bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rpgrip1 is required for rod outer segment development and ciliary protein trafficking in zebrafish
Authors: Raghupathy Rakesh K. , Zhang Xun , Liu Fei , Alhasani Reem H. , Biswas Lincoln , Akhtar Saeed , Pan Luyuan , Moens Cecilia B. , Li Wenchang , Liu Mugen , Kennedy Breandan N. , Shu Xinhua 
Published: November 2017

AbstractMutations in the RPGR-interacting protein 1 (RPGRIP1) gene cause recessive Leber congenital amaurosis (LCA), juvenile retinitis pigmentosa (RP) and cone-rod dystrophy. RPGRIP1 interacts with other retinal disease-causing proteins and has been proposed to have a role in ciliary protein transport; however, its function remains elusive. Here, we describe a new zebrafish model carrying a nonsense mutation in the rpgrip1 gene. Rpgrip1homozygous mutants do not form rod outer segments and display mislocalization of rhodopsin, suggesting a role for RPGRIP1 in rhodopsin-bearing vesicle trafficking. Furthermore, Rab8, the key regulator of rhodopsin ciliary trafficking, was mislocalized in photoreceptor cells of rpgrip1 mutants. The degeneration of rod cells is early onset, followed by the death of cone cells. These phenotypes are similar to that observed in LCA and juvenile RP patients. Our data indicate RPGRIP1 is necessary for rod outer segment development through regulating ciliary protein trafficking. The rpgrip1 mutant zebrafish may provide a platform for developing therapeutic treatments for RP patients.
Glandular Morphometrics for Objective Grading of Colorectal Adenocarcinoma Histology Images
Authors: Awan Ruqayya , Sirinukunwattana Korsuk , Epstein David , Jefferyes Samuel , Qidwai Uvais , Aftab Zia , Mujeeb Imaad , Snead David , Rajpoot Nasir 
Published: November 2017

AbstractDetermining the grade of colon cancer from tissue slides is a routine part of the pathological analysis. In the case of colorectal adenocarcinoma (CRA), grading is partly determined by morphology and degree of formation of glandular structures. Achieving consistency between pathologists is difficult due to the subjective nature of grading assessment. An objective grading using computer algorithms will be more consistent, and will be able to analyse images in more detail. In this paper, we measure the shape of glands with a novel metric that we call the Best Alignment Metric (BAM). We show a strong correlation between a novel measure of glandular shape and grade of the tumour. We used shape specific parameters to perform a two-class classification of images into normal or cancerous tissue and a three-class classification into normal, low grade cancer, and high grade cancer. The task of detecting gland boundaries, which is a prerequisite of shape-based analysis, was carried out using a deep convolutional neural network designed for segmentation of glandular structures. A support vector machine (SVM) classifier was trained using shape features derived from BAM. Through cross-validation, we achieved an accuracy of 97% for the two-class and 91% for three-class classification.
Temperature Dependence in Heterogeneous Nucleation with Application to the Direct Determination of Cluster Energy on Nearly Molecular Scale
Authors: McGraw Robert L. , Winkler Paul M. , Wagner Paul E. 
Published: November 2017

AbstractA re-examination of measurements of heterogeneous nucleation of water vapor on silver nanoparticles is presented here using a model-free framework that derives the energy of critical cluster formation directly from measurements of nucleation probability. Temperature dependence is correlated with cluster stabilization by the nanoparticle seed and previously found cases of unusual increasing nucleation onset saturation ratio with increasing temperature are explained. A necessary condition for the unusual positive temperature dependence is identified, namely that the critical cluster be more stable, on a per molecule basis, than the bulk liquid to exhibit the effect. Temperature dependence is next examined in the classical Fletcher model, modified here to make the energy of cluster formation explicit in the model. The contact angle used in the Fletcher model is identified as the microscopic contact angle, which can be directly obtained from heterogeneous nucleation experimental data by a recently developed analysis method. Here an equivalent condition, increasing contact angle with temperature, is found necessary for occurrence of unusual temperature dependence. Our findings have immediate applications to atmospheric particle formation and nanoparticle detection in condensation particle counters (CPCs).
A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness
Authors: Lai John , Moya Leire , An Jiyuan , Hoffman Andrea , Srinivasan Srilakshmi , Panchadsaram Janaththani , Walpole Carina , Perry-Keene Joanna L. , Chambers Suzanne ,   Australian Prostate Cancer BioResource, Yeadon T. , Saunders P. , Eckert A. , Heathcote P. , Wood G. , Malone G. , Samaratunga H. , Collins A. , Turner M. , Kerr K. , Lehman Melanie L. , Nelson Colleen C. , Clements Judith A. , Batra Jyotsna 
Published: November 2017

