bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of DNA methylation in hybrid vigor in
Arabidopsis thaliana
Authors: Kawanabe Takahiro , Ishikura Sonoko , Miyaji Naomi , Sasaki Taku , Wu Li Min , Itabashi Etsuko , Takada Satoko , Shimizu Motoki , Takasaki-Yasuda Takeshi , Osabe Kenji , Peacock W. James , Dennis Elizabeth S. , Fujimoto Ryo 
Published: October 2016

Significance
Hybrid vigor is an important phenomenon in basic genetics and in agricultural practice, but the bases of the superior performance of the hybrid relative to its parents in biomass and seed production remain elusive. In recent years, it has been suggested that epigenetic controls on levels of gene action are involved. Using mutants of genes involved in DNA methylation, we show that RNA polymerase IV or methyltransferase I do not contribute to the generation of the heterotic phenotype but that decrease in DNA methylation 1, a nucleosome remodeller with an effect on DNA methylation level, is required to produce a full level of hybrid vigor.
Age and Stock Analysis Using Otolith Shape in Gags from the Southern Gulf of Mexico
Authors: Renán Ximena , Montero‐Muñoz Jorge , Garza‐Pérez Joaquin R. , Brulé Thierry 
Published: October 2016

AbstractOn Campeche Bank (CB) in the southern Gulf of Mexico, Gags Mycteroperca microlepis are captured as part of a sequential multispecies fishery. Limited scientific data suggest that the Gag is the third most important commercial species in the region, contributing 21% (total weight) of the overall grouper catch. Neither age nor stock data are currently available for Gags in this region, making it impossible to determine how this species is affected by current fishing practices. Such information is vital for the CB stock since it acts as a genetic source for a mixed Gag population on the west Florida shelf through a constant unidirectional flow of larvae. The goal of this study was to generate baseline age and stock structure data for Gags on CB. Age was quantified from otoliths by counting the number of annuli (indicated by the number of opaque zones from the otolith core to the margin) in thin sections. Otolith shape was analyzed by using discrete wavelet transforms, linear otolith morphometrics, and shape indices. In each of 198 specimens, age was determined based on examination of the right sagittal otolith, and shape analysis was conducted on the left sagittal otolith. Individual age ranged from 4 to 17 years, and otolith opaque band deposition occurred annually between December and February. Using principal components analysis and linear discriminant analysis, two distinct groups were identified (discrimination success = 98%), indicating the presence of substructure in the CB stock of Gags. Otolith analysis clearly assisted in achieving a better understanding of the CB Gag stock and in identifying the complexity within the stock, demonstrating that otolith analysis is a useful tool in characterizing fish populations. The study results highlight the urgent need for Gag stock assessment in this region and for the application of a cautious approach to fishery management given the immense gaps in biological data for this species.Received January 13, 2016; accepted July 18, 2016 Published online October 7, 2016
Development of Habitat Suitability Indices for the Candy Darter, with Cross‐Scale Validation across Representative Populations
Authors: Dunn Corey G. , Angermeier Paul L. 
Published: October 2016

AbstractUnderstanding relationships between habitat associations for individuals and habitat factors that limit populations is a primary challenge for managers of stream fishes. Although habitat use by individuals can provide insight into the adaptive significance of selected microhabitats, not all habitat parameters will be significant at the population level, particularly when distributional patterns partially result from habitat degradation. We used underwater observation to quantify microhabitat selection by an imperiled stream fish, the Candy Darter Etheostoma osburni, in two streams with robust populations. We developed multiple‐variable and multiple‐life‐stage habitat suitability indices (HSIs) from microhabitat selection patterns and used them to assess the suitability of available habitat in streams where Candy Darter populations were extirpated, localized, or robust. Next, we used a comparative framework to examine relationships among (1) habitat availability across streams, (2) projected habitat suitability of each stream, and (3) a rank for the likely long‐term viability (robustness) of the population inhabiting each stream. Habitat selection was characterized by ontogenetic shifts from the low‐velocity, slightly embedded areas used by age‐0 Candy Darters to the swift, shallow areas with little fine sediment and complex substrate, which were used by adults. Overall, HSIs were strongly correlated with population rank. However, we observed weak or inverse relationships between predicted individual habitat suitability and population robustness for multiple life stages and variables. The results demonstrated that microhabitat selection by individuals does not always reflect population robustness, particularly when based on a single life stage or season, which highlights the risk of generalizing habitat selection that is observed during nonstressful periods or for noncritical resources. These findings suggest that stream fish managers may need to be cautious when implementing conservation measures based solely on observations of habitat selection by individuals and that detailed study at the individual and population levels may be necessary to identify habitat that limits populations.Received March 30, 2016; accepted July 19, 2016Published online October 7, 2016
Hospitalization event notifications and reductions in readmissions of Medicare fee-for-service beneficiaries in the Bronx, New York
Authors: Unruh Mark Aaron , Jung Hye-Young , Kaushal Rainu , Vest Joshua R 
Published: October 2016

