bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Authors: Croucher Nicholas J. , Page Andrew J. , Connor Thomas R. , Delaney Aidan J. , Keane Jacqueline A. , Bentley Stephen D. , Parkhill Julian , Harris Simon R. 
Published: November 2014

AbstractThe emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.
Adaptation to larval crowding inDrosophila ananassaeandDrosophila nasuta nasuta: increased larval competitive ability without increased larval feeding rate
Authors: Nagarajan Archana , Natarajan Sharmila Bharathi , Jayaram Mohan , Thammanna Ananda , Chari Sudarshan , Bose Joy , Jois Shreyas V. , Joshi Amitabh 
Published: November 2014

AbstractThe standard view of adaptation to larval crowding in fruitflies, built on results from 25 years of multiple experimental evolution studies onD. melanogaster, is that enhanced competitive ability evolves primarily through increased larval feeding and foraging rate, at the cost of efficiency of food conversion to biomass, and increased larval tolerance to nitrogenous wastes. These results, moreover, were at odds from the predictions of classicalK-selection theory, notably the expectation that selection at high density should result in the increase of efficiency of conversion of food to biomass, and were better interpreted through the lens ofα-selection. We show here that populations ofD. ananassaeandD. n. nasutasubjected to extreme larval crowding evolve greater competitive ability and pre-adult survivorship at high density primarily through a combination of reduced larval duration, faster attainment of minimum critical size for pupation, greater time efficiency of food conversion to biomass, increased pupation height with a relatively small role of increased urea/ammonia tolerance, if at all. This is a very different suite of traits than that seen to evolve under similar selection inD.melanogasterand seems to be closer to the expectations from the canonical theory ofK-selection. We discuss possible reasons for these differences in results across the three species. Overall, the results reinforce the view that our understanding of the evolution of competitive ability in fruitflies needs to be more nuanced than before, with an appreciation that there may be multiple evolutionary routes through which higher competitive ability can be attained.
Personality traits and party identification over time
Authors: Bakker Bert N. , Hopmann David Nicolas , Persson Mikael 
Published: November 2014

AbstractWhy do some people stably identify with a party while others do not? This study tests whether and how the direction, stability and strength of party identification are associated with big five personality traits, using panel data from a representative sample of German citizens. First, the study confirms that personality traits are related to identification with different political parties. Second, it moves beyond previous research by showing that personality traits are related to the strength and variation in party identification over time. The implications of the study for the classical perspectives on party identification, as well as the personality and politics literature, are discussed.
Hyperandrogenism and phenotypes of polycystic ovary syndrome are not associated with differences in obstetric outcomes
Authors: Mumm Hanne , Jensen Dorte Møller , Sørensen Jens Aage , Andersen Lise Lotte Torvin , Ravn Pernille , Andersen Marianne , Glintborg Dorte 
Published: November 2014

AbstractObjectivesTo investigate obstetric outcomes in Danish women with different phenotypes of polycystic ovary syndrome (PCOS) and isolated hyperandrogenism (HA) and describe the risk of adverse obstetric outcomes in women with PCOS and HA compared to controls.DesignCohort study.SettingOdense University Hospital, Denmark.PopulationWomen with PCOS were identified prospectively starting in 1997. Singleton pregnancies in women with PCOS and HA during 2003–2011 were included (n = 199). A control group was matched to the patient cohort according to date of childbirth (n = 995).MethodsData on clinical characteristics and obstetric outcomes were collected in patients with PCOS and HA and controls. In PCOS and HA, total and free testosterone, sex hormone binding globulin, and hemoglobin A1c were measured outside pregnancy. During pregnancy, oral glucose tolerance tests were performed in 39 patients and 123 controls according to Danish national guidelines. PCOS phenotypes were based on the Rotterdam criteria.Main outcome measuresGestational diabetes mellitus, pregnancy‐induced hypertension, preeclampsia, delivery by emergency cesarean section, preterm delivery and anthropometric measures in the newborn.ResultsThe incidence of adverse obstetric outcomes and anthropometric measures among the newborns were comparable between different phenotypes of PCOS and patients with HA. In the oral glucose tolerance test, patients had a higher risk of gestational diabetes mellitus compared with controls; the odds ratio (95% confidence interval) was 3.3 (1.5–6.9) after adjustment for age, parity, and body mass index (p = 0.002). The incidence of other adverse obstetric outcomes was similar in patients and controls.ConclusionsObstetric outcomes were comparable in women with different PCOS phenotypes.
Tofacitinib withdrawal and retreatment in moderate-to-severe chronic plaque psoriasis: a randomized controlled trial
Authors: Bissonnette R. , Iversen L. , Sofen H. , Griffiths C.E.M. , Foley P. , Romiti R. , Bachinsky M. , Rottinghaus S.T. , Tan H. , Proulx J. , Valdez H. , Gupta P. , Mallbris L. , Wolk R. 
Published: November 2014

