bluuebunny/crossref_metadata_2025_split huggingface dataset:
GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features
Authors: Li Fuyi , Li Chen , Revote Jerico , Zhang Yang , Webb Geoffrey I. , Li Jian , Song Jiangning , Lithgow Trevor 
Published: October 2016

AbstractGlycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features, while little work has been done to systematically assess the importance of structural features to glycosylation prediction. Here, we propose a novel bioinformatics method called GlycoMinestruct(http://glycomine.erc.monash.edu/Lab/GlycoMine_Struct/) for improved prediction of human N- and O-linked glycosylation sites by combining sequence and structural features in an integrated computational framework with a two-step feature-selection strategy. Experiments indicated that GlycoMinestruct outperformed NGlycPred, the only predictor that incorporated both sequence and structure features, achieving AUC values of 0.941 and 0.922 for N- and O-linked glycosylation, respectively, on an independent test dataset. We applied GlycoMinestruct to screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestruct can be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies.
Orthotropic Piezoelectricity in 2D Nanocellulose
Authors: García Y. , Ruiz-Blanco Yasser B. , Marrero-Ponce Yovani , Sotomayor-Torres C. M. 
Published: October 2016

AbstractThe control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V−1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.
PTEN ameliorates autoimmune arthritis through down-regulating STAT3 activation with reciprocal balance of Th17 and Tregs
Authors: Lee Seung Hoon , Park Jin-Sil , Byun Jae-Kyung , Jhun JooYeon , Jung KyungAh , Seo Hyeon-Beom , Moon Young-Mee , Kim Ho-Youn , Park Sung-Hwan , Cho Mi-La 
Published: October 2016

AbstractPTEN is a tyrosine phosphatase with significant function in inhibiting STAT3 activation. Recently, inactivation of STAT3 has been demonstrated as a therapeutic candidate for autoimmune arthritis. The expression of PTEN controlled by p53 regulates autoimmune arthritis through modulating the balance between Th17 and Treg. We hypothesized that PTEN regulated by p53 might reduce CIA severity and inflammatory response via inhibiting STAT3 activation. Our results revealed that PTEN could ameliorate experimental autoimmune arthritis by reducing STAT3 activity and Th17 differentiation. Systemic infusion of PTEN overexpression downregulated CIA severity. In addition, PTEN overexpression decreased the activation of T cells and modulated reciprocal differentiation of Th17 and Treg cells. We observed that PTEN expression downregulated by p53 deficiency induced the activation of STAT3. Loss of p53 exacerbated autoimmune arthritis and dysregulated the population of Th17 and Treg. These data suggest that induction of STAT3-modulatory activity of PTEN may be a therapeutic target for rheumatoid arthritis therapy.
An rs4705342 T>C polymorphism in the promoter of miR-143/145 is associated with a decreased risk of ischemic stroke
Authors: Wei Ye-Sheng , Xiang Yang , Liao Pin-Hu , Wang Jun-Li , Peng You-Fan 
Published: October 2016

AbstractThe expression of miR-143/miR-145 was up-regulated in ischemic stroke (IS), which may be used as biomarkers and/or therapeutic targets for IS. We aimed to investigate the association of rs4705342 and rs4705343 polymorphisms in the promoter of miR-143/145 with risk of IS. The study population comprised 445 patients with IS and 518 controls. The rs4705342 genotype was analyzed by using a TaqMan Assay and the rs4705343 genotype was determined by using a polymerase chain reaction-restriction fragment length polymorphism assay. Relative expression of miR-143/miR-145 was measured by quantitative real-time PCR. We found that the rs4705342 was associated with a decreased risk of IS (TC vs. TT: adjusted OR = 0.74, 95% CI, 0.57–0.97; CC vs. TT: adjusted OR = 0.53, 95% CI, 0.34–0.83). Haplotype analysis showed that the TC haplotype was associated with an increased risk of IS risk (OR = 1.33, 95% CI, 1.01–1.75), whereas the CT haplotype was associated with a decreased risk of IS risk (OR = 0.68, 95% CI, 0.50–0.92). Importantly, patients carrying the rs4705342TC/CC genotypes had a lower level of miR-145 (P = 0.03). We found for the first time that the rs4705342 CC was a protective factor for IS, probably by reducing the level of miR-145.
Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function
Authors: Liao Y. , Williams T. J. , Walsh J. C. , Ji M. , Poljak A. , Curmi P. M. G. , Duggin I. G. , Cavicchioli R. 
Published: October 2016

