bluuebunny/crossref_metadata_2025_split huggingface dataset:
Truncus arteriosus communis in combination with cor triatriatum sinsitrum
Authors: Klusmeier Elmar , Haas Nikolaus A. , Sandica Eugen 
Published: April 2015

AbstractTruncus arteriosus communis is a rare CHD, accounting for only 1% of all congenital cardiac abnormalities. It has been associated with other malformations of the heart, mainly truncal valve (bicuspid/quadricuspid) and aortic arch abnormalities such as right, interrupted, and hypoplastic aortic arch. Cor tratriatrum sinistrum is another rare CHD, and it has been associated with other cardiac defects such as anomalous pulmonary venous drainage, ventricular septal defect, coarctation of the aorta, and tetralogy of Fallot. The combination of truncus arteriosus communis and cor tratriatrum sinistrum has not been reported so far. This case study describes the diagnosis of a unique case, including these two very rare cardiac defects and the successful surgical treatment thereafter.
Designing Dual-functionalized Gels for Self-reconfiguration and Autonomous Motion
Authors: Kuksenok Olga , Balazs Anna C. 
Published: April 2015

AbstractHuman motion is enabled by the concerted expansion and contraction of interconnected muscles that are powered by inherent biochemical reactions. One of the challenges in the field of biomimicry is eliciting this form of motion from purely synthetic materials, which typically do not generate internalized reactions to drive mechanical action. Moreover, for practical applications, this bio-inspired motion must be readily controllable. Herein, we develop a computational model to design a new class of polymer gels where structural reconfigurations and internalized reactions are intimately linked to produce autonomous motion, which can be directed with light. These gels contain both spirobenzopyran (SP) chromophores and the ruthenium catalysts that drive the oscillatory Belousov-Zhabotinsky (BZ) reaction. Importantly, both the SP moieties and the BZ reaction are photosensitive. When these dual-functionalized gels are exposed to non-uniform illumination, the localized contraction of the gel (due to the SP moieties) in the presence of traveling chemical waves (due to the BZ reaction) leads to new forms of spontaneous, self-sustained movement, which cannot be achieved by either of the mono-functionalized networks.
Argininosuccinate synthetase 1 suppression and arginine restriction inhibit cell migration in gastric cancer cell lines
Authors: Shan Yan-Shen , Hsu Hui-Ping , Lai Ming-Derg , Yen Meng-Chi , Chen Wei-Ching , Fang Jung-Hua , Weng Tzu-Yang , Chen Yi-Ling 
Published: April 2015

AbstractGastric cancer metastasis remains a major cause of cancer-related deaths. There is an urgent need to develop new therapeutic approaches targeting metastatic gastric cancer. Argininosuccinate synthetase 1 (ASS1) expression is increased in gastric cancer. We detected the protein expression of ASS1 in human gastric cancer cell lines (AGS, NCI-N87 and MKN45) and in murine gastric cancer cell lines (3I and 3IB2). We used vector-mediated short hairpin RNA (shRNA) expression to silence ASS1 expression in the MKN45 and 3IB2 cell lines and analyzed the effects of this protein on cell migration and metastasis. We demonstrated that ASS1 silencing suppressed cell migration in the MKN45 and 3IB2 cell lines. ASS1 knockdown significantly reduced liver metastasis in mice after the intrasplenic implantation of 3IB2 cancer cell clones. To determine whether arginine restriction may represent a therapeutic approach to treat gastric cancer, the sensitivity of tumor cells to arginine depletion was determined in gastric cancer cells. Arginine depletion significantly inhibited cell migration in the gastric cancer cell line. The silencing of ASS1 expression in MKN45 and 3IB2 gastric cancer cells markedly decreased STAT3 protein expression. In conclusion, our results indicate that the ASS1 protein is required for cell migration in gastric cancer cell lines.
Preclinical Study of Locoregional Therapy of Hepatocellular Carcinoma by Bioelectric Ablation with Microsecond Pulsed Electric Fields (μsPEFs)
Authors: Chen Xinhua , Ren Zhigang , Li Chengxiang , Guo Fei , Zhou Dianbo , Jiang Jianwen , Chen Xinmei , Sun Jihong , Yao Chenguo , Zheng Shusen 
Published: April 2015

