bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global geographic patterns of sexual size dimorphism in birds: Support for a latitudinal trend?
Authors: Friedman Nicholas R. , Remeš Vladimír 
Published: December 2014

AbstractSexual size dimorphism (SSD) is widespread among animals, and is a common indication of differential selection among males and females. Sexual selection theory predicts that SSD should increase as one sex competes more fiercely for access to mates, but it is unclear what effect spatial variation in ecology may have on this behavioral process. Here, we examine SSD across the class Aves in a spatial and phylogenetic framework, and test several a priori hypotheses regarding its relationship with climate. We mapped the global distribution of SSD from published descriptions of body size, distribution, and phylogenetic relationships across 2581 species of birds. We examined correlations between SSD and nine predictor variables representing a priori models of physical geography, climate, and climate variability. Our results show guarded support for a global latitudinal trend in SSD based on a weak prevalence of species with low or female-biased SSD in the North, but substantial spatial heterogeneity. While several stronger relationships were observed between SSD and climate predictors within zoogeographical regions, no global relationship emerged that was consistent across multiple methods of analysis. While we found support for a global relationship between climate and SSD, this support lacked consistency and explanatory power. Furthermore the strong phylogenetic signal and conspicuous lack of support from phylogenetically corrected analyses suggests that any such relationship in birds is likely due to the idiosyncratic histories of different lineages. In this manner, our results broadly agree with studies in other groups, leading us to conclude that the relationship between climate and SSD is at best complex. This suggests that SSD is linked to behavioral dynamics that may at a global scale be largely independent of environmental conditions.
SpeedSeq: Ultra-fast personal genome analysis and interpretation
Authors: Chiang Colby , Layer Ryan M , Faust Gregory G , Lindberg Michael R , Rose David B , Garrison Erik P , Marth Gabor T , Quinlan Aaron R , Hall Ira M 
Published: December 2014

AbstractComprehensive interpretation of human genome sequencing data is a challenging bioinformatic problem that typically requires weeks of analysis, with extensive hands-on expert involvement. This informatics bottleneck inflates genome sequencing costs, poses a computational burden for large-scale projects, and impedes the adoption of time-critical clinical applications such as personalized cancer profiling and newborn disease diagnosis, where the actionable timeframe can measure in hours or days. We developed SpeedSeq, an open-source genome analysis platform that vastly reduces computing time. SpeedSeq accomplishes read alignment, duplicate removal, variant detection and functional annotation of a 50X human genome in <24 hours, even using one low-cost server. SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants (SNVs), indels, and structural variants (SVs) and includes novel functionality for SV genotyping, SV annotation, fusion gene detection, and rapid identification of actionable mutations. SpeedSeq will help bring timely genome analysis into the clinical realm.Availability:SpeedSeq is available athttps://github.com/cc2qe/speedseq.
Networks that learn the precise timing of event sequences
Authors: Veliz-Cuba Alan , Shouval Harel , Josić Krešimir , Kilpatrick Zachary P. 
Published: December 2014

AbstractNeuronal circuits can learn and replay firing patterns evoked by sequences of sensory stimuli. After training, a brief cue can trigger a spatiotemporal pattern of neural activity similar to that evoked by a learned stimulus sequence. Network models show that such sequence learning can occur through the shaping of feedforward excitatory connectivity via long term plasticity. Previous models describe how event order can be learned, but they typically do not explain how precise timing can be recalled. We propose a mechanism for learning both the order and precise timing of event sequences. In our recurrent network model, long term plasticity leads to the learning of the sequence, while short term facilitation enables temporally precise replay of events. Learned synaptic weights between populations determine the time necessary for one population to activate another. Long term plasticity adjusts these weights so that the trained event times are matched during playback. While we chose short term facilitation as a time-tracking process, we also demonstrate that other mechanisms, such as spike rate adaptation, can fulfill this role. We also analyze the impact of trial-to-trial variability, showing how observational errors as well as neuronal noise result in variability in learned event times. The dynamics of the playback process determine how stochasticity is inherited in learned sequence timings. Future experiments that characterize such variability can therefore shed light on the neural mechanisms of sequence learning.
Consequences of a Deficit in Vitamin B6 Biosynthesis de Novo for Hormone Homeostasis and Root Development in Arabidopsis
Authors: Boycheva Svetlana , Dominguez Ana , Rolcik Jakub , Boller Thomas , Fitzpatrick Teresa B. 
Published: December 2014

