bluuebunny/crossref_metadata_2025_split huggingface dataset:
From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists
Authors: Gomariz María , Martínez-García Manuel , Santos Fernando , Rodriguez Francisco , Capella-Gutiérrez Salvador , Gabaldón Toni , Rosselló-Móra Ramon , Meseguer Inmaculada , Antón Josefa 
Published: June 2014

Abstract
The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to &gt;40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.
Epigenetic Modification of the Leptin Promoter in Diet-Induced Obese Mice and the Effects of N-3 Polyunsaturated Fatty Acids
Authors: Shen Wenwen , Wang Cui , Xia Lulu , Fan Chaonan , Dong Hua , Deckelbaum Richard J. , Qi Kemin 
Published: June 2014

AbstractWe report evidence of a detailed epigenetic modification of the leptin promoter and the effects of n-3 polyunsaturated fatty acids (n-3 PUFAs), which is closely associated with the leptin gene transcription in obesity. In the adipose tissue of diet induced obese (DIO) mice, methylation of the CpG island and the binding of methyl-CpG-binding domain protein 2 (MBD2) and DNA methyltransferases (DNMTs) at the leptin promoter are increased and RNA Pol II is decreased. Additionally, histones H3 and H4 are hypoacetylated, lysine 4 of histone H3 (H3K4) is hypomethylated and the binding of histone deacetylases (HDACs) 1, 2 and 6 is increased at the leptin promoter in the DIO mice. These modifications may serve a feedback role to maintain leptin concentrations within a normal range. The regulation of leptin transcriptional expression by n-3 PUFAs is mediated, at least in part, by epigenetic targets, such as MBD2 and histone modifications.
Molecular weight dependent vertical composition profiles of PCDTBT:PC71BM blends for organic photovoltaics
Authors: Kingsley James W. , Marchisio Pier Paolo , Yi Hunan , Iraqi Ahmed , Kinane Christy J. , Langridge Sean , Thompson Richard L. , Cadby Ashley J. , Pearson Andrew J. , Lidzey David G. , Jones Richard A. L. , Parnell Andrew J. 
Published: June 2014

AbstractWe have used Soxhlet solvent purification to fractionate a broad molecular weight distribution of the polycarbazole polymer PCDTBT into three lower polydispersity molecular weight fractions. Organic photovoltaic devices were made using a blend of the fullerene acceptor PC71BM with the molecular weight fractions. An average power conversion efficiency of 5.89% (peak efficiency of 6.15%) was measured for PCDTBT blend devices with a number average molecular weight of Mn = 25.5 kDa. There was significant variation between the molecular weight fractions with low (Mn = 15.0 kDa) and high (Mn = 34.9 kDa) fractions producing devices with average efficiencies of 5.02% and 3.70% respectively. Neutron reflectivity measurements on these polymer:PC71BM blend layers showed that larger molecular weights leads to an increase in the polymer enrichment layer thickness at the anode interface, this improves efficiency up to a limiting point where the polymer solubility causes a reduction of the PCDTBT concentration in the active layer.
Thermal loss in high‐Q antennas
Authors: Caporal Del Barrio S. , Bahramzy P. , Svendsen S. , Jagielski O. , Pedersen G.F. 
Published: June 2014

Tunable antennas are very promising for future generations of mobile communications, where antennas are required to cover a wide range of operating bands. This reported work was aimed at characterising the loss mechanism of tunable antennas. Tunable antennas typically exhibit a high quality factor (Q), which can lead to thermal loss due to the conductivity of the metal. The investigation shows that copper loss is non‐negligible for high‐Q values. In the proposed design, the copper loss is 2 dB, for a Q of 260 at 700 MHz.
Hybrid optimisation method for optimal power flow using flexible AC transmission system devices
Authors: Huang Chao‐Ming , Huang Yann‐Chang 
Published: June 2014

This study proposes a hybrid optimisation method for optimal power flow using a flexible AC transmission system (FACTS). The FACTS plays an important role in the dynamic stability and steady‐state control of power systems. This study achieves steady‐state control by determining the types and the optimal locations of the FACTS devices and their associated values in the transmission lines. To determine the optimal solutions to the FACTS allocation problem, a hybrid optimisation method that combines a harmony search algorithm and an ant system is proposed. The objective functions of power flow considered are the active power transmission loss, the performance index of the active power flow in the transmission lines and the performance index of the voltage difference between buses. The proposed method was verified on the IEEE 30‐bus and Taiwan Power Company 345 kV simplified systems. The results demonstrate that the proposed method improves the total transfer capability and provides better steady‐state control of power systems than existing methods do.
Multilevel cascaded transformerless inverter for connecting distributed‐generation sources to network
Authors: Ebadi Mazdak , Joorabian Mahmood , Moghani Javad Shokrollahi 
Published: June 2014

