processes underlying IBD. Scientific text was curated by using Biological Expression Language (BEL) and compiled with OpenBEL 3.0.0. Network properties were analysed by Cytoscape. Network perturbation amplitudes were computed to score the network models with transcriptomic data from public data repositories. The IBD network model suite consists of three independent models that represent signalling pathways that contribute to IBD. In the “intestinal permeability” model, programmed cell death factors were downregulated in CD and upregulated in UC. In the “inflammation” model, PPARG, IL6, and IFN-associated pathways were prominent regulatory factors in both diseases. In the “wound healing” model, factors promoting wound healing were upregulated in CD and downregulated in UC. Scoring of publicly available transcriptomic datasets onto these network models demonstrated that the IBD models capture the perturbation in each dataset accurately. The IBD network model suite can provide better mechanistic insights of the transcriptional changes in IBD and constitutes a valuable tool in personalized medicine to further understand individual drug responses in IBD.
Impacts of Atlantic multidecadal variability on the tropical Pacific: a multi-model study
Authors: Ruprich-Robert Yohan , Moreno-Chamarro Eduardo , Levine Xavier , Bellucci Alessio , Cassou Christophe , Castruccio Frederic , Davini Paolo , Eade Rosie , Gastineau Guillaume , Hermanson Leon , Hodson Dan , Lohmann Katja , Lopez-Parages Jorge , Monerie Paul-Arthur , Nicolì Dario , Qasmi Said , Roberts Christopher D. , Sanchez-Gomez Emilia , Danabasoglu Gokhan , Dunstone Nick , Martin-Rey Marta , Msadek Rym , Robson Jon , Smith Doug , Tourigny Etienne 
Published: June 2021

AbstractAtlantic multidecadal variability (AMV) has been linked to the observed slowdown of global warming over 1998–2012 through its impact on the tropical Pacific. Given the global importance of tropical Pacific variability, better understanding this Atlantic–Pacific teleconnection is key for improving climate predictions, but the robustness and strength of this link are uncertain. Analyzing a multi-model set of sensitivity experiments, we find that models differ by a factor of 10 in simulating the amplitude of the Equatorial Pacific cooling response to observed AMV warming. The inter-model spread is mainly driven by different amounts of moist static energy injection from the tropical Atlantic surface into the upper troposphere. We reduce this inter-model uncertainty by analytically correcting models for their mean precipitation biases and we quantify that, following an observed 0.26 °C AMV warming, the equatorial Pacific cools by 0.11 °C with an inter-model standard deviation of 0.03 °C.
Numerical investigations of the compressible Navier-Stokes system
Authors: Al-Taki Bilal , Atsou Kevin , Casanova Jean-Jéróme , Goudon Thierry , Lafitte Pauline , Lagoutière Frédéric , Minjeaud Sebastian 
Published: June 2021

In this paper we write, analyze and experimentally compare three different numerical schemes dedicated to the one dimensional barotropic Navier-Stokes equations:
a staggered scheme based on the Rusanov one for the inviscid (Euler) system,a staggered pseudo-Lagrangian scheme in which the mesh “follows” the fluid,the Eulerian projection (on a fixed mesh) of the preceding scheme.
All these schemes only involve the resolution of linear systems (all the nonlinear terms are solved in an explicit way). We propose numerical illustrations of their behaviors on particular solutions in which the density has discontinuities (hereafter called Hoff solutions). We show that the three schemes seem to converge to the same solutions, and we compare the evolution of the amplitude of the discontinuity of the numerical solution (with the pseudo-Lagrangian scheme) with the one predicted by Hoff and observe a good agreement.