Summary

Background
Tofacitinib is an oral Janus kinase inhibitor being investigated for the treatment of moderate-to-severe plaque psoriasis.

Objectives
To compare outcomes following tofacitinib withdrawal with outcomes of continuation.

Methods
In this phase 3 study (NCT01186744), patients received tofacitinib 5 mg (n =331) or 10 mg (n =335) twice daily for 24 weeks. The patients who achieved both ≥ 75% reduction in Psoriasis Area and Severity Index (PASI 75) score from baseline and Physician's Global Assessment (PGA) of ‘clear’ or ‘almost clear’ (PGA response) received a placebo (withdrawal) or the previous dose. At relapse (&gt; 50% reduction in the PASI improvement during initial treatment) or week 40, the patients received the initial dose.

Results
Initial treatment: 33·5% and 55·2% achieved both PASI 75 and PGA responses with tofacitinib 5 and 10 mg twice daily, respectively, making them eligible for the treatment-withdrawal period. Withdrawal: 56·2%, 62·3%, 23·3% and 26·1% maintained PASI 75 responses with tofacitinib 5, 10 mg, placebo (5 mg) and placebo (10 mg) twice daily, respectively; 49·9%, 63·9%, 22·9% and 18·0% maintained PGA responses; and 92·3%, 93·0%, 32·8% and 42·9% did not relapse. Elevations in low-density lipoprotein–cholesterol levels following initial treatment (mean increase: 8·71 mg dL−1 with 5 mg twice daily, 10·26 mg dL−1 with 10 mg twice daily) were reversed upon withdrawal. Retreatment: 36·8% and 61·0% of patients who relapsed achieved PASI 75 responses with tofacitinib 5 or 10 mg after 16 weeks; 44·8% and 57·1% regained PGA responses.

Conclusions
Patients who received continuous treatment maintained a response more effectively when compared with placebo recipients. Safety profiles were comparable in both the continuous treatment group and retreatment group. Of those patients who relapsed, up to 60% recaptured a response with tofacitinib.
Methylation‐induced downregulation of TFPI‐2 causes TMPRSS4 overexpression and contributes to oncogenesis in a subset of non‐small‐cell lung carcinoma
Authors: Hamamoto Junko , Soejima Kenzo , Naoki Katsuhiko , Yasuda Hiroyuki , Hayashi Yuichiro , Yoda Satoshi , Nakayama Sohei , Satomi Ryosuke , Terai Hideki , Ikemura Shinnosuke , Sato Takashi , Arai Daisuke , Ishioka Kota , Ohgino Keiko , Betsuyaku Tomoko 
Published: November 2014

We identified transmembrane protease, serine 4 (TMPRSS4) as a putative, druggable target by screening surgically resected samples from 90 Japanese non‐small‐cell lung cancer (NSCLC) patients using cDNA microarray. TMPRSS4 has two druggable domains and was upregulated in 94.5% of the lung cancer specimens. Interestingly, we found that TMPRSS4 expression was associated with tissue factor pathway inhibitor 2 (TFPI‐2) expression in these clinical samples. In contrast to TMPRSS4, TFPI‐2 expression was downregulated in NSCLC samples. The in vitro induction of TFPI‐2 in lung cancer cell lines decreased the expression of TMPRSS4 mRNA levels. Reporter assay showed that TFPI‐2 inhibited transcription of TMPRSS4, although partially. Knockdown of TMPRSS4 reduced the proliferation rate in several lung cancer cell lines. When lung cancer cell lines were treated with 5‐aza‐2′‐deoxycytidine or trichostatin A, their proliferation rate and TMPRSS4 mRNA expression levels were also reduced through the upregulation of TFPI‐2 by decreasing its methylation in vitro. The TFPI‐2 methylation level in the low TMPRSS4 group appeared to be significantly low in NSCLC samples (P = 0.02). We found a novel molecular mechanism that TFPI‐2 negatively regulates cell growth by inhibiting transcription of TMPRSS4. We suggest that TMPRSS4 is upregulated by silencing of TFPI‐2 through aberrant DNA methylation and contributes to oncogenesis in NSCLC.
Women on Corporate Boards in Italy: The Role of Family Connections
Authors: Bianco Magda , Ciavarella Angela , Signoretti Rossella 
Published: November 2014

