bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway
Authors: Thierry Sylvain , Thierry Eloïse , Subra Frédéric , Deprez Eric , Leh Hervé , Bury-Moné Stéphanie , Delelis Olivier 
Published: May 2016

AbstractIntegration of HIV-1 linear DNA into host chromatin is required for high levels of viral expression, and constitutes a key therapeutic target. Unintegrated viral DNA (uDNA) can support only limited transcription but may contribute to viral propagation, persistence and/or treatment escape under specific situations. The molecular mechanisms involved in the differential expression of HIV uDNA vs integrated genome (iDNA) remain to be elucidated. Here, we demonstrate, for the first time, that the expression of HIV uDNA is mainly supported by 1-LTR circles, and regulated in the opposite way, relatively to iDNA, following NF-κB pathway modulation. Upon treatment activating the NF-κB pathway, NF-κB p65 and AP-1 (cFos/cJun) binding to HIV LTR iDNA correlates with increased iDNA expression, while uDNA expression decreases. On the contrary, inhibition of the NF-κB pathway promotes the expression of circular uDNA, and correlates with Bcl-3 and AP-1 binding to its LTR region. Finally, this study identifies NF-κB subunits and Bcl-3 as transcription factors binding the HIV promoter differently depending on viral genome topology, and opens new insights on the potential roles of episomal genomes during the HIV-1 latency and persistence.
Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules
Authors: Tursch Anja , Mercadante Davide , Tennigkeit Jutta , Gräter Frauke , Özbek Suat 
Published: May 2016

AbstractThe stinging capsules of cnidarians, nematocysts, function as harpoon-like organelles with unusual biomechanical properties. The nanosecond discharge of the nematocyst requires a dense protein network of the capsule structure withstanding an internal pressure of up to 150 bar. Main components of the capsule are short collagens, so-called minicollagens, that form extended polymers by disulfide reshuffling of their cysteine-rich domains (CRDs). Although CRDs have identical cysteine patterns, they exhibit different structures and disulfide connectivity at minicollagen N and C-termini. We show that the structurally divergent CRDs have different cross-linking potentials in vitro and in vivo. While the C-CRD can participate in several simultaneous intermolecular disulfides and functions as a cystine knot after minicollagen synthesis, the N-CRD is monovalent. Our combined experimental and computational analyses reveal the cysteines in the C-CRD fold to exhibit a higher structural propensity for disulfide bonding and a faster kinetics of polymerization. During nematocyst maturation, the highly reactive C-CRD is instrumental in efficient cross-linking of minicollagens to form pressure resistant capsules. The higher ratio of C-CRD folding types evidenced in the medusozoan lineage might have fostered the evolution of novel, predatory nematocyst types in cnidarians with a free-swimming medusa stage.
Cloud-based Electronic Health Records for Real-time, Region-specific Influenza Surveillance
Authors: Santillana M. , Nguyen A. T. , Louie T. , Zink A. , Gray J. , Sung I. , Brownstein J. S. 
Published: May 2016

AbstractAccurate real-time monitoring systems of influenza outbreaks help public health officials make informed decisions that may help save lives. We show that information extracted from cloud-based electronic health records databases, in combination with machine learning techniques and historical epidemiological information, have the potential to accurately and reliably provide near real-time regional estimates of flu outbreaks in the United States.
Highly Robust Neutral Plane Oxide TFTs Withstanding 0.25 mm Bending Radius for Stretchable Electronics
Authors: Kim Yong-Hwan , Lee Eunji , Um Jae Gwang , Mativenga Mallory , Jang Jin 
Published: May 2016

