bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Heating-Induced Deterioration of Electromechanical Performance in Polymer-Supported Metal Films for Flexible Electronics
Authors: Jang Dong-Won , Lee Jeong-Hwan , Kim Ansoon , Lee Soon-Bok , Hong Seong-Gu 
Published: September 2017

AbstractThe retention of electrical performance under the combined conditions of mechanical strain and an electrical current is essential for flexible electronics. Here, we report that even below the critical current density required for electromigration, the electrical current can significantly deteriorate the electromechanical performance of metal film/polymer substrate systems. This leads to a loss of stretchability, and this effect becomes more severe with increasing strain as well as increasing current. The local increase of electrical resistance in the metal film caused by damage, such as localized deformations, cracks, etc., locally raises the temperature of the test sample via Joule heating. This weakens the deformation resistance of the polymer substrate, accelerating the necking instability, and consequently leading to a rapid loss of electrical conductivity with strain. To minimize such a current-induced deterioration of the polymer-supported metal films, we develop and demonstrate the feasibility of two methods that enhance the deformation resistance of the polymer substrate at elevated temperatures: increasing the thickness of the polymer substrate, and utilizing a polymer substrate with a high glass transition temperature.
EUF1 – a newly identified gene involved in erythritol utilization in Yarrowia lipolytica
Authors: Rzechonek Dorota A. , Neuvéglise Cécile , Devillers Hugo , Rymowicz Waldemar , Mirończuk Aleksandra M. 
Published: September 2017

AbstractThe gene YALI0F01562g was identified as an important factor involved in erythritol catabolism of the unconventional yeast Yarrowia lipolytica. Its putative role was identified for the first time by comparative analysis of four Y. lipolytica strains: A-101.1.31, Wratislavia K1, MK1 and AMM. The presence of a mutation that seriously damaged the gene corresponded to inability of the strain Wratislavia K1 to utilize erythritol. RT-PCR analysis of the strain MK1 demonstrated a significant increase in YALI0F01562g expression during growth on erythritol. Further studies involving deletion and overexpression of the selected gene showed that it is indeed essential for efficient erythritol assimilation. The deletion strain Y. lipolytica AMM∆euf1 was almost unable to grow on erythritol as the sole carbon source. When the strain was applied in the process of erythritol production from glycerol, the amount of erythritol remained constant after reaching the maximal concentration. Analysis of the YALI0F01562g gene sequence revealed the presence of domains characteristic for transcription factors. Therefore we suggest naming the studied gene Erythritol Utilization Factor – EUF1.
Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC)
Authors: von Mentzer Astrid , Tobias Joshua , Wiklund Gudrun , Nordqvist Stefan , Aslett Martin , Dougan Gordon , Sjöling Åsa , Svennerholm Ann-Mari 
Published: September 2017

AbstractThe ability to colonize the small intestine is essential for enterotoxigenic Escherichia coli (ETEC) to cause diarrhea. Although 22 antigenically different colonization factors (CFs) have been identified and characterized in ETEC at least 30% of clinical ETEC isolates lack known CFs. Ninety-four whole genome sequenced “CF negative” isolates were searched for novel CFs using a reverse genetics approach followed by phenotypic analyses. We identified a novel CF, CS30, encoded by a set of seven genes, csmA-G, related to the human CF operon CS18 and the porcine CF operon 987P (F6). CS30 was shown to be thermo-regulated, expressed at 37 °C, but not at 20 °C, by SDS-page and mass spectrometry analyses as well as electron microscopy imaging. Bacteria expressing CS30 were also shown to bind to differentiated human intestinal Caco-2 cells. The genes encoding CS30 were located on a plasmid (E873p3) together with the genes encoding LT and STp. PCR screening of ETEC isolates revealed that 8.6% (n = 13) of “CF negative” (n = 152) and 19.4% (n = 13) of “CF negative” LT + STp (n = 67) expressing isolates analyzed harbored CS30. Hence, we conclude that CS30 is common among “CF negative” LT + STp isolates and is associated with ETEC that cause diarrhea.
Neoproterozoic rifting in the Upper Yangtze Continental Block: Constraints from granites in the Well W117 borehole, South China
Authors: He Deng-Fa , Li Di , Li Chuan-Xin , Li Ying-Qiang , Mei Qing-Hua 
Published: September 2017

