bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean‐specific genes
Authors: Orsini Luisa , Brown James B. , Shams Solari Omid , Li Dong , He Shan , Podicheti Ram , Stoiber Marcus H. , Spanier Katina I. , Gilbert Donald , Jansen Mieke , Rusch Douglas B. , Pfrender Michael E. , Colbourne John K. , Frilander Mikko J. , Kvist Jouni , Decaestecker Ellen , De Schamphelaere Karel A. C. , De Meester Luc 
Published: July 2017

AbstractNatural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype‐specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co‐expression network analysis. We discovered that approximately one‐third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype‐ and/or condition‐specific transcriptional response with a strong genotype‐by‐environment interaction. Intriguingly, genotype‐ and condition‐specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche‐specific adaptation.
Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
Authors: Fuentes‐Pardo Angela P. , Ruzzante Daniel E. 
Published: July 2017

AbstractWhole‐genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled‐individual DNA (Pool‐seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
Structure and stability of genetic variance–covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three‐spined stickleback
Authors: Siren J. , Ovaskainen O. , Merilä J. 
Published: July 2017

AbstractThe genetic variance–covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G‐matrices is limited for two reasons. First, phenotypes are high‐dimensional, whereas traditional statistical methods are tuned to estimate and analyse low‐dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high‐dimensional G‐matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half‐sib breeding design of three‐spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low‐temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability—as well as the similarity among G‐matrices—may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G‐matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G‐matrices, the BSFG method can improve predicted evolutionary responses to selection.
A unique invertase is important for sugar absorption of an obligate biotrophic pathogen during infection
Authors: Chang Qing , Liu Jie , Lin Xiaohong , Hu Shoujun , Yang Yang , Li Dan , Chen Liyang , Huai Baoyu , Huang Lili , Voegele Ralf T. , Kang Zhensheng 
Published: July 2017

Summary

An increased invertase activity in infected plant tissue has been observed in many plant–pathogen interactions. However, the origin of this increased invertase activity (plant and/or pathogen) is still under debate. In addition, the role of pathogen invertases in the infection process is also unclear.

We identified and cloned a gene with homology to invertases from Puccinia striiformis f. sp. tritici (Pst). Transcript levels of PsINV were analyzed by quantitative reverse transcription PCR in both compatible and incompatible Pst–wheat interactions . Function of the gene product was confirmed by heterologous expression, and its function in Pst infection was analyzed by host‐induced gene silencing (HIGS).

Pst abundantly secretes invertase during its invasion attempts whether in a compatible or incompatible interaction with wheat. Further research into the different domains of this protein indicated that the rust‐specific sequence contributes to a higher efficiency of sucrose hydrolysis. With PsINV silenced by HIGS during the infection process, growth of Pst is inhibited and conidial fructification incomplete. Finally, pathogenicity of Pst is impaired and spore yield significantly reduced.

Our results clearly demonstrate that this Pst invertase plays a pivotal role in this plant–pathogen interaction probably by boosting sucrose hydrolysis to secure the pathogen's sugar absorption.
Oil rent, the Rentier State/Resource Curse Narrative and the GCC Countries
Authors: Rutledge Emilie 
Published: July 2017

AbstractDespite the fact that ‘rent’ underpins both Rentier State (RS) and Resource Curse (RC) theses, external factors that help shape perceptions of it and determine its value, are rarely factored in. The purpose of this article is to suggest reasons for this shortcoming and, with particular reference to the ‘archetypal candidate’ Gulf Cooperation Council countries, question the utility per se of the RS/RC paradigm (RS outcomes can only manifest within RC contexts). To explain the default and long‐standing utilisation of the construct across the social sciences—in spite of the frequent need to detour around contrary data—this paper points firstly to the way in which rent is now popularly perceived (from logically grounded, to excessively unwarranted) and secondly, to the fact that ‘oil’ lies at the paradigm's heart. It is a commodity that various Western polities once had unfettered control over; no other depletable natural resource in the past century has held such global economic significance (external actors clearly have a vested interest). Lastly, to underscore the need for a reappraisal of the RS/RC analytical framework, some data are presented that demonstrate that the GCC countries have not, comparatively speaking, suffered the deleterious consequences that the paradigm stipulates.
Impact of timing of recurrence following catheter ablation of scar‐related ventricular tachycardia on subsequent mortality
Authors: Muser Daniele , Mendelson Todd , Fahed Joe , Liang Jackson J. , Castro Simon A. , Zado Erica , Marchlinski Francis E. , Santangeli Pasquale 
Published: July 2017