Objective: Follow-up with a primary care provider after hospital discharge has been associated with a reduced likelihood of readmission. However, primary care providers are frequently unaware of their patients’ hospitalizations. Event notification may be an effective tool for reducing readmissions by notifying primary care providers when their patients have been admitted to and discharged from a hospital.Materials and Methods: We examined the effect of an event notification system on 30-day readmissions in the Bronx, New York. The Bronx has among the highest readmission rates in the country and is a particularly challenging setting to improve care due to the low socioeconomic status of the county and high rates of poor health behaviors among its residents. The study cohort included 2559 Medicare fee-for-service beneficiaries associated with 14 141 hospital admissions over the period January 2010 through June 2014. Linear regression models with beneficiary-level fixed-effects were used to estimate the impact of event notifications on readmissions by comparing the likelihood of rehospitalization for a beneficiary before and after event notifications were active.Results: The unadjusted 30-day readmission rate when event notifications were not active was 29.5% compared to 26.5% when alerts were active. Regression estimates indicated that active hospitalization alert services were associated with a 2.9 percentage point reduction in the likelihood of readmission (95% confidence interval: −5.5, −0.4).Conclusions: Alerting providers through event notifications may be an effective tool for improving the quality and efficiency of care among high-risk populations.
Impact of commercial computerized provider order entry (CPOE) and clinical decision support systems (CDSSs) on medication errors, length of stay, and mortality in intensive care units: a systematic review and meta-analysis
Authors: Prgomet Mirela , Li Ling , Niazkhani Zahra , Georgiou Andrew , Westbrook Johanna I 
Published: October 2016

Objective: To conduct a systematic review and meta-analysis of the impact of commercial computerized provider order entry (CPOE) and clinical decision support systems (CDSSs) on medication errors, length of stay (LOS), and mortality in intensive care units (ICUs).
Methods: We searched for English-language literature published between January 2000 and January 2016 using Medline, Embase, and CINAHL. Titles and abstracts of 586 unique citations were screened. Studies were included if they: (1) reported results for an ICU population; (2) evaluated the impact of CPOE or the addition of CDSSs to an existing CPOE system; (3) reported quantitative data on medication errors, ICU LOS, hospital LOS, ICU mortality, and/or hospital mortality; and (4) used a randomized controlled trial or quasi-experimental study design.
Results: Twenty studies met our inclusion criteria. The transition from paper-based ordering to commercial CPOE systems in ICUs was associated with an 85% reduction in medication prescribing error rates and a 12% reduction in ICU mortality rates. Overall meta-analyses of LOS and hospital mortality did not demonstrate a significant change.
Discussion and Conclusion: Critical care settings, both adult and pediatric, involve unique complexities, making them vulnerable to medication errors and adverse patient outcomes. The currently limited evidence base requires research that has sufficient statistical power to identify the true effect of CPOE implementation. There is also a critical need to understand the nature of errors arising post-CPOE and how the addition of CDSSs can be used to provide greater benefit to delivering safe and effective patient care.
Varieties of Voice-Hearing: Psychics and the Psychosis Continuum
Authors: Powers Albert R. , Kelley Megan S. , Corlett Philip R. 
Published: October 2016

