bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deformation analysis of lipid membranes subjected to general forms of intra-membrane viscous flow and interactions with an elliptical-cross-section substrate
Authors: Liu Zhe , Kim Chun-il 
Published: January 2020

AbstractWe study the morphology of lipid membranes subjected to intra-membrane viscous flows and interactions with elliptical cylinder substrates. From the non-linear theory of elastic surfaces, a linearized shape equation and admissible boundary conditions are formulated in elliptical coordinates via the Monge representation of a surface. In particular, the intra-membrane viscosity terms are linearized and mapped into elliptic coordinates in order to accommodate more general forms of viscous flow. The assimilated viscous flow is characterized by potential functions which satisfies the continuity condition. A complete solution in terms of Mathieu function is then obtained within the prescription of incremental deformations superposed on large. The results describe smooth morphological transitions over the domain of interest and, more importantly, predicts wrinkle formations in the presence of intra-membrane viscous flow in the surface. Lastly, the obtained solution accommodates the results from the circular cases in the limit of vanishing eccentricity and intra-membrane viscous flow.
Decision-making process during collective movement initiation in golden snub-nosed monkeys (Rhinopithecus roxellana)
Authors: Wang Chengliang , Pan Ruliang , Wang Xiaowei , Qi Xiaoguang , Zhao Haitao , Guo Songtao , Ren Yi , Fu Weiwei , Zhu Zirui , Li Baoguo 
Published: January 2020

AbstractCollective decision-making is important for coordination and synchronization of the activities among group-living animals and the mechanisms guiding such procedure involve a great variety of characteristics of behavior and motivation. This study provides some evidence investigating collective movement initiation in a multi-level social band of the golden snub-nosed monkeys (Rhinopithecus roxellana) located in the Mts. Qinling, China. We collect 1223 datum records relevant to decision initiation from six OMUs. The results indicate that collective movement initiation could be divided into two continual but relatively independent processes: decisions on moving direction and movement implementation. In both processes, adult individuals are more likely to initiate the decision-making, while other adults vote on initiator’s preference, with a threshold, a supporting number required for a success. Thus, voting behavior and quorum fulfillment contribute to a successful decision-making. Adult individuals play important role in making decisions for moving direction and implementation. For a successful collective movement initiation, the individuals being more central in grooming network initiate decisions more frequently than the others, and attract voters more easily. Furthermore, following the initiation, at least four positive voters are required for a direction decision and at least three positive voters are needed for the decision on movement implementation, which could be considered as the threshold of quorum numbers required for a successful decision. This study has provided some very interesting information and scientific evidence in understanding social structure and behaviors of the nonhuman primates with a social structure very similar to humans’. Thus, some results can directly be referred to the comprehension of human social structure and behavior.
Neural Networks Mediating Perceptual Learning in Congenital Blindness
Authors: Chebat Daniel-Robert , Schneider Fabien C. , Ptito Maurice 
Published: January 2020

AbstractDespite the fact that complete visual deprivation leads to volumetric reductions in brain structures associated with spatial learning, blind individuals are still able to navigate. The neural structures involved in this function are not fully understood. Our study aims to correlate the performance of congenitally blind individuals (CB) and blindfolded sighted controls (SC) in a life-size obstacle-course using a visual-to-tactile sensory substitution device, with the size of brain structures (voxel based morphometry-VBM-) measured through structural magnetic resonance Imaging (MRI). VBM was used to extract grey matter volumes within several a-priori defined brain regions in all participants. Principal component analysis was utilized to group brain regions in factors and orthogonalize brain volumes. Regression analyses were then performed to link learning abilities to these factors. We found that (1) both CB and SC were able to learn to detect and avoid obstacles; (2) their learning rates for obstacle detection and avoidance correlated significantly with the volume of brain structures known to be involved in spatial skills. There is a similar relation between regions of the dorsal stream network and avoidance for both SC and CB whereas for detection, SC rely more on medial temporal lobe structures and CB on sensorimotor areas.
Transcriptome analyses revealed molecular responses of Cynanchum auriculatum leaves to saline stress
Authors: Zhang Ming , Hong Li-Zhou , Gu Min-Feng , Wu Cheng-Dong , Zhang Gen 
Published: January 2020

