bluuebunny/crossref_metadata_2025_split huggingface dataset:
The caspase-1 inhibitor AC-YVAD-CMK attenuates acute gastric injury in mice: involvement of silencing NLRP3 inflammasome activities
Authors: Zhang Fang , Wang Liang , Wang Jun-jie , Luo Peng-fei , Wang Xing-tong , Xia Zhao-fan 
Published: April 2016

AbstractThis study evaluated the protective effects of inhibiting caspase-1 activity or gastric acid secretion on acute gastric injury in mice. AC-YVAD-CMK, omeprazole, or vehicle were administered to mice before cold-restraint stress- or ethanol-induced gastric injury. Survival rates and histological evidence of gastric injury of mice pretreated with AC-YVAD-CMK or omeprazole and exposed to cold-restraint stress, improved significantly relative to the vehicle group. The increased levels of tumour necrosis factor-α, interleukin (IL)-1β, IL-6 and IL-18 following cold-stress injury were decreased by AC-YVAD-CMK, but not omeprazole, pretreatment. The increased expression of CD68 in gastric tissues was inhibited significantly by AC-YVAD-CMK pretreatment. Inhibiting caspase-1 activity in the NLRP3 inflammasome decreased gastric cell apoptosis and the expression of Bax and cleaved caspase-3. AC-YVAD-CMK pretreatment significantly inhibited cold-restraint stress-induced increases in the expression of phosphorylated IκB-alpha and P38. General anatomy and histological results showed the protective effect of AC-YVAD-CMK on ethanol-induced acute gastric injury. Overall, our results showed that the caspase-1 inhibitor AC-YVAD-CMK protected against acute gastric injury in mice by affecting the NLRP3 inflammasome and attenuating inflammatory processes and apoptosis. This was similar to the mechanism associated with NF-κB and P38 mitogen-activated protein kinase signalling pathways.
Dynamics of 2013 Sudden Stratospheric Warming event and its impact on cold weather over Eurasia: Role of planetary wave reflection
Authors: Nath Debashis , Chen Wen , Zelin Cai , Pogoreltsev Alexander Ivanovich , Wei Ke 
Published: April 2016

AbstractIn the present study, we investigate the impact of stratospheric planetary wave reflection on tropospheric weather over Central Eurasia during the 2013 Sudden Stratospheric Warming (SSW) event. We analyze EP fluxes and Plumb wave activity fluxes to study the two and three dimensional aspects of wave propagation, respectively. The 2013 SSW event is excited by the combined influence of wavenumber 1 (WN1) and wavenumber 2 (WN2) planetary waves, which makes the event an unusual one and seems to have significant impact on tropospheric weather regime. We observe an extraordinary development of a ridge over the Siberian Tundra and the North Pacific during first development stage (last week of December 2012) and later from the North Atlantic in the second development stage (first week of January 2013), and these waves appear to be responsible for the excitation of the WN2 pattern during the SSW. The wave packets propagated upward and were then reflected back down to central Eurasia due to strong negative wind shear in the upper stratospheric polar jet, caused by the SSW event. Waves that propagated downward led to the formation of a deep trough over Eurasia and brought extreme cold weather over Kazakhstan, the Southern part of Russia and the Northwestern part of China during mid-January 2013.
Targeting HCCR expression resensitizes gastric cancer cells to chemotherapy via down-regulating the activation of STAT3
Authors: Zhang Jun-Ling , Liu Xiang-Zheng , Wang Peng-Yuan , Chen Guo-Wei , Jiang Yong , Qiao Shu-Kai , Zhu Jing , Wang Xin , Pan Yi-Sheng , Liu Yu-Cun 
Published: April 2016

AbstractThe human cervical cancer oncogene (HCCR) has been found to be overexpressed in a variety of human cancers. However, the level of expression of HCCR and its biological function in gastric cancer are largely unknown. In this study, we evaluated HCCR expression in several gastric cancer cell lines and in one normal gastric mucosal cell line. We established a 5-FU-resistant gastric cancer cell subline, and we evaluated its HCCR expression. HCCR expression levels were high in gastric cancer lines, and expression was significantly increased in the 5-FU-resistant cancer cell subline. HCCR expression affected cell growth by regulating apoptosis in the cancer cells, and it had a positive correlation with p-STAT3 expression. Western blot and luciferase reporter assays showed that the activation of STAT3 upregulated HCCR expression in a positive feedback loop model. In vivo and in vitro studies showed that HCCR plays an important role in the apoptosis induced by 5-FU. Our data demonstrate that HCCR is probably involved in apoptosis and cancer growth and that it functions as a p-STAT3 stimulator in a positive feedback loop model. In gastric cancer cells, HCCR confers a more aggressive phenotype and resistance to 5-FU-based chemotherapy.
Novel mechanism of enhancing IRE1α-XBP1 signalling via the PERK-ATF4 pathway
Authors: Tsuru Akio , Imai Yasutaka , Saito Michiko , Kohno Kenji 
Published: April 2016