AbstractVitamin B6 (pyridoxal 5′-phosphate) is an essential cofactor of many metabolic enzymes. Plants biosynthesize the vitamin de novo employing two enzymes, pyridoxine synthase1 (PDX1) and PDX2. In Arabidopsis (Arabidopsis thaliana), there are two catalytically active paralogs of PDX1 (PDX1.1 and PDX1.3) producing the vitamin at comparable rates. Since single mutants are viable but the pdx1.1 pdx1.3 double mutant is lethal, the corresponding enzymes seem redundant. However, the single mutants exhibit substantial phenotypic differences, particularly at the level of root development, with pdx1.3 being more impaired than pdx1.1. Here, we investigate the differential regulation of PDX1.1 and PDX1.3 by identifying factors involved in their disparate phenotypes. Swapped-promoter experiments clarify the presence of distinct regulatory elements in the upstream regions of both genes. Exogenous sucrose (Suc) triggers impaired ethylene production in both mutants but is more severe in pdx1.3 than in pdx1.1. Interestingly, Suc specifically represses PDX1.1 expression, accounting for the stronger vitamin B6 deficit in pdx1.3 compared with pdx1.1. Surprisingly, Suc enhances auxin levels in pdx1.1, whereas the levels are diminished in pdx1.3. In the case of pdx1.3, the previously reported reduced meristem activity combined with the impaired ethylene and auxin levels manifest the specific root developmental defects. Moreover, it is the deficit in ethylene production and/or signaling that triggers this outcome. On the other hand, we hypothesize that it is the increased auxin content of pdx1.1 that is responsible for the root developmental defects observed therein. We conclude that PDX1.1 and PDX1.3 play partially nonredundant roles and are differentially regulated as manifested in disparate root growth impairment morphologies.
A novel pathway for the synthesis of inositol phospholipids uses cytidine diphosphate (CDP)‐inositol as donor of the polar head group
Authors: Jorge Carla D. , Borges Nuno , Santos Helena 
Published: December 2014

SummaryWe describe a novel biosynthetic pathway for glycerophosphoinositides in Rhodothermus marinus in which inositol is activated by cytidine triphosphate (CTP); this is unlike all known pathways that involve activation of the lipid group instead. This work was motivated by the detection in the R. marinus genome of a gene with high similarity to CTP:L‐myo‐inositol‐1‐phosphate cytidylyltransferase, the enzyme that synthesizes cytidine diphosphate (CDP)‐inositol, a metabolite only known in the synthesis of di‐myo‐inositol phosphate. However, this solute is absent in R. marinus. The fate of radiolabelled CDP‐inositol was investigated in cell extracts to reveal that radioactive inositol was incorporated into the chloroform‐soluble fraction. Mass spectrometry showed that the major lipid product has a molecular mass of 810 Da and contains inositol phosphate and alkyl chains attached to glycerol by ether bonds. The occurrence of ether‐linked lipids is rare in bacteria and has not been described previously in R. marinus. The relevant synthase was identified by functional expression of the candidate gene in Escherichia coli. The enzyme catalyses the transfer of L‐myo‐inositol‐1‐phosphate from CDP‐inositol to dialkylether glycerol yielding dialkylether glycerophosphoinositol. Database searching showed homologous proteins in two bacterial classes, Sphingobacteria and Alphaproteobacteria. This is the first report of the involvement of CDP‐inositol in phospholipid synthesis.
Risk assessment for preeclampsia in nulliparous women at 11–13 weeks gestational age: prospective evaluation of two algorithms
Authors: Skråstad RB , Hov GG , Blaas H‐GK , Romundstad PR , Salvesen KÅ 
Published: December 2014

