bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative study of afterpulsing behavior and models in single photon counting avalanche photo diode detectors
Authors: Ziarkash Abdul Waris , Joshi Siddarth Koduru , Stipčević Mario , Ursin Rupert 
Published: March 2018

AbstractSingle-photon avalanche diode (SPAD) detectors, have a great importance in fields like quantum key distribution, laser ranging, florescence microscopy, etc. Afterpulsing is a non-ideal behavior of SPADs that adversely affects any application that measures the number or timing of detection events. Several studies based on a few individual detectors, derived distinct mathematical models from semiconductor physics perspectives. With a consistent testing procedure and statistically large data sets, we show that different individual detectors - even if identical in type, make, brand, etc. - behave according to fundamentally different mathematical models. Thus, every detector must be characterized individually and it is wrong to draw universal conclusions about the physical meaning behind these models. We also report the presence of high-order afterpulses that are not accounted for in any of the standard models.
Multi-nanolayered VO2/Sapphire Thin Film via Spinodal Decomposition
Authors: Sun Guangyao , Cao Xun , Yue Yuanzheng , Gao Xiang , Long Shiwei , Li Ning , Li Rong , Luo Hongjie , Jin Ping 
Published: March 2018

AbstractCoating of VO2-based thin film has been extensively studied for fabricating energy-saving smart windows. One of the most efficient ways for fabricating high performance films is to create multi-nanolayered structure. However, it has been highly challenge to make such layers in the VO2-based films using conventional methods. In this work, a facile two-step approach is established to fabricate multilayered VO2-TiO2thin films. We first deposited the amorphous thin films upon sputtering, and then anneal them to transform the amorphous phase into alternating Ti- and V-rich multilayered nanostructure via a spinodal decomposition mechanism. In particular, we take advantage of different sapphire substrate planes (A-plane (11–20), R-plane (1–102), C-plane (0001), and M-plane (10-10)) to achieve different decomposition modes. The new approach has made it possible to tailoring the microstructure of the thin films for optimized performances by controlling the disorder-order transition in terms of both kinetic and thermodynamic aspects. The derived thin films exhibit superior optical modulation upon phase transition, significantly reduced transition temperature and hysteresis loop width, and high degradation resistance, these improvements indicate a high potential to be used for fabricating the next generation of energy saving smart windows.
Transcription factor PAX6 as a novel prognostic factor and putative tumour suppressor in non-small cell lung cancer
Authors: Kiselev Yury , Andersen Sigve , Johannessen Charles , Fjukstad Bjørn , Standahl Olsen Karina , Stenvold Helge , Al-Saad Samer , Donnem Tom , Richardsen Elin , Bremnes Roy M. , Rasmussen Busund Lill-Tove 
Published: March 2018

AbstractLung cancer is the leading cause of cancer deaths. Novel predictive biomarkers are needed to improve treatment selection and more accurate prognostication. PAX6 is a transcription factor with a proposed tumour suppressor function. Immunohistochemical staining was performed on tissue microarrays from 335 non-small cell lung cancer (NSCLC) patients for PAX6. Multivariate analyses of clinico-pathological variables and disease-specific survival (DSS) was carried out, and phenotypic changes of two NSCLC cell lines with knockdown of PAX6 were characterized. While PAX6 expression was only associated with a trend of better disease-specific survival (DSS) (p = 0.10), the pN+ subgroup (N = 103) showed significant correlation between high PAX6 expression and longer DSS (p = 0.022). Median survival for pN + patients with high PAX6 expression was 127.4 months, versus 22.9 months for patients with low PAX6 expression. In NCI-H661 cells, knockdown of PAX6 strongly activated serum-stimulated migration. In NCI-H460 cells, PAX6 knockdown activated anchorage-independent growth. We did not observe any significant effect of PAX6 on proliferation in either of cell lines. Our findings strongly support the proposition of PAX6 as a valid and positive prognostic marker in NSCLC in node-positive patients. There is a need for further studies, which should provide mechanistical explanation for the role of PAX6 in NSCLC.
Bacteriophages are more virulent to bacteria with human cells than they are in bacterial culture; insights from HT-29 cells
Authors: Shan Jinyu , Ramachandran Ananthi , Thanki Anisha M. , Vukusic Fatima B. I. , Barylski Jakub , Clokie Martha R. J. 
Published: March 2018

