bluuebunny/crossref_metadata_2025_split huggingface dataset:
Second-trimester urine nephrin:creatinine ratio versus soluble fms-like tyrosine kinase-1:placental growth factor ratio for prediction of preeclampsia among asymptomatic women
Authors: Zhai Tianyue , Furuta Itsuko , Nakagawa Kinuko , Kojima Takashi , Umazume Takeshi , Ishikawa Satoshi , Yamada Takahiro , Morikawa Mamoru , Minakami Hisanori 
Published: November 2016

AbstractThis prospective observational study compare urine nephrin:creatinine ratio (NCR, ng/mg) with serum soluble fms-like tyrosine kinase-1:placental growth factor ratio (FPR, pg/pg) for preeclampsia (PE) prediction among unselected asymptomatic pregnant women in 2nd trimester. NCR and FPR were determined in 254 paired urine/blood samples collected simultaneously from 254 women at median gestational week (GW) 24 (range, 22–27) without hypertension or significant proteinuria in pregnancy (SPIP). Fifteen (5.9%) developed SPIP and hypertension at GW 34.0 (26.0–38.6) and 35.3 (27.6–38.6), respectively, and were diagnosed with PE at GW 35.7 (27.6–38.6). The 90th percentile level determined in 239 women normotensive throughout pregnancy gave NCR (139) sensitivity and positive predictive values (PPV) of 60% (9/15) and 27% (9/33), while those for serum FPR (4.85) were 40% (6/15) and 20% (6/30), respectively. Relative risks (95%CI) of later PE were 10.0 (3.82–26.4; 27% [9/33] vs. 2.7% [6/221]) and 4.98 (1.91–13.0; 20% [6/30] vs. 4.0% [9/224]) for NCR-positive and FPR-positive women, respectively. Cut-offs suggested by ROC gave NCR (86.6) sensitivity and PPV of 87% (13/15) and 17% (13/79), and FPR (8.8) values of 40% (6/15) and 40% (6/15), respectively. Thus, 2nd trimester NCR was superior to FPR for PE prediction.
Identifying mutations in Tunisian families with retinal dystrophy
Authors: Habibi Imen , Chebil Ahmed , Falfoul Yosra , Allaman-Pillet Nathalie , Kort Fedra , Schorderet Daniel F. , El Matri Leila 
Published: November 2016

AbstractRetinal dystrophies (RD) are a rare genetic disorder with high genetic heterogeneity. This study aimed at identifying disease-causing variants in fifteen consanguineous Tunisian families. Full ophthalmic examination was performed. Index patients were subjected to IROme analysis or whole exome sequencing followed by homozygosity mapping. All detected variations were confirmed by direct Sanger sequencing. Mutation analysis in our patients revealed two compound heterozygous mutations p.(R91W);(V172D) in RPE65, and five novel homozygous mutations: p.R765C in CNGB1, p.H337R in PDE6B, splice site variant c.1129-2A > G and c.678_681delGAAG in FAM161A and c.1133 + 3_1133 + 6delAAGT in CERKL. The latter mutation impacts pre-mRNA splicing of CERKL. The other changes detected were six previously reported mutations in CNGB3 (p.R203*), ABCA4 (p.W782*), NR2E3 (p.R311Q), RPE65 (p.H182Y), PROM1 (c.1354dupT) and EYS (c.5928-2A > G). Segregation analysis in each family showed that all affected individuals were homozygotes and unaffected individuals were either heterozygote carriers or homozygous wild type allele. These results confirm the involvement of a large number of genes in RD in the Tunisian population.
Glutamate dehydrogenase activator BCH stimulating reductive amination prevents high fat/high fructose diet-induced steatohepatitis and hyperglycemia in C57BL/6J mice
Authors: Han Seung Jin , Choi Sung-E , Yi Sang-A , Jung Jong Gab , Jung Ik-Rak , Shin Maureen , Kang Seok , Oh Hyunhee , Kim Hae Jin , Kim Dae Jung , Kwon Ji Eun , Choi Cheol Soo , Lee Kwan Woo , Kang Yup 
Published: November 2016