AbstractUnresectable hepatocellular carcinoma (HCC) needs locoregional ablation as a curative or downstage therapy. Microsecond Pulsed Electric Fields (μsPEFs) is an option. A xenograft tumor model was set up on 48 nude mice by injecting human hepatocellular carcinoma Hep3B cells subcutaneously. The tumor-bearing mice were randomly divided into 3 groups: μsPEFs treated, sham and control group. μsPEFs group was treated by μsPEFs twice in 5 days. Tumor volume, survival, pathology, mitochondria function and cytokines were followed up. μsPEFs was also conducted on 3 swine to determine impact on organ functions. The tumors treated by μsPEFs were completely eradicated while tumors in control and sham groups grew up to 2 cm3 in 3 weeks. The μsPEFs-treated group indicated mitochondrial damage and tumor necrosis as shown in JC-1 test, flow cytometry, H&E staining and TEM. μsPEFs activates CD56+ and CD68+ cells and inhibits tumor proliferating cell nuclear antigen. μsPEFs inhibits HCC growth in the nude mice by causing mitochondria damage, tumor necrosis and non-specific inflammation. μsPEFs treats porcine livers without damaging vital organs. μsPEFs is a feasible minimally invasive locoregional ablation option.
TIGAR regulates DNA damage and repair through pentosephosphate pathway and Cdk5-ATM pathway
Authors: Yu Hong-Pei , Xie Jia-Ming , Li Bin , Sun Yi-Hui , Gao Quan-Geng , Ding Zhi-Hui , Wu Hao-Rong , Qin Zheng-Hong 
Published: April 2015

AbstractPrevious study revealed that the protective effect of TIGAR in cell survival is mediated through the increase in PPP (pentose phosphate pathway) flux. However, it remains unexplored if TIGAR plays an important role in DNA damage and repair. This study investigated the role of TIGAR in DNA damage response (DDR) induced by genotoxic drugs and hypoxia in tumor cells. Results showed that TIGAR was increased and relocated to the nucleus after epirubicin or hypoxia treatment in cancer cells. Knockdown of TIGAR exacerbated DNA damage and the effects were partly reversed by the supplementation of PPP products NADPH, ribose, or the ROS scavenger NAC. Further studies with pharmacological and genetic approaches revealed that TIGAR regulated the phosphorylation of ATM, a key protein in DDR, through Cdk5. The Cdk5-AMT signal pathway involved in regulation of DDR by TIGAR defines a new role of TIGAR in cancer cell survival and it suggests that TIGAR may be a therapeutic target for cancers.
Vasectomy and prostate cancer risk: a meta-analysis of cohort studies
Authors: Shang Yonggang , Han Guangwei , Li Jia , Zhao Jiang , Cui Dong , Liu Chengcheng , Yi Shanhong 
Published: April 2015

AbstractSome studies have suggested that vasectomy is associated with the increased risk of prostate cancer, however, this conclusion is not supported by all the published studies. In order to examine the relationship between vasectomy and prostate cancer risk, we conducted a meta-analysis of cohort studies to clarify this controversial association. PubMed and Medline were used to identify the cohort studies that reported the association of vasectomy with prostate cancer risk from 1980 to January 2015. Based on a random effects model, the RR and 95% CI were used to assess the combined risk. In total, 10 cohort studies involving more than 7027 cases and 429914 participants were included. There was no significant relationship between vasectomy and prostate cancer risk, the pooled RR (95%CI) was 1.11[0.98, 1.27] (P = 0.109). In subgroup-analysis, the relationship between vasectomy and prostate cancer risk was not significantly modified by the length of follow-up and population distribution except Americans. Omission of any single study had little effect on the pooled risk estimate. Little evidence of publication bias was found. In conclusion, our meta-analysis suggests that vasectomy is not associated with the increased risk of prostate cancer. More studies based on other populations including the Chinese are needed.
Cardioprotective effects and pharmacokinetic properties of a controlled release formulation of a novel hydrogen sulfide donor in rats with acute myocardial infarction
Authors: Tran Ba Hieu , Huang Chengrong , Zhang Qiuyan , Liu Xu , Lin Shizhou , Liu Hongrui , Wang Shujun , Zhu Yi Zhun 
Published: April 2015