AbstractManuscript TypeEmpiricalResearch Question/IssueThis paper sets out to shed light on female representation on Italian corporate boards before the introduction of gender quota legislation in 2012, as well as on the relevance of family connections. We investigate the potential determinants of having boards with diverse representation and the correlation between female directorship and family connections, with a focus on governance measures.Research FindingsUsing data on all directors of Italian publicly traded companies from 2008 to 2010, we identify two different models. In the majority of gender‐diverse boards, at least one woman has a family connection to the controlling shareholder. Family‐affiliated women are more common in companies that are small, have a concentrated ownership, are in the consumer sector, and have a larger board. Conversely, non‐family‐affiliated women are more common on the boards of companies that are widely held, have younger and more educated boards, have a higher proportion of independent directors, and have a smaller number of interlocked directors. With reference to governance‐related outcomes, the number of board meetings appears to be negatively correlated to both the presence of family members and female directors. Additionally, women show lower attendance than men at board meetings.Theoretical/Academic ImplicationsThe paper provides support for theories on the differences between the governance of family‐owned and non‐family‐owned companies.Practitioner/Policy ImplicationThe study offers insights to policymakers implementing gender quota legislation. Substantial effort should be devoted to ensuring that board diversity is associated with actual independence of board members.
Analysis of edge crack behaviour influenced by non‐symmetrical contact tractions and bulk tension
Authors: Kim H.‐K. 
Published: November 2014

AbstractThis paper analyses a crack growth behaviour, which is initiated from the contact edge between a square punch with rounded edges and a half plane. Investigated are the influences of the contact profile, magnitude of the bulk tension and, crack obliquity, in particular, misalignment between the punch and half plane on the variation of the stress intensity factors KI and KII during the crack growth. The misalignment is simulated by a tilting of the punch. A partial slip regime is considered for the contact shear force to accommodate a general fretting fatigue condition. It was found that a crack closure occurs if only the contact forces are applied. The crack grows longer before it is closed if the punch is tilted (clockwise, in this paper) such that it initiates at the opposite site with respect to the direction of tilting. The closure phenomenon disappears when the bulk tension is added and exceeds a certain magnitude, which significantly depends on not only the contact profile but also the degree and direction of tilting. Provided are the lowest values of the bulk tensile stress due to a fatigue load necessary to extend the crack without a closure for each condition of the contact profile and misalignment. This may be used as a design guideline to restrain the contact‐induced failure.
The hippopotamus conveyor belt: vectors of carbon and nutrients from terrestrial grasslands to aquatic systems in sub‐Saharan Africa
Authors: Subalusky Amanda L. , Dutton Christopher L. , Rosi‐Marshall Emma J. , Post David M. 
Published: November 2014

Summary

Hippopotami can play a significant role as ecosystem engineers and may play an important role as carbon and nutrient vectors from savanna grasslands to aquatic systems.

We coupled the results of a feeding study of captive hippopotami, faeces leaching/mineralisation experiments, hippopotamus consumption estimates and the stoichiometry of savanna grasses to calculate excretion and egestion rates of hippopotami. We then used time budgets and population estimates to calculate nutrient loading by hippopotami in the Mara River, Kenya.

In captivity, hippopotami consumed 11.0 g dry matter (DM) kg hippopotamus−1 day−1 (110.6 C; 6.8 N; 1.0 P) and egested 5.3 g DM kg−1 day−1. They excreted or egested 2.72 g C, 0.28 g N and 0.04 g P kg hippopotamus−1 day−1, and urine comprised 12% of C, 70% of N and 33% of P of total excretion and egestion.