ObjectiveTo evaluate two algorithms for prediction of preeclampsia in a population of nulliparous women in Norway.DesignProspective screening study.SettingNational Centre for Fetal Medicine in Trondheim, Norway.PopulationFive hundred and forty‐one nulliparous women.MethodsThe women were examined between 11+0 and 13+6 weeks with interviews for maternal characteristics and measurements of mean arterial pressure, uterine artery pulsatility index, pregnancy‐associated plasma protein A and placental growth factor. The First Trimester Screening Program version 2.8 by The Fetal Medicine Foundation (FMF) was compared with the Preeclampsia Predictor TM version 1 revision 2 by Perkin Elmer (PREDICTOR).Main outcome measuresPrediction of preeclampsia requiring delivery before 37 weeks, before 42 weeks and late preeclampsia (delivery after 34 weeks).ResultsThe performance of the two algorithms was similar, but quite poor, for prediction of preeclampsia requiring delivery before 42 weeks with an area under the curve of 0.77 (0.67–0.87) and sensitivity 40% (95% CI 19.1–63.9) at a fixed 10% false positive rate for FMF and 0.74 (0.63–0.84) and sensitivity 30% (95% CI 11.9–54.3) at a fixed 10% false positive rate for PREDICTOR. The FMF algorithm for preeclampsia requiring delivery <37 weeks had an area under the curve of 0.94 (0.86–1.0) and sensitivity of 80% (95% CI 28.4–99.5) at a 10% fixed false positive rate.ConclusionsFetal Medicine Foundation and PREDICTOR algorithms had similar and only modest performance in predicting preeclampsia. The results indicate that the FMF algorithm is suitable for prediction of preterm preeclampsia.
Temporal dynamics of active Archaea in oxygen‐depleted zones of two deep lakes
Authors: Hugoni Mylène , Domaizon Isabelle , Taib Najwa , Biderre‐Petit Corinne , Agogué Hélène , Galand Pierre E. , Debroas Didier , Mary Isabelle 
Published: December 2014

SummaryDeep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.
The exopolysaccharide Psl–eDNA interaction enables the formation of a biofilm skeleton in Pseudomonas aeruginosa
Authors: Wang Shiwei , Liu Xi , Liu Hongsheng , Zhang Li , Guo Yuan , Yu Shan , Wozniak Daniel J. , Ma Luyan Z. 
Published: December 2014

SummaryA hallmark of bacterial biofilms is a self‐produced extracellular matrix of exopolysaccharide, extracellular DNA (eDNA) and proteins that hold bacterial cells together in the community. However, interactions among matrix components and how the interactions contribute to the formation of matrix remain unclear. Here, we show the physical interaction between exopolysaccharide Psl and eDNA, the two key biofilm matrix components of the opportunistic pathogen Pseudomonas aeruginosa. The interaction allows the two components to combine to form a web of eDNA–Psl fibres, which resembles a biofilm skeleton in the centre of pellicles to give bacteria structural support and capability against agents targeted on one matrix component. The web of eDNA–Psl fibres was also found in flow‐cell biofilms at microcolonies initiation stage. The colocalization of eDNA or Psl fibres with bacterial cell membrane stain suggests that fibre‐like eDNA is likely derived from the lysis of dead bacteria in biofilms. Psl can interact with DNA from diverse sources, suggesting that P. aeruginosa has the ability to use DNA of other organisms (such as human neutrophils and other bacterial species) to form its own communities, which might increase the survival of P. aeruginosa in multispecies biofilms or within a human host.
Low frequency of endospore‐specific genes in subseafloor sedimentary metagenomes
Authors: Kawai Mikihiko , Uchiyama Ikuo , Takami Hideto , Inagaki Fumio 
Published: December 2014