There are many types of distributed‐generation (DG) sources that cannot be connected to the network directly and use an inverter‐based interface. In harmonic compensators [like active power filters (APFs)], the coupling transformer disrupts the compensation capability, therefore the transformerless inverter schemes have grown up in recent years. A new cascaded multilevel transformerless inverter topology is introduced in this study to connect the DG sources to power utility. The proposed circuit of this study can compensate the current harmonic of the non‐linear load (as in APF) and inject maximum possible active power as a DG source interface, simultaneously. A fixed gain called KC is obtained based on the load nature, and is used to adjust the set point of the inverter between two operating modes. Proposed scheme has been simulated in Matlab/Simulink to evaluate the circuit performance both in the maximum active power injection mode and the load harmonic compensation mode. Then a 2.2 kW single‐phase prototype of the circuit is used for experimental evaluation of the study. Both simulative and experimental results prove that such a circuit minimises the total harmonic distortion of the source side current to an acceptable margin, while injecting the maximum possible active power.
Attenuation of migration properties of CD4+ T cells from aged mice correlates with decrease in chemokine receptor expression, response to retinoic acid, and RALDH expression compared to young mice
Authors: Park Jihyun , Miyakawa Takuya , Shiokawa Aya , Nakajima-Adachi Haruyo , Tanokura Masaru , Hachimura Satoshi 
Published: June 2014

Abstract
Aging results in attenuation of abilities to mount appropriate immune responses. The influence of aging on CD4+ T cell migration ability toward chemokines was investigated with young and aged mice. We found functional decline in migration ability toward CCL19 and also decreased CCR7 expression level in antigen-stimulated CD4+ T cells from aged mice compared with those from young mice. Upon addition of retinoic acid (RA), CD4+ T cells from aged mice showed decreased CCR9 expression level compared to young mice and the migration ability of CD4+ T cells from aged mice toward CCL25 was attenuated compared to young mice. We also observed that the expression of RALDH2 mRNA was decreased in mesenteric lymph node dendritic cells from aged mice compared to those from young mice. These results demonstrate that attenuated migration abilities of CD4+ T cells were observed in aged mice, which correlated with decreased chemokine receptor expression. Furthermore, the reduced production and response to RA by aging may be one of the causes of such attenuated migration abilities in the intestinal immune system.
Detection of mutations by fill-in ligation reaction with enzyme-linked immunosorbent assay for rapid medical diagnosis
Authors: Tang Yi-Tong , Xiao Na , Li Zhi-Shan , Zou Jiu-Ming , Cao Rui , Zhao Xue-Hong , Shao Jin-Hui 
Published: June 2014

Abstract
Several approaches for parallel genotyping have been developed with increasingly available information on DNA variation. However, these methods require either complex laboratory procedures or expensive instrumentation. None of these procedures is readily performed in local clinical laboratories. In this study, we developed a flexible genotyping method involving fill-in ligation reaction with enzyme-linked immunosorbent assay successfully applied to detect important single-nucleotide polymorphisms (SNPs) for EGFR c.2573T &gt; G (L858R), EGFR c.2582T &gt; A (L861Q), and EGFR c.2155G &gt; T (G719C). This assay exhibited excellent specificity, with a sensitivity as low as 0.5%. Eight out of 62 clinical samples were identified as heterozygotes for the SNP site of L858R, whereas only two samples were identified as heterozygotes by direct sequencing. The developed method enabled accurate identification of SNP in a simple and cost-effective manner adapted to routine analysis.
Predicting dynamic signaling network response under unseen perturbations
Authors: Zhu Fan , Guan Yuanfang 
Published: June 2014

