bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodiversity dynamics and environmental occupancy of fossil azooxanthellate and zooxanthellate scleractinian corals
Authors: Kiessling Wolfgang , Kocsis Ádám T. 
Published: April 2015

AbstractScleractinian corals have two fundamentally different life strategies, which can be inferred from morphological criteria in fossil material. In the non-photosymbiotic group nutrition comes exclusively from heterotrophic feeding, whereas the photosymbiotic group achieves a good part of its nutrition from algae hosted in the coral’s tissue. These ecologic differences arose early in the evolutionary history of corals but with repeated evolutionary losses and presumably also gains of symbiosis since then. We assessed the biodiversity dynamics and environmental occupancy of both ecologic groups to identify times when the evolutionary losses of symbiosis as inferred from molecular analyses might have occurred and if these can be linked to environmental change. Two episodes are likely: The first was in the mid-Cretaceous when non-symbiotic corals experienced an origination pulse and started to become more common in deeper, non-reef habitats and on siliciclastic substrates initiating a long-term offshore trend in occupancy. The second was around the Cretaceous/Paleogene boundary with another origination pulse and increased occupancy of deep-water settings in the non-symbiotic group. Environmental factors such as rapid global warming associated with mid-Cretaceous anoxic events and increased nutrient concentrations in Late Cretaceous–Cenozoic deeper waters are plausible mechanisms for the shift. Turnover rates and durations are not significantly different between the two ecologic groups when compared over the entire history of scleractinians. However, the deep-water shift of non-symbiotic corals was accompanied by reduced extinction rates, supporting the view that environmental occupancy is a prominent driver of evolutionary rates.
Democracy under the Caliphs: Alfarabi's Unusual Understanding of Popular Rule
Authors: Orwin Alexander I. 
Published: April 2015

AbstractThe account of “democracy” presented in the writings of Alfarabi differs considerably from all other treatments of the subject, both ancient and modern. The goal of this article is to elucidate thefalāsifa's view of democracy and account for its unusual character, by showing how appropriate it is to both the meaning of the term in medieval Arabic and the political situation of their own time. Questions such as internal order, war, immigration, philosophy, and their relationship to democracy as understood by thefalāsifaare all duly considered. The article concludes with the suggestion that this peculiar sort of democracy nonetheless resembles modern democracy in one small but crucial respect.
Similar vegetation structure in protected and non-protected wetlands in Central Brazil: conservation significance
Authors: MOREIRA SUZANA N. , EISENLOHR PEDRO V. , POTT ARNILDO , POTT VALI J. , OLIVEIRA-FILHO ARY T. 
Published: April 2015

SUMMARYAppropriate legislation based on in-depth ecological evidence is essential for ecosystem conservation. Wetland areas in the BrazilianCerradohotspot are facing difficulties in terms of status under environmental law: only those wetlands with the palmMauritia flexuosa(veredas) are recognized as protected. Comprehensive fieldwork in central-western Brazil (72 50-m transects) coupled with both exploratory and confirmatory analyses showed that communities with (MP) and without (MA)M. flexuosaare similar in terms of the floristics and ecology. The results demonstrate that the analysed wetlands are part of a continuum, in which a gradual replacement of species and community structure occurs without a pattern related to physiognomy. Considering such floristic and structure patterns when legally defining the ecosystem would promote a more comprehensive and realistic view of the ecosystem's characteristics and functions, and result in laws with a stronger scientific support. Conservationists should further examine the lack of consistent separation of plant community attributes between the MP and MA areas, and reconsider the scientific definition of veredas.
The militarization of anti-poaching: undermining long term goals?
Authors: DUFFY ROSALEEN , ST JOHN FREYA A. V. , BÜSCHER BRAM , BROCKINGTON DAN 
Published: April 2015

SummaryConservation is at a critical juncture because of the increase in poaching which threatens key species. Poaching is a major public concern, as indicated by the rises in rhino and elephant poaching, the United for Wildlife Initiative and the London Declaration, signed by 46 countries in February 2014. This is accompanied by an increasing calls for a more forceful response, especially to tackle the involvement of organized crime in wildlife trafficking. However, there is a risk that this will be counter-productive. Further, such calls are based on a series of assumptions which are worthy of greater scrutiny. First, calls for militarization are based on the idea that poverty drives poaching. Yet, poaching and trafficking are changing because of the shifting dynamics of poverty in supply countries, coupled with changing patterns of wealth in consumer markets. Second, the ways increases in poaching are being linked to global security threats, notably from Al Shabaab are poorly evidenced and yet circulate in powerful policy circles. There is a risk that militarization will place more heavily armed rangers in the centre of some of the most complex regional conflicts in the world (such as the Horn of Africa and Central Africa/Sahel region).
Effects of Tributyltin Chloride on Developing Mouse Oocytes and Preimplantation Embryos
Authors: Huang Xian-Ju , Shen Ming , Wang Lizhong , Yu Fengxiang , Wu Wangjun , Liu Hong-lin 
Published: April 2015

