bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phinch: An interactive, exploratory data visualization framework for –Omic datasets
Authors: Bik Holly M. ,   Pitch Interactive Inc.
Published: October 2014

AbstractUsing environmental sequencing approaches, we now have the ability to deeply characterize biodiversity and biogeographic patterns in understudied, uncultured microbial taxa (investigations of bacteria, archaea, and microscopic eukaryotes using 454/Illumina sequencing platforms). However, the sheer volume of data produced from these new technologies requires fundamentally different approaches and new paradigms for effective data analysis. Scientific visualization represents an innovative method towards tackling the current bottleneck in bioinformatic workflows. In addition to giving researchers a unique approach for exploring large datasets, it stands to empower biologists with the ability to conduct powerful analyses without requiring a deep level of computational knowledge. Here we present Phinch, an interactive, browser-based visualization framework that can be used to explore and analyze biological patterns in high-throughput -Omic datasets. This project takes advantage of standard file formats from computational pipelines in order to bridge the gap between biological software (e.g. microbial ecology pipelines) and existing data visualization capabilities (harnessing the flexibility and scalability of technologies such as HTML5).
Fitting the Balding-Nichols model to forensic databases
Authors: Rohlfs Rori V. , Aguiar Vitor R. C. , Lohmueller Kirk E. , Castro Amanda M. , Ferreira Alessandro C. S. , Almeida Vanessa C. O. , Louro Iuri D. , Nielsen Rasmus 
Published: October 2014

AbstractLarge forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how the specific implementation of the Balding-Nichols model must be considered when applied to database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.
Ongoing worldwide homogenization of human pathogens
Authors: Poisot T , Nunn C , Morand S 
Published: October 2014

AbstractBackgroundInfectious diseases are a major burden on human population, especially in low- and middle-income countries. The increase in the rate of emergence of infectious outbreaks necessitates a better understanding of the worldwide distribution of diseases through space and time.MethodsWe analyze 100 years of records of diseases occurrence worldwide. We use a graph-theoretical approach to characterize the worldwide structure of human infectious diseases, and its dynamics over the Twentieth Century.FindingsSince the 1960s, there is a clear homogenizing of human pathogens worldwide, with most diseases expanding their geographical area. The occurrence network of human pathogens becomes markedly more connected, and less modular.InterpretationHuman infectious diseases are steadily expanding their ranges since the 1960s, and disease occurrence has become more homogenized at a global scale. Our findings emphasize the need for international collaboration in designing policies for the prevention of outbreaks.FundingT.P. is funded by a FRQNT-PBEE post-doctoral fellowship, and through a Marsden grant from the Royal Academy of Sciences of New-Zealand. Funders had no input in any part of the study.
DevoWorm: differentiation waves and computation in C. elegans embryogenesis
Authors: Alicea Bradly , McGrew Steven , Gordon Richard , Larson Stephen , Warrington Tim , Watts Mark 
Published: October 2014

AbstractDevelopment is a complex process that, under normal circumstances, proceeds in a stable and patterned fashion. Developmental morphogenesis (called embryogenesis) can tell us a great deal about the function and structure of an adult organism. One of the most important aspects of development to understand is the progression of cell division and differentiation in what will become an adult worm. This is where the DevoWorm project can both address multiple outstanding theoretical issues and provide graphical clarity to the embryogenetic process. As a representative of mosaic development,C. elegansembryogenesis is both tractable in terms of cell number and relatively well-characterized. In this paper, we will lay out a theoretical re-interpretation of embryogenesis in addition to developing an RDF-based computational framework for visualizing the results of this theoretical effort. Our theoretical efforts will ultimately involve the construction of a differentiation tree and data analyses that support the concept of differentiation waves acting to coordinate cellular differentiation and embryonic form. The differentiation tree will also feature a means to perturb development in a manner that mimics phenotypic mutagenesis. This will allow us to understand the selective variability that is inherent in biological development, but that remains so poorly understood. In tandem, these developments will allow us to construct a conceptual and computational framework which can be applied to both mosaic and regulative development.
Deep Sequencing revealed ‘Plant Like Transcripts’ in mosquitoAnopheles culicifacies: an Evolutionary Puzzle
Authors: Sharma Punita , Sharma Swati , Mishra Ashwani Kumar , Thomas Tina , Das De Tanwee , Verma Sonia , Kumari Vandana , Rohilla Suman Lata , Singh Namita , Pandey Kailash C , Dixit Rajnikant 
Published: October 2014

