bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sorting Nexin 9 facilitates podocin endocytosis in the injured podocyte
Authors: Sasaki Yu , Hidaka Teruo , Ueno Takashi , Akiba-Takagi Miyuki , Oliva Trejo Juan Alejandro , Seki Takuto , Nagai-Hosoe Yoshiko , Tanaka Eriko , Horikoshi Satoshi , Tomino Yasuhiko , Suzuki Yusuke , Asanuma Katsuhiko 
Published: March 2017

AbstractThe irreversibility of glomerulosclerotic changes depends on the degree of podocyte injury. We have previously demonstrated the endocytic translocation of podocin to the subcellular area in severely injured podocytes and found that this process is the primary disease trigger. Here we identified the protein sorting nexin 9 (SNX9) as a novel facilitator of podocin endocytosis in a yeast two-hybrid analysis. SNX9 is involved in clathrin-mediated endocytosis, actin rearrangement and vesicle transport regulation. Our results revealed and confirmed that SNX9 interacts with podocin exclusively through the Bin–Amphiphysin–Rvs (BAR) domain of SNX9. Immunofluorescence staining revealed the expression of SNX9 in response to podocyte adriamycin-induced injury both in vitro and in vivo. Finally, an analysis of human glomerular disease biopsy samples demonstrated strong SNX9 expression and co-localization with podocin in samples representative of severe podocyte injury, such as IgA nephropathy with poor prognosis, membranous nephropathy and focal segmental glomerulosclerosis. In conclusion, we identified SNX9 as a facilitator of podocin endocytosis in severe podocyte injury and demonstrated the expression of SNX9 in the podocytes of both nephropathy model mice and human patients with irreversible glomerular disease.
SeqTU: A Web Server for Identification of Bacterial Transcription Units
Authors: Chen Xin , Chou Wen-Chi , Ma Qin , Xu Ying 
Published: March 2017

AbstractA transcription unit (TU) consists of K ≥ 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA molecule under certain conditions. Their identification is an essential step in elucidation of transcriptional regulatory networks. We have recently developed a machine-learning method to accurately identify TUs from RNA-seq data, based on two features of the assembled RNA reads: the continuity and stability of RNA-seq coverage across a genomic region. While good performance was achieved by the method on Escherichia coli and Clostridium thermocellum, substantial work is needed to make the program generally applicable to all bacteria, knowing that the program requires organism specific information. A web server, named SeqTU, was developed to automatically identify TUs with given RNA-seq data of any bacterium using a machine-learning approach. The server consists of a number of utility tools, in addition to TU identification, such as data preparation, data quality check and RNA-read mapping. SeqTU provides a user-friendly interface and automated prediction of TUs from given RNA-seq data. The predicted TUs are displayed intuitively using HTML format along with a graphic visualization of the prediction.
Size and stochasticity in irrigated social-ecological systems
Authors: Puy Arnald , Muneepeerakul Rachata , Balbo Andrea L. 
Published: March 2017

AbstractThis paper presents a systematic study of the relation between the size of irrigation systems and the management of uncertainty. We specifically focus on studying, through a stylized theoretical model, how stochasticity in water availability and taxation interacts with the stochastic behavior of the population within irrigation systems. Our results indicate the existence of two key population thresholds for the sustainability of any irrigation system: "Equation missing"or the critical population size required to keep the irrigation system operative, andN* or the population threshold at which the incentive to work inside the irrigation system equals the incentives to work elsewhere. Crossing"Equation missing"irretrievably leads to system collapse.N* is the population level with a sub-optimal per capita payoff towards which irrigation systems tend to gravitate. When subjected to strong stochasticity in water availability or taxation, irrigation systems might suffer sharp population drops and irreversibly disintegrate into a system collapse, via a mechanism we dub ‘collapse trap’. Our conceptual study establishes the basis for further work aiming at appraising the dynamics between size and stochasticity in irrigation systems, whose understanding is key for devising mitigation and adaptation measures to ensure their sustainability in the face of increasing and inevitable uncertainty.
Sequential activation of different pathway networks in ischemia-affected and non-affected myocardium, inducing intrinsic remote conditioning to prevent left ventricular remodeling
Authors: Pavo Noemi , Lukovic Dominika , Zlabinger Katrin , Zimba Abelina , Lorant David , Goliasch Georg , Winkler Johannes , Pils Dietmar , Auer Katharina , Jan Ankersmit Hendrik , Giricz Zoltán , Baranyai Tamas , Sárközy Márta , Jakab András , Garamvölgyi Rita , Emmert Maximilian Y. , Hoerstrup Simon P. , Hausenloy Derek J. , Ferdinandy Péter , Maurer Gerald , Gyöngyösi Mariann 
Published: March 2017

