bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo evidence of functional and anatomical stripe-based subdivisions in human V2 and V3
Authors: Dumoulin Serge O. , Harvey Ben M. , Fracasso Alessio , Zuiderbaan Wietske , Luijten Peter R. , Wandell Brian A. , Petridou Natalia 
Published: April 2017

AbstractVisual cortex contains a hierarchy of visual areas. The earliest cortical area (V1) contains neurons responding to colour, form and motion. Later areas specialize on processing of specific features. The second visual area (V2) in non-human primates contains a stripe-based anatomical organization, initially defined using cytochrome-oxidase staining of post-mortem tissue. Neurons in these stripes have been proposed to serve distinct functional specializations, e.g. processing of color, form and motion. These stripes represent an intermediate stage in visual hierarchy and serve a key role in the increasing functional specialization of visual areas. Using sub-millimeter high-field functional and anatomical MRI (7T), we provide in vivo evidence for stripe-based subdivisions in humans. Using functional MRI, we contrasted responses elicited by stimuli alternating at slow and fast temporal frequencies. We revealed stripe-based subdivisions in V2 ending at the V1/V2 border. The human stripes reach into V3. Using anatomical MRI optimized for myelin contrast within gray matter, we also observe a stripe pattern. Stripe subdivisions preferentially responding to fast temporal frequencies are more myelinated. As such, functional and anatomical measures provide independent and converging evidence for functional organization into striped-based subdivisions in human V2 and V3.
DNA word analysis based on the distribution of the distances between symmetric words
Authors: Tavares Ana H. M. P. , Pinho Armando J. , Silva Raquel M. , Rodrigues João M. O. S. , Bastos Carlos A. C. , Ferreira Paulo J. S. G. , Afreixo Vera 
Published: April 2017

AbstractWe address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short distances between symmetric word pairs may allow the occurrence of non-standard DNA conformations, such as hairpin/cruciform structures. We focused on the human genome, and analysed both the complete genome as well as a version with known repetitive sequences masked out. We reported several well-defined features in the distributions of distances, which can be classified into three different profiles, showing enrichment in distinct distance ranges. We analysed in greater detail certain pairs of symmetric words of length seven, found by our procedure, characterised by the surprising fact that they occur at single distances more frequently than expected.
Associations of metabolic disorder factors with the risk of uncontrolled hypertension: a follow-up cohort in rural China
Authors: Xiao Jing , Hua Tianqi , Shen Huan , Zhang Min , Wang Xiao-Jian , Gao Yue-Xia , Lu Qinyun , Wu Chuanli 
Published: April 2017

AbstractWe evaluated how metabolic disorders affected antihypertension therapy. 2,912 rural Chinese patients with hypertension who provided blood samples, demographic and clinical data at baseline and after 1 year of antihypertension therapy were evaluated. At baseline, 1,515 patients (52.0%) were already receiving drug therapy and 11.4% of them had controlled blood pressure (BP). After 1 year, all 2,912 patients were receiving antihypertension therapy that was administered by community physicians, and 59.42% of them had controlled BP. Central obesity and abnormal triglyceride, high-density lipoprotein cholesterol, and glucose were associated with 15–70% higher risks of uncontrolled hypertension. Metabolic syndrome using the JIS criteria was associated with poor BP control (odds ratio: 1.71 and 1.54 for the baseline and follow-up datasets, respectively). The risk of uncontrolled hypertension increased with the number of metabolic disorders (p for trend <0.01). The presence of ≥3 metabolic disorder factors was associated with higher risks of poor BP control. The associations of metabolic factors and uncontrolled hypertension were stronger for the standard and modified ATP III criteria, compared to the IDF and JIS criteria. Metabolic factors were associated with less effective antihypertension therapy, and all definitions of metabolic syndrome helped identify patients with elevated risks of uncontrolled hypertension.
RNA sequence analysis of rat acute experimental pancreatitis with and without fatty liver: a gene expression profiling comparative study
Authors: Wang Qian , Yan Hongkai , Wang Gang , Qiu Zhaoyan , Bai Bin , Wang Shiqi , Yu Pengfei , Feng Quanxin , Zhao Qingchuan , He Xianli , Liu Chaoxu 
Published: April 2017

AbstractFatty liver (FL) is one of the risk factors for acute pancreatitis and is also indicative of a worse prognosis as compared to acute pancreatitis without fatty liver (AP). The aim of the present study was to analyze, at the hepatic level, the differentially expressed genes (DEGs) between acute pancreatitis with fatty liver (APFL) rats and AP rats. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses of these DEGs indicated that PPARα signalling pathway and fatty acid degradation pathway may be involved in the pathological process of APFL, which indicated that fatty liver may aggravate pancreatitis through these pathways. Moreover, the excessive activation of JAK/STAT signaling pathway and toll-like receptor signaling pathway was also found in APFL group as shown in heat map. In conclusion, the inhibition of PPARα signaling pathway and the fatty acid degradation pathway may lead to the further disorder of lipid metabolism, which can aggravate pancreatitis.
Improving Optical Temperature Sensing Performance of Er3+ Doped Y2O3 Microtubes via Co-doping and Controlling Excitation Power
Authors: Wang Xiangfu , Wang Ye , Marques-Hueso Jose , Yan Xiaohong 
Published: April 2017