We previously reported that S-propargyl-cysteine (SPRC) exerts cardioprotective effects by elevating H2S levels via the CSE/H2S pathway. In the present study, we investigated the cardioprotective effects and pharmacokinetic properties of a controlled release formulation of SPRC (CR-SPRC) in an in vivo rat model of myocardial infarction (MI). Rats were randomly assigned to seven groups that were pre-treated with CR-SPRC daily for 7 days prior to ligation of the left anterior descending coronary artery to induce MI. Cardiac function and infarct size were determined after MI, and we examined the activity of antioxidant enzymes, expression of anti-inflammation proteins and hydrogen sulfide levels. Mixed-mode, reversed-phase and cation-exchange HPLC–MS/MS were used to compare the pharmacokinetic properties of CR-SPRC and SPRC. CR-SPRC significantly reduced infarct size and creatine kinase (CK) and lactate dehydrogenase (LDH) leakage and it preserved cardiac function during MI. CR-SPRC displayed antioxidant properties, preserving glutathione (GSH), catalase (CAT) and superoxide dismutase (SOD) levels whereas reducing malondialdehyde (MDA) levels. Moreover, CR-SPRC significantly reduced the protein levels of inflammatory biomarkers (phospho-NF-κB p65/NF-κB p65, TNF-α) and increased cystathionine-γ-lyase (CSE) and Iκ-Bα protein levels. CR-SPRC had better pharmacokinetic properties than SPRC, with a reduced concentration peak (Cmax), prolonged time to reach peak concentration (Tmax), prolonged mean residence time (MRTinf) and increased AUC0–t. CR-SPRC showed protective effects against MI via the CSE/H2S pathway and demonstrated better cardioprotective effects than SPRC by prolonging the release of endogenous H2S.
Hydration water mobility is enhanced around tau amyloid fibers
Authors: Fichou Yann , Schirò Giorgio , Gallat François-Xavier , Laguri Cedric , Moulin Martine , Combet Jérôme , Zamponi Michaela , Härtlein Michael , Picart Catherine , Mossou Estelle , Lortat-Jacob Hugues , Colletier Jacques-Philippe , Tobias Douglas J. , Weik Martin 
Published: April 2015

Significance
Protein aggregation into amyloid fibers and oligomers is observed in a variety of neurodegenerative diseases. The fibers formed by the intrinsically disordered human protein tau, for instance, are one of the hallmarks of Alzheimer disease. In this work, we report on the dynamic behavior of tau hydration water, which we found to be more mobile in tau fibers than in nonaggregated tau. This increase in mobility could promote fiber formation through an increase in hydration water entropy. That hydration water is more mobile around the pathological form of tau corroborates that methodologies sensitive to the diffusion of water, such as diffusion magnetic resonance imaging, could be used to diagnose Alzheimer patients in an early stage of the disease.
Ligand deconstruction: Why some fragment binding positions are conserved and others are not
Authors: Kozakov Dima , Hall David R. , Jehle Stefan , Luo Lingqi , Ochiana Stefan O. , Jones Elizabeth V. , Pollastri Michael , Allen Karen N. , Whitty Adrian , Vajda Sandor 
Published: April 2015

Significance
Fragment-based drug discovery (FBDD), in which initial screening is done with low-molecular-weight compounds called fragments, relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. We describe a remarkably simple condition for fragment binding conservation that can be tested computationally. The condition can be used for detecting whether a protein is suitable for FBDD, for predicting the size of fragments required for screening, and for determining if a fragment hit can be extended into a higher affinity ligand. The findings also reveal general properties of binding sites, highlighting the role that critical interactions between anchor sites and anchor fragments play in protein–ligand interactions in general.
Artemin promotes functional long-distance axonal regeneration to the brainstem after dorsal root crush
Authors: Wong Laura Elisabeth , Gibson Molly E. , Arnold H. Moore , Pepinsky Blake , Frank Eric 
Published: April 2015