SummarySpore formation is considered to be one of the microbial strategies for long‐term survival in subseafloor sedimentary habitats. However, our knowledge of the genetic and physiological characteristics of subseafloor microbes is limited. Here, we studied the distribution and frequency of genes that are related to endospore formation in 10 subseafloor sedimentary metagenomes from Site C9001 off Japan and Site 1229 off Peru. None or very low frequencies of endospore‐specific genes (e.g. dpaA, dpaB, sspA, spo0A, spoIIGA, spoIIM, spoIIIAB, spoIVA, spoIVB, yabP, yunB, spoVM) were observed in the subseafloor metagenomes. Based on the number of universally conserved single copy genes, the frequency ratio of putative endospore‐formers was estimated to be < 10%, which is consistent with the frequency of Clostridia‐derived genomes (2–4%) but is lower than previous estimates based on the concentration of dipicolinic acid. Conceivable explanations for this discrepancy are as follows: the efficiency of lysis and DNA extraction of subseafloor endospore cells may have been lower than those of vegetative cells, conversion factor of dipicolinic acid content per cell may differ, and/or sporulation‐related genes and other functional strategies for long‐term survival in the deep subseafloor biosphere are evolutionarily distinct from known spore‐forming gene repertoires.
Empowerment and satisfaction in a multinational study of routine clinical practice
Authors: Clarke E. , Puschner B. , Jordan H. , Williams P. , Konrad J. , Kawohl W. , Bär A. , Rössler W. , Del Vecchio V. , Sampogna G. , Nagy M. , Süveges A. , Krogsgaard Bording M. , Slade M. 
Published: December 2014

ObjectiveDecision‐making between mental health clinicians and patients is under‐researched. We tested whether mental health patients are more satisfied with a decision made (i) using their preferred decision‐making style and (ii) with a clinician with the same decision‐making style preference.MethodAs part of the CEDAR Study (ISRCTN75841675), a convenience sample of 445 patients with severe mental illness from six European countries were assessed for desired clinical decision‐making style (rated by patients and paired clinicians), decision‐specific experienced style and satisfaction.ResultsPatients who experienced more involvement in decision‐making than they desired rated higher satisfaction (OR = 2.47, P = 0.005, 95% CI 1.32–4.63). Decisions made with clinicians whose decision‐making style preference was for more active involvement than the patient preference were rated with higher satisfaction (OR = 3.17, P = 0.003, 95% CI 1.48–6.82).ConclusionMore active involvement in decision‐making than the patient stated as desired was associated with higher satisfaction. A clinical orientation towards empowering, rather than shared, decision‐making may maximise satisfaction.
Prognostic Value of Speckle Tracking Echocardiography in Patients with ST‐Elevation Myocardial Infarction Treated with Late Percutaneous Intervention
Authors: Cong Tao , Sun Yinghui , Shang Zhijuan , Wang Ke , Su Dechun , Zhong Lei , Zhang Shulong , Yang Yanzong 
Published: December 2014

BackgroundLeft ventricular remodeling (LVr) is common after ST‐segment elevation myocardial infarction (STEMI). The aim of this study was to evaluate the prognostic value of speckle tracking echocardiography (STE) for predicting LVr 6–9 months after late percutaneous coronary intervention (PCI) in patients with STEMI.MethodsPatients with first STEMI who accepted late PCI were enrolled. Echocardiography was performed within 48 hours of admission. Six to nine months after MI, an echocardiography examination was repeated. LVr was defined as >15% increase in LV end‐systolic volume (LVESV) after 6 months.ResultsOne hundred and twenty‐seven patients were divided into two groups: 86 patients without LVr and 41 patients with LVr. There were significant differences in the global longitudinal strain (GLS), SD of time to peak longitudinal systolic strain (longitudinal Ts‐SD), longitudinal postsystolic index, radial strain (RS), and SD of time to peak radial systolic strain (Radial Ts‐SD). In multivariate logistic regression analysis, the GLS(odds ratio [OR] = 0.39, 95% confidence interval [CI] = 0.26–0.57, P < 0.01), and RS(OR = 1.07, 95% CI = 1.02–1.13, P = 0.01) were determinants of LVr. A receiver operating characteristic curve showed that the GLS predicted LVr with an optimal cutoff value of −10.85 (sensitivity: 89.7%, specificity: 91.7%). During clinical follow‐up for 16.9 ± 1.6 months, death or congestive heart failure developed in 12 patients (9.4%), and the baseline ejection fraction (OR = 1.91, 95% CI = 1.18–3.1, P = 0.009) and GLS (OR = 0.56, 95% CI = 0.34–0.91, P = 0.02) were independent predictors.ConclusionIn patients with STEMI treated with late percutaneous coronary intervention, the GLS as measured by STE is a strong predictor of LVr and adverse events.
Caged compounds for multichromic optical interrogation of neural systems
Authors: Amatrudo Joseph M. , Olson Jeremy P. , Agarwal Hitesh K. , Ellis‐Davies Graham C. R. 
Published: December 2014