AbstractAdvancements in thin-film transistor (TFT) technology have extended to electronics that can withstand extreme bending or even folding. Although the use of ultrathin plastic substrates has achieved considerable advancement towards this end, free-standing ultrathin plastics inevitably suffer from mechanical instability and are very difficult to handle during TFT fabrication. Here, in addition to the use of a 1.5 μm-thick polyimide (PI) substrate, a 1.5 μm-thick PI film is also deposited on top of the TFT devices to ensure that the devices are located at the neutral plane of the two PI films for high folding stability. For mechanical support during TFT fabrication up to the deposition of the top PI film, the PI substrate is spin coated on top of a carrier glass that is coated with a mixture of carbon nanotubes (CNTs) and graphene oxide (GO). The mixture of CNT and GO facilitates mechanical detachment of the neutral plane (NP) TFTs from the carrier glass before they are transferred to a polydimethylsiloxane (PDMS) substrate as islands. Being located in the neutral bending plane, the NP TFT can be transferred to the PDMS without performance degradation and exhibit excellent mechanical stability after stretching the PDMS substrate up to a 25% elastic elongation.
miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
Authors: Andrés-León Eduardo , Núñez-Torres Rocío , Rojas Ana M. 
Published: May 2016

AbstractLarge-scale RNAseq has substantially changed the transcriptomics field, as it enables an unprecedented amount of high resolution data to be acquired. However, the analysis of these data still poses a challenge to the research community. Many tools have been developed to overcome this problem, and to facilitate the study of miRNA expression profiles and those of their target genes. While a few of these enable both kinds of analysis to be performed, they also present certain limitations in terms of their requirements and/or the restrictions on data uploading. To avoid these restraints, we have developed a suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism. Additionally, it enables differential expression, miRNA-mRNA target prediction and/or functional analysis. The miARma-Seq pipeline is presented as a stand-alone tool that is both easy to install and flexible in terms of its use, and that brings together well-established software in a single bundle. Our suite can analyze a large number of samples due to its multithread design. By testing miARma-Seq in validated datasets, we demonstrate here the benefits that can be gained from this tool by making it readily accessible to the research community.
Aquaporin-3 potentiates allergic airway inflammation in ovalbumin-induced murine asthma
Authors: Ikezoe Kohei , Oga Toru , Honda Tetsuya , Hara-Chikuma Mariko , Ma Xiaojun , Tsuruyama Tatsuaki , Uno Kazuko , Fuchikami Jun-ichi , Tanizawa Kiminobu , Handa Tomohiro , Taguchi Yoshio , Verkman Alan S. , Narumiya Shuh , Mishima Michiaki , Chin Kazuo 
Published: May 2016

AbstractOxidative stress plays a pivotal role in the pathogenesis of asthma. Aquaporin-3 (AQP3) is a small transmembrane water/glycerol channel that may facilitate the membrane uptake of hydrogen peroxide (H2O2). Here we report that AQP3 potentiates ovalbumin (OVA)-induced murine asthma by mediating both chemokine production from alveolar macrophages and T cell trafficking. AQP3 deficient (AQP3−/−) mice exhibited significantly reduced airway inflammation compared to wild-type mice. Adoptive transfer experiments showed reduced airway eosinophilic inflammation in mice receiving OVA-sensitized splenocytes from AQP3−/− mice compared with wild-type mice after OVA challenge, consistently with fewer CD4+ T cells from AQP3−/− mice migrating to the lung than from wild-type mice. Additionally, in vivo and vitro experiments indicated that AQP3 induced the production of some chemokines such as CCL24 and CCL22 through regulating the amount of cellular H2O2 in M2 polarized alveolar macrophages. These results imply a critical role of AQP3 in asthma and AQP3 may be a novel therapeutic target.
Word pair classification during imagined speech using direct brain recordings
Authors: Martin Stephanie , Brunner Peter , Iturrate Iñaki , Millán José del R. , Schalk Gerwin , Knight Robert T. , Pasley Brian N. 
Published: May 2016

AbstractPeople that cannot communicate due to neurological disorders would benefit from an internal speech decoder. Here, we showed the ability to classify individual words during imagined speech from electrocorticographic signals. In a word imagery task, we used high gamma (70–150 Hz) time features with a support vector machine model to classify individual words from a pair of words. To account for temporal irregularities during speech production, we introduced a non-linear time alignment into the SVM kernel. Classification accuracy reached 88% in a two-class classification framework (50% chance level), and average classification accuracy across fifteen word-pairs was significant across five subjects (mean = 58%; p < 0.05). We also compared classification accuracy between imagined speech, overt speech and listening. As predicted, higher classification accuracy was obtained in the listening and overt speech conditions (mean = 89% and 86%, respectively; p < 0.0001), where speech stimuli were directly presented. The results provide evidence for a neural representation for imagined words in the temporal lobe, frontal lobe and sensorimotor cortex, consistent with previous findings in speech perception and production. These data represent a proof of concept study for basic decoding of speech imagery, and delineate a number of key challenges to usage of speech imagery neural representations for clinical applications.
Comprehensive evaluation of candidate reference genes for qRT-PCR studies of gene expression in mustard aphid, Lipaphis erysimi (Kalt)
Authors: Koramutla Murali Krishna , Aminedi Raghavendra , Bhattacharya Ramcharan 
Published: May 2016