AbstractWe have analyzed the pathway networks of ischemia-affected and remote myocardial areas after repetitive ischemia/reperfusion (r-I/R) injury without ensuing myocardial infarction (MI) to elaborate a spatial- and chronologic model of cardioprotective gene networks to prevent left ventricular (LV) adverse remodeling. Domestic pigs underwent three cycles of 10/10 min r-I/R by percutaneous intracoronary balloon inflation/deflation in the mid left anterior descending artery, without consecutive MI. Sham interventions (n = 8) served as controls. Hearts were explanted at 5 h (n = 6) and 24 h (n = 6), and transcriptomic profiling of the distal (ischemia-affected) and proximal (non-affected) anterior myocardial regions were analyzed by next generation sequencing (NGS) and post-processing with signaling pathway impact and pathway network analyses. In ischemic region, r-I/R induced early activation of Ca-, adipocytokine and insulin signaling pathways with key regulator STAT3, which was also upregulated in the remote areas together with clusterin (CLU) and TNF-alpha. During the late phase of cardioprotection, antigen immunomodulatory pathways were activated with upregulation of STAT1 and CASP3 and downregulation of neprilysin in both zones, suggesting r-I/R induced intrinsic remote conditioning. The temporo-spatially differently activated pathways revealed a global myocardial response, and neprilysin and the STAT family as key regulators of intrinsic remote conditioning for prevention of adverse remodeling.
Autaptic Connections Shift Network Excitability and Bursting
Authors: Wiles Laura , Gu Shi , Pasqualetti Fabio , Parvesse Brandon , Gabrieli David , Bassett Danielle S. , Meaney David F. 
Published: March 2017

AbstractWe examine the role of structural autapses, when a neuron synapses onto itself, in driving network-wide bursting behavior. Using a simple spiking model of neuronal activity, we study how autaptic connections affect activity patterns, and evaluate if controllability significantly affects changes in bursting from autaptic connections. Adding more autaptic connections to excitatory neurons increased the number of spiking events and the number of network-wide bursts. We observed excitatory synapses contributed more to bursting behavior than inhibitory synapses. We evaluated if neurons with high average controllability, predicted to push the network into easily achievable states, affected bursting behavior differently than neurons with high modal controllability, thought to influence the network into difficult to reach states. Results show autaptic connections to excitatory neurons with high average controllability led to higher burst frequencies than adding the same number of self-looping connections to neurons with high modal controllability. The number of autapses required to induce bursting was lowered by adding autapses to high degree excitatory neurons. These results suggest a role of autaptic connections in controlling network-wide bursts in diverse cortical and subcortical regions of mammalian brain. Moreover, they open up new avenues for the study of dynamic neurophysiological correlates of structural controllability.
Polymorphisms and Pharmacogenomics for the Clinical Efficacy of Methotrexate in Patients with Rheumatoid Arthritis: A Systematic Review and Meta-analysis
Authors: Qiu Qi , Huang Jing , Shu Xiaoming , Fan Huizheng , Zhou Youwen , Xiao Cheng 
Published: March 2017