AbstractBackgroundCatheter ablation (CA) has an established role in scar‐related ventricular tachycardia (VT), but the risk of recurrences is substantial and the appropriate intensity of postablation monitoring unknown. The implication of timing of postablation VT recurrence has not been adequately investigated.MethodsWe studied 120 consecutive patients with scar‐related VT (age 60 ± 15 years, left ventricular ejection fraction 39 ± 16%, 52% ischemic etiology) with at least 2 years of follow‐up. Timing of VT recurrence was classified as very early (<1 month), early (1–6 months), or late (>6 months).ResultsAt 24 months follow‐up, 53 (44%) patients had recurrent VT, with eight (15%) having very early recurrence, 17 (32%) early recurrence, and 28 (53%) late recurrence. Mortality rates at 2 years were significantly higher in patients with very early VT recurrence (38%) compared to those with early (12%), late (7%), and no (3%) recurrences (log‐rank P < 0.001). Very early VT recurrence was associated with an increased risk of death (odds ratio = 5.68, 95% confidence interval = 1.06–30.62, P = 0.04), while recurrent VT beyond 6 months was not associated with increased risk of mortality (P = 0.94).ConclusionsTiming of VT recurrence following CA of scar‐related VT impacts subsequent risk of mortality. Patients experiencing VT recurrence within 1–6 months from the procedure are at particularly high risk. These data support the importance of intense postablation monitoring for at least 6 months after the procedure to identify patients with early VT recurrence who may benefit from additional therapeutic interventions to improve outcomes.
Epicardial ablation of tachyarrhythmia in children: Experience at two academic centers
Authors: Upadhyay Shailendra , Walsh Edward P. , Cecchin Frank , Triedman John K. , Villafane Juan , Saul J. Philip 
Published: July 2017

AbstractBackgroundExperience with percutaneous epicardial ablation of tachyarrhythmia in pediatrics is limited. This case series addresses the feasibility, safety, and complications of the procedure in children.MethodsA total of nine patients underwent 10 epicardial ablation procedures from 2002 to 2013 at two academic centers. Activation mapping was performed in all cases, and electroanatomic map was utilized in nine of the 10 procedures. Patients had undergone one to three failed endocardial catheter ablations in addition to medical management, and all had symptoms, a high‐risk accessory pathway (AP), aborted cardiac arrest with Wolff‐Parkinson‐White syndrome (WPW), or ventricular dysfunction. A standard epicardial approach was used for access in all cases, using a 7‐ or 8‐ Fr sheath. Epicardial ablation modality was radiofrequency (RF) in seven, cryoablation (CRYO) in one, and CRYO plus RF in one.ResultsMedian age was 14 (range 8–19) years. Indications: drug refractory ectopic atrial tachycardia (one), ventricular tachycardia (VT) (five), high‐risk AP (two), and aborted cardiac arrest from WPW – (one). Epicardial ablation was not performed in one case despite access due to an inability to maneuver the catheter around a former pericardial scar. VT foci included the right ventricular outflow tract septum, high posterior left ventricle (LV), LV outflow tract, postero‐basal LV, and scar from previous rhabdomyoma surgery. WPW foci were in the area of the posterior septum and coronary sinus in all three cases. Overall procedural success was 70% (7/10), with epicardial ablation success in five and endocardial ablation success after epicardial mapping in two. The VT focus was close to the left anterior descending coronary artery in one of the unsuccessful cases in which both RF and CRYO were used. There was one recurrence after a successful epicardial VT ablation, which was managed with a second successful epicardial procedure. There were no other recurrences at more than 1 year of follow‐up. Complications were minimal, with one case of inadvertent pleural access requiring no specific therapy. No pericarditis or effusion was seen in any of the patients who underwent epicardial ablation.ConclusionEpicardial ablation in pediatric patients can be performed with low complications and acceptable success. It can be considered for a spectrum of tachycardia mechanisms after failed endocardial ablation attempts and suspected epicardial foci. Success and recurrence may be related to foci in proximity to the epicardial coronaries, pericardial scar, or a distant location from the closest epicardial location. Repeat procedures may be necessary.
A meta‐analysis on growth, physiological, and biochemical responses of woody species to ground‐level ozone highlights the role of plant functional types
Authors: Li Pin , Feng Zhaozhong , Catalayud Vicent , Yuan Xiangyang , Xu Yansen , Paoletti Elena 
Published: July 2017

