bluuebunny/crossref_metadata_2025_split huggingface dataset:
TonEBP modulates the protective effect of taurine in ischemia-induced cytotoxicity in cardiomyocytes
Authors: Yang Y J , Han Y Y , Chen K , Zhang Y , Liu X , Li S , Wang K Q , Ge J B , Liu W , Zuo J 
Published: December 2015

AbstractTaurine, which is found at high concentration in the heart, exerts several protective actions on myocardium. Physically, the high level of taurine in heart is maintained by a taurine transporter (TauT), the expression of which is suppressed under ischemic insult. Although taurine supplementation upregulates TauT expression, elevates the intracellular taurine content and ameliorates the ischemic injury of cardiomyocytes (CMs), little is known about the regulatory mechanisms of taurine governing TauT expression under ischemia. In this study, we describe the TonE (tonicity-responsive element)/TonEBP (TonE-binding protein) pathway involved in the taurine-regulated TauT expression in ischemic CMs. Taurine inhibited the ubiquitin-dependent proteasomal degradation of TonEBP, promoted the translocation of TonEBP into the nucleus, enhanced TauT promoter activity and finally upregulated TauT expression in CMs. In addition, we observed that TonEBP had an anti-apoptotic and anti-oxidative role in CMs under ischemia. Moreover, the protective effects of taurine on myocardial ischemia were TonEBP dependent. Collectively, our findings suggest that TonEBP is a core molecule in the protective mechanism of taurine in CMs under ischemic insult.
Predicting the impact of promoter variability on regulatory outputs
Authors: Kreamer Naomi N. , Phillips Rob , Newman Dianne K. , Boedicker James Q. 
Published: December 2015

AbstractThe increased availability of whole genome sequences calls for quantitative models of global gene expression, yet predicting gene expression patterns directly from genome sequence remains a challenge. We examine the contributions of an individual regulator, the ferrous iron-responsive regulatory element, BqsR, on global patterns of gene expression in Pseudomonas aeruginosa. The position weight matrix (PWM) derived for BqsR uncovered hundreds of likely binding sites throughout the genome. Only a subset of these potential binding sites had a regulatory consequence, suggesting that BqsR/DNA interactions were not captured within the PWM or that the broader regulatory context at each promoter played a greater role in setting promoter outputs. The architecture of the BqsR operator was systematically varied to understand how binding site parameters influence expression. We found that BqsR operator affinity was predicted by the PWM well. At many promoters the surrounding regulatory context, including overlapping operators of BqsR or the presence of RhlR binding sites, were influential in setting promoter outputs. These results indicate more comprehensive models that include local regulatory contexts are needed to develop a predictive understanding of global regulatory outputs.
Observation of an atomic exchange bias effect in DyCo4 film
Authors: Chen Kai , Lott Dieter , Radu Florin , Choueikani Fadi , Otero Edwige , Ohresser Philippe 
Published: December 2015

AbstractThe fundamental important and technologically widely employed exchange bias effect occurs in general in bilayers of magnetic thin films consisting of antiferromagnetic and ferromagnetic layers where the hard magnetization behavior of an antiferromagnetic thin film causes a shift in the magnetization curve of a soft ferromagnetic film. The minimization of the single magnetic grain size to increase the storage density and the subsequent demand for magnetic materials with very high magnetic anisotropy requires a system with high HEB. Here we report an extremely high HEB of 4 Tesla observed in a single amorphous DyCo4 film close to room temperature. The origin of the exchange bias can be associated with the variation of the magnetic behavior from the surface towards the bulk part of the film revealed by X-ray absorption spectroscopy and X-ray magnetic circular dichroism techniques utilizing the bulk sensitive transmission and the surface sensitive total electron yield modes. The competition between the atomic exchange coupling in the single film and the Zeeman interaction lead to an intrinsic exchanged coupled system and the so far highest exchange bias effect HEB = 4 Tesla reported in a single film, which is accommodated by a partial domain wall formation.
Radionuclide Gas Transport through Nuclear Explosion-Generated Fracture Networks
Authors: Jordan Amy B. , Stauffer Philip H. , Knight Earl E. , Rougier Esteban , Anderson Dale N. 
Published: December 2015