AbstractMotivation: Predicting trajectories of signaling networks under complex perturbations is one of the most valuable, but challenging, tasks in systems biology. Signaling networks are involved in most of the biological pathways, and modeling their dynamics has wide applications including drug design and treatment outcome prediction.Results: In this paper, we report a novel model for predicting the cell type-specific time course response of signaling proteins under unseen perturbations. This algorithm achieved the top performance in the 2013 8th Dialogue for Reverse Engineering Assessments and Methods (DREAM 8) subchallenge: time course prediction in breast cancer cell lines. We formulate the trajectory prediction problem into a standard regularization problem; the solution becomes solving this discrete ill-posed problem. This algorithm includes three steps: denoising, estimating regression coefficients and modeling trajectories under unseen perturbations. We further validated the accuracy of this method against simulation and experimental data. Furthermore, this method reduces computational time by magnitudes compared to state-of-the-art methods, allowing genome-wide modeling of signaling pathways and time course trajectories to be carried out in a practical time.Availability and implementation: Source code is available at http://guanlab.ccmb.med.umich.edu/DREAM/code.html and as supplementary file online.Contact: gyuanfan@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Johan Hjort: The Canadian Fisheries Expedition, International Scientific Networks, and the challenge of modernization
Authors: Hubbard Jennifer 
Published: June 2014

Abstract
By leading the Canadian Fisheries Expedition of 1914–1915 Johan Hjort took the opportunity to do far more than just survey herring, other fish stocks, and the hydrography of Canadian Atlantic waters. He also attempted to improve the backward fish-processing technologies used in the local fisheries, an agenda blocked by the Canadian government. Hjort did succeed markedly, however, in introducing Canadian scientists to the International Council for the Exploration of the Sea's new scientific methods for fisheries research. He and his colleagues offered training in the new dynamic oceanography as well as population demographic studies and biometrics for studying fish populations, races, and other units. His extroverted leadership-initiated lasting linkages between Canadian and Scandinavian scientists, and created an international network of fisheries biologists.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
Authors: Banovich Nicholas E. , Lan Xun , McVicker Graham , van de Geijn Bryce , Degner Jacob F. , Blischak John D. , Roux Julien , Pritchard Jonathan K. , Gilad Yoav 
Published: June 2014

AbstractDNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ∼300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915cismethylation QTLs (meQTLs)—i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.Author SummaryDNA methylation is an important epigenetic mark that contributes to many biological processes including the regulation of gene expression. Genetic variation has been associated with quantitative changes in DNA methylation (meQTLs). We identified thousands of meQTLs using an assay that allowed us to measure methylation levels at around 300 thousand cytosines. We found that meQTLs are enriched with loci that is also associated with quantitative changes in gene expression, DNase I hypersensitivity, PolII occupancy, and a number of histone marks. This suggests that many molecular events are likely regulated in concert. Finally, we found that changes in transcription factor binding as well as transcription factor abundance are associated with changes in DNA methylation near transcription factor binding sites. This work contributes to our understanding of the regulation of DNA methylation in the larger context of gene regulatory landscape.
Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state
Authors: Katz Yarden , Li Feifei , Lambert Nicole , Sokol Ethan , Tam Wai-Leong , Cheng Albert W. , Airoldi Edoardo M. , Lengner Christopher J. , Gupta Piyush B. , Yu Zhengquan , Jaenisch Rudolf , Burge Christopher B. 
Published: June 2014

SummaryThe conserved Musashi (Msi) family of RNA binding proteins are expressed in stem/progenitor and cancer cells, but mostly absent from differentiated cells, consistent with a role in cell state regulation. We found that Msi genes are rarely mutated but frequently overexpressed in human cancers, and associated with an epithelial-luminal cell state. Using ribosome footprint profiling and RNA-seq analysis of genetic mouse models in neuronal and mammary cell types, we found that Msis regulate translation of genes implicated in epithelial cell biology and epithelial-to-mesenchymal transition (EMT) and promote an epithelial splicing pattern. Overexpression of Msi proteins inhibited translation of genes required for EMT, including Jagged1, and repressed EMT in cell culture and in mammary glandin vivo, while knockdown in epithelial cancer cells led to loss of epithelial identity. Our results show that mammalian Msi proteins contribute to an epithelial gene expression program and promote an epithelial-luminal state in both neural and breast cell types.HighlightsMsi proteins bind UAG motifs in vitro and in 3’ UTRs of mRNAsMsi proteins are markers of epithelial state in brain and breast tumors, and cell linesThe Notch regulatorJag1mRNA is bound and translationally repressed by MsiMsi overexpression represses EMT in the mammary glandin vivo
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family
Authors: Roppolo Daniele , Boeckmann Brigitte , Pfister Alexandre , Boutet Emmanuel , Rubio Maria C. , Dénervaud-Tendon Valérie , Vermeer Joop E.M. , Gheyselinck Jacqueline , Xenarios Ioannis , Geldner Niko 
Published: June 2014