AbstractAs adult female mosquito’s salivary gland facilitate blood meal uptake and pathogen transmission e.g.Plasmodium, virus etc., a plethora of research has been focused to understand the mosquito-vertebrate-pathogen interactions. Despite the fact that mosquito spends longer time over nectar sugar source, the fundamental question ‘how adult female salivary gland’ manages molecular and functional relationship during sugar vs. blood meal uptake remains unanswered. Currently, we are trying to understand these molecular relationships under dual feeding conditions in the salivary glands of the mosquitoAnopheles culicifacies. During functional annotation of salivary transcriptome database, unexpectedly we discovered a cluster of salivary transcripts encoding plant like proteins. Our multiple experimental validations confirmed that Plant like transcripts (PLTs) are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide first evidence that how mosquito may have been benefited from its association with plant host and microbes. Future understanding of the underlying mechanism of the feeding associated molecular responses may provide new opportunity to control vector borne diseases.
PINOID AGC Kinases Are Necessary for Phytochrome-Mediated Enhancement of Hypocotyl Phototropism in Arabidopsis
Authors: Haga Ken , Hayashi Ken-ichiro , Sakai Tatsuya 
Published: October 2014

AbstractSeveral members of the AGCVIII kinase subfamily, which includes PINOID (PID), PID2, and WAVY ROOT GROWTH (WAG) proteins, have previously been shown to phosphorylate PIN-FORMED (PIN) auxin transporters and control the auxin flow in plants. PID has been proposed as a key component of the phototropin signaling pathway that induces phototropic responses, although the responses were not significantly impaired in the pid single and pid wag1 wag2 triple mutants. This raises questions about the functional roles of the PID family in phototropic responses. Here, we investigated hypocotyl phototropism in the pid pid2 wag1 wag2 quadruple mutant in detail to clarify the roles of the PID family in Arabidopsis (Arabidopsis thaliana). The pid quadruple mutants exhibited moderate responses in continuous light-induced phototropism with a decrease in growth rates of hypocotyls and normal responses in pulse-induced phototropism. However, they showed serious defects in enhancements of pulse-induced phototropic curvatures and lateral fluorescent auxin transport by red light pretreatment. Red light pretreatment significantly reduced the expression level of PID, and the constitutive expression of PID prevented pulse-induced phototropism, irrespective of red light pretreatment. This suggests that the PID family plays a significant role in phytochrome-mediated phototropic enhancement but not the phototropin signaling pathway. Red light treatment enhanced the intracellular accumulation of PIN proteins in response to the vesicle-trafficking inhibitor brefeldin A in addition to increasing their expression levels. Taken together, these results suggest that red light preirradiation enhances phototropic curvatures by up-regulation of PIN proteins, which are not being phosphorylated by the PID family.
Arabidopsis PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR Is Essential for PROTEIN PHOSPHATASE 2A Holoenzyme Assembly and Plays Important Roles in Hormone Signaling, Salt Stress Response, and Plant Development
Authors: Chen Jian , Hu Rongbin , Zhu Yinfeng , Shen Guoxin , Zhang Hong 
Published: October 2014

