bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histone deacetylases inhibition by SAHA/Vorinostat normalizes the glioma microenvironment via xCT equilibration
Authors: Wolf Ines M. L. , Fan Zheng , Rauh Manfred , Seufert Sebastian , Hore Nirjhar , Buchfelder Michael , Savaskan Nic E. , Eyüpoglu Ilker Y. 
Published: September 2014

AbstractMalignant gliomas are characterized by neurodegenerative actions leading to the destruction of surrounding brain parenchyma. The disturbance in glutamate homeostasis caused by increased expression of the glutamate transporter xCT plays a key role in glioma progression. We demonstrate that the HDAC-inhibitor SAHA specifically inhibits the xCT-transporter expression. Thereby, tumor cell stress is engendered, marked by increase in ROS. Moreover, SAHA dependent xCT-reduction correlates with the inhibition of ATF4-expression, a factor known to foster xCT expression. Since xCT/system Xc- is pivotal for the brain tumor microenvironment, normalization of this system is a key in the management of malignant gliomas. To date, the problem lay in the inability to specifically target xCT due to the ubiquitous expression of the xCT-transporter—i.e. in non-cancerously transformed cells too—as well as its essential role in physiological CNS processes. Here, we show xCT-transporter equilibration through SAHA is specific for malignant brain tumors whereas SAHA does not affect the physiological xCT levels in healthy brain parenchyma. Our data indicate that SAHA operates on gliomas specifically via normalizing xCT expression which in consequence leads to reduced extracellular glutamate levels. This in turn causes a marked reduction in neuronal cell death and normalized tumor microenvironment.
Flat Focusing Mirror
Authors: Cheng Y. C. , Kicas S. , Trull J. , Peckus M. , Cojocaru C. , Vilaseca R. , Drazdys R. , Staliunas K. 
Published: September 2014

AbstractThe control of spatial propagation properties of narrow light beams such as divergence, focusing or imaging are main objectives in optics and photonics. In this letter, we propose and demonstrate experimentally a flat focusing mirror, based on an especially designed dielectric structure without any optical axis. More generally, it also enables imaging any light pattern in reflection. The flat focusing mirror with a transversal invariance can largely increase the applicability of structured photonic materials for light beam propagation control in small-dimension photonic circuits.
Cerium; Crystal Structure and Position in The Periodic Table
Authors: Johansson Börje , Luo Wei , Li Sa , Ahuja Rajeev 
Published: September 2014

AbstractThe properties of the cerium metal have intrigued physicists and chemists for many decades. In particular a lot of attention has been directed towards its high pressure behavior, where an isostructural volume collapse (γ phase → α phase) has been observed. Two main models of the electronic aspect of this transformation have been proposed; one where the 4f electron undergoes a change from being localized into an itinerant metallic state and one where the focus is on the interaction between the 4f electron and the conduction electrons, often referred to as the Kondo volume collapse model. However, over the years it has been repeatedly questioned whether the cerium collapse really is isostructural. Most recently, detailed experiments have been able to remove this worrisome uncertainty. Therefore the isostructural aspect of the α-γ transition has now to be seriously addressed in the theoretical modeling, something which has been very much neglected. A study of this fundamental characteristic of the cerium volume collapse is made in present paper and we show that the localized ⇌ delocalized 4f electron picture provides an adequate description of this unique behavior. This agreement makes it possible to suggest that an appropriate crossroad position for cerium in The Periodic Table.
Cyst formation following disruption of intracellular calcium signaling
Authors: Kuo Ivana Y. , DesRochers Teresa M. , Kimmerling Erica P. , Nguyen Lily , Ehrlich Barbara E. , Kaplan David L. 
Published: September 2014

Significance
Autosomal dominant polycystic kidney disease is the most common cause of fluid-filled cysts within the kidney. However, how cyst formation occurs is not well understood. It is thought that proteins disrupted by this disease, such as polycystin 2, change calcium signaling, leading to the formation of cysts. In this study, we grow LLC-PK1 cells in a protein gel environment to enable the study of cysts in culture, which cannot be observed in traditional cell culture techniques. We demonstrate that loss of intracellular calcium release channels result in cyst growth and are correlated with a loss of a functional cellular component known as the primary cilia. These results demonstrate that calcium signaling is an important component in cyst development.
Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation
Authors: Kurat Christoph F. , Lambert Jean-Philippe , Petschnigg Julia , Friesen Helena , Pawson Tony , Rosebrock Adam , Gingras Anne-Claude , Fillingham Jeffrey , Andrews Brenda 
Published: September 2014