AbstractMammalian inositol-requiring enzyme 1α (IRE1α) is the most conserved of all endoplasmic reticulum (ER) stress sensors, which includes activating transcription factor (ATF) 6 and double-stranded RNA-dependent protein kinase (PKR)-like ER kinase (PERK). IRE1α has been known to splice X-box binding protein 1 (XBP1) mRNA, which is induced by ATF6 under ER stress. This spliced XBP1 mRNA is translated into the active transcription factor that promotes the expression of specific genes to alleviate ER stress. Herein, we report that in addition to the induction of XBP1 expression by ATF6, IRE1α expression is induced by ATF4, which is downstream of PERK, under ER stress. Increased IRE1α expression results in a higher splicing ratio of XBP1 mRNA. This effect was not transient and affected not only the intensity but also the duration of the activated state of this pathway. These multiple regulatory mechanisms may modulate the response to various levels or types of ER stress.
Central transthyretin acts to decrease food intake and body weight
Authors: Zheng Fenping , Kim Yonwook J. , Moran Timothy H. , Li Hong , Bi Sheng 
Published: April 2016

AbstractTransthyretin (TTR) is a blood and cerebrospinal fluid transporter of thyroxine and retinol. Gene expression profiling revealed an elevation of Ttr expression in the dorsomedial hypothalamus (DMH) of rats with exercise-induced anorexia, implying that central TTR may also play a functional role in modulating food intake and energy balance. To test this hypothesis, we have examined the effects of brain TTR on food intake and body weight and have further determined hypothalamic signaling that may underlie its feeding effect in rats. We found that intracerebroventricular (icv) administration of TTR in normal growing rats decreased food intake and body weight. This effect was not due to sickness as icv TTR did not cause a conditioned taste aversion. ICV TTR decreased neuropeptide Y (NPY) levels in the DMH and the paraventricular nucleus (P < 0.05). Chronic icv infusion of TTR in Otsuka Long-Evans Tokushima Fatty rats reversed hyperphagia and obesity and reduced DMH NPY levels. Overall, these results demonstrate a previously unknown anorectic action of central TTR in the control of energy balance, providing a potential novel target for treating obesity and its comorbidities.
Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements
Authors: Fernandez-Chamorro Javier , Lozano Gloria , Garcia-Martin Juan Antonio , Ramajo Jorge , Dotu Ivan , Clote Peter , Martinez-Salas Encarnacion 
Published: April 2016

AbstractThe function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.
Altitudinal patterns and controls of plant and soil nutrient concentrations and stoichiometry in subtropical China
Authors: He Xianjin , Hou Enqing , Liu Yang , Wen Dazhi 
Published: April 2016

AbstractAltitude is a determining factor of ecosystem properties and processes in mountains. This study investigated the changes in the concentrations of carbon (C), nitrogen (N) and phosphorus (P) and their ratios in four key ecosystem components (forest floor litter, fine roots, soil and soil microorganisms) along an altitudinal gradient (from 50 m to 950 m a.s.l.) in subtropical China. The results showed that soil organic C and microbial biomass C concentrations increased linearly with increasing altitude. Similar trends were observed for concentrations of total soil N and microbial biomass N. In contrast, the N concentration of litter and fine roots decreased linearly with altitude. With increasing altitude, litter, fine roots and soil C:N ratios increased linearly, while the C:N ratio of soil microbial biomass did not change significantly. Phosphorus concentration and C:P and N:P ratios of all ecosystem components generally had nonlinear relationships with altitude. Our results indicate that the altitudinal pattern of plant and soil nutrient status differs among ecosystem components and that the relative importance of P vs. N limitation for ecosystem functions and processes shifts along altitudinal gradients.
What makes Lymphadenopathy in Patients with Autoimmune Thyroiditis Suspicious for Malignancy?
Authors: Bouter C. , Meller B. , Meller J. , Sahlmann C. 
Published: April 2016