AbstractUnderground nuclear weapon testing produces radionuclide gases which may seep to the surface. Barometric pumping of gas through explosion-fractured rock is investigated using a new sequentially-coupled hydrodynamic rock damage/gas transport model. Fracture networks are produced for two rock types (granite and tuff) and three depths of burial. The fracture networks are integrated into a flow and transport numerical model driven by surface pressure signals of differing amplitude and variability. There are major differences between predictions using a realistic fracture network and prior results that used a simplified geometry. Matrix porosity and maximum fracture aperture have the greatest impact on gas breakthrough time and window of opportunity for detection, with different effects between granite and tuff simulations highlighting the importance of accurately simulating the fracture network. In particular, maximum fracture aperture has an opposite effect on tuff and granite, due to different damage patterns and their effect on the barometric pumping process. From stochastic simulations using randomly generated hydrogeologic parameters, normalized detection curves are presented to show differences in optimal sampling time for granite and tuff simulations. Seasonal and location-based effects on breakthrough, which occur due to differences in barometric forcing, are stronger where the barometric signal is highly variable.
A protein polymerization cascade mediates toxicity of non-pathological human huntingtin in yeast
Authors: Serpionov Genrikh V. , Alexandrov Alexander I. , Antonenko Yuri N. , Ter-Avanesyan Michael D. 
Published: December 2015

AbstractSeveral neurodegenerative amyloidoses, including Huntington disease, are caused by expansion of polyglutamine (polyQ) stretches in otherwise unrelated proteins. In a yeast model, an N-terminal fragment of mutant huntingtin with a stretch of 103 glutamine residues aggregates and causes toxicity, while its non-toxic wild type variant with a sequence of 25 glutamines (Htt25Q) does not aggregate. Here, we observed that non-toxic polymers of various proteins with glutamine-rich domains could seed polymerization of Htt25Q, which caused toxicity by seeding polymerization of the glutamine/asparagine-rich Sup35 protein thus depleting the soluble pools of this protein and its interacting partner, Sup45. Importantly, only polymers of Htt25Q, but not of the initial benign polymers, induced Sup35 polymerization, indicating an intermediary role of Htt25Q in cross-seeding Sup35 polymerization. These data provide a novel insight into interactions between amyloidogenic proteins and suggest a possible role for these interactions in the pathogenesis of Huntington and other polyQ diseases.
Secreted multifunctional Glyceraldehyde-3-phosphate dehydrogenase sequesters lactoferrin and iron into cells via a non-canonical pathway
Authors: Chauhan Anoop S. , Rawat Pooja , Malhotra Himanshu , Sheokand Navdeep , Kumar Manoj , Patidar Anil , Chaudhary Surbhi , Jakhar Priyanka , Raje Chaaya I. , Raje Manoj 
Published: December 2015

AbstractLactoferrin is a crucial nutritionally important pleiotropic molecule and iron an essential trace metal for all life. The current paradigm is that living organisms have evolved specific membrane anchored receptors along with iron carrier molecules for regulated absorption, transport, storage and mobilization of these vital nutrients. We present evidence for the existence of non-canonical pathway whereby cells actively forage these vital resources from beyond their physical boundaries, by secreting the multifunctional housekeeping enzyme Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) into the extracellular milieu. This effect’s an autocrine/paracrine acquisition of target ligand into the cell. Internalization by this route is extensively favoured even by cells that express surface receptors for lactoferrin and involves urokinase plasminogen activator receptor (uPAR). We also demonstrate the operation of this phenomenon during inflammation, as an arm of the innate immune response where lactoferrin denies iron to invading microorganisms by chelating it and then itself being sequestered into surrounding host cells by GAPDH.
Self-immunity microcapsules for corrosion protection of steel bar in reinforced concrete
Authors: Wang Yanshuai , Fang Guohao , Ding Weijian , Han Ningxu , Xing Feng , Dong Biqin 
Published: December 2015

