bluuebunny/crossref_metadata_2025_split huggingface dataset:
A preliminary exploration on DNA methylation of transgene across generations in transgenic rats
Authors: Li Qiling , Xu Wei , Cui Ye , Ma Li , Richards Jendai , Li Wenzhi , Ma Yamin , Fu Guoxing , Bythwood Tameka , Wang Yueling , Li Xu , Song Qing 
Published: February 2015

AbstractEpigenetic heritability is an important issue in the field of genetics and also in the development of many human diseases. In this study, we created a transgenic rat model and investigated the transgenerational methylation patterns in these animals. The transgene DNA fragment was unmethylated before it was injected into the pronucleus, so it is a good model to study the inheritance of DNA methylation patterns. We performed bisulfite sequencing on 23 CpG dinucleotides on the transgene across three generations in two tissues. We observed that the transgene was heavily methylated in the liver (87.53%) from the founder generation, whereas its methylation rate was much lower in the kidney (70.47%). Spearman correlation analysis showed that there was a strong correlation on the methylation status between different generations in the same tissue, which was observed in both liver and kidney and among all individuals in this pedigree. This study provided some evidence that DNA methylation patterns acquired in the founder animal can be passed to the offspring.
Fragility and basic process energies in vitrifying systems
Authors: Martinez-Garcia Julio Cesar , Rzoska Sylwester J. , Drozd-Rzoska Aleksandra , Starzonek Szymon , Mauro John C. 
Published: February 2015

AbstractThe concept of ‘fragility’ constitutes a central point of the glass transition science serving as the ‘universal’ metric linking previtreous dynamics of qualitatively distinct systems. Finding the fundamental meaning of fragility is the ‘condicio sine qua’ for reaching the long expected conceptual breakthrough in this domain. This report shows that fragility is determined by the ratio between two fundamental process energies, viz. the activation enthalpy and activation energy. The reasoning, avoiding any underlying physical model, is supported by the experimental evidence ranging from low molecular weight liquids and polymers to plastic crystals and liquid crystals. All these lead to the new general scaling plot for dynamics of arbitrary glass former. The limited adequacy of broadly used so far semi-empirical relationships between fragility and the activation energy is shown. Results presented remain valid for an arbitrary complex system and collective phenomena if their dynamics is described by the general super-Arrhenius relation.
Hyperdoping silicon with selenium: solid vs. liquid phase epitaxy
Authors: Zhou Shengqiang , Liu Fang , Prucnal S. , Gao Kun , Khalid M. , Baehtz C. , Posselt M. , Skorupa W. , Helm M. 
Published: February 2015

AbstractChalcogen-hyperdoped silicon shows potential applications in silicon-based infrared photodetectors and intermediate band solar cells. Due to the low solid solubility limits of chalcogen elements in silicon, these materials were previously realized by femtosecond or nanosecond laser annealing of implanted silicon or bare silicon in certain background gases. The high energy density deposited on the silicon surface leads to a liquid phase and the fast recrystallization velocity allows trapping of chalcogen into the silicon matrix. However, this method encounters the problem of surface segregation. In this paper, we propose a solid phase processing by flash-lamp annealing in the millisecond range, which is in between the conventional rapid thermal annealing and pulsed laser annealing. Flash lamp annealed selenium-implanted silicon shows a substitutional fraction of ~ 70% with an implanted concentration up to 2.3%. The resistivity is lower and the carrier mobility is higher than those of nanosecond pulsed laser annealed samples. Our results show that flash-lamp annealing is superior to laser annealing in preventing surface segregation and in allowing scalability.
Complete genome sequence and transcriptomics analyses reveal pigment biosynthesis and regulatory mechanisms in an industrial strain, Monascus purpureus YY-1
Authors: Yang Yue , Liu Bin , Du Xinjun , Li Ping , Liang Bin , Cheng Xiaozhen , Du Liangcheng , Huang Di , Wang Lei , Wang Shuo 
Published: February 2015