AbstractShort tandem repeats (STRs) are repetitive sequences of a polymorphic stretch of two to six nucleotides. We hypothesized that STRs are associated with prostate cancer development and/or progression. We undertook RNA sequencing analysis of prostate tumors and adjacent non-malignant cells to identify polymorphic STRs that are readily expressed in these cells. Most of the expressed STRs in the clinical samples mapped to intronic and intergenic DNA. Our analysis indicated that three of these STRs (TAAA-ACTG2, TTTTG-TRIB1, and TG-PCA3) are polymorphic and differentially expressed in prostate tumors compared to adjacent non-malignant cells. TG-PCA3 STR expression was repressed by the anti-androgen drug enzalutamide in prostate cancer cells. Genetic analysis of prostate cancer patients and healthy controls (N > 2,000) showed a significant association of the most common 11 repeat allele of TG-PCA3 STR with prostate cancer risk (OR = 1.49; 95% CI 1.11–1.99; P = 0.008). A significant association was also observed with aggressive disease (OR = 2.00; 95% CI 1.06–3.76; P = 0.031) and high mortality rates (HR = 3.0; 95% CI 1.03–8.77; P = 0.045). We propose that TG-PCA3 STR has both diagnostic and prognostic potential for prostate cancer. We provided a proof of concept to be applied to other RNA sequencing datasets to identify disease-associated STRs for future clinical exploratory studies.
Water depth affects reproductive allocation and reproductive allometry in the submerged macrophyte Vallisneria natans
Authors: Li Lei , Bonser Stephen P. , Lan Zhichun , Xu Ligang , Chen Jiakuan , Song Zhiping 
Published: November 2017

AbstractIn freshwater ecosystems, shifts in hydrological regimes have profound effects on reproductive output (R), along with vegetative biomass (V) and survival of plants. Because reproductive allocation (RA) is allometric, it remains unclear whether the observed variation of RA in response to water level variability is due to fixed patterns of development or plasticity in the developmental trajectories. Here, we investigated shifts in RA of a submerged macrophyte Vallisneria natans in response to water depth to test the hypothesis that allometric trajectories of RA are highly plastic. Plants were grown at three water depths (50, 100 and 150 cm) and measured after 26 weeks of growth. The relationships between R and V among treatments were compared. Deep water affected both biomass and number of fruits produced per plant, leading to less sexual reproduction. Plants in deep water started flowering at a smaller size and despite their small mature size, had a relatively high RA. Furthermore, these plants had a much lower log R–log V relationship than shallow- or intermediate-water plants. In conclusion, reproduction of V. natans is highly variable across water depth treatments, and variations in reproductive allometry represent different strategies under an important stress gradient for these freshwater angiosperms.
DNA metabarcoding data unveils invisible pollination networks
Authors: Pornon André , Andalo Christophe , Burrus Monique , Escaravage Nathalie 
Published: November 2017

AbstractAnimal pollination, essential for both ecological services and ecosystem functioning, is threatened by ongoing global changes. New methodologies to decipher their effects on pollinator composition to ecosystem health are urgently required. We compare the main structural parameters of pollination networks based on DNA metabarcoding data with networks based on direct observations of insect visits to plants at three resolution levels. By detecting numerous additional hidden interactions, metabarcoding data largely alters the properties of the pollination networks compared to visit surveys. Molecular data shows that pollinators are much more generalist than expected from visit surveys. However, pollinator species were composed of relatively specialized individuals and formed functional groups highly specialized upon floral morphs. We discuss pros and cons of metabarcoding data relative to data obtained from traditional methods and their potential contribution to both current and future research. This molecular method seems a very promising avenue to address many outstanding scientific issues at a resolution level which remains unattained to date; especially for those studies requiring pollinator and plant community investigations over macro-ecological scales.
Associations between general and central obesity and hypertension among children: The Childhood Obesity Study in China Mega-Cities
Authors: Zhao Yaling , Wang Liang , Xue Bo , Wang Youfa 
Published: November 2017