AbstractThe carbon‐sink strength of temperate and boreal forests at midlatitudes of the northern hemisphere is decreased by ozone pollution, but knowledge on subtropical evergreen broadleaved forests is missing. Taking the dataset from Chinese studies covering temperate and subtropical regions, effects of elevated ozone concentration ([O3]) on growth, biomass, and functional leaf traits of different types of woody plants were quantitatively evaluated by meta‐analysis. Elevated mean [O3] of 116 ppb reduced total biomass of woody plants by 14% compared with control (mean [O3] of 21 ppb). Temperate species from China were more sensitive to O3 than those from Europe and North America in terms of photosynthesis and transpiration. Significant reductions in chlorophyll content, chlorophyll fluorescence parameters, and ascorbate peroxidase induced significant injury to photosynthesis and growth (height and diameter). Importantly, subtropical species were significantly less sensitive to O3 than temperate ones, whereas deciduous broadleaf species were significantly more sensitive than evergreen broadleaf and needle‐leaf species. These findings suggest that carbon‐sink strength of Chinese forests is reduced by present and future [O3] relative to control (20–40 ppb). Given that (sub)‐tropical evergreen broadleaved species dominate in Chinese forests, estimation of the global carbon‐sink constraints due to [O3] should be re‐evaluated.
Neonatal perforated appendicitis in incarcerated inguinal hernia in the differential diagnosis of testis torsion
Authors: Erginel Basak , Soysal Feryal Gun , Celik Alaaddin , Salman Tansu 
Published: July 2017

AbstractAppendicitis in newborns is uncommon and difficult to diagnose. Reports on neonatal appendicitis subsequent to inguinal hernia incarceration are exceptionally rare. We present the case of a 26‐day‐old infant with perforated appendicitis due to incarceration of a right inguinal hernia, mimicking right testicular torsion.
Transparency in multilateral climate politics: Furthering (or distracting from) accountability?
Authors: Gupta Aarti , van Asselt Harro 
Published: July 2017

AbstractThis article analyzes the interplay between transparency and accountability in multilateral climate politics. The 2015 Paris Agreement calls for a “pledge‐and‐review” approach to collective climate action with an “enhanced transparency framework” as a key pillar of the Agreement. By making visible who is doing what, transparency is widely assumed to be vital to holding countries to account and building trust. We explore whether transparency is generating such effects in this context, by developing and applying an analytical framework to examine the link between transparency and accountability. We find that the scope and practices of climate transparency reflect (rather than necessarily reduce) broader conflicts over who should be held to account to whom and about what, with regard to responsibility and burden sharing for ambitious climate action. We conclude that the relationship between transparency and accountability is less straightforward than assumed, and that the transformative promise of transparency needs to be reconsidered in this light.
Congressional Attention and Opportunity Structures: The Select Energy Independence and Global Warming Committee
Authors: Lewallen Jonathan 
Published: July 2017

AbstractThis article examines the role that overlapping committee jurisdictions play in fostering or hindering attention to environmental and energy issues in the U.S. Congress. The Select Energy Independence and Global Warming Committee, created by House Democrats in , and its chairman Rep. Ed Markey took advantage of opportunities within the existing jurisdictional arrangement to increase attention to these issues despite lacking any legislative authority. Data from the 110th and 111th Congresses show that the Select Committee held more hearings on climate change and alternative energy, and on environmental and energy policy generally, than any other committee. The committee also increased the range of sources informing debate on these issues by calling different witnesses than other committees. These findings have important implications for the relationship between institutional structure and agendas and for Congress' policy‐making role on energy and the environment.
The Foreseeable Harms of Trump's Global Gag Rule
Authors: Bingenheimer Jeffrey B. , Skuster Patty 
Published: July 2017

