bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scalable lithography from Natural DNA Patterns via polyacrylamide gel
Authors: Qu JieHao , Hou XianLiang , Fan WanChao , Xi GuangHui , Diao HongYan , Liu XiangDon 
Published: December 2015

AbstractA facile strategy for fabricating scalable stamps has been developed using cross-linked polyacrylamide gel (PAMG) that controllably and precisely shrinks and swells with water content. Aligned patterns of natural DNA molecules were prepared by evaporative self-assembly on a PMMA substrate and were transferred to unsaturated polyester resin (UPR) to form a negative replica. The negative was used to pattern the linear structures onto the surface of water-swollen PAMG and the pattern sizes on the PAMG stamp were customized by adjusting the water content of the PAMG. As a result, consistent reproduction of DNA patterns could be achieved with feature sizes that can be controlled over the range of 40%–200% of the original pattern dimensions. This methodology is novel and may pave a new avenue for manufacturing stamp-based functional nanostructures in a simple and cost-effective manner on a large scale.
Systematic comparison of variant calling pipelines using gold standard personal exome variants
Authors: Hwang Sohyun , Kim Eiru , Lee Insuk , Marcotte Edward M. 
Published: December 2015

AbstractThe success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners—BWA-MEM, Bowtie2 and Novoalign—and four variant callers—Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500 and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes.
Tuning the properties of polyhydroxybutyrate films using acetic acid via solvent casting
Authors: Anbukarasu Preetam , Sauvageau Dominic , Elias Anastasia 
Published: December 2015

AbstractBiodegradable polyhydroxybutyrate (PHB) films were fabricated using acetic acid as an alternative to common solvents such as chloroform. The PHB films were prepared using a solvent casting process at temperatures ranging from 80 °C to 160 °C. The crystallinity, mechanical properties and surface morphology of the films cast at different temperatures were characterized and compared to PHB films cast using chloroform as a solvent. Results revealed that the properties of the PHB film varied considerably with solvent casting temperature. In general, samples processed with acetic acid at low temperatures had comparable mechanical properties to PHB cast using chloroform. This acetic acid based method is environmentally friendly, cost efficient and allows more flexible processing conditions and broader ranges of polymer properties than traditional methods.
Long-term Impact of Childhood Adiposity on Adult Metabolic Syndrome Is Modified by Insulin Resistance: The Bogalusa Heart Study
Authors: Zhang Huijie , Zhang Tao , Li Shengxu , Li Ying , Hussain Azad , Fernandez Camilo , Harville Emily , Bazzano Lydia A. , He Jiang , Chen Wei 
Published: December 2015

AbstractChildhood adiposity and insulin resistance are well-known risk factors for adult metabolic syndrome (MetS). This study aims to examine whether the association between childhood adiposity and adult MetS is modified by insulin resistance. The cohort consisted of 1,593 black and white subjects, aged 19–50 years at follow-up, who were examined 19 years apart on average as children and adults for MetS variables. The prevalence of adult MetS was compared between the insulin-sensitive obesity and insulin-resistant obesity groups in childhood. Adult MetS prevalence was higher in the insulin-resistant obesity group than in the insulin-sensitive obesity group (34.9% vs. 24.3%, p = 0.008). In multivariable logistic regression analyses adjusted for age, race, gender and follow-up years, individuals with insulin-resistant obesity in childhood were 1.7 times (p = 0.011) more likely to have MetS 19 years later on average than those with insulin-sensitive obesity in childhood. Odds ratio did not differ significantly between blacks and whites (p = 0.724). ORs for the association of childhood BMI with adult MetS significantly increased with increasing tertiles of childhood HOMA (p < 0.001 for trend). These findings suggest that insulin resistance amplifies the association between childhood adiposity and adult MetS and underscore the importance of preventing both adiposity and insulin resistance in early life.
mRNA Levels of Imprinted Genes in Bovine In Vivo Oocytes, Embryos and Cross Species Comparisons with Humans, Mice and Pigs
Authors: Jiang Zongliang , Dong Hong , Zheng Xinbao , Marjani Sadie L. , Donovan David M. , Chen Jingbo , Tian Xiuchun 
Published: December 2015