AbstractMonascus has been used to produce natural colorants and food supplements for more than one thousand years and approximately more than one billion people eat Monascus-fermented products during their daily life. In this study, using next-generation sequencing and optical mapping approaches, a 24.1-Mb complete genome of an industrial strain, Monascus purpureus YY-1, was obtained. This genome consists of eight chromosomes and 7,491 genes. Phylogenetic analysis at the genome level provides convincing evidence for the evolutionary position of M. purpureus. We provide the first comprehensive prediction of the biosynthetic pathway for Monascus pigment. Comparative genomic analyses show that the genome of M. purpureus is 13.6–40% smaller than those of closely related filamentous fungi and has undergone significant gene losses, most of which likely occurred during its specialized adaptation to starch-based foods. Comparative transcriptome analysis reveals that carbon starvation stress, resulting from the use of relatively low-quality carbon sources, contributes to the high yield of pigments by repressing central carbon metabolism and augmenting the acetyl-CoA pool. Our work provides important insights into the evolution of this economically important fungus and lays a foundation for future genetic manipulation and engineering of this strain.
Stretching Fibroblasts Remodels Fibronectin and Alters Cancer Cell Migration
Authors: Ao Mingfang , Brewer Bryson M. , Yang Lijie , Franco Coronel Omar E. , Hayward Simon W. , Webb Donna J. , Li Deyu 
Published: February 2015

AbstractMost investigations of cancer-stroma interactions have focused on biochemical signaling effects, with much less attention being paid to biophysical factors. In this study, we investigated the role of mechanical stimuli on human prostatic fibroblasts using a microfluidic platform that was adapted for our experiments and further developed for both repeatable performance among multiple assays and for compatibility with high-resolution confocal microscopy. Results show that mechanical stretching of normal tissue-associated fibroblasts (NAFs) alters the structure of secreted fibronectin. Specifically, unstretched NAFs deposit and assemble fibronectin in a random, mesh-like arrangement, while stretched NAFs produce matrix with a more organized, linearly aligned structure. Moreover, the stretched NAFs exhibited an enhanced capability for directing co-cultured cancer cell migration in a persistent manner. Furthermore, we show that stretching NAFs triggers complex biochemical signaling events through the observation of increased expression of platelet derived growth factor receptor α (PDGFRα). A comparison of these behaviors with those of cancer-associated fibroblasts (CAFs) indicates that the observed phenotypes of stretched NAFs are similar to those associated with CAFs, suggesting that mechanical stress is a critical factor in NAF activation and CAF genesis.
Effects of Walking with Blood Flow Restriction on Excess Post-exercise Oxygen Consumption
Authors: Mendonca G. , Vaz J. , Pezarat-Correia P. , Fernhall B. 
Published: February 2015

AbstractThis study determined the influence of walking with blood flow restriction (BFR) on the excess post-exercise oxygen consumption (EPOC) of healthy young men. 17 healthy young men (22.1±2.9 years) performed graded treadmill exercise to assess VO2peak. In a randomized fashion, each participant performed 5 sets of 3-min treadmill exercise at their optimal walking speed with 1-min interval either with or without BFR. Participants were then seated in a chair and remained there for 30 min of recovery. Expired gases were continuously monitored during exercise and recovery. BFR increased the O2 cost of walking as well as its relative intensity and cumulative O2 deficit (p<0.05). The EPOC magnitude after walking with BFR was greater than in the non-BFR condition (p<0.05). No differences between conditions were seen for the duration of EPOC. The EPOC magnitude was no longer different between conditions after controlling for the differences in relative intensity and in the cumulative O2 deficit (p>0.05). These data indicate that walking with BFR increases the magnitude of EPOC. Moreover, they also demonstrate that such increment in EPOC is likely explained by the effects of BFR on walking relative intensity and cumulative O2 deficit.
Age-related decrease of IF5/BTG4 in oral and respiratory cavities in mice
Authors: Mano Hiroshi , Nakatani Sachie , Kimira Yoshifumi , Mano Mikiko , Sekiguchi Yuusuke , Im Ryang-Hyock , Shimizu Jun , Wada Masahiro 
Published: February 2015

Abstract
An IF5 cDNA was isolated by expression cloning from a mouse oocyte cDNA library. It encoded a protein of 250 amino acids, and the region of it encoding amino acids 1–137 showed 86.8% alignment with the anti-proliferative domain of BTG/TOB family genes. This gene is also termed BTG4 or PC3B. Transiently expressed IF5/BTG4 induced alkaline phosphatase activity in human embryonic kidney (HEK293T) and 2T3 cells. IF5/BTG4 mRNA was detected by reverse transcription polymerase chain reaction in pharynx, larynx, trachea, oviduct, ovary, caput epididymis, and testis, but not in lung, intestine, or liver. Immunohistochemistry showed the IF5/BTG4 protein to be present in epithelial cells of the tongue, palate, pharynx, internal nose, and trachea. Both protein and mRNA levels of IF5/BTG4 were reduced by aging when comparing 4-week-old mice with 48-week-old mice. Our findings suggest that IF5/BTG4 may be an aging-related gene in epithelial cells.
Genetics of intra-species variation in avoidance behavior induced by a thermal stimulus inC. elegans
Authors: Ghosh Rajarshi , Bloom Joshua S. , Mohammadi Aylia , Schumer Molly E. , Andolfatto Peter , Ryu William , Kruglyak Leonid 
Published: February 2015