AbstractCynanchum auriculatum is a traditional herbal medicine in China and can grow in saline soils. However, little is known in relation to the underlying molecular mechanisms. In the present study, C. auriculatum seedlings were exposed to 3.75‰ and 7.5‰ salinity. Next, transcriptome profiles of leaves were compared. Transcriptome sequencing showed 35,593 and 58,046 differentially expressed genes (DEGs) in treatments with 3.75‰ and 7.5‰, compared with the control, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these DEGs enriched various defense-related biological pathways, including ROS scavenging, ion transportation, lipid metabolism and plant hormone signaling. Further analyses suggested that C. auriculatum up-regulated Na+/H+ exchanger and V-type proton ATPase to avoid accumulation of Na+. The flavonoid and phenylpropanoids biosynthesis pathways were activated, which might increase antioxidant capacity in response to saline stress. The auxin and ethylene signaling pathways were upregulated in response to saline treatments, both of which are important plant hormones. Overall, these results raised new insights to further investigate molecular mechanisms underlying resistance of C. auriculatum to saline stress.
Biodegradability of woody film produced by solvent volatilisation of Japanese Beech solution
Authors: Nishiwaki-Akine Yuri , Kanazawa Sui , Matsuura Norihisa , Yamamoto-Ikemoto Ryoko 
Published: January 2020

AbstractTo address the problem of marine pollution from discarded plastics, we developed a highly biodegradable woody film, with almost the same components as wood, from the formic acid solution of ball-milled wood. We found that the woody film was not easily degraded by cultured solution of hand bacteria (phylum Proteobacteria was dominant). However, the film was easily biodegraded when in cultured solution of soil (Firmicutes, especially class Bacilli, was dominant) for 4 weeks at 37 °C, or when buried in the soil itself, both under aerobic conditions (Acidobacteria and Proteobacteria were dominant) for 40 days at room temperature and under anaerobic conditions (Firmicutes, especially family Ruminococcaceae, was dominant) for 5 weeks at 37 °C. Moreover, when film was buried in the soil, more carbon dioxide was generated than from soil alone. Therefore, the film was not only brittle but formed of decomposable organic matter. We showed that the film does not decompose at the time of use when touched by the hand, but it decomposes easily when buried in the soil after use. We suggest that this biodegradable woody film can be used as a sustainable raw material in the future.
Evolutionary Dynamics Do Not Motivate a Single-Mutant Theory of Human Language
Authors: de Boer Bart , Thompson Bill , Ravignani Andrea , Boeckx Cedric 
Published: January 2020

AbstractOne of the most controversial hypotheses in cognitive science is the Chomskyan evolutionary conjecture that language arose instantaneously in humans through a single mutation. Here we analyze the evolutionary dynamics implied by this hypothesis, which has never been formalized before. The hypothesis supposes the emergence and fixation of a single mutant (capable of the syntactic operationMerge) during a narrow historical window as a result of frequency-independent selection under a huge fitness advantage in a population of an effective size no larger than ~15 000 individuals. We examine this proposal by combining diffusion analysis and extreme value theory to derive a probabilistic formulation of its dynamics. We find that although a macro-mutation is much more likely to go to fixation if it occurs, it is much more unlikelya priorithan multiple mutations with smaller fitness effects. The most likely scenario is therefore one where a medium number of mutations with medium fitness effects accumulate. This precise analysis of the probability of mutations occurring and going to fixation has not been done previously in the context of the evolution of language. Our results cast doubt on any suggestion that evolutionary reasoning provides an independent rationale for a single-mutant theory of language.
Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models
Authors: Saccenti Edoardo , Hendriks Margriet H. W. B. , Smilde Age K. 
Published: January 2020