AbstractTwenty-six imprinted genes were quantified in bovine in vivo produced oocytes and embryos using RNA-seq. Eighteen were detectable and their transcriptional patterns were: largely decreased (MEST and PLAGL1); first decreased and then increased (CDKN1C and IGF2R); peaked at a specific stage (PHLDA2, SGCE, PEG10, PEG3, GNAS, MEG3, DGAT1, ASCL2, NNAT and NAP1L5); or constantly low (DIRAS3, IGF2, H19 and RTL1). These patterns reflect mRNAs that are primarily degraded, important at a specific stage, or only required at low quantities. The mRNAs for several genes were surprisingly abundant. For instance, transcripts for the maternally imprinted MEST and PLAGL1, were high in oocytes and could only be expressed from the maternal allele suggesting that their genomic imprints were not yet established/recognized. Although the mRNAs detected here were likely biallelically transcribed before the establishment of imprinted expression, the levels of mRNA during these critical stages of development have important functional consequences. Lastly, we compared these genes to their counterparts in mice, humans and pigs. Apart from previously known differences in the imprinting status, the mRNA levels were different among these four species. The data presented here provide a solid reference for expression profiles of imprinted genes in embryos produced using assisted reproductive biotechnologies.
CD147 monoclonal antibody mediated by chitosan nanoparticles loaded with α-hederin enhances antineoplastic activity and cellular uptake in liver cancer cells
Authors: Zhu Rong , Zhang Chun-ge , Liu Yang , Yuan Zhi-qiang , Chen Wei-liang , Yang Shu-di , Li Ji-zhao , Zhu Wen-jing , Zhou Xiao-feng , You Ben-gang , Zhang Xue-nong 
Published: December 2015

AbstractAn antibody that specifically interacts with an antigen could be applied to an active targeting delivery system. In this study, CD147 antibody was coupled with α-hed chitosan nanoparticles (α-Hed-CS-NPs). α-Hed-CS-CD147-NPs were round and spherical in shape, with an average particle size of 148.23 ± 1.75 nm. The half-maximum inhibiting concentration (IC50) of α-Hed-CS-CD147-NPs in human liver cancer cell lines HepG2 and SMMC-7721 was lower than that of free α-Hed and α-Hed-CS-NPs. α-Hed-induced cell death was mainly triggered by apoptosis. The increase in intracellular accumulation of α-Hed-CS-CD147-NPs was also related to CD147-mediated internalization through the Caveolae-dependent pathway and lysosomal escape. The higher targeting antitumor efficacy of α-Hed-CS-CD147-NPs than that α-Hed-CS-NPs was attributed to its stronger fluorescence intensity in the tumor site in nude mice.
Outcome Assessments of Patients with Posttraumatic “Ultra-Time Vascular Injuries” of the Extremities
Authors: Sun Yi-Feng , Fang Qiong-Xuan , Zhan Hong-Yan , Wang Fan , Cao Wei , Zhao Gang 
Published: December 2015

AbstractThe management of posttraumatic vascular injury that presents after 8 h, or “ultra-time vascular injury”, is daunting and inciting recognition of this injury is vital. We retrospectively analyzed 29 patients with ultra-time vascular injuries to determine the patients’ demographic characteristics and identify the determinants for amputation and disability. The age distribution of the high-risk population was from 18 years to 40 years, which indicated that these patients had plenty of productive life remaining. Injuries to the lower limbs (79.31%) were over four times more common than injuries to the upper limbs (17.24%) and open and blunt injuries occurred most commonly. The overall rate of limb salvage was 82.76% (24/29) and limb function is excellent in 45.83% (11/24) of the patients. The remaining patients experienced different degrees of disability in their limbs, which was determined by the anatomic location of the injury and the presence of a combined arterial and venous injury, nerve injury and complex soft tissue injury, as well as the occurrence of compartment syndrome. Hence, we recommend limb-salvage treatment for patients with traumatic ultra-time vascular injuries, particularly for those aged between 18 years and 40 years. Furthermore, we encourage the development of limb-salvage techniques for ultra-time vascular injuries.
The RIFLE versus AKIN classification for incidence and mortality of acute kidney injury in critical ill patients: A meta-analysis
Authors: Xiong Jiachuan , Tang Xi , Hu Zhangxue , Nie Ling , Wang Yiqin , Zhao Jinghong 
Published: December 2015

