bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaption of the global test idea to proteomics data with missing values
Authors: Jung Klaus , Dihazi Hassan , Bibi Asima , Dihazi Gry H. , Beißbarth Tim 
Published: February 2014

AbstractMotivation: Global test procedures are frequently used in gene expression analysis to study the relationship between a functional subset of RNA transcripts and an experimental group factor. However, these procedures have been rarely used for the analysis of high-throughput data from other sources, such as proteome expression data. The main difficulties in transferring global test procedures from genomics to proteomics data are the more complicated way of obtaining functional annotations and the handling of missing values in some types of proteomics data.Results: We propose a simple mixed linear model in combination with a permutation procedure and missing values imputation to conduct global tests in proteomics experiments. This new approach is motivated by protein expression data obtained by means of 2-D gel electrophoresis within a mouse experiment of our current research. A simulation study yielded that power and testing level of the mixed model alone can be affected by missing values in the dataset. Imputation of missing values was able to correct for a bias in some simulation settings. Our new approach provides the possibility to rank Gene Ontology (GO) terms associated with protein sets. It is also helpful in the case in which a specific protein is represented by multiple spots on a 2-D gel by considering these spots also as a protein set. Analysis of our data points at correlations between the deficiency of the protein ‘calreticulin’ and protein sets related to biological processes in the heart muscle.Availability and implementation: Our proposed approach is included in the R-package ‘RepeatedHighDim’, which already contains a global test procedure for gene expression data. The package can be retrieved from http://cran.r-project.org/.Contact: klaus.jung@ams.med.uni-goettingen.de
Bayesian joint analysis of heterogeneous genomics data
Authors: Ray Priyadip , Zheng Lingling , Lucas Joseph , Carin Lawrence 
Published: February 2014

AbstractSummary: A non-parametric Bayesian factor model is proposed for joint analysis of multi-platform genomics data. The approach is based on factorizing the latent space (feature space) into a shared component and a data-specific component with the dimensionality of these components (spaces) inferred via a beta-Bernoulli process. The proposed approach is demonstrated by jointly analyzing gene expression/copy number variations and gene expression/methylation data for ovarian cancer patients, showing that the proposed model can potentially uncover key drivers related to cancer.Availability and implementation: The source code for this model is written in MATLAB and has been made publicly available at https://sites.google.com/site/jointgenomics/Contact: catherine.ll.zheng@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
Antibiotic stress-induced modulation of the endoribonucleolytic activity of RNase III and RNase G confers resistance to aminoglycoside antibiotics in Escherichia coli
Authors: Song Wooseok , Kim Yong-Hak , Sim Se-Hoon , Hwang Soonhye , Lee Jung-Hyun , Lee Younghoon , Bae Jeehyeon , Hwang Jihwan , Lee Kangseok 
Published: February 2014

Abstract
Here, we report a resistance mechanism that is induced through the modulation of 16S ribosomal RNA (rRNA) processing on the exposure of Escherichia coli cells to aminoglycoside antibiotics. We observed decreased expression levels of RNase G associated with increased RNase III activity on rng mRNA in a subgroup of E. coli isolates that transiently acquired resistance to low levels of kanamycin or streptomycin. Analyses of 16S rRNA from the aminoglycoside-resistant E. coli cells, in addition to mutagenesis studies, demonstrated that the accumulation of 16S rRNA precursors containing 3–8 extra nucleotides at the 5’ terminus, which results from incomplete processing by RNase G, is responsible for the observed aminoglycoside resistance. Chemical protection, mass spectrometry analysis and cell-free translation assays revealed that the ribosomes from rng-deleted E. coli have decreased binding capacity for, and diminished sensitivity to, streptomycin and neomycin, compared with wild-type cells. It was observed that the deletion of rng had similar effects in Salmonella enterica serovar Typhimurium strain SL1344. Our findings suggest that modulation of the endoribonucleolytic activity of RNase III and RNase G constitutes a previously uncharacterized regulatory pathway for adaptive resistance in E. coli and related gram-negative bacteria to aminoglycoside antibiotics.
Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes
Authors: Candaele Jasper , Demuynck Kirin , Mosoti Douglas , Beemster Gerrit T.S. , Inzé Dirk , Nelissen Hilde 
Published: February 2014

Abstract
DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 5′ and 3′ regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.
Insights into the Maize Pan-Genome and Pan-Transcriptome
Authors: Hirsch Candice N. , Foerster Jillian M. , Johnson James M. , Sekhon Rajandeep S. , Muttoni German , Vaillancourt Brieanne , Peñagaricano Francisco , Lindquist Erika , Pedraza Mary Ann , Barry Kerrie , de Leon Natalia , Kaeppler Shawn M. , Buell C. Robin 
Published: February 2014

AbstractGenomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
GLUTELIN PRECURSOR ACCUMULATION3Encodes a Regulator of Post-Golgi Vesicular Traffic Essential for Vacuolar Protein Sorting in Rice Endosperm
Authors: Ren Yulong , Wang Yihua , Liu Feng , Zhou Kunneng , Ding Yu , Zhou Feng , Wang Ying , Liu Kai , Gan Lu , Ma Weiwei , Han Xiaohua , Zhang Xin , Guo Xiuping , Wu Fuqing , Cheng Zhijun , Wang Jiulin , Lei Cailin , Lin Qibing , Jiang Ling , Wu Chuanyin , Bao Yiqun , Wang Haiyang , Wan Jianmin 
Published: February 2014

AbstractIn seed plants, a major pathway for sorting of storage proteins to the protein storage vacuole (PSV) depends on the Golgi-derived dense vesicles (DVs). However, the molecular mechanisms regulating the directional trafficking of DVs to PSVs remain largely elusive. Here, we report the functional characterization of the rice (Oryza sativa) glutelin precursor accumulation3 (gpa3) mutant, which exhibits a floury endosperm phenotype and accumulates excess proglutelins in dry seeds. Cytological and immunocytochemistry studies revealed that in the gpa3 mutant, numerous proglutelin-containing DVs are misrouted to the plasma membrane and, via membrane fusion, release their contents into the apoplast to form a new structure named the paramural body. Positional cloning of GPA3 revealed that it encodes a plant-specific kelch-repeat protein that is localized to the trans-Golgi networks, DVs, and PSVs in the developing endosperm. In vitro and in vivo experiments verified that GPA3 directly interacts with the rice Rab5a-guanine exchange factor VPS9a and forms a regulatory complex with Rab5a via VPS9a. Furthermore, our genetic data support the notion that GPA3 acts synergistically with Rab5a and VPS9a to regulate DV-mediated post-Golgi traffic in rice. Our findings provide insights into the molecular mechanisms regulating the plant-specific PSV pathway and expand our knowledge of vesicular trafficking in eukaryotes.
Asherman syndrome in a Danish population
Authors: Kjer Jens J. 
Published: February 2014

AbstractIntrauterine adhesions (Asherman syndrome) are rare and mainly seen after delivery or abortion in the presence of retained placental tissue. This descriptive study aimed to identify common risk factors for intrauterine adhesions. In a 10‐year period 61 women were identified with intrauterine adhesions. The pathology was suspected from symptoms, ultrasonography or on hysterosalpingography, but a final diagnosis could only be given after hysteroscopy. There was no definite evidence regarding methods for prevention and treatment of the disorder. It seems, however, that a conservative approach to curettage, hysteroscopic removal of retained tissue, and the use of distending media are important, together with gentle tissue handling when such procedures are required.
Antisecretory factor effectively and safely stops childhood diarrhoea: a placebo‐controlled, randomised study
Authors: Zaman Shakila , Aamir Khalida , Lange Stefan , Jennische Eva , Silfverdal Sven‐Arne , Hanson Lars Å 
Published: February 2014

AbstractAimWe studied the response to high doses of egg yolk containing antisecretory factor (B221®, Salovum®) in young children with acute diarrhoea, presenting to the Children's Hospital, Lahore, Pakistan.MethodsIn a randomised, placebo‐controlled trial, 36 children aged 7 to 60 months with acute diarrhoea of unknown aetiology, with mild‐to‐moderate dehydration, were randomised to the Salovum® or placebo groups. Initially, 16 grams of Salovum® or ordinary egg yolk (placebo) mixed in oral rehydration salts was given, followed by 8 g every 5 h until recovery. The number and consistency of stools were recorded.ResultsThe two groups were comparable in age, gender, duration of diarrhoea, hydration and nutritional status, although the proportion with watery stools was higher in the Salovum® group (p = 0.04). Reduction in the frequency of stools was seen at 7 versus 18 h (p < 0.0001) and normalising of stool consistency was 10 versus 18 h, p < 0.03) in the Salovum® and placebo groups. The overall effect was 35 versus 70 h in the two groups (p = 0.001). No side effects were reported.ConclusionHigh doses of AF in the form of Salovum® effectively and safely reduce childhood diarrhoea of a likely broad aetiology.
Feeling Good, Happy, and Proud: A Meta‐Analysis of Positive Ethnic–Racial Affect and Adjustment
Authors: Rivas‐Drake Deborah , Syed Moin , Umaña‐Taylor Adriana , Markstrom Carol , French Sabine , Schwartz Seth J. , Lee Richard ,   Ethnic and Racial Identity in the 21st Century Study Group
Published: February 2014