By integrating data from previously published work on hippopotamus digestion with the data we collected in the field, we estimated an average hippopotamus in the Mara River would excrete or egest 1.93–3.58 g DM, 0.78–1.47 g C, 0.13–0.19 g N and 0.01–0.02 g P kg hippopotamus−1 day−1, and that half of this excretion/egestion would enter the river.

The hippopotamus population increased by 1500% inside the Maasai Mara National Reserve, Kenya, between 1959 and 2006. We estimate that hippopotami egest 36 200 kg faeces day−1 into the Mara River (wet mass). Daily loading into the river by excretion and egestion equals 8563 kg DM, 3499 kg C, 492 kg N and 48 kg P, which is equivalent to 670% of CPOM, 15% of DOC, 27% of TN and 29% of TP of loading from the upstream catchment.

This research provides the first estimates for hippopotamus inputs to rivers that include both excretion and egestion and provides evidence that hippopotami are important resource vectors in sub‐Saharan African rivers, even when compared to other sources of carbon and nutrients.
Multiple nutrient subsidy pathways from a spawning migration of iteroparous fish
Authors: Childress Evan S. , McIntyre Peter B. 
Published: November 2014

Summary

Migratory animals can enhance ecosystem productivity through the delivery of material subsidies. Among fish, Pacific salmon are well known to deliver large quantities of nutrients to streams as they die after spawning, but the input pathways by which iteroparous species provide nutrient subsidies have not been resolved.

Our objective was to determine the importance of excretion, eggs and carcasses as nutrient sources from a large migration of longnose suckers into a stream draining a moderately agricultural catchment. Additionally, we evaluated nutrient limitation in the stream using nutrient‐diffusing substrates and determined the timing of nutrient releases during egg decomposition using a microcosm experiment.

Eggs were the largest component of the nitrogen (N, 57%) and phosphorus (P, 76%) inputs from the migration, followed by excretion by live adults (40% N, 16% P). Carcasses were a minor component of inputs.

Estimated P inputs from fish were over three times larger than the observed export of dissolved P in this P‐limited stream during the 66‐day sampling period. In contrast, sucker N inputs were <2% of dissolved N export, which was dominated by NO3. However, the dynamics of NH4 concentrations through the course of the migration were closely associated with estimated NH4 inputs from excretion and eggs.

Eggs and excretion constitute significant nutrient inputs during migrations, even in catchments with elevated nutrient loads from agriculture. Mass mortality is not required for migratory fish to enhance nutrient availability in their spawning habitats.

Given that sucker excretion rates and female reproductive investment are typical for freshwater fish, our results suggest that spawning migrations of iteroparous species in rivers around the world may deliver important nutrient subsidies when migrations are large.
The effects of flow and stream characteristics on the variation in freshwater mussel growth in a Southeast US river basin
Authors: Dycus Justin C. , Wisniewski Jason M. , Peterson James T. 
Published: November 2014

Summary

The evaluation of the age and growth of animal populations is essential for understanding and predicting how populations will respond to changes in environmental conditions and anthropogenic stressors.

We used a novel, von Bertalanffy hierarchical modelling approach to quantify relationships between the growth of three freshwater mussel species and various site‐ and watershed‐level factors including seasonal discharge, land cover and stream size in the lower Flint River Basin, Georgia, U.S.A.

Our modelling approach quantified the mussel‐to‐mussel variation in the von Bertalanffy parameters and accounted for biases associated with multiple measurements made on each mussel specimen, which are generally not accounted for as sources of bias in age and growth studies.

Modelling results suggested that maximum shell size parameter and the Brody growth coefficient varied across species, on average, 19 and 33%, respectively, among individual mussels within sample sites. The variation was related to short‐term high streamflows during the spring season, stream size, channel geomorphology and land cover in the watershed.