AbstractCorrelation coefficients are abundantly used in the life sciences. Their use can be limited to simple exploratory analysis or to construct association networks for visualization but they are also basic ingredients for sophisticated multivariate data analysis methods. It is therefore important to have reliable estimates for correlation coefficients. In modern life sciences, comprehensive measurement techniques are used to measure metabolites, proteins, gene-expressions and other types of data. All these measurement techniques have errors. Whereas in the old days, with simple measurements, the errors were also simple, that is not the case anymore. Errors are heterogeneous, non-constant and not independent. This hampers the quality of the estimated correlation coefficients seriously. We will discuss the different types of errors as present in modern comprehensive life science data and show with theory, simulations and real-life data how these affect the correlation coefficients. We will briefly discuss ways to improve the estimation of such coefficients.
Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae
Authors: Bellot Sidonie , Mitchell Thomas C. , Schaefer Hanno 
Published: January 2020

AbstractPhylogenomic studies have so far mostly relied on genome skimming or target sequence capture, which suffer from representation bias and can fail to resolve relationships even with hundreds of loci. Here, we explored the potential of phylogenetic informativeness and tree confidence analyses to interpret phylogenomic datasets. We studied Cucurbitaceae because their small genome size allows cost-efficient genome skimming, and many relationships in the family remain controversial, preventing inferences on the evolution of characters such as sexual system or floral morphology. Genome skimming and PCR allowed us to retrieve the plastome, 57 single copy nuclear genes, and the nuclear ribosomal ITS from 29 species representing all but one tribe of Cucurbitaceae. Node support analyses revealed few inter-locus conflicts but a pervasive lack of phylogenetic signal among plastid loci, suggesting a fast divergence of Cucurbitaceae tribes. Data filtering based on phylogenetic informativeness and risk of homoplasy clarified tribe-level relationships, which support two independent evolutions of fringed petals in the family. Our study illustrates how formal analysis of phylogenomic data can increase our understanding of past diversification processes. Our data and results will facilitate the design of well-sampled phylogenomic studies in Cucurbitaceae and related families.
Endogenous and artificial miRNAs explore a rich variety of conformations: a potential relationship between secondary structure and biological functionality
Authors: Gangemi C. M. A. , Alaimo S. , Pulvirenti A. , García-Viñuales Sara , Milardi D. , Falanga A. P. , Fragalà M. E. , Oliviero G. , Piccialli G. , Borbone N. , Ferro A. , D’Urso A. , Croce C. M. , Purrello R. 
Published: January 2020

AbstractMature microRNAs are short non-coding RNA sequences which upon incorporation into the RISC ribonucleoprotein complex, play a crucial role in regulation of gene expression. However, miRNAs can exist within the cell also as free molecules fulfilling their biological activity. Therefore, it is emerging that in addition to sequence even the structure adopted by mature miRNAs might play an important role to reach the target. Indeed, we analysed by several spectroscopic techniques the secondary structures of two artificial miRNAs selected by computational tool (miR-Synth) as best candidates to silence c-MET and EGFR genes and of two endogenous miRNAs (miR-15a and miR-15b) having the same seed region, but different biological activity. Our results demonstrate that both endogenous and artificial miRNAs can arrange in several 3D-structures which affect their activity and selectivity toward the targets.
HDAC10 deletion promotes Foxp3+ T-regulatory cell function
Authors: Dahiya Satinder , Beier Ulf H. , Wang Liqing , Han Rongxiang , Jiao Jing , Akimova Tatiana , Angelin Alessia , Wallace Douglas C. , Hancock Wayne W. 
Published: January 2020

AbstractFoxp3+ T-regulatory (Treg) cells are capable of suppressing immune responses. Lysine acetylation is a key mechanism of post-translational control of various transcription factors, and when acetylated, Foxp3 is stabilized and transcriptionally active. Therefore, understanding the roles of various histone/protein deacetylases (HDAC) are key to promoting Treg-based immunotherapy. Several of the 11 classical HDAC enzymes are necessary for optimal Treg function while others are dispensable. We investigated the effect of HDAC10 in murine Tregs. HDAC10 deletion had no adverse effect on the health of mice, which retained normal CD4+ and CD8+ T cell function. However, HDAC10−/− Treg exhibited increased suppressive function in vitro and in vivo. C57BL/6 Rag1−/− mice adoptively transferred with HDAC10−/− but not wild Treg, were protected from developing colitis. HDAC10−/− but not wild-type mice receiving fully MHC-mismatched cardiac transplants became tolerant and showed long-term allograft survival (>100 d). We conclude that targeting of HDAC10 may be of therapeutic value for inflammatory disorders including colitis and also for transplantation.
Entanglement Detection via Direct-Sum Majorization Uncertainty Relations
Authors: Wang Kun , Wu Nan , Song Fangmin 
Published: January 2020