AbstractBacteriophage therapeutic development will clearly benefit from understanding the fundamental dynamics of in vivo phage-bacteria interactions. Such information can inform animal and human trials, and much can be ascertained from human cell-line work. We have developed a human cell-based system using Clostridium difficile, a pernicious hospital pathogen with limited treatment options, and the phage phiCDHS1 that effectively kills this bacterium in liquid culture. The human colon tumorigenic cell line HT-29 was used because it simulates the colon environment where C. difficile infection occurs. Studies on the dynamics of phage-bacteria interactions revealed novel facets of phage biology, showing that phage can reduce C. difficile numbers more effectively in the presence of HT-29 cells than in vitro. Both planktonic and adhered Clostridial cell numbers were successfully reduced. We hypothesise and demonstrate that this observation is due to strong phage adsorption to the HT-29 cells, which likely promotes phage-bacteria interactions. The data also showed that the phage phiCDHS1 was not toxic to HT-29 cells, and phage-mediated bacterial lysis did not cause toxin release and cytotoxic effects. The use of human cell lines to understand phage-bacterial dynamics offers valuable insights into phage biology in vivo, and can provide informative data for human trials.
MEF2A regulates mGluR-dependent AMPA receptor trafficking independently of Arc/Arg3.1
Authors: Carmichael Ruth E. , Wilkinson Kevin A. , Craig Tim J. , Ashby Michael C. , Henley Jeremy M. 
Published: March 2018

AbstractDifferential trafficking of AMPA receptors (AMPARs) to and from the postsynaptic membrane is a key determinant of the strength of excitatory neurotransmission, and is thought to underlie learning and memory. The transcription factor MEF2 is a negative regulator of memory in vivo, in part by regulating trafficking of the AMPAR subunit GluA2, but the molecular mechanisms behind this have not been established. Here we show, via knockdown of endogenous MEF2A in primary neuronal culture, that MEF2A is specifically required for Group I metabotropic glutamate receptor (mGluR)-mediated GluA2 internalisation, but does not regulate AMPAR expression or trafficking under basal conditions. Furthermore, this process occurs independently of changes in expression of Arc/Arg3.1, a previously characterised MEF2 transcriptional target and mediator of mGluR-dependent long-term depression. These data demonstrate a novel MEF2A-dependent mechanism for the regulation of activity-dependent AMPAR trafficking.
Possible bite-induced abscess and osteomyelitis in Lufengosaurus (Dinosauria: sauropodomorph) from the Lower Jurassic of the Yimen Basin, China
Authors: Xing Lida , Rothschild Bruce M. , Randolph-Quinney Patrick S. , Wang Yi , Parkinson Alexander H. , Ran Hao 
Published: March 2018

AbstractWe report an osseous abnormality on a specimen of the sauropod dinosaur Lufengosaurus huenei from the Fengjiahe Formation in Yuxi Basin, China. A gross pathological defect occurs on the right third rib, which was subjected to micro-computed tomographic imaging as an aid in diagnosis. The analysis of pathological characteristics and the shape of the abnormality is incompatible with impact or healed trauma, such as a common rib fracture, and instead suggests focal penetration of the rib, possibly due to a failed predator attack. The identification of characteristics based on gross morphology and internal micro-morphology presented by the specimen, suggests an abscess with osteomyelitis as the most parsimonious explanation. Osteomyelitis is a severe infection originating in the bone marrow, usually resulting from the introduction of pyogenic (pus-producing) bacteria into the bone. Micro-tomographic imaging of the lesion suggests a degree of healing and bone remodelling following post-traumatic wound infection with evidence of sclerotic bone formation at the site of pathological focus, indicating that L. huenei survived the initial trauma. However, as osteomyelitis can express through widespread systemic effects, including a lowering of immune response and overall condition, this disease may have been a contributing factor to the eventual death of the individual.
Diffusion tensor tractography of the mammillothalamic tract in the human brain using a high spatial resolution DTI technique
Authors: Kamali Arash , Zhang Caroline C. , Riascos Roy F. , Tandon Nitin , Bonafante-Mejia Eliana E. , Patel Rajan , Lincoln John A. , Rabiei Pejman , Ocasio Laura , Younes Kyan , Hasan Khader M. 
Published: March 2018