AbstractThis work presents a new method to effectively improve the optical temperature behavior of Er3+ doped Y2O3 microtubes by co-doping of Tm3+ or Ho3+ ion and controlling excitation power. The influence of Tm3+ or Ho3+ ion on optical temperature behavior of Y2O3:Er3+ microtubes is investigated by analyzing the temperature and excitation power dependent emission spectra, thermal quenching ratios, fluorescence intensity ratios, and sensitivity. It is found that the thermal quenching of Y2O3:Er3+ microtubes is inhibited by co-doping with Tm3+ or Ho3+ ion, moreover the maximum sensitivity value based on the thermal coupled 4S3/2/2H11/2 levels is enhanced greatly and shifts to the high temperature range, while the maximum sensitivity based on 4F9/2(1)/4F9/2(2) levels shifts to the low temperature range and greatly increases. The sensitivity values are dependent on the excitation power, and reach two maximum values of 0.0529/K at 24 K and 0.0057/K at 457 K for the Y2O3:1%Er3+, 0.5%Ho3+ at 121 mW/mm2 excitation power, which makes optical temperature measurement in wide temperature range possible. The mechanism of changing the sensitivity upon different excitation densities is discussed.
Molecular classification of prostate adenocarcinoma by the integrated somatic mutation profiles and molecular network
Authors: Yang Lei , Wang Shiyuan , Zhou Meng , Chen Xiaowen , Jiang Wei , Zuo Yongchun , Lv Yingli 
Published: April 2017

AbstractProstate cancer is one of the most common cancers in men and a leading cause of cancer death worldwide, displaying a broad range of heterogeneity in terms of clinical and molecular behavior. Increasing evidence suggests that classifying prostate cancers into distinct molecular subtypes is critical to exploring the potential molecular variation underlying this heterogeneity and to better treat this cancer. In this study, the somatic mutation profiles of prostate cancer were downloaded from the TCGA database and used as the source nodes of the random walk with restart algorithm (RWRA) for generating smoothed mutation profiles in the STRING network. The smoothed mutation profiles were selected as the input matrix of the Graph-regularized Nonnegative Matrix Factorization (GNMF) for classifying patients into distinct molecular subtypes. The results were associated with most of the clinical and pathological outcomes. In addition, some bioinformatics analyses were performed for the robust subtyping, and good results were obtained. These results indicated that prostate cancers can be usefully classified according to their mutation profiles, and we hope that these subtypes will help improve the treatment stratification of this cancer in the future.
LF-MF inhibits iron metabolism and suppresses lung cancer through activation of P53-miR-34a-E2F1/E2F3 pathway
Authors: Ren Jing , Ding Liang , Xu Qianyun , Shi Guoping , Li Xiaojing , Li Xiujun , Ji Jianjian , Zhang Dongya , Wang Yaping , Wang Tingting , Hou Yayi 
Published: April 2017

AbstractOur previous studies showed that low frequency magnetic fields (LF-MF) suppressed tumor growth and influenced the function of immune system. Nevertheless the mechanisms behind the effect of LF-MF still remain to be elucidated. In this study, Tumor- bearing mice subcutaneously inoculated with Lewis lung cancer cells were exposed to a LF-MF (0.4T, 7.5 Hz) for 35 days and Survival rate, tumor growth and the tumor markers were measured. Results showed that tumor growth was obviously inhibited with a prolonged survival of tumor- bearing mice by LF-MF exposure. In vitro experiments, LF-MF was found to induce cell growth arrest, cell senescence and inhibit iron metabolism of lung cancer cells. Moreover, LF-MF stabilized p53 protein via inhibiting cell iron metabolism and the stabilized p53 protein enhanced miR-34a transcription. Furthermore, increased expression of miR-34a induced cell proliferation inhibition, cell cycle arrest and cell senescence of lung cancer cells by targeting E2F1/E2F3. We also detected the relevant indicator in tumor tissue such as the iron content, the level of miR-34a and related protein, corresponding results were obtained. Taken together, these observations imply that LF-MF suppressed lung cancer via inhibiting cell iron metabolism, stabilizing p53 protein and activation P53- miR-34a-E2F1/E2F3 pathway.
Genetic and Proteomic characterization of Bile Salt Export Pump (BSEP) in Snake Liver
Authors: Tan Xinle , Gao Fei , Su Hexiu , Gong Yajun , Zhang Jie , Sullivan Mitchell A. , Chen Jiachun 
Published: April 2017