AbstractThe sensitivity and accuracy of the Risk/Injury/Failure/Loss/End-stage (RIFLE) versus acute kidney injury Network (AKIN) criteria for acute kidney injury (AKI) in critically ill patients remains uncertain. Therefore, we performed a systematic review and meta-analysis to investigate the incidence and prognostic value of the RIFLE versus AKIN criteria for AKI in critically ill patients. Literatures were identified by searching Medline, Embase, PubMed and China National Knowledge Infrastructure (CNKI) database. Nineteen studies with 171,889 participants were included. The pooled estimates of relative risk (RR) were analyzed. We found that the RIFLE and AKIN criteria is different for the incidence of AKI in intensive care unit (ICU) patients (P = 0.02, RR = 0.88), while not for cardiac surgery patients (P = 0.30, RR = 0.93). For AKI-related hospital mortality, the AKIN criteria did not show a better ability in predicting hospital mortality in either ICU (P = 0.19, RR = 1.01) or cardiac surgery patients (P = 0.61, RR = 0.98) compared to RIFLE criteria. Our findings supported that the AKIN criteria can identify more patients in classifying AKI compared to RIFLE criteria, but not showing a better ability in predicting hospital mortality. Moreover, both RIFLE and AKIN criteria for AKI in cardiac surgery patients had better predictive ability compared with the ICU patients.
The Dynamics and Regulatory Mechanism of Pronuclear H3k9me2 Asymmetry in Mouse Zygotes
Authors: Ma Xue-Shan , Chao Shi-Bin , Huang Xian-Ju , Lin Fei , Qin Ling , Wang Xu-Guang , Meng Tie-Gang , Zhu Cheng-Cheng , Schatten Heide , Liu Hong-Lin , Sun Qing-Yuan 
Published: December 2015

AbstractH3K9 methylation is an important histone modification that is correlated with gene transcription repression. The asymmetric H3K9 dimethylation (H3K9me2) pattern between paternal and maternal genomes is generated soon after fertilization. In the present study, we carefully determined the dynamics of H3K9me2 changes in mouse zygotes and investigated the regulatory mechanisms. The results indicated that histone methyltransferase G9a, but not GLP, was involved in the regulation of asymmetric H3K9me2 and G9a was the methyltransferase that induced the appearance of H3K9me2 in the male pronucleus of the zygote treated with cycloheximide. We found that there were two distinct mechanisms that regulate H3K9me2 in the male pronucleus. Before 8 h of in vitro fertilization (IVF), a mechanism exists that inhibits the association of G9a with the H3K9 sites. After 10 h of IVF the inhibition of G9a activity depends on yet unknown novel protein(s) synthesis. The two mechanisms of transfer take place between 8–10 h of IVF and the novel protein failed to inhibit G9a activity in time, resulting in the appearance of a low level de novo H3K9me2 in the male pronucleus.
SUN2 exerts tumor suppressor functions by suppressing the Warburg effect in lung cancer
Authors: Lv Xiao-bin , Liu Lijuan , Cheng Chun , Yu Bentong , Xiong Longxin , Hu Kaishun , Tang Jianjun , Zeng Lei , Sang Yi 
Published: December 2015

AbstractSUN2, a key component of LINC (linker of nucleoskeleton and cytoskeleton) complex located at the inner nuclear membrane, plays unknown role in lung cancer. We found that SUN2 expression was decreased in lung cancer tissue compared with paired normal tissues and that higher SUN2 levels predicted better overall survival and first progression survival. Overexpression of SUN2 inhibits cell proliferation, colony formation and migration in lung cancer, whereas knockdown of SUN2 promotes cell proliferation and migration. Additionally, SUN2 increases the sensitivity of lung cancer to cisplatin by inducing cell apoptosis. Mechanistically, we showed that SUN2 exerts its tumor suppressor functions by decreasing the expression of GLUT1 and LDHA to inhibit the Warburg effect. Finally, our results provided evidence that SIRT5 acts, at least partly, as a negative regulator of SUN2.Taken together, our findings indicate that SUN2 is a key component in lung cancer progression by inhibiting the Warburg effect and that the novel SIRT5/SUN2 axis may prove to be useful for the development of new strategies for treating the patients with lung cancer.
PDGFRα plays a crucial role in connective tissue remodeling
Authors: Horikawa Shinjiro , Ishii Yoko , Hamashima Takeru , Yamamoto Seiji , Mori Hisashi , Fujimori Toshihiko , Shen Jie , Inoue Ran , Nishizono Hirofumi , Itoh Hiroshi , Majima Masataka , Abraham David , Miyawaki Toshio , Sasahara Masakiyo 
Published: December 2015

