bluuebunny/crossref_metadata_2025_split huggingface dataset:
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders
Authors: Rani Jyoti , Mittal Inna , Pramanik Atreyi , Singh Namita , Dube Namita , Sharma Smriti , Puniya Bhanwar Lal , Raghunandanan Muthukurussi Varieth , Mobeen Ahmed , Ramachandran Srinivasan 
Published: July 2017

AbstractWe performed integrative analysis of genes associated with type 2 Diabetes Mellitus (T2DM) associated complications by automated text mining with manual curation and also gene expression analysis from Gene Expression Omnibus. They were analysed for pathogenic or protective role, trends, interaction with risk factors, Gene Ontology enrichment and tissue wise differential expression. The database T2DiACoD houses 650 genes, and 34 microRNAs associated with T2DM complications. Seven genes AGER, TNFRSF11B, CRK, PON1, ADIPOQ, CRP and NOS3 are associated with all 5 complications. Several genes are studied in multiple years in all complications with high proportion in cardiovascular (75.8%) and atherosclerosis (51.3%). T2DM Patients’ skeletal muscle tissues showed high fold change in differentially expressed genes. Among the differentially expressed genes, VEGFA is associated with several complications of T2DM. A few genes ACE2, ADCYAP1, HDAC4, NCF1, NFE2L2, OSM, SMAD1, TGFB1, BDNF, SYVN1, TXNIP, CD36, CYP2J2, NLRP3 with details of protective role are catalogued. Obesity is clearly a dominant risk factor interacting with the genes of T2DM complications followed by inflammation, diet and stress to variable extents. This information emerging from the integrative approach used in this work could benefit further therapeutic approaches. The T2DiACoD is available at www.http://t2diacod.igib.res.in/.
Single vector non-leaky gene expression system for Drosophila melanogaster
Authors: Akmammedov Arslan , Geigges Marco , Paro Renato 
Published: July 2017

AbstractAn ideal transgenic gene expression system is inducible, non-leaky, and well tolerated by the target organism. While the former has been satisfactorily realized, leakiness and heavy physiological burden imposed by the existing systems are still prominent hurdles in their successful implementation. Here we describe a new system for non-leaky expression of transgenes in Drosophila. PRExpress is based on a single transgenic construct built from endogenous components, the inducible hsp70 promoter and a multimerized copy of a Polycomb response element (PRE) controlled by epigenetic chromatin regulators of the Polycomb group. We show that this system is non-leaky, rapidly and strongly inducible, and reversible. To make the application of PRExpress user-friendly, we deliver the construct via site-specific integration.
A single-channel mechanism for pharmacological potentiation of GluN1/GluN2A NMDA receptors
Authors: Chopra Divyan A. , Sapkota Kiran , Irvine Mark W. , Fang Guangyu , Jane David E. , Monaghan Daniel T. , Dravid Shashank M. 
Published: July 2017

AbstractNMDA receptors (NMDARs) contribute to several neuropathological processes. Novel positive allosteric modulators (PAMs) of NMDARs have recently been identified but their effects on NMDAR gating remain largely unknown. To this end, we tested the effect of a newly developed molecule UBP684 on GluN1/GluN2A receptors. We found that UBP684 potentiated the whole-cell currents observed under perforated-patch conditions and slowed receptor deactivation. At the single channel level, UBP684 produced a dramatic reduction in long shut times and a robust increase in mean open time. These changes were similar to those produced by NMDAR mutants in which the ligand-binding domains (LBDs) are locked in the closed clamshell conformation by incorporating a disulfide bridge. Since the locked glutamate-binding clefts primarily contributes to receptor efficacy these results suggests that UBP684 binding may induce switch in conformation similar to glutamate LBD locked state. Consistent with this prediction UBP684 displayed greater potentiation of NMDARs with only the GluN1 LBD locked compared to NMDARs with only the GluN2 LBD locked. Docking studies suggest that UBP684 binds to the GluN1 and GluN2 LBD interface supporting its potential ability in stabilizing the LBD closed conformation. Together these studies identify a novel pharmacological mechanism of facilitating the function of NMDARs.
Hypothermia Prevents Retinal Damage Generated by Optic Nerve Trauma in the Rat
Authors: Rey-Funes Manuel , Larrayoz Ignacio M. , Contartese Daniela S. , Soliño Manuel , Sarotto Anibal , Bustelo Martín , Bruno Martín , Dorfman Verónica B. , Loidl César F. , Martínez Alfredo 
Published: July 2017

