bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic hypothesis of Sphaerodoridae Malmgren, 1867 (Annelida) and its position within Phyllodocida
Authors: Capa María , Aguado M. Teresa , Bakken Torkild 
Published: September 2015

AbstractSphaerodoridae is a small, morphologically well‐defined group of annelids, with remarkable spherical tubercles covering their body surface. They have generally been considered as part of Phyllodocida, but there is no consensus about its sister group relationships. Monophyly and internal phylogenetic relationships have never been tested. We present the first phylogenetic analysis of the family, including 33 individuals of 19 species in five genera of Sphaerodoridae, and a wide representation of other Phyllodocida, based on molecular data from nuclear 18SrDNA(2240 bp), mitochondrial 16SrDNA(614 bp), and cytochrome c oxidase subunit I (657 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum parsimony, maximum likelihood and Bayesian inference. Results show maximum support for the monophyly of Sphaerodoridae, but sister group relationships remain unclear. The generaSphaerodoropsisandSphaerodoridiumare found to be paraphyletic. Monophyly ofClavodorum,EphesiellaandSphaerodorumcould not be tested because only one species was included for each of these genera. At least six of the morphotypes included in the study do not fit within current species descriptions, suggesting undescribed species. Finally, the transfer ofSphaerodoropsis minutaback toSphaerodoridiumis proposed.
Environmental cost of using poor decision metrics to prioritize environmental projects
Authors: Pannell David J. , Gibson Fiona L. 
Published: September 2015

AbstractConservation decision makers commonly use project‐scoring metrics that are inconsistent with theory on optimal ranking of projects. As a result, there may often be a loss of environmental benefits. We estimated the magnitudes of these losses for various metrics that deviate from theory in ways that are common in practice. These metrics included cases where relevant variables were omitted from the benefits metric, project costs were omitted, and benefits were calculated using a faulty functional form. We estimated distributions of parameters from 129 environmental projects from Australia, New Zealand, and Italy for which detailed analyses had been completed previously. The cost of using poor prioritization metrics (in terms of lost environmental values) was often high—up to 80% in the scenarios we examined. The cost in percentage terms was greater when the budget was smaller. The most costly errors were omitting information about environmental values (up to 31% loss of environmental values), omitting project costs (up to 35% loss), omitting the effectiveness of management actions (up to 9% loss), and using a weighted‐additive decision metric for variables that should be multiplied (up to 23% loss). The latter 3 are errors that occur commonly in real‐world decision metrics, in combination often reducing potential benefits from conservation investments by 30–50%. Uncertainty about parameter values also reduced the benefits from investments in conservation projects but often not by as much as faulty prioritization metrics.
A nationwide assessment comparing nonelective open with minimally invasive complex colorectal procedures
Authors: Schlussel A. T. , Lustik M. B. , Johnson E. K. , Maykel J. A. , Champagne B. J. , Damle A. , Ross H. M. , Steele S. R. 
Published: September 2015

AbstractAimThe use of minimally invasive colorectal surgery has increased greatly for both benign and malignant disease. Studies evaluating complex procedures have been largely limited to elective indications. We aimed to compare the outcome of a laparoscopic with an open transverse (TC) and total abdominal colectomy (TAC) in the nonelective setting.MethodComparative analysis was made using the Nationwide Inpatient Sample (2008–11) of patients undergoing a nonelective TC or TAC identified by ICD‐9‐CM procedure codes. The risk‐adjusted 30‐day outcome was assessed using regression modelling accounting for patient characteristics, comorbidity and surgical procedure.ResultsWe identified 7261 admissions including 818 laparoscopic and 6443 open procedures. The mean age of the population was 65 ± 17 years and patients in the laparoscopic group were younger (56 ± 20 vs 66 ± 17 years; P < 0.05). The rate of a single complication was lower in the laparoscopic group (26% vs 38%; P < 0.01), but this did not remain significant following a logistic regression analysis. Mortality was significantly lower in the laparoscopic group (3.1% vs 17%; P < 0.01) and this remained true after adjusting for covariates (OR = 0.62; P < 0.05). Laparoscopic cases were associated with a shorter median length of stay (10 vs 13 days; P < 0.01) and hospital charge ($75 758 vs $98 833; P < 0.01).ConclusionA nonelective laparoscopic TC or TAC is associated with an equivalent complication rate and lower mortality compared with an open operation. The results should encourage surgeons with the appropriate skills to consider a laparoscopic approach for nonelective pathology requiring a complex colectomy.
Ventral striatal gamma oscillations are highly variable from trial to trial, and are dominated by behavioural state, and only weakly influenced by outcome value
Authors: Malhotra Sushant , Cross Rob W. , Zhang Anqi , van der Meer Matthijs A. A. 
Published: September 2015