Significance
DNA replication and histone gene transcription are tightly linked and occur during the S phase of the eukaryotic cell cycle. Histone production outside of S phase is highly toxic, underscoring the importance of regulatory pathways that control histone gene expression. Although various histone regulators have been discovered, the molecular mechanisms responsible for the spatial and temporal control of histone gene expression have remained elusive. Here, we describe the discovery of Spt21 as a long-elusive cell cycle oscillator responsible for restricting histone gene transcription to the S phase of the eukaryotic cell cycle. We show here that Spt21, together with its partner protein Spt10, regulates histone gene transcription by enabling the recruitment of a roster of chromatin-remodeling proteins.
Apoptotic pore formation is associated with in-plane insertion of Bak or Bax central helices into the mitochondrial outer membrane
Authors: Westphal Dana , Dewson Grant , Menard Marie , Frederick Paul , Iyer Sweta , Bartolo Ray , Gibson Leonie , Czabotar Peter E. , Smith Brian J. , Adams Jerry M. , Kluck Ruth M. 
Published: September 2014

Significance
To trigger cell death (apoptosis), two members of the B-cell lymphoma-2 protein family, Bak and Bax, change shape and convert from inert monomers into the oligomers that disrupt the outer mitochondrial membrane, but how they perturb the membrane is poorly understood. A longstanding model is that they rearrange and insert two central helices, α5 and α6, as a hairpin through the membrane. We show, however, that the hairpin insertion model does not hold. Instead, these helices in the oligomers insert only shallowly in the membrane, in its plane. The results favor a model in which these and probably other helices of Bak and Bax crowd the outer leaflet of the membrane, producing membrane curvature that leads to its disruption.
Genomic donor cassette sharing duringVLRAandVLRCassembly in jawless vertebrates
Authors: Das Sabyasachi , Li Jianxu , Holland Stephen J. , Iyer Lakshminarayan M. , Hirano Masayuki , Schorpp Michael , Aravind L. , Cooper Max D. , Boehm Thomas 
Published: September 2014

SignificanceLampreys possess two T-like lymphocyte lineages that express either variable lymphocyte receptor (VLR) A or VLRC antigen receptors. Despite the mutually exclusive expression pattern of VLRA and VLRC, in some cases the sequences of the two receptors are partially identical. This is the result of the shared use of genomic donor cassettes that are required to convert the incompleteVLRAandVLRCgenes into functional assemblies. This feature is reminiscent of T-cell receptors of jawed vertebrates that, despite being composed of different molecular structures, also share some variable parts. The shared use of variable segments in the different antigen receptor types for T cells of all vertebrates implies a conserved functional relationship between the two prototypic T-cell lineages.
Density and Condition of Subyearling Chinook Salmon in the Lower Columbia River and Estuary in Relation to Water Temperature and Genetic Stock of Origin
Authors: Roegner G. Curtis , Teel David J. 
Published: September 2014