AbstractOcular and periocular traumatisms may result in loss of vision. Hypothermia provides a beneficial intervention for brain and heart conditions and, here, we study whether hypothermia can prevent retinal damage caused by traumatic neuropathy. Intraorbital optic nerve crush (IONC) or sham manipulation was applied to male rats. Some animals were subjected to hypothermia (8 °C) for 3 h following surgery. Thirty days later, animals were subjected to electroretinography and behavioral tests. IONC treatment resulted in amplitude reduction of the b-wave and oscillatory potentials of the electroretinogram, whereas the hypothermic treatment significantly (p < 0.05) reversed this process. Using a descending method of limits in a two-choice visual task apparatus, we demonstrated that hypothermia significantly (p < 0.001) preserved visual acuity. Furthermore, IONC-treated rats had a lower (p < 0.0001) number of retinal ganglion cells and a higher (p < 0.0001) number of TUNEL-positive cells than sham-operated controls. These numbers were significantly (p < 0.0001) corrected by hypothermic treatment. There was a significant (p < 0.001) increase of RNA-binding motif protein 3 (RBM3) and of BCL2 (p < 0.01) mRNA expression in the eyes exposed to hypothermia. In conclusion, hypothermia constitutes an efficacious treatment for traumatic vision-impairing conditions, and the cold-shock protein pathway may be involved in mediating the beneficial effects shown in the retina.
Mitigation of a nitrate reducing Pseudomonas aeruginosa biofilm and anaerobic biocorrosion using ciprofloxacin enhanced by D-tyrosine
Authors: Jia Ru , Yang Dongqing , Xu Dake , Gu Tingyue 
Published: July 2017

AbstractPseudomonas aeruginosa (PA) is a ubiquitous microbe. It can form recalcitrant biofilms in clinical and industrial settings. PA biofilms cause infections in patients. They also cause biocorrosion of medical implants. In this work, D-tyrosine (D-tyr) was investigated as an antimicrobial enhancer for ciprofloxacin (CIP) against a wild-type PA biofilm (strain PAO1) on C1018 carbon steel in a strictly anaerobic condition. Seven-day biofilm prevention test results demonstrated that 2 ppm (w/w) D-tyr enhanced 30 ppm CIP by achieving extra 2-log sessile cell reduction compared with the 30 ppm CIP alone treatment. The cocktail of 30 ppm CIP + 2 ppm D-tyr achieved similar efficacy as the 80 ppm CIP alone treatment in the biofilm prevention test. Results also indicated that the enhanced antimicrobial treatment reduced weight loss and pitting corrosion. In the 3-hour biofilm removal test, the cocktail of 80 ppm CIP + 5 ppm D-tyr achieved extra 1.5-log reduction in sessile cell count compared with the 80 ppm CIP alone treatment. The cocktail of 80 ppm CIP + 5 ppm D-tyr achieved better efficacy than the 150 ppm CIP alone treatment in the biofilm removal test.
The enzymatic epimerization of deoxynivalenol by Devosia mutans proceeds through the formation of 3-keto-DON intermediate
Authors: Hassan Yousef I. , He Jian Wei , Perilla Norma , Tang KaiJie , Karlovsky Petr , Zhou Ting 
Published: July 2017