AbstractThe human and rodent ventral striatal local field potentials show striking oscillations in the gamma band (~ 40–100 Hz), which have been linked to aspects of behaviour such as reward anticipation and delivery, movement initiation, learning from feedback, and decision‐making. These oscillations show a rich temporal organization, whose relationship with behavioural variables is not well understood. Here, we show that, in rats performing a conditioned approach task, low‐gamma and high‐gamma oscillations during an immobile reward anticipation epoch were largely insensitive to outcome value, even though rats distinguished behaviourally between different outcomes, and single units encoded outcome value. Behaviour was highly stereotyped, yet we observed large variability from trial to trial in the occurrence and timing of these oscillations. Furthermore, higher‐order features such as high‐gamma power leading low‐gamma power, and phase‐amplitude coupling to lower‐frequency bands, were only marginally modulated by outcome value. Moreover, these patterns closely resembled those found during off‐task rest periods in which no rewards could be earned. These observations suggest a new interpretation of ventral striatal gamma oscillations as reflecting a default or resting state, with only minor and highly variable modulation by specific task‐related variables.
Video Deficit in Toddlers’ Object Retrieval: What Eye Movements Reveal About Online Cognition
Authors: Kirkorian Heather L. , Lavigne Heather J. , Hanson Katherine G. , Troseth Georgene L. , Demers Lindsay B. , Anderson Daniel R. 
Published: September 2015

The purpose of this study was to determine whether toddlers exhibit different eye‐movement patterns when watching real events versus video demonstrations in an object‐retrieval task. Twenty‐four‐month‐olds (N = 36) searched for a sticker on a felt board after watching an experimenter hide it behind a felt object in person or via video. Eye movements during the hiding event were recorded. Compared to those watching in‐person events, children watching video spent more time looking at the target location overall, yet they had relatively poor search performance. Visual attention to the target location predicted search performance in the video condition only; children who watched in‐person hiding events had high success rates even if they paid relatively little visual attention to the correct location. Findings are consistent with the hypothesis that toddlers process information more quickly for in‐person (versus video) events, enabling them to learn as well (or better) despite relatively low selective attention. Thus, relatively poor encoding, as well as memory retrieval, may underlie the video deficit.
Phenotype‐associated inbreeding biases estimates of inbreeding depression in a wild bird population
Authors: Becker P. J. J. , Hegelbach J. , Keller L. F. , Postma E. 
Published: September 2015

AbstractInbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long‐term individual‐based data for white‐throated dippers (Cinclus cinclus), a bird species in which inbreeding is relatively common, to obtain an empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.
Alcohol consumption is associated with a lower incidence of acute myocardial infarction: results from a large prospective population‐based study in Norway
Authors: Gémes K. , Janszky I. , Laugsand L. E. , László K. D. , Ahnve S. , Vatten L. J. , Mukamal K. J. 
Published: September 2015

AbstractAimsCompelling evidence suggests that light‐to‐moderate alcohol consumption is associated with a reduced risk of acute myocardial infarction (AMI), but several issues from previous studies remain to be addressed. The aim of this study was to investigate some of these key issues related to the association between alcohol consumption andAMIrisk, including the strength and shape of the association in a low‐drinking setting, the roles of quantity, frequency and beverage type, the importance of confounding by medical and psychiatric conditions, and the lack of prospective data on previous drinking.MethodsA population‐based prospective cohort study of 58 827 community‐dwelling individuals followed for 11.6 years was conducted. We assessed the quantity and frequency of consumption of beer, wine and spirits at baseline in 1995–1997 and the frequency of alcohol intake approximately 10 years earlier.ResultsA total of 2966 study participants had anAMIduring the follow‐up period. Light‐to‐moderate alcohol consumption was inversely and linearly associated withAMIrisk. After adjusting for major cardiovascular disease risk factors, the hazard ratio for a one‐drink increment in daily consumption was 0.72 (95% confidence interval 0.62–0.86). Accounting for former drinking or comorbidities had almost no effect on the association. Frequency of alcohol consumption was more strongly associated with lowerAMIrisk than overall quantity consumed.ConclusionsLight‐to‐moderate alcohol consumption was linearly associated with a decreased risk ofAMIin a population in which abstaining from alcohol is not socially stigmatized. Our results suggest that frequent alcohol consumption is most cardioprotective and that this association is not driven by misclassification of former drinkers.
Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests
Authors: Ding Junjun , Zhang Yuguang , Wang Mengmeng , Sun Xin , Cong Jing , Deng Ye , Lu Hui , Yuan Tong , Van Nostrand Joy D. , Li Diqiang , Zhou Jizhong , Yang Yunfeng 
Published: September 2015