Significance
Recovery after a spinal cord injury requires that axons regenerate and reconnect with their original targets. Here we report that after interruption of sensory axons in dorsal roots, systemic treatment with a naturally occurring growth factor, artemin (ARTN), promotes regeneration of these axons 3–4 cm away from their original target region in the brainstem, where they reestablish functional connections. In contrast to earlier studies, we also find that GDNF family receptor, a known receptor for ARTN, is expressed on both myelinated and unmyelinated sensory neurons, consistent with ARTN’s ability to promote regeneration of large and small sensory neurons.
Ribosomal protein S6 kinase 1 signaling in prefrontal cortex controls depressive behavior
Authors: Dwyer Jason M. , Maldonado-Avilés Jaime G. , Lepack Ashley E. , DiLeone Ralph J. , Duman Ronald S. 
Published: April 2015

Significance
The molecular pathophysiology associated with depression remains largely unknown. Recent evidence suggests that signaling pathways downstream of mechanistic target of rapamycin complex 1, such as p70 S6 kinase 1 (S6K1), can lead to structural changes in the medial prefrontal cortex (mPFC) of rats, which are associated with antidepressant responses. We used a viral-mediated approach to control S6K1 activity in the mPFC. Enhanced S6K1 activity produced antidepressant-like effects and resilience to chronic stress, whereas decreased S6K1 activity produced prodepressive behavior. Together, these studies demonstrate that aberrant activity of protein synthesis pathways may underlie the pathology of depression, and demonstrate that direct modulation of this pathway can control depressive behavior in a bidirectional manner. Further understanding of these signaling pathways may contribute to improved treatments for major depressive disorder.
Therapeutic effects of cell-permeant peptides that activate G proteins downstream of growth factors
Authors: Ma Gary S. , Aznar Nicolas , Kalogriopoulos Nicholas , Midde Krishna K. , Lopez-Sanchez Inmaculada , Sato Emi , Dunkel Ying , Gallo Richard L. , Ghosh Pradipta 
Published: April 2015

Significance
Most common diseases (e.g., cancer, inflammatory disorders, diabetes) are driven by not one, but multiple cell surface receptors that trigger and sustain a pathologic signaling network. The largest fraction of therapeutic agents that target individual receptors/pathways often eventually fail due to the emergence of compensatory mechanisms. Recently, we identified GIV protein as a central platform for receptor cross-talk which integrates signals downstream of a myriad of upstream receptors, and modulates several key pathways within downstream signaling network, all via activation of trimeric G proteins. Here we provide the proof-of-concept that nongenetic exogenous modulation of the GIV-Gi signaling interface using cell-penetrable GIV-derived peptides is an effective strategy to reset pathologic signaling networks downstream of multiple receptors in a diverse array of pathophysiologic conditions.
Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure
Authors: Lerch Michael T. , López Carlos J. , Yang Zhongyu , Kreitman Margaux J. , Horwitz Joseph , Hubbell Wayne L. 
Published: April 2015

Significance
High pressure has emerged as a powerful tool for exploring the energy landscape of proteins, but structural origins of the pressure response remain controversial. The results of this study on a cavity mutant of T4 lysozyme (L99A) provide direct evidence for a structure-relaxation mechanism wherein pressure shifts conformational equilibria toward states with alternative packing arrangements that fill cavities or voids in the core. Both structure relaxation and cavity hydration can occur in response to pressure, and which dominates is found to depend on details of the energy landscape. The results also address conflicting views regarding the pressure response of L99A that have recently been published.
Polyester: simulating RNA-seq datasets with differential transcript expression
Authors: Frazee Alyssa C. , Jaffe Andrew E. , Langmead Ben , Leek Jeffrey T. 
Published: April 2015