AbstractThe mammillary bodies as part of the hypothalamic nuclei are in the central limbic circuitry of the human brain. The mammillary bodies are shown to be directly or indirectly connected to the amygdala, hippocampus, and thalami as the major gray matter structures of the human limbic system. Although it is not primarily considered as part of the human limbic system, the thalamus is shown to be involved in many limbic functions of the human brain. The major direct connection of the thalami with the hypothalamic nuclei is known to be through the mammillothalamic tract. Given the crucial role of the mammillothalamic tracts in memory functions, diffusion tensor imaging may be helpful in better visualizing the surgical anatomy of this pathway noninvasively. This study aimed to investigate the utility of high spatial resolution diffusion tensor tractography for mapping the trajectory of the mammillothalamic tract in the human brain. Fifteen healthy adults were studied after obtaining written informed consent. We used high spatial resolution diffusion tensor imaging data at 3.0 T. We delineated, for the first time, the detailed trajectory of the mammillothalamic tract of the human brain using deterministic diffusion tensor tractography.
Lack of evidence supporting a role of TMC4-rs641738 missense variant—MBOAT7- intergenic downstream variant—in the Susceptibility to Nonalcoholic Fatty Liver Disease
Authors: Sookoian Silvia , Flichman Diego , Garaycoechea Martin E. , Gazzi Carla , Martino Julio San , Castaño Gustavo O. , Pirola Carlos J. 
Published: March 2018

AbstractCurrent knowledge on the genetic basis of nonalcoholic fatty liver disease (NAFLD) suggests that variants contributing not only to the disease predisposition but histological severity as well are located in genes that regulate lipid metabolism. We explored the role of rs641738 C/T located in TMC4 (transmembrane channel-like 4) exon 1 (p.Gly17Glu) and 500 bases- downstream of MBOAT7 gene (TMC4/MBOAT7), in the genetic risk for developing NAFLD in a case-control study. Our sample included 634 individuals (372 patients with NAFLD diagnosed by liver biopsy and 262 control subjects); genotyping was performed by a Taqman assay. Genotype frequencies in controls (CC: 84, CT: 137, TT: 41) and patients (CC: 134, CT: 178, TT: 60) were in Hardy-Weinberg equilibrium; minor allele frequency 40.8%. Our sample had 84–99% power if an additive genetic model is assumed for estimated odds ratios of 1.3–1.5, respectively. We found no evidence of association between rs641738 and either NAFLD (Cochran-Armitage test for trend, p = 0.529) or the disease severity (p = 0.61). Low levels of MBOAT7 protein expression were found in the liver of patients with NAFLD, which were unrelated to the rs641738 genotypes. In conclusion, the role of rs641738 in the pathogenesis of NAFLD is inconclusive.
Pattern Formation through Temporal Fractional Derivatives
Authors: Yin Hongwei , Wen Xiaoqing 
Published: March 2018

AbstractIt is well known that temporal first-derivative reaction-diffusion systems can produce various fascinating Turing patterns. However, it has been found that many physical, chemical and biological systems are well described by temporal fractional-derivative reaction-diffusion equations. Naturally arises an issue whether and how spatial patterns form for such a kind of systems. To address this issue clearly, we consider a classical prey-predator diffusive model with the Holling II functional response, where temporal fractional derivatives are introduced according to the memory character of prey’s and predator’s behaviors. In this paper, we show that this fractional-derivative system can form steadily spatial patterns even though its first-derivative counterpart can’t exhibit any steady pattern. This result implies that the temporal fractional derivatives can induce spatial patterns, which enriches the current mechanisms of pattern formation.
Metabolomics coupled with pathway analysis characterizes metabolic changes in response to BDE-3 induced reproductive toxicity in mice
Authors: Wei Ziheng , Xi Jing , Gao Songyan , You Xinyue , Li Na , Cao Yiyi , Wang Liupeng , Luan Yang , Dong Xin 
Published: March 2018