AbstractA novel microcapsule-based self-immunity system for reinforced concrete is proposed. Its feasibility for hindering the corrosion of steel rebar by means of lifting the threshold value of [Cl−]/[OH−] is discussed. Precisely controlled release behavior enables corrosion protection in the case of depassivation. The release process is characterized over a designated range of pH values and its release characteristics of the microcapsules, triggered by decreasing pH value, are captured by observing that the core crystals are released when exposed to a signal (stimulus). The aim of corrosion protection of steel bar is achieved through the constantly-stabilized passive film and its stability is promoted using continuous calcium hydroxide released from the microcapsule, restoring alkaline conditions. The test results exhibited that the release process of the microcapsules is a function of time. Moreover, the release rate of core materials could interact with environmental pH value, in which the release rate is found to increase remarkably with decreasing pH value, but is inhibited by high pH levels.
Measurement of the Nucleus Area and Nucleus/Cytoplasm and Mitochondria/Nucleus Ratios in Human Colon Tissues by Dual-Colour Two-Photon Microscopy Imaging
Authors: Su Lim Chang , Sun Kim Eun , Yeon Kim Ji , Taek Hong Seung , Jai Chun Hoon , Eun Kang Dong , Rae Cho Bong 
Published: December 2015

AbstractWe developed two-photon (TP) probes for DNA (ABI-Nu), cytoplasm (Pyr-CT) and mitochondria (BF-MT). We found that ABI-Nu binds to AT in the minor groove, while ABI-Nu and BF-MT are effective for tracking in the cytoplasm and mitochondria, respectively. These probes showed very large effective two-photon action cross section values of 2230, 1555 and 790 Göppert-Mayer units (1 GM  =  10−50 cm4 s photon−1molecule−1) at 740 nm with emission maxima at 473, 561 and 560 nm, respectively, in each organelle. Using these probes, we quantitatively estimated the mean nuclear area and the ratios of nuclei to cytoplasm and mitochondria to nuclei in human colon tissues by dual-colour two-photon microscopy imaging within 2  h after biopsy. The mean nuclear area and the nuclei to cytoplasm and mitochondria to cytoplasm ratios increased in the following order: normal colon mucosa <colon adenoma <colon adenocarcinoma. Furthermore, the nuclear areas of these tissues showed significant differences that were well outside of the ranges of experimental errors, indicating the diagnostic potential of this method.
Tubby-like protein superfamily member PLSCR3 functions as a negative regulator of adipogenesis in mouse 3T3-L1 preadipocytes by suppressing induction of late differentiation stage transcription factors
Authors: Inokawa Akira , Inuzuka Tatsutoshi , Takahara Terunao , Shibata Hideki , Maki Masatoshi 
Published: December 2015

PLSCR3 (phospholipid scramblase 3, Scr3) belongs to the superfamily of membrane-associated transcription regulators named Tubby-like proteins (TULPs). Physiological phospholipid scrambling activities of PLSCRs in vivo have been skeptically argued, and knowledge of the biological functions of Scr3 is limited. We investigated the expression of Scr3 during differentiation of mouse 3T3-L1 preadipocytes by Western blotting (WB) and by reverse-transcription and real-time quantitative PCR (RT-qPCR). The Scr3 protein decreased during 3T3-L1 differentiation accompanied by a reduction in the mRNA level, and there was a significant increase in the amount of Scr3 protein secreted into the culture medium in the form of extracellular microvesicles (exosomes). On the other hand, Scr3 expression did not significantly decrease, and the secretion of Scr3 in 3T3 Swiss-albino fibroblasts (a parental cell-line of 3T3-L1) was not increased by differentiation treatment. Overexpression of human Scr3 during 3T3-L1 differentiation suppressed triacylglycerol accumulation and inhibited induction of the mRNAs of late stage pro-adipogenic transcription factors [CCAAT/enhancer-binding protein α (C/EBPα) and peroxisome proliferator-activated receptor γ (PPARγ)] and X-box-binding protein 1 (XBP1). Expression of early stage pro-adipogenic transcription factors (C/EBPβ and C/EBPδ) was not significantly affected. These results suggest that Scr3 functions as a negative regulator of adipogenesis in 3T3-L1 cells at a specific differentiation stage and that decrease in the intracellular amount of Scr3 protein caused by reduction in Scr3 mRNA expression and enhanced secretion of Scr3 protein appears to be important for appropriate adipocyte differentiation.
Dilemma of Approaches to Thoracic and Lumbar Spine: Our 10 Years' Review
Authors: Barman Debajit Roy , Varshney Rahul , Mukherjee Shuvankar , Sen Sarmila , Sen Nani , Ghosh Santanu , Mohanty B. C. , Deb Pulak , Datta Parthasarathi 
Published: December 2015