AbstractMethotrexate (MTX) is widely used and considered a first-line disease modifying anti-rheumatic drug (DMARD) for the treatment of rheumatoid arthritis (RA). Many of the relevant genes have been investigated to estimate the association between gene polymorphisms and MTX effectiveness in RA patients, although inconsistent results have been reported. A systematic review and meta-analysis were performed to identify genetic variants associated with MTX efficacy. A total of 30 publications that included 34 genes and 125 SNPs associated with the transporters, enzymes, and metabolites of MTX or the progression of RA were included in the systematic review (SR), and 21 studies were included in 9 meta-analyses. Associations between MTX response in RA patients in MTHFR 1298A > C (rs1801131), ATIC 347C > G (rs2372536), RFC-1 80G > A (rs1051266), SLC19A1 A > G (rs2838956) and SLC19A1 G > A (rs7499) genetic polymorphisms were found, but not observed between the MTHFR 677C > T (rs1801133), TYMS 28 bp VNTR (rs34743033), MTRR 66A > G (rs1801394), and ABCB1 3435C > T (rs1045642). However, for the polymorphisms not being associated following meta-analysis could still be associated if larger cohorts were used, and studies of other polymorphisms are necessary in large cohorts and a rigorous way, which may provide more accurate results for the effect of the gene polymorphisms on the MTX response.
Genetic signatures of natural selection in a model invasive ascidian
Authors: Lin Yaping , Chen Yiyong , Yi Changho , Fong Jonathan J. , Kim Won , Rius Marc , Zhan Aibin 
Published: March 2017

AbstractInvasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.
A reduced lymphocyte ratio as an early marker for predicting acute pancreatitis
Authors: Qi Xiuzhong , Yang Fangyong , Huang Haitao , Du Yiqi , Chen Yan , Wang Meitang , Zhu Dezeng , Yue Xiaoqiang , Wang Lina 
Published: March 2017

AbstractThe early diagnosis and severity grading for acute pancreatitis (AP) are difficult to determine because of the complexity and differences in disease process. To date, few studies have investigated the role of lymphocyte ratio (LR) in AP. Therefore, the objective of the present study was to investigate the prognostic value of LR as an indicator in AP, as well as determine an optimal cut-off value for the severity prediction. There were two hundred four patients involved in this study, ninety-two of whom had severe acute pancreatitis (SAP). The LR was analyzed on admission and correlated with severity, which was determined using the Atlanta classification. The optimal cut-off value for LR was generated using receiving operator characteristic (ROC) curves. The results showed that the LR in the SAP group decreased significantly compared to the mild acute pancreatitis (MAP) group (8.82 vs. 13.43). The optimal cut-off value obtained from ROC curves was 0.081, with a sensitivity of 80.4%, a specificity of 53.3%, a positive likelihood ratio of 1.722, and a negative likelihood ratio of 0.368. In conclusion, the LR is obviously related to the condition of AP patients and is valuable for the differential diagnosis of SAP in early stages of AP.
Position and orientation measurement adopting camera calibrated by projection geometry of Plücker matrices of three-dimensional lines
Authors: Xu Guan , Zheng Anqi , Li Xiaotao , Su Jian 
Published: March 2017

AbstractA position and orientation measurement method is investigated by adopting a camera calibrated by the projection geometry of the skew-symmetric Plücker matrices of 3D lines. The relationship between the Plücker matrices of the dual 3D lines and the 2D projective lines is provided in two vertical world coordinate planes. The transform matrix is generated from the projections of the 3D lines. The differences between the coordinates of the reprojective lines and the coordinates of extracted lines are employed to verify the calibration validity. Moreover, the differences between the standard movement distance of the target and the measurement distance are also presented to compare the calibration accuracy of the 3D line to 2D line method and the point-based method. Furthermore, we also explore the noise immunity of the two methods by adding Gaussian noises. Finally, an example to measure the position and orientation of a cart is performed as an application case of this method. The results are tabled for the reproduction by the readers. The results demonstrate that the line to line method contributes higher calibration accuracy and better noise immunity. The position and orientation measurement adopting the line to line method is valid for the future applications.
Efficient frequency generation in phoXonic cavities based on hollow whispering gallery mode resonators
Authors: Farnesi Daniele , Righini Giancarlo , Nunzi Conti Gualtiero , Soria Silvia 
Published: March 2017