AbstractWell W117 in the Sichuan Basin reveals a suite of ~814 Ma quartz monzonites, unconformably overlain by Sinian clastic and carbonate sediments. The quartz monzonites contain no muscovite and amphibole, and are characterized by high SiO2 (72.26–77.93%), total alkali, and TFe2O3/MgO content, and low P2O5 and CaO abundance, with variable A/CNK ratio (0.93–1.19), classified as metaluminous to weakly aluminous highly fractionated I-type granites. They are preserved in the Neoproterozoic rift and exhibit restricted negative εNd(t) values (−7.0 to −5.2) and variable zircon εHf(t) values (−13.9 to 2.3), suggesting their generation via melting of both ancient and juvenile crustal materials in an extensional setting. Their parent magmas were formed in a low-temperature condition (831–650 °C) and finally emplaced at ca. 9–10 km below the surface, indicating that the intrusion underwent exhumation before the deposition of Sinian sag basin. Such geological processes, together with evidence for Neoproterozoic structures in the surrounding area, support that the Upper Yangtze craton experienced two main phases of rifting from 830–635 Ma. The Well W117 granites and its overlying sediments record a geodynamic evolution from orogenic collapse to continental rifting, and to thermal subsidence, probably related to the Rodinia supercontinent breakup.
Influence of mismatched and bulged nucleotides on SNP-preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes
Authors: Magner Dorota , Biala Ewa , Lisowiec-Wachnicka Jolanta , Kierzek Ryszard 
Published: September 2017

AbstractThis study focused on determining design rules for gapmer-type antisense oligonucleotides (ASOs), that can differentiate cleavability of two SNP variants of RNA in the presence of ribonuclease H based on the mismatch type and position in the heteroduplex. We describe the influence of structural motifs formed by several arrangements of multiple mismatches (various types of mismatches and their position within the ASO/target RNA duplex) on RNase H cleavage selectivity of five different SNP types. The targets were mRNA fragments of APP, SCA3, SNCA and SOD1 genes, carrying C-to-G, G-to-C, G-to-A, A-to-G and C-to-U substitutions. The results show that certain arrangements of mismatches enhance discrimination between wild type and mutant SNP alleles of RNA in vitro as well as in HeLa cells. Among the over 120 gapmers tested, we found two gapmers that caused preferential degradation of the mutant allele APP 692 G and one that led to preferential cleavage of the mutant SNCA 53 A allele, both in vitro and in cells. However, several gapmers promoted selective cleavage of mRNA mutant alleles in in vitro experiments only.
Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat
Authors: Nirmal Ravi C. , Furtado Agnelo , Rangan Parimalan , Henry Robert J. 
Published: September 2017

AbstractA large portion of the global wheat crop is milled to produce flour for use in the production of foods such as bread. Pressure to increase food supplies sustainably can be address directly by reducing post-harvest losses during processes such as flour milling. The recovery of flour in the milling of wheat is genetically determined but difficult to assess in wheat breeding due to the requirement for a large sample. Here we report the discovery that human selection for altered expression of putative cell adhesion proteins is associated with wheats that give high yields of flour on milling. Genes encoding fasciclin-like arabinogalactan proteins are expressed at low levels in high milling wheat genotypes at mid grain development. Thirty worldwide wheat genotypes were grouped into good and poor millers based flour yield obtained from laboratory scale milling of mature seeds. Differentially expressed genes were identified by comparing transcript profiles at 14 and 30 days post anthesis obtained from RNA-seq data of all the genotypes. Direct selection for genotypes with appropriate expression of these genes will greatly accelerate wheat breeding and ensure high recoveries of flour from wheat by resulting in grains that break up more easily on milling.
Polarized super-resolution structural imaging inside amyloid fibrils using Thioflavine T
Authors: Shaban Haitham A. , Valades-Cruz Cesar A. , Savatier Julien , Brasselet Sophie 
Published: September 2017

AbstractThioflavin T (ThT) is standardly used as a fluorescent marker to detect aggregation of amyloid fibrils by conventional fluorescence microscopy, including polarization resolved imaging that brings information on the orientational order of the fibrils. These techniques are however diffraction limited and cannot provide fine structural details at the fibrils scales of 10–100 nm, which lie beyond the diffraction limit. In this work, we evaluate the capacity of ThT to photoswitch when bound to insulin amyloids by adjusting the redox properties of its environment. We demonstrate that on-off duty cycles, intensity and photostability of the ThT fluorescence emission under adequate buffer conditions permit stochastic super-resolution imaging with a localization precision close to 20 nm. We show moreover that signal to noise conditions allow polarized orientational imaging of single ThT molecules, which reveals ultra-structure signatures related to protofilaments twisting within amyloid fibrils.
A pathway analysis of genome-wide association study highlights novel type 2 diabetes risk pathways
Authors: Liu Yang , Zhao Jing , Jiang Tao , Yu Mei , Jiang Guohua , Hu Yang 
Published: September 2017