AbstractIndividuals with non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes (T2D) induced by high calorie western diet are characterized by enhanced lipogenesis and gluconeogenesis in the liver. Stimulation of reductive amination may shift tricarboxylic acid cycle metabolism for lipogenesis and gluconeogenesis toward glutamate synthesis with increase of NAD+/NADH ratio and thus, ameliorate high calorie diet-induced fatty liver and hyperglycemia. Stimulation of reductive amination through glutamate dehydrogenase (GDH) activator 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH) reduced both de novo lipogenesis and gluconeogenesis but increased the activities of sirtuins and AMP-activated kinase in primary hepatocytes. Long-term BCH treatment improved most metabolic alterations induced by high fat/high fructose (HF/HFr) diet in C57BL/6J mice. BCH prevented HF/HFr-induced fat accumulation and activation of stress/inflammation signals such as phospho-JNK, phospho-PERK, phospho-p38 and phospho-NFκB in liver tissues. Furthermore, BCH treatment reduced the expression levels of inflammatory cytokines such as TNF-α and IL-1β in HF/HFr-fed mouse liver. BCH also reduced liver collagen and plasma levels of alanine transaminase and aspartate transaminase. On the other hand, BCH significantly improved fasting hyperglycemia and glucose tolerance in HF/HFr-fed mice. In conclusion, stimulation of reductive amination through GDH activation can be used as a strategy to prevent high calorie western diet-induced NAFLD and T2D.
Enterohemorrhagic Escherichia coli promotes the invasion and tissue damage of enterocytes infected with Candida albicans in vitro
Authors: Yang Weiming , Zhou Yanjun , Wu Chunrong , Tang Jianguo 
Published: November 2016

AbstractThe principal aim of this study was to investigate the in vitro co-infection of Caco-2 cells with Candida albicans and enterohemorrhage Escherichia coli (EHEC). The ability of both species to colonize or invade the Caco-2 cells was evaluated by indirect immunofluorescence and inverted microscopy. The damage to Caco-2 cells was evaluated by measuring lactate dehydrogenase (LDH) activity. C. albicans virulence gene expression (HWP1, ALS3, PLB1, SAP4, and EFG1) was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). Compared to single infections with enterohemorrhage Escherichia coli or C. albicans, a co-infection colonized or invaded Caco-2 cells more quickly, and C. albicans tended to accumulate more easily, accompanied by the upregulation of related genes. In addition, the LDH activity in the co-infected group was higher than in cells infected with C. albicans or with enterohemorrhage Escherichia coli, accompanied by the upregulation of toxicity-related genes. Using Caco-2 cells as an infection model, this study demonstrated that co-infecting in vitro enterocytes with C. albicans and enterohemorrhage Escherichia coli enhanced the invasiveness and tissue damaging effects of C. albicans.
Pre-dispersal strategies by Quercus schottkyana to mitigate the effects of weevil infestation of acorns
Authors: Xia Ke , Harrower William L. , Turkington Roy , Tan Hong-Yu , Zhou Zhe-Kun 
Published: November 2016

AbstractWe investigated how pre-dispersal strategies may mitigate the effects of weevil infestation of acorns in a population of Quercus schottkyana, a dominant oak in Asian evergreen broad-leaved forests, and assess if weevil infestation contributes to low seedling recruitment. We counted the number of acorns produced, daily from the end of August to mid-late November for 9 years from 2006–2014. We also recorded the rate of acorn infestation by weevils and acorn germination rates of weekly collections. Annual acorn production was variable, but particularly low in 2011 and 2013. There was no trade-off between acorn production and acorn dry mass. However, acorns produced later in the season were significantly heavier. For most years: (i) the rate of weevil infestation was negatively density dependent (a greater proportion of acorns died with increased acorn density), (ii) the percentage germination of acorns was positively density dependent (proportionately more acorns germinated with increased density), and (iii) as the season progressed, the percentage of infested acorns declined while germination rates increased. Finally, (iv) maximum acorn production, percentage infestation and percentage germination were asynchronous. Although pre-dispersal mortality is important it is unlikely to be the primary factor leading to low recruitment of oak seedlings.
Stable Upconversion Nanohybrid Particles for Specific Prostate Cancer Cell Immunodetection
Authors: Shi Yu , Shi Bingyang , Dass Arun V. Everest , Lu Yiqing , Sayyadi Nima , Kautto Liisa , Willows Robert D. , Chung Roger , Piper James , Nevalainen Helena , Walsh Bradley , Jin Dayong , Packer Nicolle H. 
Published: November 2016