AbstractCaged compounds are widely used by neurophysiologists to study many aspects of cellular signaling in glia and neurons. Biologically inert before irradiation, they can be loaded into cells via patch pipette or topically applied in situ to a defined concentration; photolysis releases the caged compound in a very rapid and spatially defined way. As caged compounds are exogenous optical probes, they include not only natural products such neurotransmitters, calcium and IP3 but non‐natural products such as fluorophores, drugs and antibodies. In this Technical Spotlight we provide a short introduction to the uncaging technique by discussing the nitroaromatic caging chromophores most widely used in such experiments [e.g. α‐carboxy‐ortho‐nitrobenyl (CNB), dimethoxynitrobenzyl (DMNB), 4‐methoxy‐7‐nitroindolinyl (MNI) and 4‐carboxymethoxy‐7‐nitroindolinyl (CDNI)]. We show that recently developed caging chromophores [rutheniumbipyridial (RuBi) and 7‐diethylaminocoumarin (DEAC)450] that are photolyzed with blue light (~ 430–480 nm range) can be combined with traditional nitroaromatic caged compounds to enable two‐color optical probing of neuronal function. For example, one‐photon uncaging of either RuBi‐GABA or DEAC450‐GABA with a 473‐nm laser is facile, and can block nonlinear currents (dendritic spikes or action potentials) evoked by two‐photon uncaging of CDNI‐Glu at 720 nm. We also show that two‐photon uncaging of DEAC450‐Glu and CDNI‐GABA at 900 and 720 nm, respectively, can be used to fire and block action potentials. Our experiments illustrate that recently developed chromophores have taken uncaging out of the ‘monochrome era’, in which it has existed since 1978, so as to enable multichromic interrogation of neuronal function with single‐synapse precision.
Soil warming and CO2 enrichment induce biomass shifts in alpine tree line vegetation
Authors: Dawes Melissa A. , Philipson Christopher D. , Fonti Patrick , Bebi Peter , Hättenschwiler Stephan , Hagedorn Frank , Rixen Christian 
Published: December 2014

AbstractResponses of alpine tree line ecosystems to increasing atmospheric CO2 concentrations and global warming are poorly understood. We used an experiment at the Swiss tree line to investigate changes in vegetation biomass after 9 years of free air CO2 enrichment (+200 ppm; 2001–2009) and 6 years of soil warming (+4 °C; 2007–2012). The study contained two key tree line species, Larix decidua and Pinus uncinata, both approximately 40 years old, growing in heath vegetation dominated by dwarf shrubs. In 2012, we harvested and measured biomass of all trees (including root systems), above‐ground understorey vegetation and fine roots. Overall, soil warming had clearer effects on plant biomass than CO2 enrichment, and there were no interactive effects between treatments. Total plant biomass increased in warmed plots containing Pinus but not in those with Larix. This response was driven by changes in tree mass (+50%), which contributed an average of 84% (5.7 kg m−2) of total plant mass. Pinus coarse root mass was especially enhanced by warming (+100%), yielding an increased root mass fraction. Elevated CO2 led to an increased relative growth rate of Larix stem basal area but no change in the final biomass of either tree species. Total understorey above‐ground mass was not altered by soil warming or elevated CO2. However, Vaccinium myrtillus mass increased with both treatments, graminoid mass declined with warming, and forb and nonvascular plant (moss and lichen) mass decreased with both treatments. Fine roots showed a substantial reduction under soil warming (−40% for all roots <2 mm in diameter at 0–20 cm soil depth) but no change with CO2 enrichment. Our findings suggest that enhanced overall productivity and shifts in biomass allocation will occur at the tree line, particularly with global warming. However, individual species and functional groups will respond differently to these environmental changes, with consequences for ecosystem structure and functioning.