Abstract
PROTEIN PHOSPHATASE 2A (PP2A) is a major group of serine/threonine protein phosphatases in eukaryotes. It is composed of three subunits: scaffolding subunit A, regulatory subunit B, and catalytic subunit C. Assembly of the PP2A holoenzyme in Arabidopsis (Arabidopsis thaliana) depends on Arabidopsis PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR (AtPTPA). Reduced expression of AtPTPA leads to severe defects in plant development, altered responses to abscisic acid, ethylene, and sodium chloride, and decreased PP2A activity. In particular, AtPTPA deficiency leads to decreased methylation in PP2A-C subunits (PP2Ac). Complete loss of PP2Ac methylation in the suppressor of brassinosteroid insensitive1 mutant leads to 30% reduction of PP2A activity, suggesting that PP2A with a methylated C subunit is more active than PP2A with an unmethylated C subunit. Like AtPTPA, PP2A-A subunits are also required for PP2Ac methylation. The interaction between AtPTPA and PP2Ac is A subunit dependent. In addition, AtPTPA deficiency leads to reduced interactions of B subunits with C subunits, resulting in reduced functional PP2A holoenzyme formation. Thus, AtPTPA is a critical factor for committing the subunit A/subunit C dimer toward PP2A heterotrimer formation.
Differentially Phased Leaf Growth and Movements in Arabidopsis Depend on Coordinated Circadian and Light Regulation
Authors: Dornbusch Tino , Michaud Olivier , Xenarios Ioannis , Fankhauser Christian 
Published: October 2014

Abstract
In contrast to vastly studied hypocotyl growth, little is known about diel regulation of leaf growth and its coordination with movements such as changes in leaf elevation angle (hyponasty). We developed a 3D live-leaf growth analysis system enabling simultaneous monitoring of growth and movements. Leaf growth is maximal several hours after dawn, requires light, and is regulated by daylength, suggesting coupling between growth and metabolism. We identify both blade and petiole positioning as important components of leaf movements in Arabidopsis thaliana and reveal a temporal delay between growth and movements. In hypocotyls, the combination of circadian expression of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5 and their light-regulated protein stability drives rhythmic hypocotyl elongation with peak growth at dawn. We find that PIF4 and PIF5 are not essential to sustain rhythmic leaf growth but influence their amplitude. Furthermore, EARLY FLOWERING3, a member of the evening complex (EC), is required to maintain the correct phase between growth and movement. Our study shows that the mechanisms underlying rhythmic hypocotyl and leaf growth differ. Moreover, we reveal the temporal relationship between leaf elongation and movements and demonstrate the importance of the EC for the coordination of these phenotypic traits.
Critical Function of a Chlamydomonas reinhardtii Putative Polyphosphate Polymerase Subunit during Nutrient Deprivation
Authors: Aksoy Munevver , Pootakham Wirulda , Grossman Arthur R. 
Published: October 2014

Abstract
Forward genetics was used to isolate Chlamydomonas reinhardtii mutants with altered abilities to acclimate to sulfur (S) deficiency. The ars76 mutant has a deletion that eliminates several genes, including VACUOLAR TRANSPORTER CHAPERONE1 (VTC1), which encodes a component of a polyphosphate polymerase complex. The ars76 mutant cannot accumulate arylsulfatase protein or mRNA and shows marked alterations in levels of many transcripts encoded by genes induced during S deprivation. The mutant also shows little acidocalcisome formation compared with wild-type, S-deprived cells and dies more rapidly than wild-type cells following exposure to S-, phosphorus-, or nitrogen (N)-deficient conditions. Furthermore, the mutant does not accumulate periplasmic l-amino acid oxidase during N deprivation. Introduction of the VTC1 gene specifically complements the ars76 phenotypes, suggesting that normal acidocalcisome formation in cells deprived of S requires VTC1. Our data also indicate that a deficiency in acidocalcisome function impacts trafficking of periplasmic proteins, which can then feed back on the transcription of the genes encoding these proteins. These results and the reported function of vacuoles in degradation processes suggest a major role of the acidocalcisome in reshaping the cell during acclimation to changing environmental conditions.
ArabidopsisATG8-INTERACTING PROTEIN1 Is Involved in Autophagy-Dependent Vesicular Trafficking of Plastid Proteins to the Vacuole
Authors: Michaeli Simon , Honig Arik , Levanony Hanna , Peled-Zehavi Hadas , Galili Gad 
Published: October 2014