AbstractWe examined the hypotheses that density and morphometric condition of subyearling juvenile Chinook Salmon Oncorhynchus tshawytscha would decline during periods of high water temperature in the lower Columbia River and estuary. The hypotheses were tested using salmon density measurements and a condition anomaly calculated from residuals of the length–weight linear regression based on 5,536 subyearlings collected from brackish estuarine and tidal freshwater (TFW) habitats. We captured Chinook Salmon at all temperatures encountered (4.2–23.5°C). In the TFW zone, densities were highest at optimal temperatures and lowest at suboptimal and supraoptimal temperatures; in the estuary, density did not differ among temperature regimes. Fish condition was lowest in winter, when temperatures were suboptimal, and highest in summer, when temperatures were supraoptimal. Pairwise comparisons of fish condition between periods of optimal temperature (spring) and supraoptimal or stressful temperature (summer) showed little change in the estuary but a large, positive increase with temperature in the TFW zone. Similarly, we examined seasonal differences in the condition of 50–60‐mm fry and again found condition to be lowest in winter and highest in summer. Finally, using genetic information, we identified stock‑specific differences in migration timing and concluded that most large yearlings and many subyearlings migrated in late winter or spring and therefore were never exposed to high temperatures. Other prevalent stocks persisted in the estuary during periods of elevated temperature; however, the condition of those fish also tended to be higher or neutral in summer than in spring. High temperatures appeared to influence migration timing, as evidenced by reduced density in TFW reaches during summer. However, we found little support for the hypothesis that condition of juvenile Chinook Salmon is reduced during periods of high water temperature in the lower Columbia River and estuary.Received April 5, 2014; accepted April 11, 2014
Diel Behavior in White Perch Revealed using Acoustic Telemetry
Authors: McCauley M. M. , Cerrato R. M. , Sclafani M. , Frisk M. G. 
Published: September 2014

AbstractAcoustic telemetry was used to investigate small‐scale movement and behavior of semi‐anadromous White Perch Morone americana in New York's Great South Bay system. Fifteen Vemco VR2 acoustic receivers were deployed in the main channel of the lower Carmans River. Of the 40 fish that were tagged with Vemco V9 acoustic transmitters from August 2010 to 2011, 15 fish returned at least 28 d of movement data. Acoustic tracking revealed that adult White Perch exhibited upstream and downstream diel movement within the Carmans River, a behavior that has not been previously described in adults of this species. Movements were tested for cyclical patterns by using autocorrelation analysis. The frequency of diel behavior (f) across individuals was found to be dependent on season: frequency was significantly reduced in winter (f = 13.8%) and was maximized in summer (f = 49.4% in 2010; f = 57.5% in 2011). Directionality in diel movement was also seasonal; nightly upstream movements were favored in summer and fall months, and nightly downstream movements were preferred in winter. Diel behavior was affected by temperature and salinity, with high salinities and low temperatures reducing the frequency of occurrence.Received March 24, 2014; accepted June 17, 2014
Risk Estimation Modeling and Feasibility Testing for A Mobile Ehealth Intervention for Binge Drinking among Young People: The D-ARIANNA (Digital-Alcohol Risk Alertness Notifying Network for Adolescents and Young Adults) Project
Authors: Carrà Giuseppe , Crocamo Cristina , Schivalocchi Alessandro , Bartoli Francesco , Carretta Daniele , Brambilla Giulia , Clerici Massimo 
Published: September 2014

Background Binge drinking is common among young people but often relevant risk factors are not recognized. eHealth apps, attractive for young people, may be useful to enhance awareness of this problem. We aimed at developing a current risk estimation model for binge drinking, incorporated into an eHealth app—D-ARIANNA (Digital-Alcohol RIsk Alertness Notifying Network for Adolescents and young adults)—for young people. Methods A longitudinal approach with phase 1 (risk estimation), phase 2 (design), and phase 3 (feasibility) was followed. Risk/protective factors identified from the literature were used to develop a current risk estimation model for binge drinking. Relevant odds ratios were subsequently pooled through meta-analytic techniques with a random-effects model, deriving weighted estimates to be introduced in a final model. A set of questions, matching identified risk factors, were nested in a questionnaire and assessed for wording, content, and acceptability in focus groups involving 110 adolescents and young adults. Results Ten risk factors (5 modifiable) and 2 protective factors showed significant associations with binge drinking and were included in the model. Their weighted coefficients ranged between −0.71 (school proficiency) and 1.90 (cannabis use). The model, nested in an eHealth app questionnaire, provides in percent an overall current risk score, accompanied by appropriate images. Factors that mostly contribute are shown in summary messages. Minor changes have been realized after focus groups review. Most of the subjects (74%) regarded the eHealth app as helpful to assess binge drinking risk. Conclusions We could produce an evidence-based eHealth app for young people, evaluating current risk for binge drinking. Its effectiveness will be tested in a large trial.
Identification of Genes Involved in Taura Syndrome Virus Resistance in Litopenaeus Vannamei
Authors: Boube I. , Lotz J. M. , Pozhitkov A. E. , Li S. , Griffitt R. J. 
Published: September 2014