AbstractAs one of his first acts as President of the United States, Donald Trump signed an executive order reinstating a version of the global gag rule. Under this rule, US grantees are barred from receiving global health funding if they engage in abortion‐related work: not only abortion services, but also abortion referrals and counseling or advocacy for the liberalization of abortion laws. Critics of the Trump global gag rule generally raise three classes of objections: (1) that the rule fails to accomplish its presumed objective of reducing the number of abortions; (2) that it negatively affects the health and well‐being of individuals and populations in affected countries; and (3) that it interferes with governments’ ability to meet their international obligations. In this commentary, we examine the scientific and policy bases for these criticisms.
An open task to promote students to create statistical concepts through modelling
Authors: Albarracín Lluís , Aymerich Àngels , Gorgorió Núria 
Published: July 2017

SummaryThis article reports on the solutions of a group of 22 students, aged 15/16 years old, when facing a statistical modelling activity. They were given the salary lists of 5 companies and were asked what could be said about their salary structure; no hint was given. The results show that students not only used a wide range of data concepts and procedures but also developed their own criteria to measure dispersion.
The LexA transcription factor regulates fatty acid biosynthetic genes in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Kizawa Ayumi , Kawahara Akihito , Takashima Kosuke , Takimura Yasushi , Nishiyama Yoshitaka , Hihara Yukako 
Published: July 2017

SummarySpecific transcription factors have been identified in various heterotrophic bacterial species that regulate the sets of genes required for fatty acid metabolism. Here, we report that expression of the fab genes, encoding fatty acid biosynthetic enzymes, is regulated by the global regulator LexA in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803. Sll1626, an ortholog of the well‐known LexA repressor involved in the SOS response in heterotrophic bacteria, was isolated from crude extracts of Synechocystis by DNA affinity chromatography, reflecting its binding to the upstream region of the acpP‐fabF and fabI genes. An electrophoresis mobility shift assay revealed that the recombinant LexA protein can bind to the upstream region of each fab gene tested (fabD, fabH, fabF, fabG, fabZ and fabI). Quantitative RT‐PCR analysis of the wild type and a lexA‐disrupted mutant strain suggested that LexA acts as a repressor of the fab genes involved in initiation of fatty acid biosynthesis (fabD, fabH and fabF) and the first reductive step in the subsequent elongation cycle (fabG) under normal growth conditions. Under nitrogen‐depleted conditions, downregulation of fab gene expression is partly achieved through an increase in LexA‐repressing activity. In contrast, under phosphate‐depleted conditions, fab gene expression is upregulated, probably due to the loss of repression by LexA. We further demonstrate that elimination of LexA largely increases the production of fatty acids in strains modified to secrete free fatty acids.
The role of T‐type calcium channels in the subiculum: to burst or not to burst?
Authors: Joksimovic Srdjan M. , Eggan Pierce , Izumi Yukitoshi , Joksimovic Sonja Lj. , Tesic Vesna , Dietz Robert M. , Orfila James E. , DiGruccio Michael R. , Herson Paco S. , Jevtovic‐Todorovic Vesna , Zorumski Charles F. , Todorovic Slobodan M. 
Published: July 2017

Key points
Pharmacological, molecular and genetic data indicate a prominent role of low‐voltage‐activated T‐type calcium channels (T‐channels) in the firing activity of both pyramidal and inhibitory interneurons in the subiculum.
Pharmacological inhibition of T‐channels switched burst firing with lower depolarizing stimuli to regular spiking, and fully abolished hyperpolarization‐induced burst firing.
Our molecular studies showed that CaV3.1 is the most abundantly expressed isoform of T‐channels in the rat subiculum.
Consistent with this finding, both regular‐spiking and burst firing patterns were profoundly depressed in the mouse with global deletion of CaV3.1 isoform of T‐channels.
Selective inhibition of T‐channels and global deletion of CaV3.1 channels completely suppressed development of long‐term potentiation (LTP) in the CA1–subiculum, but not in the CA3–CA1 pathway.
AbstractSeveral studies suggest that voltage‐gated calcium currents are involved in generating high frequency burst firing in the subiculum, but the exact nature of these currents remains unknown. Here, we used selective pharmacology, molecular and genetic approaches to implicate Cav3.1‐containing T‐channels in subicular burst firing, in contrast to several previous reports discounting T‐channels as major contributors to subicular neuron physiology. Furthermore, pharmacological antagonism of T‐channels, as well as global deletion of CaV3.1 isoform, completely suppressed development of long‐term potentiation (LTP) in the CA1–subiculum, but not in the CA3–CA1 pathway. Our results indicate that excitability and synaptic plasticity of subicular neurons relies heavily on T‐channels. Hence, T‐channels may be a promising new drug target for different cognitive deficits.