AbstractPolybrominated diphenyl ethers (PBDEs) may affect male reproductive function. 4-bromodiphenyl ether (BDE-3), the photodegradation products of higher brominated PBDEs, is the most fundamental mono-BDE in environment but is less studied. The purpose of this study was to investigate the reproductive toxicity induced by BDE-3 and explore the mechanism by metabolomics approach. In this study, mice were treated intragastrically with BDE-3 for consecutive six weeks at the dosages of 0.0015, 1.5, 10 and 30 mg/kg. The reproductive toxicity was evaluated by sperm analysis and histopathology examinations. UPLC-Q-TOF/MS was applied to profile the metabolites of testis tissue, urine and serum samples in the control and BDE-3 treated mice. Results showed the sperm count was dose-dependently decreased and percentage of abnormal sperms increased by the treatment of BDE-3. Histopathology examination also revealed changes in seminiferous tubules and epididymides in BDE-3 treated mice. Metabolomics analysis revealed that different BDE-3 groups showed metabolic disturbances to varying degrees. We identified 76, 38 and 31 differential metabolites in testis tissue, urine and serum respectively. Pathway analysis revealed several pathways including Tyrosine metabolism, Purine metabolism and Riboflavin metabolism, which may give a possible explanation for the toxic mechanism of BDE-3. This study indicates that UHPLC-Q-TOFMS-based metabolomics approach provided a better understanding of PBDEs-induced toxicity dynamically.
Structural and Functional Connectivity Changes Beyond Visual Cortex in a Later Phase of Visual Perceptual Learning
Authors: Kang Dong-Wha , Kim Dongho , Chang Li-Hung , Kim Yong-Hwan , Takahashi Emi , Cain Matthew S. , Watanabe Takeo , Sasaki Yuka 
Published: March 2018

AbstractThe neural mechanisms of visual perceptual learning (VPL) remain unclear. Previously we found that activation in the primary visual cortex (V1) increased in the early encoding phase of training, but returned to baseline levels in the later retention phase. To examine neural changes during the retention phase, we measured structural and functional connectivity changes using MRI. After weeks of training on a texture discrimination task, the fractional anisotropy of the inferior longitudinal fasciculus, a major tract connecting visual and anterior areas, was increased, as well as the functional connectivity between V1 and anterior regions mediated by the ILF. These changes were strongly correlated with behavioral performance improvements. These results suggest a two-phase model of VPL in which localized functional changes in V1 in the encoding phase of training are followed by changes in both structural and functional connectivity in ventral visual processing, perhaps leading to the long-term stabilization of VPL.
Schramm-Loewner evolution and perimeter of percolation clusters of correlated random landscapes
Authors: de Castro C. P. , Luković M. , Pompanin G. , Andrade R. F. S. , Herrmann H. J. 
Published: March 2018

AbstractMotivated by the fact that many physical landscapes are characterized by long-range height-height correlations that are quantified by the Hurst exponent H, we investigate the statistical properties of the iso-height lines of correlated surfaces in the framework of Schramm-Loewner evolution (SLE). We show numerically that in the continuum limit the external perimeter of a percolating cluster of correlated surfaces with H ∈ [−1, 0] is statistically equivalent to SLE curves. Our results suggest that the external perimeter also retains the Markovian properties, confirmed by the absence of time correlations in the driving function and the fact that the latter is Gaussian distributed for any specific time. We also confirm that for all H the variance of the winding angle grows logarithmically with size.
Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation
Authors: Jia Linpei , Fu Wenjing , Jia Rufu , Wu Leiyun , Li Xiaoxia , Jia Qiang , Zhang Hongliang 
Published: March 2018

AbstractWe aim to identify the key protein interaction networks and implicated pathways of BK virus nephropathy (BKVN) via bioinformatic methods. The microarray dataGSE75693of 30 patients with stable kidney transplantation and 15 with BKVN were downloaded and analyzed by using thelimmapackage to identify differentially expressed genes (DEGs). Then the gene ontology (GO) functional enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were done to investigate the molecular function (MF), biological process (BP), cellular components (CC) and pathways of DEGs. Finally, protein-protein interactions (PPIs) were constructed, and the hub proteins were identified. As a result, 249 up-regulated genes and 253 down-regulated genes of BKVN patients were selected based on criteria ofP > 0.01 and fold change >2.0. GO and KEGG showed that DEGs were mainly located in nucleus and cytosol, and were implicated in the immune responses. In the PPI analysis, 26 up-regulated and 8 down-regulated proteins composed the pivotal interaction network. CXCL10, EGF and STAT1 were identified as hub proteins in BKVN. In conclusion, CXCL10, EGF and STAT1 may induce kidney injuries by promoting inflammation and prohibiting reparation of tissue damage in BKVN.
Using spatial mark-recapture for conservation monitoring of grizzly bear populations in Alberta
Authors: Boulanger John , Nielsen Scott E. , Stenhouse Gordon B. 
Published: March 2018