This study provides insight to the factors affecting the growth of stream‐dwelling freshwater mussels. Although hierarchical von Bertalanffy growth models are rarely used for freshwater mussel age and growth studies, this approach can provide important information regarding the ecology of freshwater mussels.
Boron isotope geochemistry ofNa‐bicarbonate,Na‐chloride, andCa‐chloride waters from theNorthernApennineForedeep basin: other pieces of the sedimentary basin puzzle
Authors: Boschetti T. , Toscani L. , Salvioli Mariani E. 
Published: November 2014

AbstractThe boron stable isotope ratio δ11Bof 12 water samples representative of three chemical facies (freshNa‐bicarbonate, brackishNa‐chloride, saline, and brineCa‐chloride) has been analyzed. Interpretation of the δ11Bdata, along with the chemical compositions, reveals thatNa‐carbonate waters from theNorthernApennine are of meteoric origin, with boron contributions from clay desorption and mixing with seawater‐derived fluids ofNa‐chloride orCa‐chloride compositions. The comparison of our new results with the literature data on other sedimentary basins ofMediterranean, and worldwide, confirms the contribution ofNa‐bicarbonate waters to the genesis of mud volcano fluids. TheNa‐chloride sample ofSalvarola (SAL), which may represent the end‐member of the mud volcanoes, and theCa‐chloride brine water fromSalsomaggiore (SM) indicate boron release from clays compatible with the diagenetic process. The empirical equation:urn:x-wiley:14688115:media:gfl12124:gfl12124-math-0001relating boron concentration and the stable isotope composition of the fluids observed in this study and the literature is proposed to trace the effect of diagenesis in sedimentary basins. A geothermometer associated to the diagenetic equation is also proposed:urn:x-wiley:14688115:media:gfl12124:gfl12124-math-0002The application of this equation to obtain reservoir temperatures from δ11B compositions of waters should be carefully evaluated against the results obtained from other chemical and isotopic geothermometers from other basins around the world.
The prevalence of culture‐confirmed toenail onychomycosis in at‐risk patient populations
Authors: Gupta A.K. , Daigle D. , Foley K.A. 
Published: November 2014

AbstractOnychomycosis is a fungal infection of the nail and is the most common nail affliction in the general population. Certain patient populations are at greater risk of infection and the prevalence of onychomycosis reported in the literature has yet to be summarized across these at‐risk groups. We performed a systematic review of the literature and calculated pooled prevalence estimates of onychomycosis in at‐risk patient populations. The prevalence of dermatophyte toenail onychomycosis was as follows: general population 3.22% (3.07, 3.38), children 0.14% (0.11, 0.18), the elderly 10.28% (8.63, 12.18), diabetic patients 8.75% (7.48, 10.21), psoriatic patients 10.22% (8.61, 12.09), HIV positive patients 10.40% (8.02, 13.38), dialysis patients 11.93% (7.11, 19.35) and renal transplant patients 5.17% (1.77, 14.14). Dialysis patients had the highest prevalence of onychomycosis caused by dermatophytes, elderly individuals had the highest prevalence of onychomycosis caused by yeasts (6.07%; 95% CI = 3.58, 10.11) and psoriatic patients had the highest prevalence of onychomycosis caused by non‐dermatophyte moulds (2.49%; 95% CI = 1.74, 3.55). An increased prevalence of onychomycosis in certain patient populations may be attributed to impaired immunity, reduced peripheral circulation and alterations to the nail plate which render these patients more susceptible to infection.
Guillain‐Barré syndrome associated with CASPR2 antibodies: two paediatric cases
Authors: Rosch Richard E. , Bamford Alasdair , Hacohen Yael , Wraige Elizabeth , Vincent Angela , Mewasingh Leena , Lim Ming 
Published: November 2014

AbstractThe pathogenesis of Guillain‐Barré syndrome (GBS) is considered to be, at least in part, mediated by autoantibodies directed against neuronal antigens. Antibodies to contactin‐associated protein‐like 2 (CASPR2), part of the voltage‐gated potassium channel complex (VGKC‐complex), are associated with neurological disease predominantly affecting the peripheral nervous system but are not known to be associated with GBS. We report two cases of ganglioside antibody‐negative paediatric GBS associated with CASPR2 antibodies. Both patients made a complete clinical recovery. The tissue distribution and function of CASPR2 make it a biologically plausible autoimmune target in GBS and its clinical relevance in GBS should be determined in further studies.