AbstractWe report on nonlinear optical effects on phoxonic cavities based on hollow whispering gallery mode resonators pumped with a continuous wave laser. We observed stimulated scattering effects such as Brillouin and Raman, Kerr effects such as degenerated and non-degenerated four wave mixing, and dispersive wave generation. These effects happened concomitantly. Hollow resonators give rise to a very rich nonlinear scenario due to the coexistence of several family modes.
Striatal phosphodiesterase 10A and medial prefrontal cortical thickness in patients with schizophrenia: a PET and MRI study
Authors: Bodén R , Persson J , Wall A , Lubberink M , Ekselius L , Larsson E-M , Antoni G 
Published: March 2017

AbstractThe enzyme phosphodiesterase 10A (PDE10A) is abundant in striatal medium spiny neurons and has been implicated in the pathophysiology of schizophrenia in animal models and is investigated as a possible new pharmacological treatment target. A reduction of prefrontal cortical thickness is common in schizophrenia, but how this relates to PDE10A expression is unknown. Our study aim was to compare, we believe for the first time, the striatal non-displaceable binding potential (BPND) of the new validated PDE10A ligand [11C]Lu AE92686 between patients with schizophrenia and healthy controls. Furthermore, we aimed to assess the correlation of PDE10A BPND to cortical thickness. Sixteen healthy male controls and 10 male patients with schizophrenia treated with clozapine, olanzapine or quetiapine were investigated with positron emission tomography (PET) and magnetic resonance imaging (MRI). Striatal binding potential (BPND) of [11C]Lu AE92686 was acquired through dynamic PET scans and cortical thickness by structural MRI. Clinical assessments of symptoms and cognitive function were performed and the antipsychotic dosage was recorded. Patients with schizophrenia had a significantly lower BPND of [11C]Lu AE92686 in striatum (P=0.003) than healthy controls. The striatal BPND significantly correlated to cortical thickness in the medial prefrontal cortex and superior frontal gyrus across patients with schizophrenia and healthy controls. No significant correlation was observed between the BPND for [11C]Lu AE92686 in striatum and age, schizophrenia symptoms, antipsychotic dosage, coffee consumption, smoking, duration of illness or cognitive function in the patients. In conclusion, PDE10A may be important for functioning in the striato-cortical interaction and in the pathophysiology of schizophrenia.
Elevated hair cortisol concentrations in recently fled asylum seekers in comparison to permanently settled immigrants and non-immigrants
Authors: Mewes R , Reich H , Skoluda N , Seele F , Nater U M 
Published: March 2017

AbstractRecently fled asylum seekers generally live in stressful conditions. Their residency status is mostly insecure and, similar to other immigrants, they experience stress due to acculturation. Moreover, they often suffer from traumatization and posttraumatic stress disorder (PTSD). All of these factors can result in chronic maladaptive biological stress responses in terms of hyper- or hypocortisolism and, ultimately, illness. We believe the current study is the first to compare hair cortisol concentration (HCC) of recently fled asylum seekers with PTSD to those without PTSD, and to compare HCC of asylum seekers to HCC of permanently settled immigrants and non-immigrant individuals. HCC of the previous 2 months was compared between 24 asylum seekers without PTSD, 32 asylum seekers with PTSD, 24 permanently settled healthy Turkish immigrants and 28 non-immigrant healthy Germans as the reference group. Statistical comparisons were controlled for age, sex and body mass index. No significant difference in HCC was found between asylum seekers with and without PTSD. However, the asylum seekers showed a 42% higher HCC than the reference group. In contrast, the permanently settled immigrants exhibited a 23% lower HCC than the reference group. We found relative hypercortisolism in recently fled asylum seekers, but no difference between persons with and without PTSD. These findings add to the very few studies investigating HCC in groups with recent traumatization and unsafe living conditions. Contrary to the findings in asylum seekers, permanently settled immigrants showed relative hypocortisolism. Both hyper- and hypocortisolism may set the stage for the development of stress-related illnesses.
New dimensions and new tools to realize the potential of RDoC: digital phenotyping via smartphones and connected devices
Authors: Torous J , Onnela J-P , Keshavan M 
Published: March 2017