AbstractIndividuals within a species vary in their responses to a wide range of stimuli, partly as a result of differences in their genetic makeup. Relatively little is known about the genetic and neuronal mechanisms contributing to diversity of behavior in natural populations. By studying animal-to-animal variation in innate avoidance behavior to thermal stimuli in the nematodeCaenorhabditis elegans, we uncovered genetic principles of how different components of a behavioral response can be altered in nature to generate behavioral diversity. Using a thermal pulse assay, we uncovered heritable variation in responses to a transient temperature increase. Quantitative trait locus mapping revealed that separate components of this response were controlled by distinct genomic loci. The loci we identified contributed to variation in components of thermal pulse avoidance behavior in an additive fashion. Our results show that the escape behavior induced by thermal stimuli is composed of simpler behavioral components that are influenced by at least six distinct genetic loci. The loci that decouple components of the escape behavior reveal a genetic system that allows independent modification of behavioral parameters. Our work sets the foundation for future studies of evolution of innate behaviors at the molecular and neuronal level.
The biological functions of Naa10 – from amino-terminal acetylation to human disease
Authors: Doerfel Max , Lyon Gholson J. 
Published: February 2015

1AbstractN-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40 % of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
Do Read Errors Matter for Genome Assembly?
Authors: Shomorony Ilan , Courtade Thomas , Tse David 
Published: February 2015

AbstractWhile most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read length and error rate in terms of the information needed for the perfect assembly of the genome. Using an adversarial erasure error model, we make progress on this problem by establishing a critical read length, as a function of the genome and the error rate, above which perfect assembly is guaranteed. For several real genomes, including those from the GAGE dataset, we verify that this critical read length is not significantly greater than the read length required for perfect assembly from reads without errors.
Crossmodal integration improves sensory detection thresholds in the ferret
Authors: Hollensteiner Karl J. , Pieper Florian , Engler Gerhard , König Peter , Engel Andreas K. 
Published: February 2015

AbstractDuring the last two decades ferrets (Mustela putorius) have been established as a highly efficient animal model in different fields in neuroscience. Here we asked whether ferrets integrate sensory information according to the same principles established for other species. Since only few methods and protocols are available for behaving ferrets we developed a head-free, body-restrained approach allowing a standardized stimulation position and the utilization of the ferret’s natural response behavior. We established a behavioral paradigm to test audiovisual integration in the ferret. Animals had to detect a brief auditory and/or visual stimulus presented either left or right from their midline. We first determined detection thresholds for auditory amplitude and visual contrast. In a second step, we combined both modalities and compared psychometric fits and the reaction times between all conditions. We employed Maximum Likelihood Estimation (MLE) to model bimodal psychometric curves and to investigate whether ferrets integrate modalities in an optimal manner. Furthermore, to test for a redundant signal effect we pooled the reaction times of all animals to calculate a race model. We observed that bimodal detection thresholds were reduced and reaction times were faster in the bimodal compared to unimodal conditions. The race model and MLE modeling showed that ferrets integrate modalities in a statistically optimal fashion. Taken together, the data indicate that principles of multisensory integration previously demonstrated in other species also apply to crossmodal processing in the ferret.
An Atlas of Genetic Correlations across Human Diseases and Traits
Authors: Bulik-Sullivan Brendan , Finucane Hilary K , Anttila Verneri , Gusev Alexander , Day Felix R. , Duncan Laramie , Perry John R. B. , Patterson Nick , Robinson Elise B. , Daly Mark J. , Price Alkes L. , Neale Benjamin M. ,   ReproGen Consortium,   Psychiatric Genomics Consortium,   Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3
Published: February 2015

AbstractIdentifying genetic correlations between complex traits and diseases can provide useful etiological insights and help prioritize likely causal relationships. The major challenges preventing estimation of genetic correlation from genome-wide association study (GWAS) data with current methods are the lack of availability of individual genotype data and widespread sample overlap among meta-analyses. We circumvent these difficulties by introducing a technique for estimating genetic correlation that requires only GWAS summary statistics and is not biased by sample overlap. We use our method to estimate 300 genetic correlations among 25 traits, totaling more than 1.5 million unique phenotype measurements. Our results include genetic correlations between anorexia nervosa and schizophrenia, anorexia and obesity and associations between educational attainment and several diseases. These results highlight the power of genome-wide analyses, since there currently are no genome-wide significant SNPs for anorexia nervosa and only three for educational attainment.
Harsh Environments and “Fast” Human Life Histories: What Does the Theory Say?
Authors: Baldini Ryan 
Published: February 2015