AbstractIn this paper we investigate the relationship between direct-sum majorization formulation of uncertainty relations and entanglement, for the case of two observables. Our primary results are entanglement detection methods based on direct-sum majorization uncertainty relations. These detectors provide a set of sufficient conditions for detecting entanglement whose number grows linearly with the dimension of the state being detected.
White matter microstructural changes in tuberous sclerosis: Evaluation by neurite orientation dispersion and density imaging (NODDI) and diffusion tensor images
Authors: Taoka Toshiaki , Aida Noriko , Fujii Yuta , Ichikawa Kazushi , Kawai Hisashi , Nakane Toshiki , Ito Rintaro , Naganawa Shinji 
Published: January 2020

AbstractNeurite orientation dispersion and density imaging (NODDI) is a novel diffusion method for evaluating tissue microstructure, and may provide additional information over conventional diffusion tensor imaging (DTI). We evaluated NODDI and DTI parameters in cases of tuberous sclerosis (TS) to assess microstructural changes in the white matter. Eleven cases of tuberous sclerosis and eight age-matched controls underwent NODDI and DTI. We performed qualitative analysis and tract-based spatial statistics (TBSS) analysis of the NODDI parameters (Ficv: intracellular volume fraction, Fiso: isotropic fraction, ODI: orientation dispersion index) as well as DTI parameters (MD: mean diffusivity, FA: fractional anisotropy). We also performed a correlation analysis between clinical symptoms and parameters. The qualitative analysis indicated that the Ficv had a lower value in TS cases particularly in the tubers adjacent to the white matter. The TBSS analysis showed that the TS cases had decreased Ficv in a greater area compared to the other parameters including MD. In particular, the Ficv was decreased in deep white matter, such as the superior longitudinal fascicles (SLF). The application of NODDI to TS cases revealed tissue microstructural changes, and particularly the Ficv could detect more widespread abnormalities in white matter structure compared to DTI parameters.
Landscape of transcriptome variations uncovering known and novel driver events in colorectal carcinoma
Authors: Pira Giovanna , Uva Paolo , Scanu Antonio Mario , Rocca Paolo Cossu , Murgia Luciano , Uleri Elena , Piu Claudia , Porcu Alberto , Carru Ciriaco , Manca Alessandra , Persico Ivana , Muroni Maria Rosaria , Sanges Francesca , Serra Caterina , Dolei Antonia , Angius Andrea , De Miglio Maria Rosaria 
Published: January 2020

AbstractWe focused on an integrated view of genomic changes in Colorectal cancer (CRC) and distant normal colon tissue (NTC) to test the effectiveness of expression profiling on identification of molecular targets. We performed transcriptome on 16 primary coupled CRC and NTC tissues. We identified pathways and networks related to pathophysiology of CRC and selected potential therapeutic targets. CRC cells have multiple ways to reprogram its transcriptome: a functional enrichment analysis in 285 genes, 25% mutated, showed that they control the major cellular processes known to promote tumorigenesis. Among the genes showing alternative splicing, cell cycle related genes were upregulated (CCND1, CDC25B, MCM2, MCM3), while genes involved in fatty acid metabolism (ACAAA2, ACADS, ACAT1, ACOX, CPT1A, HMGCS2) were downregulated. Overall 148 genes showed differential splicing identifying 17 new isoforms. Most of them are involved in the pathogenesis of CRC, although the functions of these variants remain unknown. We identified 2 in-frame fusion events, KRT19-KRT18 and EEF1A1-HSP90AB1, encoding for chemical proteins in two CRC patients. We draw a functional interactome map involving integrated multiple genomic features in CRC. Finally, we underline that two functional cell programs are prevalently deregulated and absolutely crucial to determinate and sustain CRC phenotype.
Metabolomics Reveals that Cysteine Metabolism Plays a Role in Celastrol-Induced Mitochondrial Apoptosis in HL-60 and NB-4 Cells
Authors: Chen Minjian , Yang Jing , Li Lei , Hu Yanhui , Lu Xiaomei , Sun Rongli , Wang Yubang , Wang Xinru , Zhang Xiaoling 
Published: January 2020