Abstract
Hearing voices that are not present is a prominent symptom of serious mental illness. However, these experiences may be common in the non-help-seeking population, leading some to propose the existence of a continuum of psychosis from health to disease. Thus far, research on this continuum has focused on what is impaired in help-seeking groups. Here we focus on protective factors in non-help-seeking voice-hearers. We introduce a new study population: clairaudient psychics who receive daily auditory messages. We conducted phenomenological interviews with these subjects, as well as with patients diagnosed with a psychotic disorder who hear voices, people with a diagnosis of a psychotic disorder who do not hear voices, and matched control subjects (without voices or a diagnosis). We found the hallucinatory experiences of psychic voice-hearers to be very similar to those of patients who were diagnosed. We employed techniques from forensic psychiatry to conclude that the psychics were not malingering. Critically, we found that this sample of non-help-seeking voice hearers were able to control the onset and offset of their voices, that they were less distressed by their voice-hearing experiences and that, the first time they admitted to voice-hearing, the reception by others was much more likely to be positive. Patients had much more negative voice-hearing experiences, were more likely to receive a negative reaction when sharing their voices with others for the first time, and this was subsequently more disruptive to their social relationships. We predict that this sub-population of healthy voice-hearers may have much to teach us about the neurobiology, cognitive psychology and ultimately the treatment of voices that are distressing.
The PhytoClust Tool for Metabolic Gene Clusters Discovery in Plant Genomes
Authors: Töpfer Nadine , Fuchs Lisa-Maria , Aharoni Asaph 
Published: October 2016

AbstractThe existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs computational approaches are essential. Here we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MBCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism.
Head and gaze tracking of unrestrained marmosets
Authors: Turesson Hjalmar K. , Conceição Thamiris Botelho Ribeiro , Ribeiro Sidarta 
Published: October 2016

AbstractNew technologies for manipulating and recording the nervous system allow us to perform unprecedented experiments. However, the influence of our experimental manipulations on psychological processes must be inferred from their effects on behavior. Today, quantifying behavior has become the bottleneck for large-scale, high-throughput, experiments. The method presented here addresses this issue by using deep learning algorithms for video-based animal tracking. Here we describe a reliable automatic method for tracking head position and orientation from simple video recordings of the common marmoset (Callithrix jacchus). This method for measuring marmoset behavior allows for the estimation of gaze within foveal error, and can easily be adapted to a wide variety of similar tasks in biomedical research. In particular, the method has great potential for the simultaneous tracking of multiple marmosets to quantify social behaviors.
An efficient field and laboratory workflow for plant phylotranscriptomic projects1
Authors: Yang Ya , Moore Michael J. , Brockington Samuel F. , Timoneda-Monfort Alfonso , Feng Tao , Marx Hannah E. , Walker Joseph F. , Smith Stephen A. 
Published: October 2016

ABSTRACTPremise of the study:We describe a field and lab workflow developed for plant phylotranscriptomic projects, involving field collected cryogenic tissues, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation.Methods and Results:216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens and were subjected to RNA extraction, stranded mRNA library preparation and sequencing on Illumina HiSeq platforms. These include difficult mucilaginous tissues such as those of Cactaceae and Droseraceae.Conclusions:Our workflow is not only cost effective (~$270 per sample, as of August 2016, from tissue to reads) and time efficient (~5 hours a sample including all lab work and sample curation), but has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds.
Genetic Information Relationship Network (GIRN): A Force-directed graphing tool for gene expression analysis
Authors: Rondeau Gaelle , Welsh John 
Published: October 2016

AbstractWe present a web-based tool, Genetic Information Relationship Network (GIRN), for mapping genes to a global protein interaction network for humans, and for further annotating this map with gene ontology, pathway, disease, and user-generated terms. These annotations can be adjusted according to enrichment within a subset of genes. Additionally, drugs that interact with genes in the subset can be added to the graph. The maps are force-directed graphs in which highly connected nodes tend toward the center, and highly interconnected nodes tend toward each other. Icons of different shapes and colors are employed to indicate whether the node represents a protein, a gene, or one of the various types of annotation. Coordinated interaction of genes and functional inference can be identified by visual inspection. Each node in the graph is associated with a menu of links to external data sources. Collectively, these tools provide an efficient portal to gene-associated public data for any group of genes specified by the user. The site can be found atwww.voxvill.org/relnet.
Atmospheric deposition exposes pandas to toxic pollutants
Authors: Chen Yi-ping , Zheng Ying-juan , Liu Qiang , Song Yi , An Zhi-sheng , Ma Qing-yi , Ellison Aaron M. 
Published: October 2016