AbstractTributyltin, an organotin, is ubiquitous in estuaries and freshwater systems. Previous reports suggest that tributyltin is an endocrine disruptor in many wildlife species and it inhibits aromatase in mammalian placental and granulosa-like tumor cell lines. However, no evidence showing the effects of tributyltin on oocytes or preimplantation embryonic developmental competence exists. Therefore, we investigated the role of tributyltin chloride (TBTCl) in the development of female oocytes and preimplantation embryos. Briefly, female ICR mice were gavaged with 0 (vehicle), 4, and 8 mg/kg of TBTCl each day for 18 days. The fluorescence intensity analysis showed that the 5-methylcytosine level decreased after TBTCl treatment, indicating that the general DNA methylation level decreased in the treated oocytes. Our results demonstrate that TBTCl treatment results in decreased mRNA levels of imprinted genes H19, Igf2r, and Peg3 during oocyte growth. The TBTCl-treated oocytes showed a significant increase in reactive oxygen species levels in germinal vesicle oocytes. In TBTCl-treated oocytes, there was no difference in GPx and Sod1 expression, but a decreased mRNA level of Cat occurred when compared with control. Moreover, the blastocysts with TBTCl exposure displayed higher apoptotic signals. These results suggest that TBTCl induces developmental defects in oocytes and preimplantation embryos.
Psychological Treatment of Obsessive-Compulsive Disorder in Children and Adolescents: a Meta-Analysis
Authors: Rosa-Alcázar Ana I. , Sánchez-Meca Julio , Rosa-Alcázar Ángel , Iniesta-Sepúlveda Marina , Olivares-Rodríguez José , Parada-Navas José L. 
Published: April 2015

AbstractAlthough several meta-analyses have investigated the efficacy of psychological treatments for pediatric obsessive-compulsive disorder (OCD), there is not yet a consensus on the most efficacious treatment components. A meta-analysis was carried out to examine the efficacy of the different treatment techniques used in the psychological interventions of pediatric OCD. An exhaustive literature search from 1983 to February 2014 enabled us to locate 46 published articles that applied some kind of cognitive-behavioral therapy (CBT). For each group the effect size was the standardized pretest-posttest mean change, and it was calculated for obsessive-compulsive symptoms and for other outcome measures. The results clearly showed large effect sizes for CBT in reducing obsessive-compulsive symptoms and, to a lesser extent, other outcome measures (d+= 1.860; 95% CI: 1.639; 2.081). The most promising treatments are those based on multicomponent programs comprising ERP, cognitive strategies, and relapse prevention. The analysis of other potential moderator variables and the implications for clinical practice are discussed.
Tonic endocannabinoid-mediated modulation of GABA release is independent of the CB1 content of axon terminals
Authors: Lenkey Nora , Kirizs Tekla , Holderith Noemi , Máté Zoltán , Szabó Gábor , Vizi E. Sylvester , Hájos Norbert , Nusser Zoltan 
Published: April 2015

AbstractThe release of GABA from cholecystokinin-containing interneurons is modulated by type-1 cannabinoid receptors (CB1). Here we tested the hypothesis that the strength of CB1-mediated modulation of GABA release is related to the CB1 content of axon terminals. Basket cell boutons have on average 78% higher CB1 content than those of dendritic-layer-innervating (DLI) cells, a consequence of larger bouton surface and higher CB1 density. The CB1 antagonist AM251 caused a 54% increase in action potential-evoked [Ca2+] in boutons of basket cells, but not in DLI cells. However, the effect of AM251 did not correlate with CB1 immunoreactivity of individual boutons. Moreover, a CB1 agonist decreased [Ca2+] in a cell type- and CB1-content-independent manner. Replica immunogold labelling demonstrated the colocalization of CB1 with the Cav2.2 Ca2+ channel subunit. Our data suggest that only a subpopulation of CB1s, within nanometre distances from their target Cav2.2 channels, are responsible for endocannabinoid-mediated modulation of GABA release.
Eco-evolutionary feedbacks during experimental range expansions
Authors: Fronhofer Emanuel A. , Altermatt Florian 
Published: April 2015