AbstractIn this study, we examined the associations of general and central obesity and hypertension among Chinese children. Data was collected from 1626 children aged 7–16 years and their parents in four mega-cities across China. Mixed effect models examined associations of general and central obesity with hypertension, and between body mass index (BMI), waist circumference (WC), waist-to-height ratio (WHtR), systolic blood pressure (SBP) and diastolic blood pressure (DBP). The prevalence of general obesity, central obesity, and hypertension among the children was 11.1%, 19.7%, and 9.0%, respectively. More boys had general and central obesity than girls (15.2% vs. 6.9%; 27.4% vs. 11.7%, respectively; both P < 0.0001). Sex difference in hypertension rate was not statistically significant (9.3% in boys vs. 8.8% in girls, P = 0.7341). Both SBP and DBP were positively associated with BMI, WC, and WHtR, regardless of sex and region. General obesity (OR = 5.94, 95% confidence interval [CI]: 3.69–9.55) and central obesity (OR = 3.45, 95% CI: 2.27–5.23) were strongly associated with hypertension. The prevalence of general obesity, central obesity, and hypertension was high among Chinese children in the four mega-cities across China. Children’s BMI, WC, and WHtR were positively associated with their SBP and DBP. Obese children were 3–6 times more likely to have hypertension.
Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles
Authors: Hutzler Stefan , Erbar Stephanie , Jabulowsky Robert A. , Hanauer Jan R. H. , Schnotz Jürgen H. , Beissert Tim , Bodmer Bianca S. , Eberle Regina , Boller Klaus , Klamp Thorsten , Sahin Ugur , Mühlebach Michael D. 
Published: November 2017

AbstractRecombinant vaccine strain-derived measles virus (MV) is clinically tested both as vaccine platform to protect against other pathogens and as oncolytic virus for tumor treatment. To investigate the potential synergism in anti-tumoral efficacy of oncolytic and vaccine properties, we chose Ovalbumin and an ideal tumor antigen, claudin-6, for pre-clinical proof of concept. To enhance immunogenicity, both antigens were presented by retroviral virus-like particle produced in situ during MV-infection. All recombinant MV revealed normal growths, genetic stability, and proper expression and presentation of both antigens. Potent antigen-specific humoral and cellular immunity were found in immunized MV-susceptible IFNAR−/−-CD46Ge mice. These immune responses significantly inhibited metastasis formation or increased therapeutic efficacy compared to control MV in respective novel in vivo tumor models using syngeneic B16-hCD46/mCLDN6 murine melanoma cells. These data indicate the potential of MV to trigger selected tumor antigen-specific immune responses on top of direct tumor lysis for enhanced efficacy.
CP and CP-PGN protect mice against MRSA infection by inducing M1 macrophages
Authors: Zhang Yang , Li Xiang-Xiang , Ma Yuan , Xu Jie , Zhao Li-Na , Qian Xue-Feng , Zhang Xian-Feng , Shi Jin-Fang , Han Qing-Zhen 
Published: November 2017

AbstractCorynebacterium pyruviciproducens (C. pyruviciproducens, CP), as a newly discovered immunomodulator, has been confirmed to have a stronger immunoregulation than Propionibacterium acnes (P. acnes) of the traditional immune adjuvant, by previous experiments with model antigen ovalbumin and sheep red blood cells. Here, it was designed to assess its ability to resist methicillin-resistant Staphylococcus aureus (MRSA), since MRSA as a vital gram positive pathogen is characterized by high morbidity and mortality. In this report, it was indicated that C. pyruviciproducens and its peptidoglycan (CP-PGN) could help to be against bloodstream infection of MRSA with raised survival rate, decreased bacteria load and alleviated systemic inflammation, and these effects of CP-PGN were more pronounced. However, the whole CP was inclined to prevent localized abdominal infection of MRSA from progressing to a systemic infection. And they showed the potential as a therapeutic drug alone or combined with vancomycin. The diversity of capacity of activating macrophages induced by CP and CP-PGN may result in distinct resistance to MRSA in different infection models. Furthermore, both CP and CP-PGN induced M1 macrophages. In conclusion, CP and its PGN could act as promising immune agents to treat and prevent MRSA infection.
Construction of a system using a deep learning algorithm to count cell numbers in nanoliter wells for viable single-cell experiments
Authors: Kamatani Takashi , Fukunaga Koichi , Miyata Kaede , Shirasaki Yoshitaka , Tanaka Junji , Baba Rie , Matsusaka Masako , Kamatani Naoyuki , Moro Kazuyo , Betsuyaku Tomoko , Uemura Sotaro 
Published: November 2017