AbstractSnake gallbladder, a traditional Chinese medicine, has been believed in various Asian countries to improve visual acuity and alleviate rheumatism. Bile acids, a major component of the gallbladder, are toxic to the liver and kidney in humans and animals due to its detergent effects, while also exhibiting therapeutic effects due to an increase in the gallbladder contractions of muscle strips in patients with cholesterol gallstones. Secretion of bile acids in human and mammals depends on the bile salt export pump (BSEP), a liver-specific adenosine triphosphate (ATP)-binding cassette transporter encoded by ABCB11. However, the presence of BSEP in snakes has not been thoroughly explored. Here we confirm the existence of BSEP and its coding DNA sequence in snakes on both the proteomic and genetic level. This work provides information on the snake ABCB11 sequence and helps further potential genetic manipulation to affect bile salt metabolism. Our study provides the foundation for research on bile acid production from snakes by using modern genetic and proteomic methodologies.
Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China
Authors: Lv Yang , Hu Guangyao , Wang Chunyang , Yuan Wenjie , Wei Shanshan , Gao Jiaoqi , Wang Boyuan , Song Fangchao 
Published: April 2017

AbstractThe microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation.
Rapid, simple and direct detection of Meloidogyne hapla from infected root galls using loop-mediated isothermal amplification combined with FTA technology
Authors: Peng Huan , Long Haibo , Huang Wenkun , Liu Jing , Cui Jiangkuan , Kong Lingan , Hu Xianqi , Gu Jianfeng , Peng Deliang 
Published: April 2017

AbstractThe northern root-knot nematode (Meloidogyne hapla) is a damaging nematode that has caused serious economic losses worldwide. In the present study, a sensitive, simple and rapid method was developed for detection of M. hapla in infested plant roots by combining a Flinders Technology Associates (FTA) card with loop-mediated isothermal amplification (LAMP). The specific primers of LAMP were designed based on the distinction of internal transcribed spacer (ITS) sequences between M. hapla and other Meloidogyne spp. The LAMP assay can detect nematode genomic DNA at concentrations low to 1/200 000, which is 100 times more sensitive than conventional PCR. The LAMP was able to highly specifically distinguish M. hapla from other closely related nematode species. Furthermore, the advantages of the FTA-LAMP assay to detect M. hapla were demonstrated by assaying infected root galls that were artificially inoculated. In addition, M. hapla was successfully detected from six of forty-two field samples using FTA-LAMP technology. This study was the first to provide a simple diagnostic assay for M. hapla using the LAMP assay combined with FTA technology. In conclusion, the new FTA-LAMP assay has the potential for diagnosing infestation in the field and managing the pathogen M. hapla.
The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization
Authors: Messina Giovanni , Atterrato Maria Teresa , Prozzillo Yuri , Piacentini Lucia , Losada Ana , Dimitri Patrizio 
Published: April 2017

AbstractThe human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the first in vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
Identification and expression of cuticular protein genes based on Locusta migratoria transcriptome
Authors: Zhao Xiaoming , Gou Xin , Qin Zhongyu , Li Daqi , Wang Yan , Ma Enbo , Li Sheng , Zhang Jianzhen 
Published: April 2017

AbstractMany types of cuticular proteins are found in a single insect species, and their number and features are very diversified among insects. The cuticle matrix consists of many different proteins that confer the physical properties of the exoskeleton. However, the number and properties of cuticle proteins in Locusta migratoria remain unclear. In the present study, Illumina sequencing and de novo assembly were combined to characterize the transcriptome of L. migratoria. Eighty-one cuticular protein genes were identified and divided into five groups: the CPR family (51), Tweedle (2), CPF/CPFLs (9), CPAP family (9), and other genes (10). Based on the expression patterns in different tissues and stages, most of the genes as a test were distributed in the integument, pronotum and wings, and expressed in selected stages with different patterns. The results showed no obvious correlation between the expression patterns and the conservative motifs. Additionally, each cluster displayed a different expression pattern that may possess a different function in the cuticle. Furthermore, the complexity of the large variety of genes displayed differential expression during the molting cycle may be associated with cuticle formation and may provide insights into the gene networks related to cuticle formation.
Generation of Aptamers from A Primer-Free Randomized ssDNA Library Using Magnetic-Assisted Rapid Aptamer Selection
Authors: Tsao Shih-Ming , Lai Ji-Ching , Horng Horng-Er , Liu Tu-Chen , Hong Chin-Yih 
Published: April 2017

AbstractAptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences. The Magnetic-Assisted Rapid Aptamer Selection (MARAS) is a newly developed protocol for generating single-strand DNA aptamers. No repeat selection cycle is required in the protocol. This study proposes and demonstrates a method to isolate aptamers for C-reactive proteins (CRP) from a randomized ssDNA library containing no fixed sequences at 5′ and 3′ termini using the MARAS platform. Furthermore, the isolated primer-free aptamer was sequenced and binding affinity for CRP was analyzed. The specificity of the obtained aptamer was validated using blind serum samples. The result was consistent with monoclonal antibody-based nephelometry analysis, which indicated that a primer-free aptamer has high specificity toward targets. MARAS is a feasible platform for efficiently generating primer-free aptamers for clinical diagnoses.
DOSCATs: Double standards for protein quantification
Authors: Bennett Richard J. , Simpson Deborah M. , Holman Stephen W. , Ryan Sheila , Brownridge Philip , Eyers Claire E. , Colyer John , Beynon Robert J. 
Published: April 2017

AbstractThe two most common techniques for absolute protein quantification are based on either mass spectrometry (MS) or on immunochemical techniques, such as western blotting (WB). Western blotting is most often used for protein identification or relative quantification, but can also be deployed for absolute quantification if appropriate calibration standards are used. MS based techniques offer superior data quality and reproducibility, but WB offers greater sensitivity and accessibility to most researchers. It would be advantageous to apply both techniques for orthogonal quantification, but workflows rarely overlap. We describe DOSCATs (DOuble Standard conCATamers), novel calibration standards based on QconCAT technology, to unite these platforms. DOSCATs combine a series of epitope sequences concatenated with tryptic peptides in a single artificial protein to create internal tryptic peptide standards for MS as well as an intact protein bearing multiple linear epitopes. A DOSCAT protein was designed and constructed to quantify five proteins of the NF-κB pathway. For three target proteins, protein fold change and absolute copy per cell values measured by MS and WB were in excellent agreement. This demonstrates that DOSCATs can be used as multiplexed, dual purpose standards, readily deployed in a single workflow, supporting seamless quantitative transition from MS to WB.
Extracellular Vesicle-functionalized Decalcified Bone Matrix Scaffolds with Enhanced Pro-angiogenic and Pro-bone Regeneration Activities
Authors: Xie Hui , Wang Zhenxing , Zhang Liming , Lei Qian , Zhao Aiqi , Wang Hongxiang , Li Qiubai , Cao Yilin , Jie Zhang Wen , Chen Zhichao 
Published: April 2017

AbstractVascularization is crucial for bone regeneration after the transplantation of tissue-engineered bone grafts in the clinical setting. Growing evidence suggests that mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) are potently pro-angiogenic both in vitro and in vivo. In the current study, we fabricated a novel EV-functionalized scaffold with enhanced pro-angiogenic and pro-bone regeneration activities by coating decalcified bone matrix (DBM) with MSC-derived EVs. EVs were harvested from rat bone marrow-derived MSCs and the pro-angiogenic potential of EVs was investigated in vitro. DBM scaffolds were then coated with EVs, and the modification was verified by scanning electron microscopy and confocal microscopy. Next, the pro-angiogenic and pro-bone regeneration activities of EV-modified scaffolds were evaluated in a subcutaneous bone formation model in nude mice. Micro-computed tomography scanning analysis showed that EV-modified scaffolds with seeded cells enhanced bone formation. Enhanced bone formation was confirmed by histological analysis. Immunohistochemical staining for CD31 proved that EV-modified scaffolds promoted vascularization in the grafts, thereby enhancing bone regeneration. This novel scaffold modification method provides a promising way to promote vascularization, which is essential for bone tissue engineering.
Important roles of Vilse in dendritic architecture and synaptic plasticity
Authors: Lee Jin-Yu , Lee Li-Jen , Fan Chih-Chen , Chang Ho-Ching , Shih Hsin-An , Min Ming-Yuan , Chang Mau-Sun 
Published: April 2017

AbstractVilse/Arhgap39 is a Rho GTPase activating protein (RhoGAP) and utilizes its WW domain to regulate Rac/Cdc42-dependent morphogenesis in Drosophila and murine hippocampal neurons. However, the function of Vilse in mammalian dendrite architecture and synaptic plasticity remained unclear. In the present study, we aimed to explore the possible role of Vilse in dendritic structure and synaptic function in the brain. Homozygous knockout of Vilse resulted in premature embryonic lethality in mice. Changes in dendritic complexity and spine density were noticed in hippocampal neurons of Camk2a-Cre mediated forebrain-specific Vilse knockout (VilseΔ/Δ) mice. VilseΔ/Δ mice displayed impaired spatial memory in water maze and Y-maze tests. Electrical stimulation in hippocampal CA1 region revealed that the synaptic transmission and plasticity were defected in VilseΔ/Δ mice. Collectively, our results demonstrate that Vilse is essential for embryonic development and required for spatial memory.