AbstractLymphadenopathy in Robbins level II-IV and VI is common in autoimmune thyroiditis but the diagnostic strategy of a distinct lymphadenopathy exceeding the known features in autoimmune thyroiditis patients is unknown. The aim of this study was to determine how the extent of cervical lymphadenopathy in autoimmune thyroiditis affects the diagnostic management.The study comprises one index-patient with autoimmune thyroiditis and distinct suspicious lymphadenopathy in all cervical levels as well as retroclavicular. In addition 10 patients with autoimmune thyroiditis and distinct suspicious lymphadenopathy limited to level VI were evaluated.Findings of high resolution ultrasound, fine-needle aspiration cytology, serological testing and clonal analysis are reported here. Further diagnostics of the index-patient included histology, immunohistochemistry, bcl-2-expression analysis and PET/CT.The index-patient showed distinct lymphadenopathy in level I-VI and retroclavicular. Lymph nodes did not display any sonographic malignancy criteria. Molecular analysis and immunohistochemistry revealed monoclonal CD10- and CD20-positive, Bcl-2 expressing follicular B-cells confirming the diagnosis of a follicular B-cell Non-Hodgkin lymphoma.10 additional patients with limited lymphadenopathy showed typical features of autoimmune thyroiditis and lymph nodes did not display sonographic malignancy criteria in all cases. Further tests excluded lymph node malignancies.Extensive diagnostics in autoimmune thyroiditis and distinct cervical lymphadenopathy is crucial. Whereas limited lymphadenopathy in AIT was proven benign, extensive lymphadenopathy exceeding the known amount and/or spreading to retroclavicular/mediastinal compartments is suspicious for malignancy. Even in the absence of sonographic malignancy criteria further tests have to be performed.
Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding
Authors: Fabbretti Attilio , Schedlbauer Andreas , Brandi Letizia , Kaminishi Tatsuya , Giuliodori Anna Maria , Garofalo Raffaella , Ochoa-Lizarralde Borja , Takemoto Chie , Yokoyama Shigeyuki , Connell Sean R. , Gualerzi Claudio O. , Fucini Paola 
Published: April 2016

Significance
Eubacterial protein synthesis entails formation of an unlocked preinitiation complex consisting of the 30S ribosomal subunit, initiation factors, mRNA, and initiator tRNA. A conformational change in the subunit accompanies mRNA–tRNA codon–anticodon base-pairing generating a locked 30S complex. If correctly formed, this complex associates with the 50S ribosomal subunit forming a 70S complex, and the initiation factors are ejected. We show that the translational inhibitor GE81112 targets this essential step, hampering formation of a canonical codon–anticodon interaction and stalling the 30S in an unlocked state. Moreover, in the presence of GE81112 three rRNA helices, h44/h45/h24a, are stabilized in a disengaged conformation, suggesting that their conformation is associated with tRNA/mRNA decoding and transition of the 30S from unlocked to locked state.
Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species
Authors: Kim Sang-Chul , Kim Jung Sung , Kim Joo-Hwan 
Published: April 2016

Abstract
Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, a trnI -CAU gene duplication event was reported from Paris verticillata , a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of two Trillium species representing two subgenera: Trillium and Phyllantherum . In Trillium tschonoskii (subgenus Trillium ), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence of T. maculatum (subgenus Phyllantherum ) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that of T. tschonoskii . The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome of T. maculatum contained a 3.4-kb inverted sequence between ndhC and rbcL in the LSC region, and it was a unique feature for subgenera Phyllantherum . In addition, we found three different types of gene duplication in the intergenic spacer between rpl23 and ycf2 containing trnI -CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excluding T. govanianum . These genomic features provide informative molecular markers for identifying the infrageneric taxa of Trillium and improve our understanding of the evolution patterns of Parideae in Melanthiaceae.
Discovery of two new pulsars in 47 Tucanae (NGC 104)
Authors: Pan Z. , Hobbs G. , Li D. , Ridolfi A. , Wang P. , Freire P. 
Published: April 2016