AbstractMustard aphid, also known as turnip aphid (Lipaphis erysimi) is a major insect pest of rapeseed-mustard group of crops. Tremendous economic significance has led to substantial basic research involving gene-expression studies in this insect species. In qRT-PCR analysis of gene-expression, normalization of data against RNA variation by using appropriate reference gene is fundamental. However, appropriate reference genes are not known in case of L. erysimi. We evaluated 11 candidate reference genes for their expression stability in 21 samples of L. erysimi subjected to various regimes of experimental treatments. Unlike other studies, we validated true effects of the treatments on the samples either by gene-expression study of an associated marker gene or by biochemical tests. In the validated samples, expression stability of the reference genes was analysed by employing four different statistical softwares geNorm, NormFinder, BestKeeper and deltaCt. Drawing consensus on the results from different softwares, we recommend three best reference genes 16S, RPS18 and RPL13 for normalization of qRT-PCR data in L. erysimi. This study provides for the first time a comprehensive list of suitable reference genes for mustard aphid and demonstrates the advantage of using more than one reference gene in combination for certain experimental conditions.
Control factors and scale analysis of annual river water, sediments and carbon transport in China
Authors: Song Chunlin , Wang Genxu , Sun Xiangyang , Chang Ruiying , Mao Tianxu 
Published: May 2016

AbstractUnder the context of dramatic human disturbances on river system, the processes that control the transport of water, sediment, and carbon from river basins to coastal seas are not completely understood. Here we performed a quantitative synthesis for 121 sites across China to find control factors of annual river exports (Rc: runoff coefficient; TSSC: total suspended sediment concentration; TSSL: total suspended sediment loads; TOCL: total organic carbon loads) at different spatial scales. The results indicated that human activities such as dam construction and vegetation restoration might have a greater influence than climate on the transport of river sediment and carbon, although climate was a major driver of Rc. Multiple spatial scale analyses indicated that Rc increased from the small to medium scale by 20% and then decreased at the sizable scale by 20%. TSSC decreased from the small to sizeable scale but increase from the sizeable to large scales; however, TSSL significantly decreased from small (768 g·m−2·a−1) to medium spatial scale basins (258 g·m−2·a−1), and TOCL decreased from the medium to large scale. Our results will improve the understanding of water, sediment and carbon transport processes and contribute better water and land resources management strategies from different spatial scales.
Catalpol inhibits apoptosis in hydrogen peroxide-induced cardiac myocytes through a mitochondrial-dependent caspase pathway
Authors: Hu Ling-ai , Sun Yu-kun , Zhang Hong-sheng , Zhang Jin-guo , Hu Jian 
Published: May 2016

Catalpol, an iridoid glucoside, has been reported to inhibit apoptosis of neuron and endothelial cells. In the present study, we investigated the mechanism of catalpol-mediated cardioprotection. The rat embryonic ventricular myocardial cell line (H9c2) cells were first incubated with catalpol, and then exposed to hydrogen peroxide (H2O2). The concentration of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) were all determined by using commercially available kits. Apoptotic cells were assessed by Hoechst 33258 and Annexin V-fluorescein isothiocyanate binding assay. Synthesis of Bcl-2, Bax, cytochrome c and caspase-3 were analysed by real-time semiquantitative reverse transcription-PCR and Western blotting. We observed that apoptosis in H9c2 was associated with increased Bax, cytochrome c, caspase-3, decreased Bcl-2 activity after 24 h of H2O2 exposure. Catalpol pretreatment afforded a marked protection against the above H2O2-mediated cytotoxicity and apoptosis in H9c2 cells. Moreover, the catalpol pretreatment led to a great reduction in H2O2-induced MDA release and increased SOD. These findings indicated for the first time that pretreatment of H9c2 cells with catalpol can be against H2O2-induced apoptosis, and the protective effect of catalpol involves the mitochondrial-dependent caspase pathway and is associated with increased Bcl-2 and decreased Bax expression.
Graphene‐based THz modulator analysed by equivalent circuit model
Authors: Xiao Binggang , Chen Jing , Xie Zhiyi , Xiao Sanshui 
Published: May 2016