One point of intersection in ethnic and racial identity research is the conceptual attention paid to how positively youth feel about their ethnicity or race, or positive ethnic–racial affect. This article reports results of a series of meta‐analyses based on 46 studies of this dimension and psychosocial, academic, and health risk outcomes among ethnic and racial minority youth. The overall pattern of results suggests that positive ethnic–racial affect exhibited small to medium associations (r range = |.11| to |.37|) with depressive symptoms, positive social functioning, self‐esteem, well‐being, internalizing, externalizing, academic achievement, academic attitudes, and health risk outcomes. Implications for theory and research about the role of positive ethnic–racial affect among youth growing up in an increasingly diverse society are discussed.
Validating a script concordance test for assessing neurological localization and emergencies
Authors: Tan K. , Tan N. C. K. , Kandiah N. , Samarasekera D. , Ponnamperuma G. 
Published: February 2014

Background and purposeClinical judgment is the ability to weigh clinical information and make decisions under conditions of uncertainty. Although neurological localization (NL) and neurological emergencies (NE) present such uncertainties, no validated method is reported to assess these decision‐making skills. A script concordance test (SCT) was designed and validated to assess clinical judgment in NL and NE.MethodsOur SCT comprised 14 clinical scenarios (53 questions). Candidates picked the response they considered the best for the questions in each scenario. Undergraduates and internal medicine residents completed the SCT; their responses were scored against the scoring key derived from an expert panel of accredited neurologists. Scores were expressed as a percentage of the maximum score.ResultsMean total scores for undergraduates (n = 52), residents (n = 37) and experts (n = 15) were 61.0 ± 0.9, 68.3 ± 1.1 and 76.6 ± 1.1 (mean ± standard error of the mean, P < 0.001). Mean scores for undergraduates, residents and experts were 59.3 ± 1.1, 66.4 ± 1.4 and 76.1 ± 1.8 (P < 0.001) for NL, and 62.9 ± 1.3, 70.4 ± 1.3 and 77.2 ± 1.6 (P < 0.001) for NE. Senior residents scored higher than junior residents (postgraduate years 2–5 versus postgraduate year 1, 69.7 ± 1.4 vs. 65.3 ± 1.1, P = 0.035). The higher scores with increasing clinical experience supports the construct validity of the SCT. The SCT showed acceptable reliability (G coefficient 0.74 ± 0.05).ConclusionsOur SCT is validated to reliably assess NL and NE in undergraduate and postgraduate learners; it is generalizable and feasible. It has potential as a valuable adjunct assessment tool for clinical judgment. Future plans to design SCTs to evaluate other topics in clinical neurology, as a multi‐center study, are under way.
Ending overfishing while catching more fish
Authors: Zhou Shijie , Smith Anthony DM , Knudsen E Eric 
Published: February 2014

AbstractThe world's seas and oceans are a vital source of animal protein from fishing and a major contributor to global food security. It has been argued that global wild‐catch production has reached its limit, and there is concern that many species are overfished. Concerns are also mounting about the state of marine ecosystems and the ecological impacts of fishing on them, with increasing efforts to protect marine biodiversity. Fisheries appear to be at an impasse – demand for seafood is rising but so is concern about the impacts of fishing. However, through a simple analysis, we show that global exploitation rates are well below long‐term sustainable levels at a whole ecosystem level. The oceans can support considerably higher sustainable catch than currently harvested. Overfishing has happened but only to a small fraction of species as a result of intensive and selective fishing. Shifting fishing effort away from highly targeted stocks towards currently underutilized species would reduce pressure on overfished species, result in fewer adverse ecosystem effects of fishing and increase overall fisheries production. This shift requires significant changes to our views about seafood, particularly in the developed world. We suggest ways in which this paradigm shift could happen and the range of expertise that would be required to achieve higher global yields with less ecological impact.
Global warming will reshuffle the areas of high prevalence and richness of three genera of avian blood parasites
Authors: Pérez‐Rodríguez Antón , de la Hera Iván , Fernández‐González Sofía , Pérez‐Tris Javier 
Published: February 2014