AbstractNo systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
Increasing The Genetic Admixture of Available Lines of Human Pluripotent Stem Cells
Authors: Tofoli Fabiano A. , Dasso Maximiliano , Morato-Marques Mariana , Nunes Kelly , Pereira Lucas Assis , da Silva Giselle Siqueira , Fonseca Simone A. S. , Costas Roberta Montero , Santos Hadassa Campos , da Costa Pereira Alexandre , Lotufo Paulo A. , Bensenor Isabela M. , Meyer Diogo , Pereira Lygia Veiga 
Published: October 2016

AbstractHuman pluripotent stem cells (hPSCs) may significantly improve drug development pipeline, serving as anin vitrosystem for the identification of novel leads, and for testing drug toxicity. Furthermore, these cells may be used to address the issue of differential drug response, a phenomenon greatly influenced by genetic factors. This application depends on the availability of hPSC lines from populations with diverse ancestries. So far, it has been reported that most lines of hPSCs derived worldwide are of European or East Asian ancestries. We have established 23 lines of hPSCs from Brazilian individuals, and we report the analysis of their genomic ancestry. We show that embryo-derived PSCs are mostly of European descent, while induced PSCs derived from participants of a national-wide Brazilian cohort study present high levels of admixed European, African and Native American genomic ancestry. Additionally, we use high density SNP data and estimate local ancestries, particularly those of CYP genes loci. Such information will be of key importance when interpreting variation among cell lines with respect to cellular phenotypes of interest. The availability of genetically admixed lines of hPSCs will be of relevance when setting up futurein vitrostudies of drug response.
Design and fabrication of high-performance diamond triple-gate field-effect transistors
Authors: Liu Jiangwei , Ohsato Hirotaka , Wang Xi , Liao Meiyong , Koide Yasuo 
Published: October 2016

AbstractThe lack of large-area single-crystal diamond wafers has led us to downscale diamond electronic devices. Here, we design and fabricate a hydrogenated diamond (H-diamond) triple-gate metal-oxide-semiconductor field-effect transistor (MOSFET) to extend device downscaling and increase device output current. The device’s electrical properties are compared with those of planar-type MOSFETs, which are fabricated simultaneously on the same substrate. The triple-gate MOSFET’s output current (174.2 mA mm−1) is much higher than that of the planar-type device (45.2 mA mm−1), and the on/off ratio and subthreshold swing are more than 108 and as low as 110 mV dec−1, respectively. The fabrication of these H-diamond triple-gate MOSFETs will drive diamond electronic device development forward towards practical applications.
Evidence for nuclear interaction of a cytoskeleton protein (OsIFL) with metallothionein and its role in salinity stress tolerance
Authors: Soda Neelam , Sharan Ashutosh , Gupta Brijesh K. , Singla-Pareek Sneh L. , Pareek Ashwani 
Published: October 2016