A terahertz (THz) modulator based on graphene is proposed and analysed by use of equivalent transmission line of a homogeneous medium and the local anisotropic model of the graphene conductivity. The result calculated by the equivalent circuit is consistent with that obtained by Fresnel transfer matrices. For the modulator proposed here, when the frequency of carrier wave is 0.6 THz, the theoretical analysis indicates that the modulation bandwidth is 55.5 kHz and the modulation depth is 81.3% for voltage change from 0 to 50 V.
Assessment of the Learning Curve for Microendoscopic Decompression Surgery for Lumbar Spinal Canal Stenosis through an Analysis of 480 Cases Involving a Single Surgeon
Authors: Nomura Kazunori , Yoshida Munehito 
Published: May 2016

Study Design  Retrospective study. Objective  To assess the learning curve of microendoscopic decompression surgery for lumbar spinal canal stenosis (LSCS). Methods  Four hundred eighty LSCS cases involving 753 stenotic lesions limited to the intraspinal canal were treated with microendoscopic decompression by a single surgeon at an institution between November 2006 and January 2015. They were numbered chronologically, and the operating time, intraoperative blood loss, and perioperative complications were investigated. Surgical outcomes were evaluated using the Japanese Orthopedic Association (JOA) score for low back pain before and 1 year after the operation. Results  The mean operating time per level was 66.1 minutes. There was a progressive reduction in the operating time through the case series, and the approximate curve seemed to be y =  − 9.4Ln( x) + 115.0. The blood loss per level, which showed a mean value of 15.0 mL, was more than 50 mL in only 2.7% of the cases after case no. 30 and in 20% of the cases before it. There were 10 (2.1%) cases of perioperative complications, which occurred even after the surgeon had gained mastery of the procedure. The median JOA score improved significantly from 17 points preoperatively to 26 points postoperatively. Conclusions  The learning curve of microendoscopic decompression surgery for LSCS has been defined with data for a single surgeon in an institution. The operating time seems to decrease along a natural logarithmic function. The intraoperative blood loss stabilizes after the first 30 cases, whereas perioperative complications can occur at any time even after mastery of the technique.
Deep-brain photoreception links luminance detection to motor output in
Xenopus
frog tadpoles
Authors: Currie Stephen P. , Doherty Gayle H. , Sillar Keith T. 
Published: May 2016

Significance
Detecting and responding to light are basic requirements of nearly all life forms. Species from bacteria to man use light to regulate diverse behaviors from acute phototropism and visual processing to seasonal breeding cycles. Here, we describe a previously unidentified form of photoreception in the brain of frog tadpoles. The photoreceptors are preferentially activated by UV light and link ambient light levels to swimming activity. The pathway may be a simple method to optimize lighting conditions for feeding and avoiding predation, or may overlay and reinforce classical circadian systems. Deep-brain photoreception is of broad significance because the proteins involved are phylogenetically conserved.
Collisionless pitch-angle scattering of runaway electrons
Authors: Liu Jian , Wang Yulei , Qin Hong 
Published: May 2016

Abstract
It is discovered that the tokamak field geometry generates a toroidicity induced broadening of the pitch-angle distribution of runaway electrons. This collisionless pitch-angle scattering is much stronger than the collisional scattering and invalidates the gyro-center model for runaway electrons. As a result, the energy limit of runaway electrons is found to be larger than the prediction of the gyro-center model and to depend heavily on the background magnetic field.
A Network Approach to Psychosis: Pathways Between Childhood Trauma and Psychotic Symptoms
Authors: Isvoranu Adela-Maria , van Borkulo Claudia D. , Boyette Lindy-Lou , Wigman Johanna T. W. , Vinkers Christiaan H. , Borsboom Denny ,   Group Investigators
Published: May 2016