AbstractThe importance of parasitism for host populations depends on local parasite richness and prevalence: usually host individuals face higher infection risk in areas where parasites are most diverse, and host dispersal to or from these areas may have fitness consequences. Knowing how parasites are and will be distributed in space and time (in a context of global change) is thus crucial from both an ecological and a biological conservation perspective. Nevertheless, most research articles focus just on elaborating models of parasite distribution instead of parasite diversity. We produced distribution models of the areas where haemosporidian parasites are currently highly diverse (both at community and at within‐host levels) and prevalent among Iberian populations of a model passerine host: the blackcapSylvia atricapilla; and how these areas are expected to vary according to three scenarios of climate change. On the basis of these models, we analysed whether variation among populations in parasite richness or prevalence are expected to remain the same or change in the future, thereby reshuffling the geographic mosaic of host‐parasite interactions as we observe it today. Our models predict a rearrangement of areas of high prevalence and richness of parasites in the future, withHaemoproteusandLeucocytozoonparasites (today the most diverse genera in blackcaps) losing areas of high diversity andPlasmodiumparasites (the most virulent ones) gaining them. Likewise, the prevalence of multiple infections and parasite infracommunity richness would be reduced. Importantly, differences among populations in the prevalence and richness of parasites are expected to decrease in the future, creating a more homogeneous parasitic landscape. This predicts an altered geographic mosaic of host‐parasite relationships, which will modify the interaction arena in which parasite virulence evolves.
A commentary on ‘Mineral soil carbon fluxes in forests and implications for carbon balance assessments’: a deeper look at the data
Authors: Hoover Coeli M. , Heath Linda S. 
Published: February 2014

AbstractForestry practitioners contacted us with their concerns about a recent review article by Buchholz T, Friedland AJ, Hornig CE, Keeton WS, Zanchi G, Nunery J (2013) GCB Bioenergy who questioned the way soil carbon is treated in many models and protocols, and indicated that an increasing number of research studies showed meaningful soil organic carbon (SOC) loss as a result of forest management. We revisit the major studies cited in the review and present a more complete look at the results, consistently treat forest floor carbon as a separate pool, discuss differences in interpretation, and suggest opportunities to advance the state of knowledge regarding SOC and forest carbon accounting. Overall, we conclude that the literature continues to support the current default assumption of little or no change in mineral SOC when sound forest management practices are followed.
Artificial Sinks: Opportunities and Challenges for Managing Offsite Nitrogen Losses
Authors: Gold Arthur J. , Addy Kelly , David Mark B. , Schipper Louis A. , Needelman Brian A. 
Published: February 2014

AbstractAdvanced control measures are needed after nitrogen (N) leaves agricultural fields and begins to flow through a catchment. Bioreactors – simple, wood‐chip filled trenches – and constructed wetlands afford additional treatment to reduce N from agricultural lands, but their success requires informed adoption and placement. Rates of N removal in field studies of bioreactors vary based on carbon substrate, hydrologic setting, temperature, N loading and hydraulic residence time. From limited measures in constructed wetlands, N removal can be substantial and influenced by seasonality. Additional research is needed to understand uncertainty and variability associated with these systems. Further synthesis of data from research and demonstration sites combined with geospatial tools will help guide the design and siting of these systems at regional and local scales. Professional and student training and web‐based data information exchange will advance the adoption and strategic placement of appropriate bioreactor and constructed wetland designs to remove edge‐of‐field N contributions.
Texas High Plains Initiative for Strategic and Innovative Irrigation Management and Conservation
Authors: Weinheimer Justin , Johnson Phillip , Mitchell Donna , Johnson Jeff , Kellison Rick 
Published: February 2014

AbstractThe strategic management of irrigation applications to improve water‐use efficiency and meet economic objectives has been identified as a key factor in the conservation of water resources in the Texas High Plains region. Two field level demonstration projects have been ongoing in the Texas High Plains to evaluate advantages and disadvantages of irrigation water conservation methods. Since 2010, the North Plains Groundwater Conservation District has evaluated corn production using 12 acre‐inches or less of applied irrigation water with a goal to produce 200 bushels per acre. In the South Plains, the Texas Alliance for Water Conservation (TAWC) has worked directly with 24 producers in Hale and Floyd Counties on 29 sites over the past seven years to monitor water use, soil moisture, crop productivity and economic returns on various cropping systems on over 4,000 acres. Both of these demonstration projects take an innovative approach to strategic irrigation management that uses new technologies with an overall goal to practice water conservation while maintaining economic profitability.
The Seminole Project: Renewable Energy for Municipal Water Desalination
Authors: Rainwater Ken , Nash Phil , Song Lianfa , Schroeder John 
Published: February 2014

AbstractThis demonstration project addresses the continuing depletion of the Ogallala aquifer, the current principal source of potable ground water for much of the Texas High Plains. The project site is Seminole, Gaines County, Texas. Brackish ground water from the much deeper Santa Rosa aquifer in the Dockum group is produced and treated by reverse osmosis (RO) for potential use in the city's municipal supply. The electrical power for the well pump and RO system is assisted by a 50‐kW wind turbine. Financial support was from the City of Seminole, Department of Energy, Texas Water Development Board, Bureau of Reclamation, Texas Department of Agriculture, and State Energy Conservation Office. The Santa Rosa well and wind turbine were installed in 2011, and the RO system, turbine, well, and related infrastructure were ready for continuous operation in early 2013. A one‐year demonstration will follow to document the seasonal electricity contributions from wind and grid sources.