AbstractProstate cancer is one of the male killing diseases and early detection of prostate cancer is the key for better treatment and lower cost. However, the number of prostate cancer cells is low at the early stage, so it is very challenging to detect. In this study, we successfully designed and developed upconversion immune-nanohybrids (UINBs) with sustainable stability in a physiological environment, stable optical properties and highly specific targeting capability for early-stage prostate cancer cell detection. The developed UINBs were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS) and luminescence spectroscopy. The targeting function of the biotinylated antibody nanohybrids were confirmed by immunofluorescence assay and western blot analysis. The UINB system is able to specifically detect prostate cancer cells with stable and background-free luminescent signals for highly sensitive prostate cancer cell detection. This work demonstrates a versatile strategy to develop UCNPs based sustainably stable UINBs for sensitive diseased cell detection.
An ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge
Authors: Ueda Nobuo , Richards Gemma S. , Degnan Bernard M. , Kranz Alexandrea , Adamska Maja , Croll Roger P. , Degnan Sandie M. 
Published: November 2016

AbstractIn many marine invertebrates, larval metamorphosis is induced by environmental cues that activate sensory receptors and signalling pathways. Nitric oxide (NO) is a gaseous signalling molecule that regulates metamorphosis in diverse bilaterians. In most cases NO inhibits or represses this process, although it functions as an activator in some species. Here we demonstrate that NO positively regulates metamorphosis in the poriferanAmphimedon queenslandica. High rates ofA. queenslandicametamorphosis normally induced by a coralline alga are inhibited by an inhibitor of nitric oxide synthase (NOS) and by a NO scavenger. Consistent with this, an artificial donor of NO induces metamorphosis even in the absence of the alga. Inhibition of the ERK signalling pathway prevents metamorphosis in concert with, or downstream of, NO signalling; a NO donor cannot override the ERK inhibitor.NOSgene expression is activated late in embryogenesis and in larvae, and is enriched in specific epithelial and subepithelial cell types, including a putative sensory cell, the globular cell; DAF-FM staining supports these cells being primary sources of NO. Together, these results are consistent with NO playing an activating role in induction ofA. queenslandicametamorphosis, evidence of its highly conserved regulatory role in metamorphosis throughout the Metazoa.
Combinational Immunotherapy with Allo-DRibble Vaccines and Anti-OX40 Co-Stimulation Leads to Generation of Cross-Reactive Effector T Cells and Tumor Regression
Authors: Yu Guangjie , Li Yuhuan , Cui Zhihua , Morris Nicholas P. , Weinberg Andrew D. , Fox Bernard A. , Urba Walter J. , Wang Lixin , Hu Hong-Ming 
Published: November 2016

AbstractIt is well-known that vaccines comprising of irradiated whole tumor cells or tumor-derived heat shock proteins can generate tumor-specific immune responses. In contrast, we showed recently that vaccines composed of autophagosomes (DRibbles) derived from syngeneic sarcomas could induce cross-reactive T-cell responses and cross-protection against the tumor. This unusual property of DRibbles was related to the selective recruitment of defective ribosomal products (DRiPs) and other short-lived proteins (SLiPs) into autophagosomes via sequestosome (SQSTM1, p62) mediated association of ubiquitinated SLiPs to the autophagy gene product LC3. Here, we extend our observations to mammary carcinomas from mice of different genetic background. We demonstrated that combined of intranodal administration of autologous or allogeneic DRibbles together with anti-OX40 antibody led to robust proliferation, expansion, and differentiation of memory and effector T cells. We also showed that SLiPs is an excellent source of antigen for cross-priming of CD8+ T-cells that recognize shared tumor antigens in the context of host MHC class I molecules. Thus, our results provide a strong basis for novel clinical trials that combine allogeneic “off-the-shelf” DRibble vaccines together with antibodies against co-stimulatory molecules.
A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Authors: Davidsson Marcus , Diaz-Fernandez Paula , Schwich Oliver D. , Torroba Marcos , Wang Gang , Björklund Tomas 
Published: November 2016

AbstractDetailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.
A Rapid Response Thin-Film Plasmonic-Thermoelectric Light Detector
Authors: Pan Ying , Tagliabue Giulia , Eghlidi Hadi , Höller Christian , Dröscher Susanne , Hong Guo , Poulikakos Dimos 
Published: November 2016

AbstractLight detection and quantification is fundamental to the functioning of a broad palette of technologies. While expensive avalanche photodiodes and superconducting bolometers are examples of detectors achieving single-photon sensitivity and time resolutions down to the picosecond range, thermoelectric-based photodetectors are much more affordable alternatives that can be used to measure substantially higher levels of light power (few kW/cm2). However, in thermoelectric detectors, achieving broadband or wavelength-selective performance with high sensitivity and good temporal resolution requires careful design of the absorbing element. Here, combining the high absorptivity and low heat capacity of a nanoengineered plasmonic thin-film absorber with the robustness and linear response of a thermoelectric sensor, we present a hybrid detector for visible and near-infrared light achieving response times of the order of 100 milliseconds, almost four times shorter than the same thermoelectric device covered with a conventional absorber. Furthermore, we show an almost two times higher light-to-electricity efficiency upon replacing the conventional absorber with a plasmonic absorber. With these improvements, which are direct results of the efficiency and ultra-small thickness of the plasmonic absorber, this hybrid detector constitutes an ideal component for various medium-intensity light sensing applications requiring spectrally tailored absorption coatings with either broadband or narrowband characteristics.
Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations
Authors: Zuo Zhicheng , Liu Jin 
Published: November 2016

AbstractThe CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (spCas9) along with a single guide RNA (sgRNA) has emerged as a versatile toolbox for genome editing. Despite recent advances in the mechanism studies on spCas9-sgRNA-mediated double-stranded DNA (dsDNA) recognition and cleavage, it is still unclear how the catalytic Mg2+ ions induce the conformation changes toward the catalytic active state. It also remains controversial whether Cas9 generates blunt-ended or staggered-ended breaks with overhangs in the DNA. To investigate these issues, here we performed the first all-atom molecular dynamics simulations of the spCas9-sgRNA-dsDNA system with and without Mg2+ bound. The simulation results showed that binding of two Mg2+ ions at the RuvC domain active site could lead to structurally and energetically favorable coordination ready for the non-target DNA strand cleavage. Importantly, we demonstrated with our simulations that Cas9-catalyzed DNA cleavage produces 1-bp staggered ends rather than generally assumed blunt ends.
Cordyceps collected from Bhutan, an appropriate alternative of Cordyceps sinensis
Authors: Wu Ding-Tao , Lv Guang-Ping , Zheng Jian , Li Qian , Ma Shuang-Cheng , Li Shao-Ping , Zhao Jing 
Published: November 2016

AbstractNaturalCordycepscollected in Bhutan has been widely used as naturalCordyceps sinensis, an official species of Cordyceps used as Chinese medicines, around the world in recent years. However, whether Cordyceps from Bhutan could be really used as naturalC. sinensisremains unknown. Therefore, DNA sequence, bioactive components including nucleosides and polysaccharides in twelve batches of Cordyceps from Bhutan were firstly investigated, and compared with naturalC. sinensis. Results showed that the fungus of Cordyceps from Bhutan wasC. sinensisand the host insect belonged toHepialidaesp. In addition, nucleosides and their bases such as guanine, guanosine, hypoxanthine, uridine, inosine, thymidine, adenine, and adenosine, as well as compositional monosaccharides, partial acid or enzymatic hydrolysates, molecular weights and contents of polysaccharides in Cordyceps from Bhutan were all similar to those of naturalC. sinensis. All data suggest that Cordyceps from Bhutan is a rational alternative of naturalC. sinensis, which is beneficial for the improvement of their performance in health and medicinal food areas.
Silicon deposition in nanopores using a liquid precursor
Authors: Masuda Takashi , Tatsuda Narihito , Yano Kazuhisa , Shimoda Tatsuya 
Published: November 2016