AbstractRecently, celastrol has shown great potential for inducing apoptosis in acute myeloid leukemia cells, especially acute promyelocytic leukaemia cells. However, the mechanism is poorly understood. Metabolomics provides an overall understanding of metabolic mechanisms to illustrate celastrol's mechanism of action. We treated both nude mice bearing HL-60 cell xenografts in vivo and HL-60 cells as well as NB-4 cells in vitro with celastrol. Ultra-performance liquid chromatography coupled with mass spectrometry was used for metabolomics analysis of HL-60 cells in vivo and for targeted L-cysteine analysis in HL-60 and NB-4 cells in vitro. Flow cytometric analysis was performed to assess mitochondrial membrane potential, reactive oxygen species and apoptosis. Western blotting was conducted to detect the p53, Bax, cleaved caspase 9 and cleaved caspase 3 proteins. Celastrol inhibited tumour growth, induced apoptosis, and upregulated pro-apoptotic proteins in the xenograft tumour mouse model. Metabolomics showed that cysteine metabolism was the key metabolic alteration after celastrol treatment in HL-60 cells in vivo. Celastrol decreased L-cysteine in HL-60 cells. Acetylcysteine supplementation reversed reactive oxygen species accumulation and apoptosis induced by celastrol and reversed the dramatic decrease in the mitochondrial membrane potential and upregulation of pro-apoptotic proteins in HL-60 cells. In NB-4 cells, celastrol decreased L-cysteine, and acetylcysteine reversed celastrol-induced reactive oxygen species accumulation and apoptosis. We are the first to identify the involvement of a cysteine metabolism/reactive oxygen species/p53/Bax/caspase 9/caspase 3 pathway in celastrol-triggered mitochondrial apoptosis in HL-60 and NB-4 cells, providing a novel underlying mechanism through which celastrol could be used to treat acute myeloid leukaemia, especially acute promyelocytic leukaemia.
Analysis of histological and microRNA profiles changes in rabbit skin development
Authors: Ding Haisheng , Cheng Guanglong , Leng Jianjian , Yang Yongxin , Zhao Xiaowei , Wang Xiaofei , Qi Yunxia , Huang Dongwei , Zhao Huiling 
Published: January 2020

AbstractThe periodic regrowth of rabbit fur is economically important. Here, we aimed to characterise the histological traits and microRNA (miRNA) expression profiles in the skin tissue of Wan Strain Angora rabbits at different weeks after plucking. Haematoxylin-eosin staining showed that hair follicles were in the telogen phase in the first week, while they were in the anagen phase from the fourth to twenty-fourth weeks. In addition, two small RNA libraries derived from skin samples of Wan Strain Angora rabbits at telogen and anagen stages yielded over 24 million high-quality reads. Specifically, 185 miRNAs were differentially expressed between the telogen and anagen phases. The function of the differentially expressed miRNAs was explored by comparing them with known mammalian miRNAs and by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of their predicted targets. Five new functional miRNAs were validated using quantitative real-time PCR. Moreover, the fibroblast growth factor 5 (FGF5) gene was verified to be a target of conservative_NC_013672.1_9290 and conservative_NC_013675.1_10734. We investigated differential miRNA profiles between the telogen and anagen phases of the hair cycle and our findings provide a basis for future studies focusing on the mechanisms of miRNA-mediated regulation of rabbit hair follicle cycling.