AbstractSelective autophagy has been extensively studied in various organisms, but knowledge regarding its functions in plants, particularly in organelle turnover, is limited. We have recently discovered ATG8-INTERACTING PROTEIN1 (ATI1) from Arabidopsis thaliana and showed that following carbon starvation it is localized on endoplasmic reticulum (ER)-associated bodies that are subsequently transported to the vacuole. Here, we show that following carbon starvation ATI1 is also located on bodies associating with plastids, which are distinct from the ER ATI bodies and are detected mainly in senescing cells that exhibit plastid degradation. Additionally, these plastid-localized bodies contain a stroma protein marker as cargo and were observed budding and detaching from plastids. ATI1 interacts with plastid-localized proteins and was further shown to be required for the turnover of one of them, as a representative. ATI1 on the plastid bodies also interacts with ATG8f, which apparently leads to the targeting of the plastid bodies to the vacuole by a process that requires functional autophagy. Finally, we show that ATI1 is involved in Arabidopsis salt stress tolerance. Taken together, our results implicate ATI1 in autophagic plastid-to-vacuole trafficking through its ability to interact with both plastid proteins and ATG8 of the core autophagy machinery.
Chromatin-Dependent Repression of theArabidopsisFloral Integrator Genes Involves Plant Specific PHD-Containing Proteins
Authors: López-González Leticia , Mouriz Alfonso , Narro-Diego Laura , Bustos Regla , Martínez-Zapater José Miguel , Jarillo Jose A. , Piñeiro Manuel 
Published: October 2014

AbstractThe interplay among histone modifications modulates the expression of master regulatory genes in development. Chromatin effector proteins bind histone modifications and translate the epigenetic status into gene expression patterns that control development. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific proteins with a plant homeodomain (PHD) motif, SHORT LIFE (SHL) and EARLY BOLTING IN SHORT DAYS (EBS), function in the chromatin-mediated repression of floral initiation and play independent roles in the control of genes regulating flowering. Previous results showed that repression of the floral integrator FLOWERING LOCUS T (FT) requires EBS. We establish that SHL is necessary to negatively regulate the expression of SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), another floral integrator. SHL and EBS recognize di- and trimethylated histone H3 at lysine 4 and bind regulatory regions of SOC1 and FT, respectively. These PHD proteins maintain an inactive chromatin conformation in SOC1 and FT by preventing high levels of H3 acetylation, bind HISTONE DEACETYLASE6, and play a central role in regulating flowering time. SHL and EBS are widely conserved in plants but are absent in other eukaryotes, suggesting that the regulatory module mediated by these proteins could represent a distinct mechanism for gene expression control in plants.
Genomic characterization of ϕRS603, a filamentous bacteriophage that is infectious to the phytopathogen Ralstonia solanacearum
Authors: Van Truong Thi Bich , Yoshida Shohei , Miki Kaito , Kondo Akihiro , Kamei Kaeko 
Published: October 2014

AbstractA filamentous bacteriophage (ϕ), ϕRS603, which is infectious to the phytopathogen Ralstonia solanacearum was isolated. ϕRS603 was found to have a circular single‐stranded DNA genome composed of 7679 nucleotides and to contain 13 putative open reading frames (ORFs). The ϕRS603 genome showed strong similarity with those of Ralstonia phages ϕRSM1 and ϕRSM3, as reported by Askora et al. The ϕRS603 genome had no ORFs corresponding to ORFs 2, 3, 13 and 14 (integrase) of ϕRSM3. ϕRS603 had an ORF that was homologous to other Ralstonia phages ϕRSS0 and ϕRSS1; however, ϕRSM1 and ϕRSM3 did not.
Development of an Activity Card Sort for Australian adults aged 18–64 years
Authors: Gustafsson Louise , de Jonge Desleigh , Lai Yvonne , Muuse Jessica , Naude Nicola , Hoyle Melanie 
Published: October 2014