AbstractThe enzymatic detoxification of deoxynivalenol (DON) is a promising mitigation strategy for addressing this mycotoxin contamination of cereal grains. A recently described bacterium, Devosia mutans 17-2-E-8, capable of transforming DON into its non-toxic stereoisomer 3-epi-DON, holds promise for the development of such applications. Earlier observations suggested that DON epimerization proceeds via a two-step catalysis with 3-keto-DON as an intermediate. The results of this study indicate that NADPH is required for DON epimerization by cell-free protein extracts of D. mutans, while high concentrations of glucose and sucrose have a suppressive effect. Chemically synthesized 3-keto-DON incubated with D. mutans protein fractions enriched by ammonium sulfate precipitation at 35–55% saturation selectively reduced 3-keto-DON to 3-epi-DON, but fell short of supporting the complete epimerization of DON. In addition, seven Devosia species investigated for DON epimerization were all able to reduce 3-keto-DON to 3-epi-DON, but only a few were capable of epimerizing DON. The above observations collectively confirm that the enzymes responsible for the oxidation of DON to 3-keto-DON are physically separate from those involved in 3-keto-DON reduction to 3-epi-DON. The enzymatic nature of DON epimerization suggests that the process could be used to develop genetically engineered crops or microorganisms, ultimately reducing foodborne exposure of consumers and farm animals to DON.
Xylapeptide A, an Antibacterial Cyclopentapeptide with an Uncommon L-Pipecolinic Acid Moiety from the Associated Fungus Xylaria sp. (GDG-102)
Authors: Xu Wei-Feng , Hou Xue-Mei , Yao Fei-Hua , Zheng Na , Li Jun , Wang Chang-Yun , Yang Rui-Yun , Shao Chang-Lun 
Published: July 2017

AbstractTwo new cyclopentapeptides, xylapeptide A (1) with an uncommon L-pipecolinic acid moiety, and xylapeptide B (2) having a common L-proline residue were identified from an associated fungus Xylaria sp. isolated from the Chinese medicinal plant Sophora tonkinensis. Their planar structures were elucidated by a comprehensive analysis of NMR and MS spectroscopic spectra. The absolute configurations were determined by Marfey’s method and single-crystal X-ray diffraction (Cu Kα) analysis. Xylapeptide A (1) is the first example of cyclopentapeptide with L-Pip of terrestrial origin and showed strong antibacterial activity against Bacillus subtilis and B. cereus with MIC value of 12.5 μg/mL.
Identification of reference genes for qRT-PCR in granulosa cells of healthy women and polycystic ovarian syndrome patients
Authors: Lv Yue , Zhao Shi Gang , Lu Gang , Leung Chi Kwan , Xiong Zhi Qiang , Su Xian Wei , Ma Jin Long , Chan Wai Yee , Liu Hong Bin 
Published: July 2017

AbstractComparative gene expression analysis by qRT-PCR is commonly used to detect differentially expressed genes in studies of PCOS pathology. Impaired GC function is strongly associated with PCOS pathogenesis, and a growing body of studies has been dedicated to identifying differentially expressed genes in GCs in PCOS patients and healthy women by qRT-PCR. It is necessary to validate the expression stability of the selected reference genes across the tested samples for target gene expression normalization. We examined the variability and stability of expression of the 15 commonly used reference genes in GCs from 44 PCOS patients and 45 healthy women using the GeNorm, BestKeeper, and NormFinder statistical algorithms. We combined the rankings of the three programs to produce a final ranking based on the geometric means of their stability scores. We found thatHPRT1,RPLP0, andHMBSout of 15 examined commonly used reference genes are stably expressed in GCs in both controls and PCOS patients and can be used for normalization in gene expression profiling by qRT-PCR. Future gene-expression studies should consider using these reference genes in GCs in PCOS patients for more accurate quantitation of target gene expression and data interpretation.
Cytologically indeterminate thyroid nodules: increased diagnostic performance with combination of US TI-RADS and a new scoring system
Authors: He Ya-Ping , Xu Hui-Xiong , Zhao Chong-Ke , Sun Li-Ping , Li Xiao-Long , Yue Wen-Wen , Guo Le-Hang , Wang Dan , Ren Wei-Wei , Wang Qiao , Qu Shen 
Published: July 2017

AbstractTo investigate the diagnostic performance of combination of ultrasound (US) thyroid imaging reporting and data system (TI-RADS) and a new US scoring system for diagnosing thyroid nodules (TNs) with indeterminate results (Bethesda categories III, IV and V) on fine-needle aspiration (FNA) cytology. 453 patients with 453 cytologically indeterminate TNs were included in this study. Multivariate analyses were performed to construct the scoring system. The diagnostic performances of TI-RADS and the combined method were evaluated and compared. Multivariate analyses revealed that marked hypoechogenicity, taller than wide shape and absence of halo sign were independent predictors for malignancy in cytologically indeterminate TNs. Scoring system was thereafter defined as follows: risk score (RS) = 3.2 x (if marked hypoechogenicity) + 2.8 x (if taller than wide shape) + 1.3 x (if absence of halo sign). Compared with TI-RADS alone, the areas under the receiver operating characteristic curves (AUC), specificity, accuracy and positive predictive value (PPV) of the combined method increased significantly with 0.731 versus 0.569, 48.5% versus 14.1%, 76.2% versus 62.3%, and 70.9% versus 59.9%, respectively (all P < 0.05). The combination of TI-RADS and new US scoring system showed superior diagnostic performances in predicting malignant TNs with indeterminate FNA cytology results in comparison with TI-RADS alone.
Image Cytometric Analysis of Algal Spores for Evaluation of Antifouling Activities of Biocidal Agents
Authors: Il Koo Bon , Lee Yun-Soo , Seo Mintae , Seok Choi Hyung , Leng Seah Geok , Nam Taegu , Nam Yoon Sung 
Published: July 2017