AbstractChildhood trauma (CT) has been identified as a potential risk factor for the onset of psychotic disorders. However, to date, there is limited consensus with respect to which symptoms may ensue after exposure to trauma in early life, and whether specific pathways may account for these associations. The aim of the present study was to use the novel network approach to investigate how different types of traumatic childhood experiences relate to specific symptoms of psychotic disorders and to identify pathways that may be involved in the relationship between CT and psychosis. We used data of patients diagnosed with a psychotic disorder (n = 552) from the longitudinal observational study Genetic Risk and Outcome of Psychosis Project and included the 5 scales of the Childhood Trauma Questionnaire-Short Form and all original symptom dimensions of the Positive and Negative Syndrome Scale. Our results show that all 5 types of CT and positive and negative symptoms of psychosis are connected through symptoms of general psychopathology. These findings are in line with the theory of an affective pathway to psychosis after exposure to CT, with anxiety as a main connective component, but they also point to several additional connective paths between trauma and psychosis: eg, through poor impulse control (connecting abuse to grandiosity, excitement, and hostility) and motor retardation (connecting neglect to most negative symptoms). The results of the current study suggest that multiple paths may exist between trauma and psychosis and may also be useful in mapping potential transdiagnostic processes.
The Effects of Personal Pharmacogenetic Testing on the Effects of Pharmacy Student Perceptions of Knowledge and Attitudes Towards Precision Medicine
Authors: Surofchy Dalga , Oh Sam S. , Galanter Joshua , Xiang Pin , Li Megan , Guo Su , Desai Tejal , Guglielmo Joseph B. , Giacomini Kathy , Long-Boyle Janel , Wu Alan HB , Burchard Esteban G 
Published: May 2016

ABSTRACTObjectiveTo evaluate if pharmacy students’ participation in personal pharmacogenetic (Pgx) testing enhances their knowledge and attitude towards precision medicine (PM).MethodsFirst-year pharmacy students were offered personalized pharmacogenetic testing as a supplement to a required curricular pharmacogenomics course. Ninety-eight of 122 (80%) students completed pre- and post-course surveys assessing knowledge and attitudes regarding PM; 73 students also volunteered for personal pharmacogenetic testing of the following drug metabolizing enzymes (CYP2C19,CYP2D6,UGT1A1) and pharmacodynamics-relevant proteins (interleukin (IL)-28B & human lymphocyte antigen HLAB*5701).ResultsAmong the 122 students, we found that incorporating pharmacogenetic testing improved mean knowledge and attitude by 1.0 and 0.3 Likert points, respectively. We observed statistically significant improvements in 100% of knowledge and 70% of attitude-related statements for students who decided to undergo personal pharmacogenetic testing. Students who were enrolled in the course but did not partake in personalized pharmacogenetic testing had similar gains in knowledge and attitude.ConclusionThis study demonstrates the feasibility and importance of educating future pharmacists by incorporating pharmacogenetic testing into professional school curricula. Students who opt not to participate in genotyping may still benefit by learning vicariously through the shared learning environment created by genotyped students.
Male density and rapid evolution of genital morphology in the seed beetleCallosobruchus maculatus
Authors: Soper D. M. , Macy W. L. 
Published: May 2016

SummaryMale reproductive structures are known to be extremely diverse, particularly in insect taxa. Male genital structures are thought to be some of the fastest evolving traits, but the processes responsible for this pattern remain unclear. In the present study we manipulated the mating regimes ofCallosobruchus maculatus, a seed beetle, to determine if male genital structures would be altered under forced monogamy and polyandry. Males in this species have an intromittent organ that contains spines that are known to puncture the female reproductive tract. We measured both testes size and genital spine length in monogamous and polyandrous treatments over seven generations. We found that testes size was not significantly different between treatments, but that genital spine length was significantly longer in the polyandrous treatment within seven generations. These results highlight the fact that evolution can occur rapidly when under strong sexual selection, a process that has been implicated in leading to morphological differences in male genitalia.