AbstractAs two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as ‘The Oriental Botanic Garden’ for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.
Under‐recognised co‐morbidities in idiopathic pulmonary fibrosis: A review
Authors: de Boer Kaïssa , Lee Joyce S. 
Published: September 2015

AbstractCo‐morbidities in idiopathic pulmonary fibrosis are common. These co‐morbidities include obstructive sleep apnoea, gastro‐oesophageal reflux disease, pulmonary hypertension and depression. The presence of co‐morbidities among patients with idiopathic pulmonary fibrosis contributes to worse quality of life, morbidity and mortality. Despite the high prevalence of certain co‐morbidities in idiopathic pulmonary fibrosis, the optimal screening and management of many of these conditions remains unclear. The impact of co‐morbidities on this patient population is becoming more apparent. Their relevance will only increase as significant effort is being made to develop novel therapeutics that will alter the disease trajectory of patients with idiopathic pulmonary fibrosis. The purpose of this review is to focus on the epidemiology, pathophysiology, diagnosis and management of select co‐morbidities, including obstructive sleep apnoea, gastro‐oesophageal reflux disease, pulmonary hypertension and depression, in idiopathic pulmonary fibrosis.
A “Sorted” America? Geographic Polarization and Value Overlap in the American Electorate*
Authors: Strickler Ryan 
Published: September 2015

ObjectiveGeographic political polarization is an increasingly salient topic of academic and popular discourse. Using Bill Bishop's bestseller The Big Sort as a foil, this article tests the claim that America has split into “ideologically inbred” “red” and “blue” communities.MethodDrawing on Bishop's concept of “landslide” Democratic and Republican counties, the article uses survey data to measure the overlap in opinion between respondents from opposing “landslide” counties. This is done both graphically and with a quantitative measure developed by Levendusky and Pope (2011).ResultsAcross economic, social, and cultural value dimensions, there is vastly more common ground than difference between respondents from “landslide” Democratic and Republican counties.ConclusionHyperbolic claims of a “sorted” country aside, geographic polarization in the United States is limited at best. Partisan polarization could be a real and consequential phenomenon in the electorate, but it has little geographic, “red versus blue” manifestation.
To treat or not to treat: a rare case of pseudo‐thrombotic thrombocytopenic purpura in a Jehovah's Witness
Authors: Malla Midhun , Seetharam Mahesh 
Published: September 2015

BACKGROUNDThrombotic thrombocytopenic purpura (TTP) is a rare microvascular occlusive disorder characterized by systemic intravascular aggregation of platelets, thrombocytopenia, and mechanical injury to red blood cells. We report a rare case of pernicious anemia presenting as TTP in a Jehovah's Witness.CASE REPORTA 46‐year‐old Jehovah's Witness female presented with epigastric pain, vomiting, and diarrhea for 2 days and fatigue and paresthesias for 4 weeks. Initial laboratory evaluation showed severe anemia and thrombocytopenia with elevated total bilirubin and lactate dehydrogenase. Peripheral blood smear showed schistocytes, macroovalocytes, and hypersegmented neutrophils. TTP was suspected and plasmapheresis was offered. The patient refused it due to her religious beliefs. Due to the presence of macroovalocytes and hypersegmented neutrophils, vitamin B12 level was checked and found to be extremely low. Anti‐intrinsic factor antibodies and anti‐parietal cell antibodies were also positive; hence a diagnosis of pernicious anemia was established. Treatment with intramuscular vitamin B12 was initiated, which resulted in dramatic neurologic and hematologic improvement.DISCUSSIONVitamin B12 deficiency can lead to elevated levels of homocysteine in the blood. Homocysteine can cause endothelial dysfunction, which can lead to formation of microvascular thrombi. Due to this phenomenon, vitamin B12 deficiency can rarely present with schistocytes and thrombocytopenia, which combined with other stigmata of vitamin B12 deficiency, can be misdiagnosed as TTP.
Masitinib monotherapy in canine epitheliotropic lymphoma
Authors: Holtermann N. , Kiupel M. , Kessler M. , Teske E. , Betz D. , Hirschberger J. 
Published: September 2015