AbstractChemical biocides have been widely used as marine antifouling agents, but their environmental toxicity impose regulatory restriction on their use. Although various surrogate antifouling biocides have been introduced, their comparative effectiveness has not been well investigated partly due to the difficulty of quantitative evaluation of their antifouling activity. Here we report an image cytometric method to quantitatively analyze the antifouling activities of seven commercial biocides using Ulva prolifera as a target organism, which is known to be a dominant marine species causing soft fouling. The number of spores settled on a substrate is determined through image analysis using the intrinsic fluorescence of chlorophylls in the spores. Pre-determined sets of size and shape of spores allow for the precise determination of the number of settled spores. The effects of biocide concentration and combination of different biocides on the spore settlement are examined. No significant morphological changes of Ulva spores are observed, but the amount of adhesive pad materials is appreciably decreased in the presence of biocides. It is revealed that the growth rate of Ulva is not directly correlated with the antifouling activities against the settlement of Ulva spores. This work suggests that image cytometric analysis is a very convenient, fast-processable method to directly analyze the antifouling effects of biocides and coating materials.
Development of Series of Affinity Tags in Streptomyces
Authors: Mao Xu-Ming , Sun Ning , Zheng Yang , Li Yong-Quan 
Published: July 2017

AbstractStreptomycesare of great biological and industrial significance due to their complex morphological development and ability to produce numerous secondary metabolites. However, the intrinsic biochemical mechanisms underlying morphogenesis and secondary metabolism are rarely revealed, partially because of the limited availability of the biochemical tools inStreptomyces. Here we provided series of integrative vectors with various affinity tags, including single tags 3×FLAG, 3×HA, 3×Strep-tag II, 18×His, 13×Myc, and dual tags, all of which were driven from a strong constitutive promoterermEp*. Using a sigma factor SigT fromS. coelicoloras a model, we successfully expressed and immuno-detected SigT fused with all tags. Moreover, after SigT was N-terminally tagged with 3×FLAG and C-terminally tagged with 18×His, we isolated SigT-interactive proteins from theS. coelicolorlysate based on the tandem affinity purification (TAP). Particularly, among the proteins purified, the SigT cognate anti-sigma factor RstA ranked the top with the most total independent spectra. These data suggested the feasibility of these affinity tags inStreptomyces, which will be widely employed to explore the biochemical mechanisms to further understand the dynamic and elaborate regulation in this genus.
Soluble Epoxide Hydrolase Inhibition Protected against Angiotensin II-induced Adventitial Remodeling
Authors: Zhou Chi , Huang Jin , Li Qing , Nie Jiali , Xu Xizhen , Wang Dao Wen 
Published: July 2017

AbstractEpoxyeicosatrienoic acids (EETs), the metabolites of cytochrome P450 epoxygenases derived from arachidonic acid, exert important biological activities in maintaining cardiovascular homeostasis. Soluble epoxide hydrolase (sEH) hydrolyzes EETs to less biologically active dihydroxyeicosatrienoic acids. However, the effects of sEH inhibition on adventitial remodeling remain inconclusive. In this study, the adventitial remodeling model was established by continuous Ang II infusion for 2 weeks in C57BL/6 J mice, before which sEH inhibitor 1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl) urea (TPPU) was administered by gavage. Adventitial remodeling was evaluated by histological analysis, western blot, immunofluorescent staining, calcium imaging, CCK-8 and transwell assay. Results showed that Ang II infusion significantly induced vessel wall thickening, collagen deposition, and overexpression of α-SMA and PCNA in aortic adventitia, respectively. Interestingly, these injuries were attenuated by TPPU administration. Additionally, TPPU pretreatment overtly prevented Ang II-induced primary adventitial fibroblasts activation, characterized by differentiation, proliferation, migration, and collagen synthesis via Ca2+-calcineurin/NFATc3 signaling pathway in vitro. In summary, our results suggest that inhibition of sEH could be considered as a novel therapeutic strategy to treat adventitial remodeling related disorders.
The research infrastructure of Chinese foundations, a database for Chinese civil society studies
Authors: Ma Ji , Wang Qun , Dong Chao , Li Huafang 
Published: July 2017