AbstractUnderstanding biological range expansions and invasions is of great ecological and economical interest. Importantly, spatial dynamics can be deeply affected by rapid evolution depending on the ecological context. Using experimental evolution in replicated microcosm landscapes and numerical analyses we show experimentally that the ecological process of range expansions leads to the evolution of increased dispersal. This evolutionary change counter-intuitively feeds back on (macro-)ecological patterns affecting the spatial distribution of population densities. While existing theory suggests that densities decrease from range cores to range margins due to K-selection, we show the reverse to be true when competition is considered explicitly including resource dynamics. We suggest that a dispersal-foraging trade-off, leading to more ‘prudent’ foraging at range margins, is the driving mechanism behind the macroecological pattern reported. In conclusion, rapid multi-trait evolution and eco-evolutionary feedbacks are highly relevant for understanding macroecological patterns and designing appropriate conservation strategies.
Accelerated sintering in phase-separating nanostructured alloys
Authors: Park Mansoo , Schuh Christopher A. 
Published: April 2015

AbstractSintering of powders is a common means of producing bulk materials when melt casting is impossible or does not achieve a desired microstructure, and has long been pursued for nanocrystalline materials in particular. Acceleration of sintering is desirable to lower processing temperatures and times, and thus to limit undesirable microstructure evolution. Here we show that markedly enhanced sintering is possible in some nanocrystalline alloys. In a nanostructured W–Cr alloy, sintering sets on at a very low temperature that is commensurate with phase separation to form a Cr-rich phase with a nanoscale arrangement that supports rapid diffusional transport. The method permits bulk full density specimens with nanoscale grains, produced during a sintering cycle involving no applied stress. We further show that such accelerated sintering can be evoked by design in other nanocrystalline alloys, opening the door to a variety of nanostructured bulk materials processed in arbitrary shapes from powder inputs.
Strong influence of behavioral dynamics on the ability of testing and treating HIV to stop transmission
Authors: Henry Christopher J. , Koopman James S. 
Published: April 2015

AbstractChoosing between strategies to control HIV transmission with antivirals requires understanding both the dynamics affecting those strategies' effectiveness and what causes those dynamics. Alternating episodes of high and low contact rates (episodic risk) interact with increased transmission probabilities during early infection to strongly influence HIV transmission dynamics. To elucidate the mechanics of this interaction and how these alter the effectiveness of universal test and treat (UT8T) strategies, we formulated a model of UT8T effects. Analysis of this model shows how and why changing the dynamics of episodic risk changes the fraction of early transmissions (FET) and the basic reproduction number (R0) and consequently causes UT8T to vary from easily eliminating transmission to having little effect. As the length of risk episodes varies from days to lifetimes, FET first increases, then falls. Endemic prevalence varies similarly.R0, in contrast, increases monotonically and is the major determinant of UT8T effects. At some levels of episodic risk, FET can be high, but eradication is easy becauseR0is low. At others FET is lower, but a highR0makes eradication impossible and control ineffective. Thus changes in individual risk over time must be measured and analyzed to plan effective control strategies with antivirals.
Mechanism of the Antigen-Independent Cytokinergic SPE-7 IgE Activation of Human Mast Cells in Vitro
Authors: Bax Heather J. , Bowen Holly , Dodev Tihomir S. , Sutton Brian J. , Gould Hannah J. 
Published: April 2015

AbstractRelease of pro-inflammatory mediators by mast cells is a key feature of allergic disease. The ‘dogma’ is that IgE molecules merely sensitise mast cells by binding FcεRI prior to cross-linking by multivalent allergen, receptor aggregation and mast cell activation. However, certain monoclonal IgE antibodies have been shown to elicit mast cell activation in an antigen-independent cytokinergic manner and DNP-specific murine SPE-7 IgE is the most highly cytokinergic antibody known. We show that both monovalent hapten and recombinant SPE-7 IgE Fab inhibit its cytokinergic activity as measured by mast cell degranulation and TNF-α release. Using SPE-7 IgE, a non-cytokinergic human IgE and a poorly cytokinergic murine IgE, we reveal that interaction of the Fab region of ‘free’ SPE-7 IgE with the Fab of FcεRI-bound SPE-7 IgE is the basis of its cytokinergic activity. We rule out involvement of IgE Fc, Cε1 and Cλ/κ domains and propose that ‘free’ SPE-7 IgE binds to FcεRI-bound SPE-7 IgE by an Fv-Fv interaction. Initial formation of a tri-molecular complex (one ‘free’ IgE molecule cross-linking two receptor-bound IgE molecules) leads to capture of further ‘free’ and receptor-bound IgEs to form larger clusters that trigger mast cell activation.
CRISPR/Cas9-mediated endogenous protein tagging for RESOLFT super-resolution microscopy of living human cells
Authors: Ratz Michael , Testa Ilaria , Hell Stefan W. , Jakobs Stefan 
Published: April 2015