AbstractMobile and connected devices like smartphones and wearable sensors can facilitate the collection of novel naturalistic and longitudinal data relevant to psychiatry at both the personal and population level. The National Institute of Mental Health’s Research Domain Criteria framework offers a useful roadmap to organize, guide and lead new digital phenotyping data towards research discoveries and clinical advances.
Effects of naltrexone are influenced by childhood adversity during negative emotional processing in addiction recovery
Authors: Savulich G , Riccelli R , Passamonti L , Correia M , Deakin J F W , Elliott R , Flechais R S A , Lingford-Hughes A R , McGonigle J , Murphy A , Nutt D J , Orban C , Paterson L M , Reed L J , Smith D G , Suckling J , Tait R , Taylor E M , Sahakian B J , Robbins T W , Ersche K D ,   ICCAM Platform
Published: March 2017

AbstractNaltrexone is an opioid receptor antagonist used in the management of alcohol dependence. Although the endogenous opioid system has been implicated in emotion regulation, the effects of mu-opioid receptor blockade on brain systems underlying negative emotional processing are not clear in addiction. Individuals meeting criteria for alcohol dependence alone (n=18, alcohol) and in combination with cocaine and/or opioid dependence (n=21, alcohol/drugs) and healthy individuals without a history of alcohol or drug dependence (n=21) were recruited. Participants were alcohol and drug abstinent before entered into this double-blind, placebo-controlled, randomized, crossover study. Functional magnetic resonance imaging was used to investigate brain response while viewing aversive and neutral images relative to baseline on 50 mg of naltrexone and placebo. We found that naltrexone modulated task-related activation in the medial prefrontal cortex and functional connectivity between the anterior cingulate cortex and the hippocampus as a function of childhood adversity (for aversive versus neutral images) in all groups. Furthermore, there was a group-by-treatment-by-condition interaction in the right amygdala, which was mainly driven by a normalization of response for aversive relative to neutral images under naltrexone in the alcohol/drugs group. We conclude that early childhood adversity is one environmental factor that influences pharmacological response to naltrexone. Pharmacotherapy with naltrexone may also have some ameliorative effects on negative emotional processing in combined alcohol and drug dependence, possibly due to alterations in endogenous opioid transmission or the kappa-opioid receptor antagonist actions of naltrexone.
Nanosecond pulse discharge based nitrogen oxides treatment using different electrode configurations
Authors: Mohapatro Sankarsan , Allamsetty Srikanth , Madhukar Apeksha , Sharma Nikhil Kumar 
Published: March 2017

Nowadays, the intensity of air pollution, due to the industries and automobiles, has been increasing continuously. Nitrogen oxides (NOX) are one of the most harmful pollutants, which are getting released from both automobile and stationary diesel engines. They essentially need to be removed from the exhaust using after treatment systems. However, the energy required to remove these pollutants is one of the major considerations in selecting the technology for pollutant removal from diesel engine exhaust. A study has been carried out on the non‐thermal plasma‐based NOX removal technique using various combinations of power supply units and electrode configurations. Three different electrode configurations are tested, in which two are cylindrical electrodes with diameters 3 and 5 mm, and the other one is a square electrode with a diagonal of 5 mm. A comparison is made between the results with two different pulse power supply units, PS‐I: high‐voltage direct current test set based and PS‐II: DC–DC converter based. The square electrode with PS‐II has been found to be the optimal combination, which has removed 85% of NOX from the exhaust at an energy density of 55.5 J/L, when the initial NOX concentration in the exhaust is 388 ppm.