Background Lesions of the thoracic and lumbar spine are numerous. These lesions affect one or more columns (anterior, middle, and posterior) of the spine and compress the spinal cord either from anterior or posterior, giving rise to the features of radiculomyelopathy. These lesions can be approached either from the anterior or posterior aspect of the spine. We present our past 10 years' experience regarding the comparison between the two approaches.Methods Retrospective analysis of records of all patients with thoracic and lumbar lesion treated in our hospital between January 2005 and June 2014 was performed. Over the past 10 years, we came across 186 patients of thoracic and lumbar lesion who were operated either by anterior or posterior approach and were the focus of this study. Follow-up ranged from 6 months to 7 years.Results All the patients presented with neurological deficits. They were evaluated with investigation protocol of our hospital. Anterior approach was done in 38 cases (n = 38), and posterior approach was done in 148 cases (n = 148). We compared between the two groups in terms of perioperative complications, recovery, persisting symptoms, and mortality.Conclusion Complete recovery is better in the posterior approach (74.3 vs. 52.6%) and morality is more in the anterior approach (7.9 vs. 1.3%).
Early Feeding by Lake Trout Fry
Authors: Ladago Bret J. , Marsden J. Ellen , Evans Allison N. 
Published: December 2015

AbstractThe restoration of Lake Trout Salvelinus namaycush in the Great Lakes and Lake Champlain has been challenging due to the bottlenecks in recruitment that occur mostly during early life stages. Among possible sources of fry mortality (e.g., predation, starvation, and disease), the least is known about the diet and starvation risk of pre‐emergent fry. The first feedings by fry are generally assumed to be delayed until close to the absorption of the yolk sac and the emergence of the fry. The stomach contents of 374 wild‐caught Lake Trout fry from Lake Champlain were examined from hatching to the exogenous feeding stage to identify the earliest occurrence of feeding relative to yolk sac absorption and to describe the diet. Within 2 weeks of hatching, 19% of fry had food in their stomachs. At 4–6 weeks and after yolk sac absorption, 98% of fry began feeding. Diet was primarily comprised of Bosmina as well as calanoid and cyclopoid copepods, and fry contained up to 215 items per stomach. Our finding that fry began feeding within 2 weeks of hatching (prior to yolk sac absorption) is relevant to current concerns that Lake Trout fry mortality in the Great Lakes is caused by thiamine deficiency syndrome: wild Lake Trout fry may be able to mitigate thiamine deficiency with early feeding on thiamine‐rich zooplankton.
Environmental Drivers of Occupancy and Detection of Olympic Mudminnow
Authors: Kuehne Lauren M. , Olden Julian D. 
Published: December 2015

AbstractThe Olympic MudminnowNovumbra hubbsiis a highly endemic freshwater fish found only in Washington State, where their distribution is limited to low‐elevation wetland habitats. The distributional extent of the Olympic Mudminnow is well established, but local and watershed environmental features associated with their presence or absence within the range are poorly understood, making it difficult to determine habitat needs versus availability. We surveyed 22 sites in 2 years along the Chehalis River with the objective of modeling environmental characteristics associated with occupancy by Olympic Mudminnows, while also accounting for incomplete detection. Occupancy and detection probabilities were highly similar between years, and occupancy that incorporated detection probabilities was 47% higher than naive estimates in a given year. Modeling with environmental covariates supported the importance of low temperatures for predicting the occurrence of Olympic Mudminnows at sites, and detection within sites was associated most strongly with shallow depths and low dissolved oxygen. These results are consistent with prior research indicating the preferential use of groundwater springs by Olympic Mudminnows, particularly in warmer summer months. Our research expands the existing knowledge of Olympic Mudminnow distributions by documenting main‐stem‐oriented populations at varying levels of abundance and suggesting habitat features that may increase occupancy and detection probabilities. The sampling and modeling approach we describe also informs development of standardized survey protocols for Olympic Mudminnows, helping to optimize resources for monitoring occupancy and abundance across their limited range.
Detailed design optimization of the MITICA negative ion accelerator in view of the ITER NBI
Authors: Agostinetti P. , Aprile D. , Antoni V. , Cavenago M. , Chitarin G. , de Esch H.P.L. , De Lorenzi A. , Fonnesu N. , Gambetta G. , Hemsworth R.S. , Kashiwagi M. , Marconato N. , Marcuzzi D. , Pilan N. , Sartori E. , Serianni G. , Singh M. , Sonato P. , Spada E. , Toigo V. , Veltri P. , Zaccaria P. 
Published: December 2015