AbstractMotivation: Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data.Results: Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.Availability and implementation: Polyester is freely available from Bioconductor (http://bioconductor.org/).Contact: jtleek@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
Toll-like receptor 9 trafficking and signaling for type I interferons requires PIKfyve activity
Authors: Hayashi Kachiko , Sasai Miwa , Iwasaki Akiko 
Published: April 2015

Abstract
Toll-like receptors (TLRs) traffic to distinct membranes for signaling. TLR7 and TLR9 recognize viral nucleic acids in the endosomes and induce robust anti-viral program. Signaling from these TLRs bifurcate at the level of distinct endosomal compartments, namely VAMP3+ and LAMP+ endosomes, to mediate the induction of cytokine and type I interferon (IFN) genes, respectively. The formation of the TLR9 endosome competent for IFNs induction requires AP-3. Phosphoinositides (PIs) mark distinct subcellular membranes and control membrane trafficking. However, their role in TLR trafficking and signaling in different dendritic cell (DC) subsets remains unclear. Here, we examined the role of phosphatidylinositol 3P 5-kinase, PIKfyve, in TLR9 trafficking and signaling. We demonstrate that inhibition of PIKfyve activity preferentially blocks TLR9 signaling for type I IFN induction in FLT3L-bone marrow-derived DCs. By confocal microscopy using RAW264.7 cells, we show that trafficking of both TLR9 and CpG to the LAMP1+ compartment was blocked by PIKfyve inhibitor treatment, whereas their trafficking to the VAMP3+ endosome remained intact. Further, AP-3 recruitment to TLR9 endosomes was impaired by PIKfyve inhibition. These data indicate that PIKfyve provides critical PIs necessary for the formation of endosome from which TLR9 signals to induce type I IFNs.
Efavirenz alters mitochondrial respiratory function in cultured neuron and glial cell lines
Authors: Funes Haryes A. , Blas-Garcia Ana , Esplugues Juan V. , Apostolova Nadezda 
Published: April 2015

Abstract

Background
The NNRTI efavirenz is among the most widely employed antiretroviral drugs. Although it is considered safe, efavirenz has been linked with several adverse effects including neurological manifestations, which appear in the majority of the patients on efavirenz-containing regimens. The molecular mechanisms responsible for these manifestations are not understood, but mounting evidence points to altered brain bioenergetics.

Methods
We evaluated the effect of short-term efavirenz treatment on the mitochondrial respiratory function of cultured glioblastoma and differentiated neuroblastoma cell lines using a Seahorse Extracellular Flux Analyzer.

Results
Incubation with efavirenz provoked a significant and concentration-dependent decrease in basal respiration and specifically in ATP production-coupled O2 consumption in both SH-SY5Y and U-251MG cells, with the effect being more pronounced in the latter. In contrast, efavirenz did not alter mitochondrial proton leakage in either of the cell types. Efavirenz led to a decrease in the respiratory control ratio as well as to a reduction in the maximal respiration rate and spare respiratory capacity in both U-251MG and SH-SY5Y cells, the former cells being more susceptible.

Conclusions
These findings reveal that efavirenz specifically alters mitochondrial respiration, which is of relevance for a better understanding of the molecular mechanisms responsible for the efavirenz-associated neurological effects that have been recorded in clinical situations.
Accrual reliability, earnings persistence, and stock prices: revisited
Authors: Dey R. Mithu , Lim Lucy 
Published: April 2015

Purpose
– The purpose of this paper is to replicate Richardson et al.’s (2005) study on how accrual components’ reliability affects earnings persistence and whether investors anticipate the lower earnings persistence through stock return. In this study, the authors use more recent data to examine whether the previous results still hold.

Design/methodology/approach
– The authors run the analysis using Richardson et al.’s (2005) design of ordinary least squares and report the results using Fama and Macbeth’s (1973) procedures.

Findings
– The results corroborate Richardson et al.’s (2005) conclusions that lower reliability of total accrual (accrual components) leads to lower earnings persistence.

Originality/value
– This study replicates Richardson et al. (2005) using more recent US data. The results in this paper confirm the general conclusion in the original study: less reliable accruals lead to lower earnings persistence.