AbstractOne of the challenges in conservation is determining patterns and responses in population density and distribution as it relates to habitat and changes in anthropogenic activities. We applied spatially explicit capture recapture (SECR) methods, combined with density surface modelling from five grizzly bear (Ursus arctos) management areas (BMAs) in Alberta, Canada, to assess SECR methods and to explore factors influencing bear distribution. Here we used models of grizzly bear habitat and mortality risk to test local density associations using density surface modelling. Results demonstrated BMA-specific factors influenced density, as well as the effects of habitat and topography on detections and movements of bears. Estimates from SECR were similar to those from closed population models and telemetry data, but with similar or higher levels of precision. Habitat was most associated with areas of higher bear density in the north, whereas mortality risk was most associated (negatively) with density of bears in the south. Comparisons of the distribution of mortality risk and habitat revealed differences by BMA that in turn influenced local abundance of bears. Combining SECR methods with density surface modelling increases the resolution of mark-recapture methods by directly inferring the effect of spatial factors on regulating local densities of animals.
Combining targeted panel-based resequencing and copy-number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies
Authors: Sanchez-Navarro Iker , R. J. da Silva Luciana , Blanco-Kelly Fiona , Zurita Olga , Sanchez-Bolivar Noelia , Villaverde Cristina , Lopez-Molina Maria Isabel , Garcia-Sandoval Blanca , Tahsin-Swafiri Saoud , Minguez Pablo , Riveiro-Alvarez Rosa , Lorda Isabel , Sanchez-Alcudia Rocío , Perez-Carro Raquel , Valverde Diana , Liu Yichuan , Tian Lifeng , Hakonarson Hakon , Avila-Fernandez Almudena , Corton Marta , Ayuso Carmen 
Published: March 2018

AbstractInherited syndromic retinopathies are a highly heterogeneous group of diseases that involve retinal anomalies and systemic manifestations. They include retinal ciliopathies, other well-defined clinical syndromes presenting with retinal alterations and cases of non-specific multisystemic diseases. The heterogeneity of these conditions makes molecular and clinical characterization of patients challenging in daily clinical practice. We explored the capacity of targeted resequencing and copy-number variation analysis to improve diagnosis of a heterogeneous cohort of 47 patients mainly comprising atypical cases that did not clearly fit a specific clinical diagnosis. Thirty-three likely pathogenic variants were identified in 18 genes (ABCC6, ALMS1, BBS1, BBS2, BBS12, CEP41, CEP290, IFT172, IFT27, MKKS, MYO7A, OTX2, PDZD7, PEX1, RPGRIP1, USH2A, VPS13B, and WDPCP). Molecular findings and additional clinical reassessments made it possible to accurately characterize 14 probands (30% of the total). Notably, clinical refinement of complex phenotypes was achieved in 4 cases, including 2 de novo OTX2-related syndromes, a novel phenotypic association for the ciliary CEP41 gene, and the co-existence of biallelic USH2A variants and a Koolen-de-Vries syndrome–related 17q21.31 microdeletion. We demonstrate that combining next-generation sequencing and CNV analysis is a comprehensive and useful approach to unravel the extensive phenotypic and genotypic complexity of inherited syndromic retinopathies.
Spatial-temporal profiling of prodiginines and serratamolides produced by endophytic Serratia marcescens harbored in Maytenus serrata
Authors: Eckelmann Dennis , Spiteller Michael , Kusari Souvik 
Published: March 2018

AbstractAn endophytic bacterium, Serratia marcescens MSRBB2, isolated from inner bark of a Cameroonian Maytenus serrata plant, was subjected to the OSMAC (One Strain Many Compounds) approach and metabolic profiling using HPLC-HRMSn. We identified 7 prodiginines along with 26 serratamolides. Their biosynthetic pathways were elucidated by feeding with labeled precursors in combination with HRMSn. Dual-culture confrontation/restriction assays of the bacterial endophyte were devised with coexisting fungal endophytes (Pestalotiopsis virgatula, Aspergillus caesiellus and Pichia spp.) as well as with unrelated, non-endophytic fungi belonging to the same genera. The assays were combined with scanning electron microscopy (SEM) as well as matrix-assisted laser desorption ionization imaging high-resolution mass spectrometry (MALDI-imaging-HRMS) for visualizing, both in high spatial and temporal resolution, the distribution and interplay of the compounds during microbial interactions. We demonstrated the effect of prodigiosin produced by endophytic S. marcescens MSRBB2 as an allelochemical that specifically inhibits coexisting endophytic fungi. Our results provide new insights into the physiological and ecological relevance of prodiginines and serratamolides within the context of allelopathy and chemical defense interaction occurring between coexisting endophytes harbored in M. serrata.