AbstractTechniques for depositing silicon into nanosized spaces are vital for the further scaling down of next-generation devices in the semiconductor industry. In this study, we filled silicon into 3.5-nm-diameter nanopores with an aspect ratio of 70 by exploiting thermodynamic behaviour based on the van der Waals energy of vaporized cyclopentasilane (CPS). We originally synthesized CPS as a liquid precursor for semiconducting silicon. Here we used CPS as a gas source in thermal chemical vapour deposition under atmospheric pressure because vaporized CPS can fill nanopores spontaneously. Our estimation of the free energy of CPS based on Lifshitz van der Waals theory clarified the filling mechanism, where CPS vapour in the nanopores readily undergoes capillary condensation because of its large molar volume compared to those of other vapours such as water, toluene, silane, and disilane. Consequently, a liquid-specific feature was observed during the deposition process; specifically, condensed CPS penetrated into the nanopores spontaneously via capillary force. The CPS that filled the nanopores was then transformed into solid silicon by thermal decomposition at 400 °C. The developed method is expected to be used as a nanoscale silicon filling technology, which is critical for the fabrication of future quantum scale silicon devices.
Local expectation violations result in global activity gain in primary visual cortex
Authors: Kok Peter , van Lieshout Lieke L.F. , de Lange Floris P. 
Published: November 2016

AbstractDuring natural perception, we often form expectations about upcoming input. These expectations are usually multifaceted – we expect a particular object at a particular location. However, expectations about spatial location and stimulus features have mostly been studied in isolation, and it is unclear whether feature-based expectation can be spatially specific. Interestingly, feature-based attention automatically spreads to unattended locations. It is still an open question whether the neural mechanisms underlying feature-based expectation differ from those underlying feature-based attention. Therefore, establishing whether the effects of feature-based expectation are spatially specific may inform this debate. Here, we investigated this by inducing expectations of a specific stimulus feature at a specific location, and probing the effects on sensory processing across the visual field using fMRI. We found an enhanced sensory response for unexpected stimuli, which was elicited only when there was a violation of expectation at the specific location where participants formed a stimulus expectation. The neural consequences of this expectation violation, however, spread to cortical locations processing the stimulus in the opposite hemifield. This suggests that an expectation violation at one location in the visual world can lead to a spatially non-specific gain increase across the visual field.
Combined administration of anisodamine and neostigmine rescued acute lethal crush syndrome through α7nAChR-dependent JAK2-STAT3 signaling
Authors: Xu Zhe-Qi , Shao Bo-Zong , Ke Ping , Liu Jian-Guo , Liu Guo-Ku , Chen Xiong-Wen , Su Ding-Feng , Liu Chong 
Published: November 2016

AbstractPreviously we showed that Ani (anisodamine)/Neo (neostigmine) combination produced anti-shock effect via activating α7 nicotinic acetylcholine receptor (α7nAChR). In this study, we aim to investigate the therapeutic effect and underlying mechanisms of Ani/Neo combination in acute lethal crush syndrome (CS). In rat and rabbit CS models, Ani/Neo combination increased the 24 h survival rates, improved hemodynamics and decreased the levels of creatine kinase, MB isoenzyme of creatine kinase, blood urea nitrogen, creatinine, K+ in serum. It also decreased the levels of H2O2, myeloperoxidase (MPO) and nitric oxide (NO) in serum and compressed muscle in rat CS model. In wild-type (WT) mice with CS, Ani/Neo combination increased 24 h survival rate and decreased the levels of H2O2, MPO, NO, TNFα, IL-6 and IL-10 in compressed muscle. These effects were attenuated by α7nAChR knockout (KO). Moreover, Ani/Neo combination prevented the decrease of phosphorylation of Janus kinase 2 (JAK2) and phosphorylation of signal transducer and activator of transcription 3 (STAT3) induced by CS. These effects of Ani/Neo in CS mice were cancelled by methyllycaconitine (α7nAChR antagonist) and α7nAChR KO. Collectively, our results demonstrate that Ani/Neo combination could produce therapeutic effects in CS. The underlying mechanism involves the activation of α7nAChR-dependent JAK2-STAT3 signaling pathway.