AbstractOverexpression is a notorious concern in conventional and especially in super-resolution fluorescence light microscopy studies because it may cause numerous artifacts including ectopic sub-cellular localizations, erroneous formation of protein complexes and others. Nonetheless, current live cell super-resolution microscopy studies generally rely on the overexpression of a host protein fused to a fluorescent protein. Here, we establish CRISPR/Cas9-mediated generation of heterozygous and homozygous human knockin cell lines expressing fluorescently tagged proteins from their respective native genomic loci at close to endogenous levels. We tagged three different proteins, exhibiting various localizations and expression levels, with the reversibly switchable fluorescent protein rsEGFP2. We demonstrate the benefit of endogenous expression levels compared to overexpression and show that typical overexpression-induced artefacts were avoided in genome-edited cells. Fluorescence activated cell sorting analysis revealed a narrow distribution of fusion protein expression levels in genome-edited cells, compared to a pronounced variability in transiently transfected cells. Using low light intensity RESOLFT (reversible saturable optical fluorescence transitions) nanoscopy we show sub-diffraction resolution imaging of living human knockin cells. Our strategy to generate human cell lines expressing fluorescent fusion proteins at endogenous levels for RESOLFT nanoscopy can be extended to other fluorescent tags and super-resolution approaches.
Substrate‐integrated waveguide phase shifter with rod‐loaded artificial dielectric slab
Authors: Djerafi T. , Wu K. , Tatu S.O. 
Published: April 2015

A substrate‐integrated waveguide (SIW) broadband phase shifter is presented and studied. The phase shift mechanism is based on the synthesis of an artificial dielectric slab using an array of metallic rods in the middle of a SIW. This technique enables a large phase shift within a compact size and enhances the density of integration. As an example, 45° and 90° phase shifters are designed and showcased on a single‐layer substrate at a centre frequency of 26 GHz. The amplitude imbalance between the two paths is also avoided while the phase error is less than 5° over a frequency band of 20–32 GHz or around 46% relative bandwidth. The measured return loss is found to be better than 12 dB over the whole frequency band.
Doubly‐fed induction generator ride‐through fault capability using resonant controllers for asymmetrical voltage sags
Authors: Mendes Victor Flores , de Sousa Clodualdo Venicio , Hofmann Wilfried , Silva Selênio Rocha 
Published: April 2015

Modern grid codes worldwide determine specific requirements for the connection of wind energy conversion systems (WECSs) to the grid. One of the requirements is the ride‐through fault capability (RTFC) or low‐voltage ride‐through (LVRT), which defines that the plants must not be disconnected from the grid at certain levels of voltage sags and also must contribute to network stabilisation. The LVRT of the doubly‐fed induction generator (DFIG) technology is a well‐known problem, mainly during unbalanced grid voltage conditions. The present study extends the studies presented in the literature, analysing the DFIG behaviour during asymmetrical voltage sags using a frequency‐domain modelling. A modified resonant controller is proposed to improve the system response during voltage sags, and the analysis of the RTFC based on the converter limits is carried out. The proposed strategy is validated with simulation results of a 2 MW‐WECS and experimental results of a 25 kW scaled test bench.
THE GBT 67–93.6 GHz SPECTRAL LINE SURVEY OF ORION-KL
Authors: Frayer D. T. , Maddalena Ronald J. , Meijer M. , Hough L. , White S. , Norrod R. , Watts G. , Stennes M. , Simon R. , Woody D. , Srikanth S. , Pospieszalski M. , Bryerton E. , Whitehead M. , Ford P. , Mello M. , Bloss M. 
Published: April 2015

ABSTRACT
We present a 67–93.6 GHz spectral line survey of Orion-KL with the new 4 mm Receiver on the Green Bank Telescope (GBT). The survey reaches unprecedented depths and covers the low-frequency end of the 3 mm atmospheric window which has been relatively unexplored previously. The entire spectral-line survey is published electronically for general use by the astronomical community. The calibration and performance of the 4 mm Receiver on the GBT is also summarized.
edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Authors: Dimont Emmanuel , Shi Jiantao , Kirchner Rory , Hide Winston 
Published: April 2015

Abstract
Summary: Next-generation sequencing platforms for measuring digital expression such as RNA-Seq are displacing traditional microarray-based methods in biological experiments. The detection of differentially expressed genes between groups of biological conditions has led to the development of numerous bioinformatics tools, but so far, few exploit the expanded dynamic range afforded by the new technologies. We present edgeRun, an R package that implements an unconditional exact test that is a more powerful version of the exact test in edgeR. This increase in power is especially pronounced for experiments with as few as two replicates per condition, for genes with low total expression and with large biological coefficient of variation. In comparison with a panel of other tools, edgeRun consistently captures functionally similar differentially expressed genes.
Availability and implementation: The package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/edgeRun).
Contact: edimont@mail.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein homology reveals new targets for bioactive small molecules
Authors: Gfeller David , Zoete Vincent 
Published: April 2015

Abstract
Motivation: The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species.
Results: Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification.
Availability and implementation: Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch.
Contact: david.gfeller@unil.ch or vincent.zoete@isb-sib.ch.
Supplementary information: Supplementary data are available at Bioinformatics online.