AbstractThis paper provides technical details and user guidance on the Research Infrastructure of Chinese Foundations (RICF), a database of Chinese foundations, civil society, and social development in general. The structure of the RICF is deliberately designed and normalized according to the Three Normal Forms. The database schema consists of three major themes: foundations’ basic organizational profile (i.e., basic profile, board member, supervisor, staff, and related party tables), program information (i.e., program information, major program, program relationship, and major recipient tables), and financial information (i.e., financial position, financial activities, cash flow, activity overview, and large donation tables). The RICF’s data quality can be measured by four criteria: data source reputation and credibility, completeness, accuracy, and timeliness. Data records are properly versioned, allowing verification and replication for research purposes.
A comprehensive data set of lake surface water temperature over the Tibetan Plateau derived from MODIS LST products 2001–2015
Authors: Wan Wei , Li Huan , Xie Hongjie , Hong Yang , Long Di , Zhao Limin , Han Zhongying , Cui Yaokui , Liu Baojian , Wang Cunguang , Yang Wenting 
Published: July 2017

AbstractLake surface water temperature (LSWT) is sensitive to long-term changes in thermal structure of lakes and regional air temperature. In the context of global climate change, recent studies showed a significant warming trend of LSWT based on investigating 291 lakes (71% are large lakes, ≥50 km2 each) globally. However, further efforts are needed to examine variation in LSWT at finer regional spatial and temporal scales. The Tibetan Plateau (TP), known as ‘the Roof of the World’ and ‘Asia’s water towers’, exerts large influences on and is sensitive to regional and even global climates. Aiming to examine detailed changing patterns and potential driven mechanisms for temperature variations of lakes across the TP region, this paper presents the first comprehensive data set of 15-year (2001–2015) nighttime and daytime LSWT for 374 lakes (≥10 km2 each), using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e., 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images. The data set itself reveals significant information on LSWT and its changes over the TP and is an indispensable variable for numerous applications related to climate change, water budget analysis (particularly lake evaporation), water storage changes, glacier melting and permafrost degradation, etc.
Factors Associated with Attention Deficit Hyperactivity Disorder in Children with Frontal Lobe Epilepsy
Authors: Sano Fumikazu , Ohyama Tetsuo , Sugita Kanji , Aihara Masao , Kanemura Hideaki 
Published: July 2017

AbstractThe relationship between attention deficit/hyperactivity disorder (ADHD) and frontal lobe epilepsy (FLE) in children is not well understood. Patients with FLE between 6 and 15 years of age were studied. Scores on the ADHD rating scale (ADHD-RS) and Wisconsin card sorting test (WCST) were obtained at baseline. Behavioral changes were evaluated using the ADHD-RS scores at 6, 12, and 24 months after seizure onset. Perseverative errors of Nelson (PEN) scales on WCST were also evaluated at same time periods. The relationships between clinical manifestations and neuropsychological disturbances were analyzed. In 34 patients, the ADHD-RS score at 24 months after onset was most strongly associated with the presence of status epilepticus (SE, p = 0.004, β = 0.490) followed by seizure frequency (p = 0.021, β = 0.382). The increase in ADHD-RS score was most strongly associated with seizure frequency (p < 0.001, β = 0.635). The PEN score on WCST at 24 months was most strongly associated with seizure frequency (p = 0.001, β = 0.724). The increase in PEN score on WCST was most strongly associated with seizure frequency (p = 0.001, β = 0.872). The only clinical factor associated with both the ADHD-RS and the PEN scores on the WCST was seizure frequency. Seizure frequency may be correlated with risk for ADHD in children with FLE.