Background/aimThe Activity Card Sort (ACS) is an interview‐based, client‐centred tool that measures the activity engagement of older adults aged 65 years and above. The tool consists of photos which clients are asked to sort into categories to reflect their previous and current level of engagement. The activities that older adults engage in may differ to that of younger adults and there is a need to explore the development of an ACS Australia for adults aged 18–64 years.MethodsThe Delphi survey method as applied by previous ACS development was used in this study. Purposeful and snowball sampling were employed to recruit participants between the ages of 18 and 64 years who were Australian citizens or residents. Demographic information was obtained via a questionnaire. There were two stages in the study. The first Delphi survey generated, selected and finalised activities and the second Delphi survey generated, selected and finalised categories.ResultsAustralian citizens and residents were involved in the development of the activities (n = 61) and categories (n = 65). The final tool includes 85 activities sorted into three broad categories representing personal care, daily life and home maintenance; rest and relaxation; and high and low impact activities.ConclusionsThis study has resulted in the development of a preliminary version of an ACS for adults aged 18–64 years. Further work is required to determine the psychometric properties of the tool.
Reduced primary care respiratory infection visits following pregnancy and infancy vitamin D supplementation: a randomised controlled trial
Authors: Grant Cameron C. , Kaur Suhina , Waymouth Ellen , Mitchell Edwin A. , Scragg Robert , Ekeroma Alec , Stewart Alistair , Crane Julian , Trenholme Adrian , Camargo Carlos A. 
Published: October 2014

AbstractAimTo determine whether vitamin D supplementation reduces primary care visits for acute respiratory infection (ARI).MethodsA randomised, double‐blind, placebo‐controlled trial was conducted in New Zealand and powered to determine the vitamin D dose needed to achieve normal vitamin D status during infancy. Healthy pregnant women, from 27 weeks’ gestation to birth, and their infants, from birth to age 6 months, were assigned to placebo or one of the two dosages of daily oral vitamin D3. Woman/infant pairs were randomised to placebo/placebo, 1000 IU/400 IU or 2000 IU/800 IU. For this ad hoc analysis, the primary care records of enrolled children were audited to age 18 months.ResultsTwo hundred and sixty pregnant women were randomised to placebo (n = 87), lower‐dose (n = 87) or higher‐dose (n = 86) vitamin D3. In comparison with the placebo group (99%), the proportion of children making any ARI visits was smaller in the higher‐dose (87%, p = 0.004), but not the lower‐dose vitamin D3 group (95%, p = 0.17). The median number of ARI visits/child was less in the higher‐dose vitamin D3 group from age 6–18 months (placebo 4, lower dose 3, higher dose 2.5; p = 0.048 for higher‐dose vitamin D3 vs. placebo).ConclusionVitamin D3 supplementation during pregnancy and infancy reduces primary care visits for ARI during early childhood.
Physiological weight loss chart helps to identify high‐risk infants who need breastfeeding support
Authors: Bertini Giovanna , Breschi Rita , Dani Carlo 
Published: October 2014

AbstractAimHealthy, full‐term, exclusively breastfed infants are expected to lose weight in the first days after birth, but experts disagree about what constitutes a physiological neonatal weight loss and there is a lack of evidence‐based data. Our study aimed to construct a centile chart of neonatal weight loss in a healthy population of exclusively breastfed term neonates.MethodsWe retrospectively studied all infants born at an Italian centre that focused on natural childbirth from April 2007 to December 2012 and who complied with World Health Organization guidance on infant feeding. The infants’ weight loss was recorded after 12, 24, 36, 48, 60 and 72 h of life.ResultsWe included 1760 healthy, full‐term, singleton babies born by vaginal delivery. Their mean weight loss was 5.95 ± 1.73%, 72.2% had maximal weight loss before discharge, only 3.9% lost more than 9% of their birthweight, and no infant lost more than 10%. We measured the percentage weight change from birth and each time the infant was examined, summarising how their weight varied in the first 72 h of life.ConclusionOur normative chart of physiological weight loss provided an important instrument for identifying high‐risk infants who required breastfeeding support.