AbstractGenome-wide association studies (GWAS) have been widely used to identify common type 2 diabetes (T2D) variants. However, the known variants just explain less than 20% of the overall estimated genetic contribution to T2D. Pathway-based methods have been applied into T2D GWAS datasets to investigate the biological mechanisms and reported some novel T2D risk pathways. However, few pathways were shared in these studies. Here, we performed a pathway analysis using the summary results from a large-scale meta-analysis of T2D GWAS to investigate more genetic signals in T2D. Here, we selected PLNK and VEGAS to perform the gene-based test and WebGestalt to perform the pathway-based test. We identified 8 shared KEGG pathways after correction for multiple tests in both methods. We confirm previous findings, and highlight some new T2D risk pathways. We believe that our results may be helpful to study the genetic mechanisms of T2D.
Intrathoracic solitary fibrous tumor – an international multicenter study on clinical outcome and novel circulating biomarkers
Authors: Ghanim Bahil , Hess Sebastian , Bertoglio Pietro , Celik Ali , Bas Aynur , Oberndorfer Felicitas , Melfi Franca , Mussi Alfredo , Klepetko Walter , Pirker Christine , Berger Walter , Harmati Imrich , Farkas Attila , Jan Ankersmit Hendrik , Dome Balazs , Fillinger Janos , Aigner Clemens , Hegedus Balazs , Renyi-Vamos Ferenc , Lang György 
Published: September 2017

AbstractIntrathoracic solitary fibrous tumor (SFT) is a rare disease. Radical resection is the standard of care. However, estimating prognosis and planning follow-up and treatment strategies remains challenging. Data were retrospectively collected by five international centers to explore outcome and biomarkers for predicting event-free-survival (EFS). 125 histological proven SFT patients (74 female; 59.2%; 104 benign; 83.2%) were analyzed. The one-, three-, five- and ten-year EFS after curative-intent surgery was 98%, 90%, 77% and 67%, respectively. Patients age (≥59 vs. <59 years hazard ratio (HR) 4.23, 95 confidence interval (CI) 1.56–11.47, p = 0.005), tumor-dignity (malignant vs. benign HR 6.98, CI 3.01–16.20, p <0.001), tumor-size (>10 cm vs. ≤10 cm HR 2.53, CI 1.10–5.83, p = 0.030), de Perrot staging (late vs. early HR 3.85, CI 1.65–8.98, p = 0.002) and resection margins (positive vs. negative HR 4.17, CI 1.15–15.17, p = 0,030) were associated with EFS. Furthermore, fibrinogen (elevated vs. normal HR 4.00, CI 1.49–10.72, p = 0.006) and the neutrophil–to-lymphocyte-ratio (NLR > 5 vs. < 5 HR 3.91, CI 1.40–10.89, p = 0.009) were prognostic after univariate analyses. After multivariate analyses tumor-dignity and fibrinogen remained as independent prognosticators. Besides validating the role of age, tumor-dignity, tumor-size, stage and resection margins, we identified for the first time inflammatory markers as prognosticators in SFT.
Biochemical efficacy, molecular docking and inhibitory effect of 2, 3-dimethylmaleic anhydride on insect acetylcholinesterase
Authors: Singh Kabrambam D. , Labala Rajendra K. , Devi Thiyam B. , Singh Ningthoujam I. , Chanu Heisnam D. , Sougrakpam Sonia , Nameirakpam Bunindro S. , Sahoo Dinabandhu , Rajashekar Yallappa 
Published: September 2017

AbstractEvolution of resistance among insects to action of pesticides has led to the discovery of several insecticides (neonicotinoids and organophosphates) with new targets in insect nervous system. Present study evaluates the mode of inhibition of acetylchlonesterase (AChE), biochemical efficacy, and molecular docking of 2,3-dimethylmaleic anhydride, against Periplaneta americana and Sitophilus oryzae. The knockdown activity of 2,3-dimethylmaleic anhydride was associated with in vivo inhibition of AChE. At KD99 dosage, the 2,3-dimethylmaleic anhydride showed more than 90% inhibition of AChE activity in test insects. A significant impairment in antioxidant system was observed, characterized by alteration in superoxide dismutase and catalase activities along with increase in reduced glutathione levels. Computational docking programs provided insights in to the possible interaction between 2,3-dimethylmaleic anhydride and AChE of P. americana. Our study reveals that 2,3-dimethylmaeic anhydride elicits toxicity in S. oryzae and P. americana primarily by AChE inhibition along with oxidative stress.
Enhancing Cell Proliferation and Osteogenic Differentiation of MC3T3-E1 Pre-osteoblasts by BMP-2 Delivery in Graphene Oxide-Incorporated PLGA/HA Biodegradable Microcarriers
Authors: Fu Chuan , Yang Xiaoyu , Tan Shulian , Song Liangsong 
Published: September 2017