AbstractFor single-cell experiments, it is important to accurately count the number of viable cells in a nanoliter well. We used a deep learning-based convolutional neural network (CNN) on a large amount of digital data obtained as microscopic images. The training set consisted of 103 019 samples, each representing a microscopic grayscale image. After extensive training, the CNN was able to classify the samples into four categories, i.e., 0, 1, 2, and more than 2 cells per well, with an accuracy of 98.3% when compared to determination by two trained technicians. By analyzing the samples for which judgments were discordant, we found that the judgment by technicians was relatively correct although cell counting was often difficult by the images of discordant samples. Based on the results, the system was further enhanced by introducing a new algorithm in which the highest outputs from CNN were used, increasing the accuracy to higher than 99%. Our system was able to classify the data even from wells with a different shape. No other tested machine learning algorithm showed a performance higher than that of our system. The presented CNN system is expected to be useful for various single-cell experiments, and for high-throughput and high-content screening.
The relationship between personality and the response to acute psychological stress
Authors: Xin Yuanyuan , Wu Jianhui , Yao Zhuxi , Guan Qing , Aleman André , Luo Yuejia 
Published: November 2017

AbstractThe present study examined the relationship between personality traits and the response to acute psychological stress induced by a standardized laboratory stress induction procedure (the Trier Social Stress Test, TSST). The stress response was measured with a combination of cardiovascular reactivity, hypothalamic–pituitary–adrenal axis reactivity, and subjective affect (including positive affect, negative affect and subjective controllability) in healthy individuals. The Generalized Estimating Equations (GEE) approach was applied to account for the relationship between personality traits and stress responses. Results suggested that higher neuroticism predicted lower heart rate stress reactivity, lower cortisol stress response, more decline of positive affect and lower subjective controllability. Individuals higher in extraversion showed smaller cortisol activation to stress and less increase of negative affect. In addition, higher openness score was associated with lower cortisol stress response. These findings elucidate that neuroticism, extraversion and openness are important variables associated with the stress response and different dimensions of personality trait are associated with different aspects of the stress response.
Asymmetric adiabatic couplers for fully-integrated broadband quantum-polarization state preparation
Authors: Chung Hung-Pin , Huang Kuang-Hsu , Wang Kai , Yang Sung-Lin , Yang Shih-Yuan , Sung Chun-I , Solntsev Alexander S. , Sukhorukov Andrey A. , Neshev Dragomir N. , Chen Yen-Hung 
Published: November 2017

AbstractSpontaneous parametric down-conversion (SPDC) is a widely used method to generate entangled photons, enabling a range of applications from secure communication to tests of quantum physics. Integrating SPDC on a chip provides interferometric stability, allows to reduce a physical footprint, and opens a pathway to true scalability. However, dealing with different photon polarizations and wavelengths on a chip presents a number of challenging problems. In this work, we demonstrate an on-chip polarization beam-splitter based on z-cut titanium-diffused lithium niobate asymmetric adiabatic couplers (AAC) designed for integration with a type-II SPDC source. Our experimental measurements reveal unique polarization beam-splitting regime with the ability to tune the splitting ratios based on wavelength. In particular, we measured a splitting ratio of 17 dB over broadband regions (>60 nm) for both H- and V-polarized lights and a specific 50%/50% splitting ratio for a cross-polarized photon pair from the AAC. The results show that such a system can be used for preparing different quantum polarization-path states that are controllable by changing the phase-matching conditions in the SPDC over a broad band. Furthermore, we propose a fully integrated electro-optically tunable type-II SPDC polarization-path-entangled state preparation circuit on a single lithium niobate photonic chip.
Uncovering the Pharmacological Mechanism of Astragalus Salvia Compound on Pregnancy-Induced Hypertension Syndrome by a Network Pharmacology Approach
Authors: Zeng Liuting , Yang Kailin , Ge Jinwen 
Published: November 2017