AbstractPlatelet derived growth factor (PDGF) plays a pivotal role in the remodeling of connective tissues. Emerging data indicate the distinctive role of PDGF receptor-α (PDGFRα) in this process. In the present study, the Pdgfra gene was systemically inactivated in adult mouse (α-KO mouse) and the role of PDGFRα was examined in the subcutaneously implanted sponge matrices. PDGFRα expressed in the fibroblasts of Pdgfra-preserving control mice (Flox mice), was significantly reduced in the sponges in α-KO mice. Neovascularized areas were largely suppressed in the α-KO mice than in the Flox mice, whereas the other parameters related to the blood vessels and endothelial cells were similar. The deposition of collagen and fibronectin and the expression of collagen 1a1 and 3a1 genes were significantly reduced in α-KO mice. There was a significantly decrease in the number and dividing fibroblasts in the α-KO mice and those of macrophages were similar between the two genotypes. Hepatocyte growth factor (Hgf) gene expression was suppressed in Pdgfra-inactivated fibroblasts and connective tissue. The findings implicate the role of PDGFRα-dependent ECM and HGF production in fibroblasts that promotes the remodeling of connective tissue and suggest that PDGFRα may be a relevant target to regulate connective tissue remodeling.
Gender differences in the association between cigarette smoking, alcohol consumption and depressive symptoms: a cross-sectional study among Chinese adolescents
Authors: Yue Yue , Hong Lingyao , Guo Lan , Gao Xue , Deng Jianxiong , Huang Jinghui , Huang Guoliang , Lu Ciyong 
Published: December 2015

AbstractThe aim of this study was to examine the association between cigarette smoking, alcohol consumption and depressive symptoms among adolescents, with a particular focus on gender differences. A total of 19,578 middle and high school students in Chongqing Province were surveyed. Self-reported cigarette smoking, alcohol consumption, depressive symptoms and family- and school-related factors were assessed. A total of 8.8% adolescents reported smoking cigarettes. Tobacco use by boys (16.5%) was significantly higher than by girls (1.9%). Approximately 23.5% of adolescents reported alcohol consumption. Consumption in boys (31.5%) was significantly higher than in girls (16.2%). Depressive symptoms were prevalent in 9.1% of the sample. Girls reported significantly more symptoms (10.4%) than boys (7.7%). Multiple logistic regression analyses showed that the association between alcohol consumption and depressive symptoms was stronger among girls (AOR = 2.1, 95% CI = 1.8–2.5) than boys (AOR = 1.7, 95% CI = 1.4–2.1). A significant association (AOR = 2.3, 95% CI = 1.6–3.4) between cigarette smoking and depressive symptoms was revealed in girls only. The significant gender differences found above may provide a basis for the early identification of individuals at high risk for depression.
Functional characteristics of the Staphylococcus aureus δ-toxin allelic variant G10S
Authors: Cheung Gordon Y. C. , Yeh Anthony J. , Kretschmer Dorothee , Duong Anthony C. , Tuffuor Kwame , Fu Chih-Lung , Joo Hwang-Soo , Diep Binh A. , Li Min , Nakamura Yuumi , Nunez Gabriel , Peschel Andreas , Otto Michael 
Published: December 2015