AbstractLack of bioactivity has seriously restricted the development of biodegradable implants for bone tissue engineering. Therefore, surface modification of the composite is crucial to improve the osteointegration for bone regeneration. Bone morphogenetic protein-2 (BMP-2), a key factor in inducing osteogenesis and promoting bone regeneration, has been widely used in various clinical therapeutic trials. In this study, BMP-2 was successfully immobilized on graphene oxide-incorporated PLGA/HA (GO-PLGA/HA) biodegradable microcarriers. Our study demonstrated that the graphene oxide (GO) facilitated the simple and highly efficient immobilization of peptides on PLGA/HA microcarriers within 120 min. To further test in vitro, MC3T3-E1 cells were cultured on different microcarriers to observe various cellular activities. It was found that GO and HA significantly enhanced cell adhesion and proliferation. More importantly, the immobilization of BMP-2 onto the GO-PLGA/HA microcarriers resulted in significantly greater osteogenic differentiation of cells in vitro, as indicated by the alkaline phosphate activity test, quantitative real-time polymerase chain reaction analysis, immunofluorescence staining and mineralization on the deposited substrates. Findings from this study revealed that the method to use GO-PLGA/HA microcarriers for immobilizing BMP-2 has a great potential for the enhancement of the osseointegration of bone implants.
Autosomal dominant transmission of complicated hereditary spastic paraplegia due to a dominant negative mutation of KIF1A, SPG30 gene
Authors: Cheon Chong Kun , Lim So-Hee , Kim Yoo-Mi , Kim Doyoun , Lee Na-Yoon , Yoon Tae-Sung , Kim Nam-Soon , Kim Eunjoon , Lee Jae-Ran 
Published: September 2017

AbstractKIF1A is a brain-specific anterograde motor protein that transports cargoes towards the plus-ends of microtubules. Many variants of the KIF1A gene have been associated with neurodegenerative diseases and developmental delay. Homozygous mutations of KIF1A have been identified in a recessive subtype of hereditary spastic paraplegia (HSP), SPG30. In addition, KIF1A mutations have been found in pure HSP with autosomal dominant inheritance. Here we report the first case of familial complicated HSP with a KIF1A mutation transmitted in autosomal dominant inheritance. A heterozygous p.T258M mutation in KIF1A was found in a Korean family through targeted exome sequencing. They displayed phenotypes of mild intellectual disability with language delay, epilepsy, optic nerve atrophy, thinning of corpus callosum, periventricular white matter lesion, and microcephaly. A structural modeling revealed that the p.T258M mutation disrupted the binding of KIF1A motor domain to microtubules and its movement along microtubules. Assays of peripheral accumulation and proximal distribution of KIF1A motor indicated that the KIF1A motor domain with p.T258M mutation has reduced motor activity and exerts a dominant negative effect on wild-type KIF1A. These results suggest that the p.T258M mutation suppresses KIF1A motor activity and induces complicated HSP accompanying intellectual disability transmitted in autosomal dominant inheritance.
Periodic and transient motions of large woodpeckers
Authors: Collins Michael D. 
Published: September 2017

AbstractTwo types of periodic and transient motions of large woodpeckers are considered. A drumming woodpecker may be modeled as a harmonic oscillator with a periodic forcing function. The transient behavior that occurs after the forcing is turned off suggests that the double knocks of Campephilus woodpeckers may be modeled in terms of a harmonic oscillator with an impulsive forcing, and this hypothesis is consistent with audio and video recordings. Wingbeats are another type of periodic and transient motion of large woodpeckers. A model for the flap rate in cruising flight is applied to the Pileated Woodpecker (Dryocopus pileatus) and the Ivory-billed Woodpecker (Campephilus principalis). During a brief transient just after taking off, the wing motion and flap rate of a large woodpecker may not be the same as in cruising flight. These concepts are relevant to videos that contain evidence for the persistence of the Ivory-billed Woodpecker.
DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests
Authors: Kang Yong , Deng Zhiyan , Zang Runguo , Long Wenxing 
Published: September 2017