AbstractThe giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas were exposed to toxins in their diet of bamboo, but the ultimate origin of these toxins is unknown. Here we show that atmospheric deposition is the origin of heavy metals and persistent organic pollutants (POPs) in the diets of captive and wild Qinling giant pandas. Atmospheric deposition averaged 115 and 49 g⋅m−2⋅yr−1at China’s Shaanxi Wild Animal Research Center (SWARC) and Foping National Nature Reserve (FNNR), respectively. Atmospheric deposition of heavy metals (As, Cd, Cr, Pb, Hg, Co, Cu, Zn, Mn and Ni) and POPs at SWARC was higher than at FNNR. Soil concentrations of the aforementioned heavy metals other than As and Zn also were significantly higher at SWARC than at FNNR. We conclude that efforts to conserve the Qinling subspecies of panda may be compromised by air pollution attendant to China’s economic development. Improvement of air quality and reductions of toxic emissions are urgently required to protect China’s iconic species.
Reproductive Isolation through Experimental Manipulation of Sexually Antagonistic Coevolution inDrosophila melanogaster
Authors: Zeeshan Ali Syed , Chatterjee Martik , Samant Manas Arun , Prasad Nagaraj Guru 
Published: October 2016

AbstractPromiscuity can drive the evolution of sexual conflict before and after mating occurs. Post-mating, the male ejaculate can selfishly manipulate female physiology leading to a chemical arms race between the sexes. Theory suggests that drift and sexually antagonistic coevolution can cause allopatric populations to evolve different chemical interactions between the sexes, thereby leading to postmating reproductive barriers and speciation. There is, however, little empirical evidence supporting this form of speciation. We tested this theory by creating an experimental evolutionary model ofDrosophila melanogasterpopulations undergoing different levels of interlocus sexual conflict. We found that allopatric populations under elevated sexual conflict show assortative mating indicating premating reproductive isolation. Further, these allopatric populations also show reduced copulation duration and sperm defense ability when mating happens between individuals between individuals across populations compared to that within the same population, indicating postmating prezygotic isolation. Sexual conflict can cause reproductive isolation in allopatric populations through the coevolution of chemical (postmating prezygotic) as well as behavioural (premating) interaction between the sexes. Thus, to our knowledge, we provide the first comprehensive evidence of postmating (as well as premating) reproductive isolation due to sexual conflict.
Control mechanisms for stochastic biochemical systems via computation of reachable sets
Authors: Lakatos Eszter , Stumpf Michael P.H. 
Published: October 2016

AbstractControlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic biology. Molecular processes, however, are notoriously noisy and frequently non-linear. We present an approach to studying the impact of control measures on motifs of molecular interactions, that addresses the problems faced in biological systems: stochasticity, parameter uncertainty, and non-linearity. We show that our reachability analysis formalism can describe the potential behaviour of biological (naturally evolved as well as engineered) systems, and provides a set of bounds on their dynamics at the level of population statistics: for example, we can obtain the possible ranges of means and variances of mRNA and protein expression levels, even in the presence of uncertainty about model parameters.
Genome-Wide Association Study of Ionomic Traits on Diverse Soybean Populations from Germplasm Collections
Authors: Ziegler Greg , Nelson Randall , Granada Stephanie , Krishnan Hari B. , Gillman Jason D. , Baxter Ivan 
Published: October 2016

AbstractThe elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate SNPs controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
Considerations and complications of mapping small RNA libraries to transposable elements
Authors: Bousios Alexandros , Gaut Brandon S. , Darzentas Nikos 
Published: October 2016

ABSTRACTThe advent of high-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. Often coupled with the availability of fully sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), and especially when such genomes are large as is often the case in plants. Here, to shed light on the challenges of mapping sRNAs to TEs, we focus on the 2,300Mb maize genome, of which >85% is derived from TEs. We compare various methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiple mapping sRNAs, and the selection among different types of sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and explore and contrast their effect on low copy regions (exons) and other popular HTS data (RNA-seq). Finally, based on our analysis, we share a series of take-home messages to help guide TE epigenetic studies specifically, but our conclusions may also apply to any work that involves mapping and analysis of HTS data.