AbstractSoil salinity is being perceived as a major threat to agriculture. Plant breeders and molecular biologist are putting their best efforts to raise salt-tolerant crops. The discovery of the Saltol QTL, a major QTL localized on chromosome I, responsible for salt tolerance at seedling stage in rice has given new hopes for raising salinity tolerant rice genotypes. In the present study, we have functionally characterized a Saltol QTL localized cytoskeletal protein, intermediate filament like protein (OsIFL), of rice. Studies related to intermediate filaments are emerging in plants, especially with respect to their involvement in abiotic stress response. Our investigations clearly establish that the heterologous expression of OsIFL in three diverse organisms (bacteria, yeast and tobacco) provides survival advantage towards diverse abiotic stresses. Screening of rice cDNA library revealed OsIFL to be strongly interacting with metallothionein protein. Bimolecular fluorescence complementation assay further confirmed this interaction to be occurring inside the nucleus. Overexpression of OsIFL in transgenic tobacco plants conferred salinity stress tolerance by maintaining favourable K+/Na+ ratio and thus showed protection from salinity stress induced ion toxicity. This study provides the first evidence for the involvement of a cytoskeletal protein in salinity stress tolerance in diverse organisms.
Unravelling the Efficient Photocatalytic Activity of Boron-induced Ti3+ Species in the Surface Layer of TiO2
Authors: Feng Ningdong , Liu Fen , Huang Min , Zheng Anmin , Wang Qiang , Chen Tiehong , Cao Gengyu , Xu Jun , Fan Jie , Deng Feng 
Published: October 2016

AbstractTi3+species are highly unstable in air owing to their facile oxidation into Ti4+species, and thus they cannot concentrate in the surface layer of TiO2but are mainly present in its bulk. We report generation of abundant and stable Ti3+species in the surface layer of TiO2by boron doping for efficient utilization of solar irradiation. The resultant photocatalysts (denoted as B-TiO2−x) exhibit extremely high and stable solar-driven photocatalytic activity toward hydrogen production. The origin of the solar-light activity enhancement in the B-TiO2−xphotocatalysts has been thoroughly investigated by various experimental techniques and density functional theory (DFT) calculations. The unique structure invoked by presence of sufficient interstitial boron atoms can lead to substantial variations in density of states of B-TiO2−x, which not only significantly narrow the band gap of TiO2to improve its visible-light absorption, but also promote the photogenerated electron mobility to enhance its solar-light photocatalytic activity.
Unidirectional superscattering by multilayered cavities of effective radial anisotropy
Authors: Liu Wei , Lei Bing , Shi Jianhua , Hu Haojun 
Published: October 2016

AbstractWe achieve unidirectional forward superscattering by multilayered spherical cavities which are effectively radially anisotropic. It is demonstrated that, relying on the large effective anisotropy, the electric and magnetic dipoles can be tuned to spectrally overlap in such cavities, which satisfies the Kerker’s condition of simultaneous backward scattering suppression and forward scattering enhancement. We show that such scattering pattern shaping can be obtained in both all-dielectric and plasmonic multilayered cavities at different spectral positions, and believe that the mechanism we have revealed provides extra freedom for scattering shaping, which may play a significant role in many scattering related applications and also in optoelectronic devices made up of intrinsically anisotropic two dimensional materials.
Aptamer-conjugated live human immune cell based biosensors for the accurate detection of C-reactive protein
Authors: Hwang Jangsun , Seo Youngmin , Jo Yeonho , Son Jaewoo , Choi Jonghoon 
Published: October 2016

AbstractC-reactive protein (CRP) is a pentameric protein that is present in the bloodstream during inflammatory events, e.g., liver failure, leukemia, and/or bacterial infection. The level of CRP indicates the progress and prognosis of certain diseases; it is therefore necessary to measure CRP levels in the blood accurately. The normal concentration of CRP is reported to be 1–3 mg/L. Inflammatory events increase the level of CRP by up to 500 times; accordingly, CRP is a biomarker of acute inflammatory disease. In this study, we demonstrated the preparation of DNA aptamer-conjugated peripheral blood mononuclear cells (Apt-PBMCs) that specifically capture human CRP. Live PBMCs functionalized with aptamers could detect different levels of human CRP by producing immune complexes with reporter antibody. The binding behavior of Apt-PBMCs toward highly concentrated CRP sites was also investigated. The immune responses of Apt-PBMCs were evaluated by measuring TNF-alpha secretion after stimulating the PBMCs with lipopolysaccharides. In summary, engineered Apt-PBMCs have potential applications as live cell based biosensors and for in vitro tracing of CRP secretion sites.
Suppression of the CD8 T cell response by human papillomavirus type 16 E7 occurs in Langerhans cell-depleted mice
Authors: Jemon K. , Leong C.-M. , Ly K. , Young S. L. , McLellan A. D. , Hibma M. H. 
Published: October 2016