Abstract
The goal of the present research was to identify the genes that are differentially expressed between two lineages of Pacific white shrimp Litopenaeus vannamei displaying different susceptibilities to Taura syndrome virus (TSV) and to understand the molecular pathways involved in resistance to the disease. An oligonucleotide microarray was constructed and used to identify several genes that were differentially expressed in the two L. vannamei lineages following infection with TSV. Individual L. vannamei from either resistant or susceptible lineages were exposed via injection to TSV. Individuals were removed at 6 and 24 h postinfection, and gene expression was assessed with the in-house microarray. The microarray data resulted in the selection of a set of 397 genes that were altered by TSV exposure between the different lineages. Significantly differentially expressed genes were subjected to hierarchical clustering and revealed a lineage-dependent clustering at 24 h postinoculation, but not at 6 h postinoculation. Discriminant analysis resulted in the identification of a set of 11 genes that were able to correctly classify Pacific white shrimp as resistant or susceptible based on gene expression data.
Received June 21, 2013; accepted October 24, 2013
Three time scale singular perturbation problems and nonsmooth dynamical systems
Authors: Cardin Pedro , da Silva Paulo , Teixeira Marco 
Published: September 2014

In this paper we study three time scale singular perturbation problems
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Temperature and entropy profiles to the virial radius of the Abell 1246 cluster observed with Suzaku
Authors: Sato Kosuke , Matsushita Kyoko , Yamasaki Noriko Y. , Sasaki Shin , Ohashi Takaya 
Published: September 2014

Abstract
We report properties of the intracluster medium (ICM) in Abell 1246 to the virial radius (r200) and further outside as observed with Suzaku. The ICM emission is clearly detected to r200, and we derive profiles of electron temperature, density, entropy, and cluster mass based on the spectral analysis. The temperature shows variation from ∼ 7 keV at the central region to ∼ 2.5 keV around r200. The total mass in r500 is (4.3 ± 0.4) × 1014 M⊙, assuming hydrostatic equilibrium. At r &gt; r500, the hydrostatic mass starts to decline and we therefore employ the total mass within r200 based on a weak-lens mass profile obtained from a sample of lower-mass clusters. This yields a gas mass fraction at r200 consistent with the cosmic baryon fraction, i.e., ∼ 17%. The entropy profile indicates a flatter slope than that of the numerical simulation, particularly in r &gt; r500. These tendencies are similar to those of other clusters observed with Suzaku. We detect no significant ICM emission outside of r200, and 2 σ upper limits of redshifted O vii and O viii line intensities are constrained to be less than 2.9 and 5.6 × 10−7 photons cm−2 s−1 arcmin−2, respectively. The O vii line upper limit indicates nH &lt; 4.7 × 10−5 cm−3 (Z/0.2 Z⊙)−1/2 (L/20 Mpc)−1/2, which corresponds to an overdensity, δ &lt; 160 (Z/0.2 Z⊙)−1/2 (L/20 Mpc)−1/2.
DNA Denaturing through Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Authors: Michaelian Karo , Santillán Padilla Norberto 
Published: September 2014

AbstractFormidable difficulties arise when attempting to explain the non-enzymatic replication, proliferation, and the acquisition of homochirality and information content, of RNA and DNA at the beginnings of life. However, new light can be shed on these problems by viewing the origin of life as a non-equilibrium thermodynamic process in which RNA, DNA and other fundamental molecules of life arose as structures to dissipate the prevailing solar spectrum. Here we present experimental results which demonstrate that the absorption and dissipation of UV-C light by DNA at temperatures below their melting temperature leads to complete and reversible denaturing for small synthetic DNA of 25 base pairs (bp), and to partial and reversible denaturing for 48 bp DNA and for large salmon sperm and yeast DNA of average size 100 kbp. This result has direct bearing on the above mentioned problems and thereby opens the door to a possible thermodynamic route to the origin of life.
Non-crossover gene conversions show strong GC bias and unexpected clustering in humans
Authors: Williams Amy L. , Genovese Giulio , Dyer Thomas , Altemose Nicolas , Truax Katherine , Jun Goo , Patterson Nick , Myers Simon R. , Curran Joanne E. , Duggirala Ravi , Blangero John , Reich David , Przeworski Molly ,   T2D-GENES Consortium
Published: September 2014