AbstractCASPARIAN STRIP MEMBRANE DOMAIN PROTEINS (CASPs) are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. CASPs show high stability in their membrane domain, which presents all the hallmarks of a membrane scaffold. Here, we characterized the large family of CASP-like (CASPL) proteins. CASPLs were found in all major divisions of land plants as well as in green algae; homologs outside of the plant kingdom were identified as members of the MARVEL protein family. When ectopically expressed in the endodermis, most CASPLs were able to integrate the CASP membrane domain, which suggests that CASPLs share with CASPs the propensity to form transmembrane scaffolds. Extracellular loops are not necessary for generating the scaffold, since CASP1 was still able to localize correctly when either one of the extracellular loops was deleted. The CASP first extracellular loop was found conserved in euphyllophytes but absent in plants lacking Casparian strips, an observation that may contribute to the study of Casparian strip and root evolution. In Arabidopsis (Arabidopsis thaliana), CASPL showed specific expression in a variety of cell types, such as trichomes, abscission zone cells, peripheral root cap cells, and xylem pole pericycle cells.
REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis
Authors: Zhao Yusheng , Xie Shaojun , Li Xiaojie , Wang Chunlei , Chen Zhongzhou , Lai Jinsheng , Gong Zhizhong 
Published: June 2014

Abstract
In Arabidopsis thaliana, active DNA demethylation is initiated by the DNA glycosylase REPRESSOR OF SILENCING1 (ROS1) and its paralogs DEMETER, DEMETER-LIKE2 (DML2), and DML3. How these demethylation enzymes are regulated, however, is poorly understood. Here, using a transgenic Arabidopsis line harboring the stress-inducible RESPONSIVE TO DEHYDRATION29A (RD29A) promoter–LUCIFERASE (LUC) reporter gene and the cauliflower mosaic virus 35S promoter (35S)–NEOMYCIN PHOSPHOTRANSFERASE II (NPTII) antibiotic resistance marker gene, we characterize a ROS locus, ROS5, that encodes a protein in the small heat shock protein family. ROS5 mutations lead to the silencing of the 35S-NPTII transgene due to DNA hypermethylation but do not affect the expression of the RD29A-LUC transgene. ROS5 physically interacts with the histone acetyltransferase ROS4/INCREASED DNA METHYLATION1 (IDM1) and is required to prevent the DNA hypermethylation of some genes that are also regulated by ROS1 and IDM1. We propose that ROS5 regulates DNA demethylation by interacting with IDM1, thereby creating a chromatin environment that facilitates the binding of ROS1 to erase DNA methylation.
Natural enemy ecology: comparing the effects of predation risk, infection risk and disease on host behaviour
Authors: Preston Daniel L. , Boland Clara E. , Hoverman Jason T. , Johnson Pieter T. J. 
Published: June 2014

SummaryGrowing interest in unifying the field of natural enemy ecology has revealed similarities between predation and parasitism. In parallel with predation, parasite infection – and even the threat of infection – can alter host traits and indirectly affect community interactions. Nonetheless, few studies have considered multiple mechanisms of natural enemy‐induced behavioural alteration in parallel (e.g. effects before and after enemy contact) or the factors that drive variation in behavioural responses.We first evaluated how the threat of infection by a virulent trematode (Ribeiroia ondatrae) compared to the well studied risk of predation in triggering inducible defences in amphibian hosts, prior to direct contact with either enemy. We then evaluated five separate factors that influenced the magnitude of parasite‐induced behavioural changes after successful transmission.In both the laboratory and an outdoor mesocosm experiment, we found no evidence that tadpoles of two species (Pseudacris regillaandAnaxyrus boreas) altered their activity levels in response to chemical cues from uninfected host snails, trematode‐infected snails, or from conspecifics actively becoming infected. In contrast, tadpoles sharply reduced their activity in response to lethal predation risks posed by caged dragonfly larvae.After infection, however,Ribeiroiacaused strong decreases in host activity and escape distance that correlated positively with infection intensity and negatively with host size and developmental stage. Five days after infection with a one‐time pulse exposure, hosts recovered to near‐normal activity levels. Hosts exposed to a chronic daily exposure of equal intensity, however, continued to decrease activity. UnlikeRibeiroia, two less virulent trematodes had no detectable effects on host behaviour.Our results highlight key distinctions between predation and parasitism. The contrasting effects prior to enemy contact may stem from the fact that unlike predation, the consequences of macroparasite infection are intensity‐dependent and unpredictable. In contrast, the strong changes in host behaviour after infection are more similar to non‐consumptive predator effects in terms of their potential influences on host fitness and community interactions.