Abstract
We report the discovery of two new millisecond pulsars (PSRs J0024−7204aa and J0024−7204ab) in the globular cluster 47 Tucanae (NGC 104). Our results bring the total number of pulsars in 47 Tucanae to 25. These pulsars were discovered by reprocessing archival observations from the Parkes radio telescope. We reprocessed the data using a standard search procedure based on the presto software package as well as using a new method in which we incoherently added the power spectra corresponding to ∼1100 h of observations. The newly discovered PSR J0024−7204aa, has a pulse frequency of ∼541 Hz (corresponding to a ∼1.84 ms period), which is higher than any other pulsars currently known in the cluster and ranks 12th amongst all the currently known pulsars. The dispersion measure of this pulsar, 24.941(7) cm−3 pc, is the highest in the cluster. The second discovered pulsar, PSR J0024−7204ab, is an isolated pulsar with a pulse frequency of ∼270 Hz (corresponding to a period of ∼3.70 ms).
A note on periodicity of long-term variations of optical continuum in active galactic nuclei
Authors: Lu Kai-Xing , Li Yan-Rong , Bi Shao-Lan , Wang Jian-Min 
Published: April 2016

Abstract
Graham et al. found a sample of active galactic nuclei (AGNs) and quasars from the Catalina Real-time Transient Survey (CRTS) that have long-term periodic variations in optical continuum. The nature of the periodicity remains uncertain. We investigate the periodic variability characteristics of the sample by testing the relations of the observed variability periods with AGN optical luminosity, black hole mass and accretion rates, and find no significant correlations. We also test the observed periods in several different aspects related to accretion discs surrounding single black holes, such as the Keplerian rotational periods of 5100 Å photon-emission regions and self-gravity dominated regions and the precessing period of warped discs. These tests shed new lights on understanding AGN variability in general. Under the assumption that the periodic behaviour is associated with supermassive black hole binary systems in particular, we compare the separations (${\scr {D}}_{\bullet }$) against characteristic radii of broad-line regions ($R_{\scriptscriptstyle {\rm BLR}}$) of the binaries and find ${\scr {D}}_{\bullet }\approx 0.05R_{\scriptscriptstyle {\rm BLR}}$. This interestingly implies that these binaries have only circumbinary BLRs.
Peripheral Intravenous Catheter Placement Is an Underrecognized Source of Staphylococcus aureus Bloodstream Infection
Authors: Austin Eloise D. , Sullivan Sean B. , Whittier Susan , Lowy Franklin D. , Uhlemann Anne-Catrin 
Published: April 2016

Abstract
Few studies have focused on the risks of peripheral intravenous catheters (PIVs) as sources for Staphylococcus aureus bacteremia (SAB), a life-threatening complication. We identified 34 PIV-related infections (7.6%) in a cohort of 445 patients with SAB. Peripheral intravenous catheter-related SAB was associated with significantly longer bacteremia duration and thrombophlebitis at old PIV sites rather than current PIVs.
Immunological Signaling During Herpes Simplex Virus-2 and Cytomegalovirus Vaginal Shedding After Initiation of Antiretroviral Treatment
Authors: Nason Martha C. , Patel Eshan U. , Kirkpatrick Allison R. , Prodger Jessica L. , Shahabi Kamnoosh , Tobian Aaron A. R. , Gianella Sara , Kalibbala Sarah , Ssebbowa Paschal , Kaul Rupert , Gray Ronald H. , Quinn Thomas C. , Serwadda David , Reynolds Steven J. , Redd Andrew D. 
Published: April 2016

Abstract
Vaginal proinflammatory cytokine expression during herpes virus reactivation was examined in human immunodeficiency virus-infected women before and after initiation of antiretroviral therapy (ART). Vaginal swabs were screened for levels of cytokines interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, tumor necrosis factor (TNF)-α, and interferon-γ. The relative risk (RR) of herpes simplex virus-2 or cytomegalovirus (CMV) shedding being associated with cytokine levels above the median were estimated. Herpes simplex virus-2 shedding was significantly associated with higher levels of IL-6 (RR = 1.4, P = .003) and TNF-α (RR = 1.3, P = .010), whereas CMV shedding was associated with higher IL-6 (RR = 1.3, P = .006) and IL-2 (RR = 1.4, P = .01). The association of viral shedding with higher IL-6 levels suggests that herpes virus reactivation may be playing a role in immune activation after ART initiation.
GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis
Authors: Stricker Georg , Engelhardt Alexander , Schulz Daniel , Schmid Matthias , Tresch Achim , Gagneur Julien 
Published: April 2016

AbstractMotivationChromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective.ResultsHere, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad-hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays.AvailabilitySoftware is available from Bioconductor:https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.htmlContactgagneur@in.tum.deSupplementary informationSupplementary information is available atBioinformaticsonline.