Abstract
The ITER Neutral Beam Test Facility (PRIMA) is presently under construction at Consorzio RFX (Padova, Italy). PRIMA includes two experimental devices: an ITER-size ion source with low voltage extraction, called SPIDER, and the full prototype of the whole ITER Heating Neutral Beams (HNBs), called MITICA.
The purpose of MITICA is to demonstrate that all operational parameters of the ITER HNB accelerator can be experimentally achieved, thus establishing a large step forward in the performances of neutral beam injectors in comparison with the present experimental devices.
The design of the MITICA extractor and accelerator grids, here described in detail, was developed using an integrated approach, taking into consideration at the same time all the relevant physics and engineering aspects. Particular care was taken also to support and validate the design on the basis of the expertise and experimental data made available by the collaborating neutral beam laboratories of CEA, IPP, CCFE, NIFS and JAEA. Considering the operational requirements and the other physics constraints of the ITER HNBs, the whole design has been thoroughly optimized and improved. Furthermore, specific innovative concepts have been introduced.
Rock-salt structure lithium deuteride formation in liquid lithium with high-concentrations of deuterium: a first-principles molecular dynamics study
Authors: Chen Mohan , Abrams T. , Jaworski M.A. , Carter Emily A. 
Published: December 2015

Abstract
Because of lithium’s possible use as a first wall material in a fusion reactor, a fundamental understanding of the interactions between liquid lithium (Li) and deuterium (D) is important. We predict structural and dynamical properties of liquid Li samples with high concentrations of D, as derived from first-principles molecular dynamics simulations. Liquid Li samples with four concentrations of inserted D atoms (LiD

,

, 0.50, 0.75, and 1.00) are studied at temperatures ranging from 470 to 1143 K. Densities, diffusivities, pair distribution functions, bond angle distribution functions, geometries, and charge transfer between Li and D atoms are calculated and analyzed. The analysis suggests liquid–solid phase transitions can occur at some concentrations and temperatures, forming rock-salt LiD within liquid Li. We also observe formation of some D2 molecules at high D concentrations.
Within-field Pathogenic Diversity of Phytophthora sojae in Commercial Soybean Fields in Iowa
Authors: Robertson Alison E. , Cianzio Silvia R. , Cerra Sarah M. , Pope Richard O. 
Published: December 2015

Phytophthora root and stem rot (PRR), caused by the oomycete Phytophthora sojae, is an economically important soybean disease in the north central region of the United States, including Iowa. Previous surveys of the pathogenic diversity of P. sojae in Iowa did not investigate whether multiple pathotypes of the pathogen existed in individual fields. Considering the many pathotypes of P. sojae that have been reported in Iowa, we hypothesized multiple pathotypes could exist within single fields. In the research reported herein, several soil samples were collected systematically from each of two commercial fields with a history of PRR in Iowa, and each soil sample was baited separately for isolates of P. sojae. Numerous pathotypes of P. sojae were detected from both fields. As many as four pathotypes were detected in some soil samples (each consisting of six to eight soil cores), which suggests that a single soybean plant could be subjected to infection by more than one pathotype. This possibility presents important implications in breeding resistant cultivars and in the management of PRR. Accepted for publication 14 July 2009. Published 8 September 2009.
Automatic genome segmentation with HMM-ANN hybrid models
Authors: Shen Li 
Published: December 2015

AbstractWe consider the problem of automatic genome segmentation (AGS) that aims to assign discrete labels to all genomic regions based on multiple ChIP-seq samples. We propose to use a hybrid model that combines a hidden Markov model (HMM) with an artificial neural network (ANN) to overcome the weaknesses of a standard HMM. Our contributions are threefold: first, we benchmark two approaches to generate targets for ANN training on an example dataset; second, we investigate many different ANN models to identify the ones with best predictions on chromatin states; third, we test different hyper-parameters and discuss how they affect the machine learning algorithms’ performance. We find our best performing models to beat two pervious state-of-the-art methods for AGS by large margins.