AbstractDNA barcoding is a useful tool for species identification and phylogenetic construction. But present studies have far reached a consistent result on the universality of DNA barcoding. We tested the universality of tree species DNA barcodes including rbcL, matK, trnH-psbA and ITS, and examined their abilities of species identification and phylogenetic construction in three tropical cloud forests. Results showed that the success rates of PCR amplification of rbcL, matK, trnH-psbA and ITS were 75.26% ± 3.65%, 57.24% ± 4.42%, 79.28% ± 7.08%, 50.31% ± 6.64%, and the rates of DNA sequencing were 63.84% ± 4.32%, 50.82% ± 4.36%, 72.87% ± 11.37%, 45.15% ± 8.91% respectively, suggesting that both rbcL and trnH-psbA are universal for tree species in the tropical cloud forests. The success rates of species identification of the four fragments were higher than 41.00% (rbcL: 41.50% ± 2.81%, matK: 42.88% ± 2.59%, trnH-psbA: 46.16% ± 5.11% and ITS: 47.20% ± 5.76%), demonstrating that these fragments have potentiality in species identification. When the phylogenetic relationships were built with random fragment combinations, optimal evolutionary tree with high supporting values were established using the combinations of rbcL + matK + trnH-psbA in tropical cloud forests.
Blood-derived macrophages prone to accumulate lysosomal lipids trigger oxLDL-dependent murine hepatic inflammation
Authors: Houben Tom , Oligschlaeger Yvonne , Bitorina Albert V. , Hendrikx Tim , Walenbergh Sofie M. A. , Lenders Marie-Hélène , Gijbels Marion J. J. , Verheyen Fons , Lütjohann Dieter , Hofker Marten H. , Binder Christoph J. , Shiri-Sverdlov Ronit 
Published: September 2017

AbstractDespite the consistent rise of non-alcoholic steatohepatitis (NASH) worldwide, the mechanisms that govern the inflammatory aspect of this disease remain unknown. Previous research showed an association between hepatic inflammation and lysosomal lipid accumulation in blood-derived hepatic macrophages. Additionally, in vitro findings indicated that lipids, specifically derived from the oxidized low-density lipoprotein (oxLDL) particle, are resistant to removal from lysosomes. On this basis, we investigated whether lysosomal lipid accumulation in blood-derived hepatic macrophages is causally linked to hepatic inflammation and assessed to what extent increasing anti-oxLDL IgM autoantibodies can affect this mechanism. By creating a proof-of-concept mouse model, we demonstrate a causal role for lysosomal lipids in blood-derived hepatic macrophages in mediating hepatic inflammation and initiation of fibrosis. Furthermore, our findings show that increasing anti-oxLDL IgM autoantibody levels reduces inflammation. Hence, therapies aimed at improving lipid-induced lysosomal dysfunction and blocking oxLDL-formation deserve further investigation in the context of NASH.
TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy
Authors: Bhat Basharat , Ganai Nazir A. , Andrabi Syed Mudasir , Shah Riaz A. , Singh Ashutosh 
Published: September 2017

AbstractMembrane proteins plays significant role in living cells. Transmembrane proteins are estimated to constitute approximately 30% of proteins at genomic scale. It has been a difficult task to develop specific alignment tools for transmembrane proteins due to limited number of experimentally validated protein structures. Alignment tools based on homology modeling provide fairly good result by recapitulating 70–80% residues in reference alignment provided all input sequences should have known template structures. However, homology modeling tools took substantial amount of time, thus aligning large numbers of sequences becomes computationally demanding. Here we present TM-Aligner, a new tool for transmembrane protein sequence alignment. TM-Aligner is based on Wu-Manber and dynamic string matching algorithm which has significantly improved its accuracy and speed of multiple sequence alignment. We compared TM-Aligner with prevailing other popular tools and performed benchmarking using three separate reference sets, BaliBASE3.0 reference set7 of alpha-helical transmembrane proteins, structure based alignment of transmembrane proteins from Pfam database and structure alignment from GPCRDB. Benchmarking against reference datasets indicated that TM-Aligner is more advanced method having least turnaround time with significant improvements over the most accurate methods such as PROMALS, MAFFT, TM-Coffee, Kalign, ClustalW, Muscle and PRALINE. TM-Aligner is freely available through http://lms.snu.edu.in/TM-Aligner/.