AbstractAlthough the past decade has seen tremendous progress in our understanding of fine-scale recombination, little is known about non-crossover (NCO) gene conversion. We report the first genome-wide study of NCO events in humans. Using SNP array data from 98 meioses, we identified 103 sites affected by NCO, of which 50/52 were confirmed in sequence data. Overlap with double strand break (DSB) hotspots indicates that the events are likely of meiotic origin. We estimate that a site is involved in a NCO at a rate of 5.7×10-6/bp/generation, consistent with sperm-typing studies, and infer that tract lengths span at least an order of magnitude. Observed NCO events show strong allelic bias at heterozygous AT/GC SNPs, with 68% (58–78%) transmitting GC alleles (P=5×10-4). Strikingly, in 4 of 15 regions for which there are also resequencing data, multiple disjoint NCO tracts cluster in close proximity (~20–30 kb), a phenomenon not previously seen in mammals.
Functional Antagonism Between CELF and Mbnl Proteins in the Cytoplasm
Authors: Wang Eric T. , Ward Amanda J. , Cherone Jennifer , Wang Thomas T. , Giudice Jimena , Cooper Thomas A. , Burge Christopher B. 
Published: September 2014

AbstractThe conserved CUGBP1, Elav-like (CELF) family of RNA binding proteins contribute to heart and skeletal muscle development and are implicated in myotonic dystrophy (DM). To understand genome-wide functions of CELF proteins, we analyzed transcriptome dynamics following induction ofCELF1orCELF2in adult mouse heart orCELF1in muscle by RNA-seq, complemented by crosslinking/immunoprecipitation-sequencing (CLIP-seq) analysis of mouse cells and tissues to distinguish direct from indirect regulatory targets. Analysis of expression and mRNA binding data revealed hundreds of mRNAs bound in their 3' UTRs by both CELF1 and and the developmentally induced Mbnl1 protein, 3-fold more than expected. The relative extent of CELF1 and Mbnl1 binding in 3' UTRs predicted the extent of repression or stabilization, respectively, following CELF induction. These findings support a “Cytoplasmic Competition” model in which CELF and Mbnl proteins compete to specify degradation or membrane localization/stabilization, respectively, of an overlapping set of targets. Several hundred messages contained proximal CELF1 and Mbnl1 binding sites (within 50 bases), and were more strongly repressed by CELF1 than messages with distal sites. Messages with different spacing of CELF and Mbnl sites in their 3' UTRs exhibited different developmental dynamics, suggesting that spacing is used to tune cytoplasmic competition between these factors to specify the timing of developmental induction. CELF1 also shared dozens of splicing targets with Mbnl1, most regulated oppositely, confirming a phenomenon observed in smaller scale studies but not previously supported by genome-wide methods, which also appears to enhance developmental transitions.
Enhanced Oxidative Stress Resistance through Activation of a Zinc Deficiency Transcription Factor inBrachypodium distachyon
Authors: Glover-Cutter Kira M. , Alderman Stephen , Dombrowski James E. , Martin Ruth C. 
Published: September 2014

AbstractIdentification of viable strategies to increase stress resistance of crops will become increasingly important for the goal of global food security as our population increases and our climate changes. Considering that resistance to oxidative stress is oftentimes an indicator of health and longevity in animal systems, characterizing conserved pathways known to increase oxidative stress resistance could prove fruitful for crop improvement strategies. This report argues for the usefulness and practicality of the model organism Brachypodium distachyon for identifying and validating stress resistance factors. Specifically, we focus on a zinc deficiency B. distachyon basic leucine zipper transcription factor, BdbZIP10, and its role in oxidative stress in the model organism B. distachyon. When overexpressed, BdbZIP10 protects plants and callus tissue from oxidative stress insults, most likely through distinct and direct activation of protective oxidative stress genes. Increased oxidative stress resistance and cell viability through the overexpression of BdbZIP10 highlight the utility of investigating conserved stress responses between plant and animal systems.