AbstractHuman papillomavirus (HPV) is an epitheliotropic virus that is the primary causal agent for cervical cancer. Langerhans cells (LC) are skin antigen presenting cells that are reduced in number in HPV-infected skin. The aim of this study was to understand the immune-modulatory effects of HPV16 E7 on LC and on the CD8 T cell response to a skin-expressed antigen. To test this, HPV16 E7 was expressed in mouse skin keratinocytes with the model antigen ovalbumin (Ova). Similar to what is observed in HPV-infected human skin, LC numbers were significantly reduced in E7-expressing mouse skin. This shows that expression of the E7 protein alone is sufficient to mediate LC depletion. Expression of E7 with Ova in keratinocytes strongly suppressed the Ova-specific CD8+ T cell response in the skin draining lymph node. When tested in LC-ablated mice, the CD8 T cell response to skin-expressed Ova in control mice was not affected, nor was the T cell response to Ova restored in E7-expressing skin. These data indicate a role for E7 in regulation of LC homeostasis in the skin and in suppression of antigen specific CD8 T cell expansion, but suggest that these two effects occur independent of each other.
Diaphanous gene mutation affects spiral cleavage and chirality in snails
Authors: Kuroda Reiko , Fujikura Kohei , Abe Masanori , Hosoiri Yuji , Asakawa Shuichi , Shimizu Miho , Umeda Shin , Ichikawa Futaba , Takahashi Hiromi 
Published: October 2016

AbstractL-R (left and right) symmetry breaking during embryogenesis and the establishment of asymmetric body plan are key issues in developmental biology, but the onset including the handedness-determining gene locus still remains unknown. Using pure dextral (DD) and sinistral (dd) strains of the pond snail Lymnaea stagnalis as well as its F2 through to F10 backcrossed lines, the single handedness-determining-gene locus was mapped by genetic linkage analysis, BAC cloning and chromosome walking. We have identified the actin-related diaphanous gene Lsdia1 as the strongest candidate. Although the cDNA and derived amino acid sequences of the tandemly duplicated Lsdia1 and Lsdia2 genes are very similar, we could discriminate the two genes/proteins in our molecular biology experiments. The Lsdia1 gene of the sinistral strain carries a frameshift mutation that abrogates full-length LsDia1 protein expression. In the dextral strain, it is already translated prior to oviposition. Expression of Lsdia1 (only in the dextral strain) and Lsdia2 (in both chirality) decreases after the 1-cell stage, with no asymmetric localization throughout. The evolutionary relationships among body handedness, SD/SI (spiral deformation/spindle inclination) at the third cleavage, and expression of diaphanous proteins are discussed in comparison with three other pond snails (L. peregra, Physa acuta and Indoplanorbis exustus).
Controllable growth of vertically aligned graphene on C-face SiC
Authors: Liu Yu , Chen Lianlian , Hilliard Donovan , Huang Qing-song , Liu Fang , Wang Mao , Böttger Roman , Hübner René , N’Diaye Alpha T. , Arenholz Elke , Heera Viton , Skorupa Wolfgang , Zhou Shengqiang 
Published: October 2016

AbstractWe investigated how to control the growth of vertically aligned graphene on C-face SiC by varying the processing conditions. It is found that, the growth rate scales with the annealing temperature and the graphene height is proportional to the annealing time. Temperature gradient and crystalline quality of the SiC substrates influence their vaporization. The partial vapor pressure is crucial as it can interfere with further vaporization. A growth mechanism is proposed in terms of physical vapor transport. The monolayer character of vertically aligned graphene is verified by Raman and X-ray absorption spectroscopy. With the processed samples, d0 magnetism is realized and negative magnetoresistance is observed after Cu implantation. We also prove that multiple carriers exist in vertically aligned graphene.
Easy on-demand single-pass self-assembly and modification to fabricate gold@graphene-based anti-inflammatory nanoplatforms
Authors: Byeon Jeong Hoon , Park Jae Hong 
Published: October 2016