AbstractA common belief among human life history researchers is that “harsher” environments - i.e., those with higher mortality rates and resource stress - select for “fast” life histories, i.e. earlier reproduction and faster senescence. I show that these “harsh environments, fast life histories” - or HEFLH - hypotheses are poorly supported by evolutionary theory. First, I use a simple model to show that effects of environmental harshness on life history evolution are incredibly diverse. In particular, small changes in basic but poorly understood variables - e.g., whether and how population density affects vital rates - can cause selection to favor very different life histories. Furthermore, I show that almost all life history theory used to justify HEFLH hypotheses is misapplied in the first place. The reason is that HEFLH hypotheses usually treat plastic responses to heterogeneous environmental conditionswithina population, whereas the theory used to justify such hypotheses treat genetic responses to environmental changes across an entire population. Counter-intuitively, the predictions of the former do not generally apply to the latter: the optimal response to a harsh environment within a large heterogeneous environment is not necessarily the optimal strategy of a population uniformly inhabiting the same harsh environment. I discuss these theoretical results in light of the current state of empirical research.
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
Authors: Hunter Samuel S. , Lyon Robert T. , Sarver Brice A. J. , Hardwick Kayla , Forney Larry J. , Settles Matthew L. 
Published: February 2015

AbstractAnalysis of High-throughput sequencing (HTS) data is a difficult problem, especially in the context of non-model organisms where comparison of homologous sequences may be hindered by the lack of a close reference genome. Current mapping-based methods rely on the availability of a highly similar reference sequence, whereasde novoassemblies produce anonymous (unannotated) contigs that are not easily compared across samples. Here, we present Assembly by Reduced Complexity (ARC) a hybrid mapping and assembly approach for targeted assembly of homologous sequences. ARC is an open-source project (http://ibest.github.io/ARC/) implemented in the Python language and consists of the following stages: 1) align sequence reads to reference targets, 2) use alignment results to distribute reads into target specific bins, 3) perform assemblies for each bin (target) to produce contigs, and 4) replace previous reference targets with assembled contigs and iterate. We show that ARC is able to assemble high quality, unbiased mitochondrial genomes seeded from 11 progressively divergent references, and is able to assemble full mitochondrial genomes starting from short, poor quality ancient DNA reads. We also show ARC compares favorably tode novoassembly of a large exome capture dataset for CPU and memory requirements; assembling 7,627 individual targets across 55 samples, completing over 1.3 million assemblies in less than 78 hours, while using under 32 Gb of system memory. ARC breaks the assembly problem down into many smaller problems, solving the anonymous contig and poor scaling inherent in somede novoassembly methods and reference bias inherent in traditional read mapping.
Long-term field experiment on the impacts of the neonicotinoid dinotefuran and the organophosphate fenitrothion on a honeybee colony
Authors: Yamada Toshiro , Yamada Yasuhiro , Yamada Kazuko , Nakamura Hiroko 
Published: February 2015

SummaryNeonicotinoides are persistent and highly toxic pesticides that have become popular instead of organophosphates, being suspected to be a trigger of massive disappearance of bees that raises concern in the world. The evaluation of the long-term influence for a whole colony in the natural environment is, however, not established yet. In this paper, we conducted a long-term field experiment and found different impacts on honeybee colonies(Apis mellifera)in an apiary between the neonicotinoid dinotefuran and the organophosphate fenitrothion even though whose concentrations in sugar syrup provided for bees were adjusted to have nearly equal short-term effects on a honeybee based on the median lethal dose (LD50) as well as the insecticidal activity to exterminate stinkbugs.The colony with administration of dinotefran (dinotefuran colony) became extinct in 26 days, while the colony with administration of fenitrothion (fenitrothion colony) survived the administration for the same period. Furthermore, the fenitrothion colony succeeded to be alive for more than 293 days after administration, and also succeeded an overwintering, which indicates that colonies exposed to fenitrothion can recover after the exposure.Meanwhile, the dinotefuran colony became extinct even though the intake of dinotefuran was estimated to be comparable with that of fenitrothion in terms of the LD50of a honeybee. Moreover, the colonies in our previous long-term experiments where dinotefuran with higher concentration were administered only for first few days (Yamada et al., 2012) became extinct in 104 days and 162 days, respectively. From these results, we speculate that colonies exposed to dinotefuran hardly recover from the damage because dinotefuran is much more persistent than fenitrothion and toxic foods stored in cells can affect a colony in a long period.