AbstractTo uncover the pharmacological mechanism of Astragalus Salvia compound (ASC) on pregnancy-induced hypertension syndrome (PIH), to provide useful information for clinical, as well as to connect the basic and clinical by a network pharmacological approach, we used network pharmacological approach. We collected ASC’s compounds by traditional Chinese Medicine databases, and input them into PharmMapper to got their targets. Then we acquired PIH targets from Genecards and OMIM, collected the interactions of all the targets and other human proteins via String and INACT. We also constructed the network by Cytoscape and analyze it by MCODE so as to get clusters. Finally, we put all the targets of clusters into DAVID to do GO enrichment analysis. After these, four networks are constructed by Cytoscape; they are PIH network, compound-compound target network of ASC, ASC-PIH network, and compound target-PIH target-other human proteins’ PPI network. According to the results, we think that ASC may directly regulate several biological processes and their genes in “endothelial cell activation and injury” and “placental or trophoblast cell ischemia” models to treat PIH. And it may indirectly act on the rest of the biological process to treat PIH or may not.
Identification of early ammonium nitrate-responsive genes in rice roots
Authors: Yang Hsiu-Chun , Kan Chia-Cheng , Hung Tzu-Huan , Hsieh Ping-Han , Wang Shi-Yun , Hsieh Wei-Yu , Hsieh Ming-Hsiun 
Published: November 2017

AbstractAmmonium has long been used as the predominant form of nitrogen source for paddy rice (Oryza sativa). Recently, increasing evidence suggests that nitrate also plays an important role for nitrogen acquisition in the rhizosphere of waterlogged paddy rice. Ammonium and nitrate have a synergistic effect on promoting rice growth. However, the molecular responses induced by simultaneous treatment with ammonium and nitrate have been less studied in rice. Here, we performed transcriptome analysis to identify genes that are rapidly regulated by ammonium nitrate (1.43 mM, 30 min) in rice roots. The combination of ammonium and nitrate preferentially induced the expression of nitrate-responsive genes. Gene ontology enrichment analysis revealed that the early ammonium nitrate-responsive genes were enriched in “regulation of transcription, DNA-dependent” and “protein amino acid phosphorylation” indicating that some of the genes identified in this study may play an important role in nitrogen sensing and signaling. Several defense/stress-responsive genes, including some encoding transcription factors and mitogen-activated protein kinase kinase kinases, were also rapidly induced by ammonium nitrate. These results suggest that nitrogen metabolism, signaling, and defense/stress responses are interconnected. Some of the genes identified here may be involved in the interaction of nitrogen signaling and defense/stress-response pathways in plants.
Relevance of MIC-1 in the Era of PSA as a Serum Based Predictor of Prostate Cancer: A Critical Evaluation
Authors: Bansal Navneeta , Kumar Deepak , Gupta Ashish , Chandra Deepak , Sankhwar Satya Narain , Mandhani Anil 
Published: November 2017

AbstractTo reduce the ambiguity of contradictory observations in different studies regarding the expression level of Macrophage Inhibitory Cytokine-1 (MIC-1) in serum in prostate cancer (PC), benign prostatic hyperplasia (BPH) and healthy controls (HC), we designed this double-blind study. The study comprises 240 sera from PC, BPH and HC subjects. The expression level of MIC-1 in PC, BPH and HC were appraised using Western blot (WB) and ELISA based approach. WB and ELISA appraisal reveals that the expression level of MIC-1 is significantly higher in PC than in HC or BPH subjects. Regression analysis revealed a significant correlation between MIC-1 vs. PSA (r = 0.09; p < 0.001) and MIC-1 vs. GS (r = 0.7; p < 0.001). ROC analysis using discriminant predicted probability revealed that the MIC-1 was better than PSA. Moreover, the combination of MIC-1 and PSA was allowing 99.1% AUC for the differentiation of BPH + PC from HC, 97.9% AUC for differentiation of BPH from HC, 98.6% AUC for differentiation of PC from HC, and 96.7% AUC for the differentiation of PC from BPH. The augmented expression of MIC-1 in PC compared to BPH and HC subjects is in concurrent of the over-expression of MIC-1 in PC reports and confiscates the contradictory findings of other studies.