AbstractThis study evaluated efficacy and side effects of masitinib in canine epitheliotropic lymphoma. Complete remission occurred in 2 of 10 dogs and lasted for median 85 days. Five dogs went into partial remission for median 60.5 days. Three pretreated dogs did not respond to therapy. Side effects occurred in six dogs and were mostly mild to moderate. Immunohistochemistry was available for eight dogs.KITreceptor was negative in all of them, six of eight lymphomas stained strongly positive for stem cell factor (SCF). platelet‐derived growth factor (PDGF)‐AAwas weakly positive in two and negative in six.PDGF‐BBwas negative in four tumours, weakly positive in one and strongly positive in three. One was strongly positive for PDGF receptor (PDGFR)‐β, seven were negative for that receptor. Five showed strong expression ofPDGFR‐α, two showed weak expression, one was negative. In conclusion, masitinib is effective in treating canine epitheliotropic lymphoma. But its effects are most likely not generated through theKITreceptor.
A Single Mutation in the Gene Responsible for the Mucoid Phenotype of Bifidobacterium animalis subsp. lactis Confers Surface and Functional Characteristics
Authors: Hidalgo-Cantabrana Claudio , Sánchez Borja , Álvarez-Martín Pablo , López Patricia , Martínez-Álvarez Noelia , Delley Michele , Martí Marc , Varela Encarna , Suárez Ana , Antolín María , Guarner Francisco , Berger Bernard , Ruas-Madiedo Patricia , Margolles Abelardo 
Published: September 2015

ABSTRACT

Exopolysaccharides (EPS) are extracellular carbohydrate polymers synthesized by a large variety of bacteria. Their physiological functions have been extensively studied, but many of their roles have not yet been elucidated. We have sequenced the genomes of two isogenic strains of
Bifidobacterium animalis
subsp.
lactis
that differ in their EPS-producing phenotype. The original strain displays a nonmucoid appearance, and the mutant derived thereof has acquired a mucoid phenotype. The sequence analysis of their genomes revealed a nonsynonymous mutation in the gene Balat_1410, putatively involved in the elongation of the EPS chain. By comparing a strain from which this gene had been deleted with strains containing the wild-type and mutated genes, we were able to show that each strain displays different cell surface characteristics. The mucoid EPS synthesized by the strain harboring the mutation in Balat_1410 provided higher resistance to gastrointestinal conditions and increased the capability for adhesion to human enterocytes. In addition, the cytokine profiles of human peripheral blood mononuclear cells and
ex vivo
colon tissues suggest that the mucoid strain could have higher anti-inflammatory activity. Our findings provide relevant data on the function of Balat_1410 and reveal that the mucoid phenotype is able to alter some of the most relevant functional properties of the cells.
Expansion of the Tetracycline-Dependent Regulation Toolbox for Helicobacter pylori
Authors: Debowski Aleksandra W. , Sehnal Miriam , Liao Tingting , Stubbs Keith A. , Marshall Barry J. , Benghezal Mohammed 
Published: September 2015

ABSTRACT

In an effort to gain greater understanding of the biology and infection processes of
Helicobacter pylori
, we have expanded the functionality of the tetracycline-dependent gene regulation (
tet
) system to provide more improved and versatile genetic control and facilitate the generation of conditional mutants to study essential genes. Second-generation tetracycline-responsive
H. pylori
uPtetO
5 promoters were based on the mutated core
ureA
promoter. Single point mutations at either the ribosomal binding site or the start codon were introduced to shift the regulatory range of three
uPtetO
5 derivatives. All promoters were tested for regulation by TetR and revTetR using
dapD
, a gene essential to peptidoglycan biosynthesis, as a reporter. All
tet
promoters were effectively regulated by both TetR and revTetR, and their regulation windows overlapped so as to cover a broad range of expression levels.
tet
promoters
uPtetO
5m1 and
uPtetO
5m2 could be sufficiently silenced by both TetR and revTetR so that the conditional mutants could not grow in the absence of diaminopimelic acid (DAP). Furthermore, through the use of these inducible promoters, we reveal that insufficient DAP biosynthesis results in viable cells with altered morphology. Overall, the development and optimization of
tet
regulation for
H. pylori
will not only permit the study of essential genes but also facilitate investigations into gene dosage effects on
H. pylori
physiology.