AbstractZwitterionic chitosan (ZC) was modified by fully (both for lateral dimension and thickness) nanodimensional gold-graphene oxide (Au@GO) flakes under visible light and the potential of the resulting materials as biomedical nanoplatforms was investigated. Fully nanodimensional GO flakes floating in nitrogen gas were incorporated with Au nanoparticles to form Au@GO nanoflakes, and the Au@GO was then incorporated with ZC droplets to form the Au@GO-ZC hybrid nanoparticles. The collected particles were exposed to visible light to induce the photocatalytic activity of the Au@GO nanoflakes towards the ZC derivatives. The visible-light-exposed particles show different chemical and surface properties from the unexposed particles, while there were no significant differences in cytotoxicity and macrophage inflammatory protein production. This work suggests that incorporating fully nanodimensional Au@GO flakes with ZC is a suitable technique for ambient photo-modification of the chitosans’ surface property without significant changes in size and shape and increases in cytotoxicity and inflammatory response.
Feedback delay reduction of Tomlinson–Harashima precoder in 14 nm CMOS via pipelined MAC units operated entirely with CSA arithmetic
Authors: Kossel M. , Brändli M. , Francese P. , Kull L. , Menolfi C. , Morf T. , Toifl T. , Cevrero A. , Luu D. , Özkaya I. , Yüksel H. 
Published: October 2016

The data rate of a Tomlinson–Harashima (TH) precoder is limited by the delay in the feedback path of its infinite impulse response (IIR) filter that cancels the channel's post‐cursor intersymbol interference (ISI). One reason for long loop delays is the requirement to perform the ISI subtraction from the data signal in binary arithmetic in order to properly execute the modulo (MOD) operation, which stabilises the IIR filter and limits the transmitter amplitude. The restriction to binary arithmetic is unfortunate, because some filter subcomponents such as, e.g. adder trees are often implemented in a faster data format that has no slow carry propagation [e.g. the carry‐save adder (CSA) format]. This paper proposes a novel architecture for TH precoders in which the MOD operation is taken out of the loop, so that the remaining IIR filtering is performed entirely in CSA arithmetic to reduce the feedback delay as no conversion to binary format is required within the loop. With the pipelining technique applied, the filter's feedback delay reduces to the propagation delay of a multiply‐accumulate unit operated with CSA arithmetic. The proposed concept was verified in a 14 nm CMOS test chip with multi‐level signalling (NRZ, 4‐/8‐/16‐PAM).
The Implications of Morphology, Mechanics, and Microstructure of Teeth for Understanding Dietary Drivers in Human Evolution
Authors: Macho Gabriele A. 
Published: October 2016

Abstract
Hominins evolved in mosaic to open habitats that experienced seasonal and larger timescale fluctuations in resources. Yet they were able to thrive and to evolve large brains that require a constant supply of high-quality foods. Analyses of overall tooth morphology and enamel microstructure indicate that mid-Pliocene hominins broadened their dietary niches and incorporated increasing amounts of abrasive foods; they probably underwent a shift towards consumption of starch-rich foods, including underground storage organs (USOs). Starches are complex carbohydrates that can be converted into simple sugars, essential for brain development and maintenance. In unheated state, however, starches are abrasive and require lengthy chewing. This conceivably explains the evolution of hominins’ large, thick-enamelled and wear-resistant teeth, as well as their relatively robust cranial morphologies. Habitat differences and competitive exclusion probably account—in large part—for differences in dietary strategies among early hominins (e.g. East and South Africa) and, hence, cranio-dental morphologies.