AbstractStaphylococcus aureus δ-toxin is a member of the phenol-soluble modulin (PSM) peptide family. PSMs have multiple functions in staphylococcal pathogenesis; for example, they lyse red and white blood cells and trigger inflammatory responses. Compared to other PSMs, δ-toxin is usually more strongly expressed but has only moderate cytolytic capacities. The amino acid sequences of S. aureus PSMs are well conserved with two exceptions, one of which is the δ-toxin allelic variant G10S. This variant is a characteristic of the subspecies S. argenteus and S. aureus sequence types ST1 and ST59, the latter representing the most frequent cause of community-associated infections in Asia. δ-toxin G10S and strains expressing that variant from plasmids or the genome had significantly reduced cytolytic and pro-inflammatory capacities, including in a strain background with pronounced production of other PSMs. However, in murine infection models, isogenic strains expressing the two δ-toxin variants did not cause measurable differences in disease severity. Our findings indicate that the widespread G10S allelic variation of the δ-toxin locus has a significant impact on key pathogenesis mechanisms, but more potent members of the PSM peptide family may overshadow that impact in vivo.
Proteomic analysis of symbiotic proteins of Glomus mosseae and Amorpha fruticosa
Authors: Song Fuqiang , Qi Dandan , Liu Xuan , Kong Xiangshi , Gao Yang , Zhou Zixin , Wu Qi 
Published: December 2015

AbstractArbuscular mycorrhiza fungi (AMF) can colonize the roots of Amorpha fruticosa, a perennial leguminous woody shrub and form arbuscular mycorrhiza (AM). AMF have significant promoting effects on A. fruticosa growth as the intensity of fungal colonization increases. Taking AMF-A. fruticosa symbionts as the experimental material, gel-free isobaric tags for relative and absolute quantification (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to investigate the expression of A. fruticosa mycorrhizal proteins at the maturation stage. A total of 3,473 proteins were identified, of which 77 showed dramatic changes in their root expression levels; 33 increased and 44 decreased. We also found nine AMF proteins that were expressed with AMF treatment. The 77 proteins were classified according to function. Plant proteins were assigned into 11 categories: metabolism-related (32%), protein folding and degradation-related (22%), energy-related (10%), protein synthesis-related (8%), stress and defense-related (24%), transcription-related (6%), membrane and transport-related (4%), cellular structure-related (2.5%), signaling transduction-related (11%) and unknown proteins (5%). The results of the study provide a foundation for further investigation of the metabolic characteristics and molecular mechanisms of AM.
Stronger warming effects on microbial abundances in colder regions
Authors: Chen Ji , Luo Yiqi , Xia Jianyang , Jiang Lifen , Zhou Xuhui , Lu Meng , Liang Junyi , Shi Zheng , Shelton Shelby , Cao Junji 
Published: December 2015

AbstractSoil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our findings therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.
Dioscin alleviates alcoholic liver fibrosis by attenuating hepatic stellate cell activation via the TLR4/MyD88/NF-κB signaling pathway
Authors: Liu Min , Xu Youwei , Han Xu , Yin Lianhong , Xu Lina , Qi Yan , Zhao Yanyan , Liu Kexin , Peng Jinyong 
Published: December 2015

AbstractThe present work aimed to investigate the activities and underlying mechanisms of dioscin against alcoholic liver fibrosis (ALF). In vivo liver fibrosis in mice was induced by an alcoholic liquid diet and in vitro studies were performed on activated HSC-T6 and LX2 cells treated with lipopolysaccharide. Our results showed that dioscin significantly attenuated hepatic stellate cells (HSCs) activation, improved collagen accumulation and attenuated inflammation through down-regulating the levels of myeloid differentiation factor 88 (MyD88), nuclear factor κB (NF-κB), interleukin (IL)-1, IL-6 and tumour necrosis factor-α by decreasing Toll-like receptor (TLR)4 expression both in vivo and in vitro. TLR4 overexpression was also decreased by dioscin, leading to the markedly down-regulated levels of MyD88, NF-κB, transforming growth factor-β1 (TGF-β1), α-smooth muscle actin (α-SMA) and type I collagen (COL1A1) in cultured HSCs. Suppression of cellular MyD88 by ST2825 or abrogation of NF-κB by pyrrolidine dithiocarbamate eliminated the inhibitory effects of dioscin on the levels of TGF-β1, α-SMA and COL1A1. In a word, dioscin exhibited potent effects against ALF via altering TLR4/MyD88/NF-κB signaling pathway, which provided novel insights into the mechanisms of this compound as an antifibrogenic candidate for the treatment of ALF in the future.