bluuebunny/crossref_metadata_2025_split huggingface dataset:
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
Authors: Mallo Diego , Oliveira Martins Leonardo de , Posada David 
Published: July 2015

AbstractWe present here a fast and flexible software –SimPhy– for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to the species tree/gene tree discordance– and gene conversion.SimPhyimplements a hierarchical phylogenetic model in which the evolution of species, locus and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled froma prioristatistical distributions.SimPhyalso incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validateSimPhy’s output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate howSimPhycan be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods.SimPhyis available athttps://github.com/adamallo/SimPhy, where users can find the source code, pre-compiled executables, a detailed manual and example cases.
Cooperative Binding Mitigates the High-Dose Hook Effect
Authors: Roy Ranjita Dutta , Rosenmund Christian , Stefan Melanie I 
Published: July 2015

AbstractBackgroundThe high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker protein in the mixture does not always increase the amount of fully formed complex. On the contrary, at a high enough concentration range the amount of fully formed complex actually decreases. It has been observed that allosterically regulated proteins seem less susceptible to this effect. The aim of this study was two-fold: First, to investigate the mathematical basis of how allostery mitigates the prozone effect. And second, to explore the consequences of allostery and the high-dose hook effect using the example of calmodulin, a calcium-sensing protein that regulates the switch between long-term potentiation and long-term depression in neurons.ResultsWe use a combinatorial model of a “perfect linker protein” (with infinite binding affinity) to mathematically describe the hook effect and its behaviour under allosteric conditions. We show that allosteric regulation does indeed mitigate the high-dose hook effect. We then turn to calmodulin as a real-life example of an allosteric protein. Using kinetic simulations, we show that calmodulin is indeed subject to a hook effect. We also show that this effect is stronger in the presence of the allosteric activator Ca2+/calmodulin-dependent kinase II (CaMKII), because it reduces the overall cooperativity of the calcium-calmodulin system. It follows that, surprisingly, there are conditions where increased amount of allosteric activator actuallydecreasethe activity of a protein.ConclusionsWe show that cooperative binding can indeed act as a protective mechanism against the hook effect. This will have implicationsin vivowhere the extent of cooperativity of a protein can be modulated, for instance, by allosteric activators or inhibitors. This can result in counterintuitive effects of decreased activity with increased concentrations of both the allosteric protein itself and its allosteric activators.
Chromatin interactions correlate with local transcriptional activity inSaccharomyces cerevisiae
Authors: Scholl Zackary , Zhong Jianling , Hartemink Alexander J. 
Published: July 2015

AbstractGenome organization is crucial for efficiently responding to DNA damage and regulating transcription. In this study, we relate the genome organization ofSaccharomyces cerevisiae(budding yeast) to its transcription activity by analyzing published circularized chromosome conformation capture (4C) data in conjunction with eight separate datasets describing genome-wide transcription rate or RNA polymerase II (Pol II) occupancy. We find that large chromosome segments are more likely to interact in areas that have high transcription rate or Pol II occupancy. Additionally, we find that groups of genes with similar transcription rates or similar Pol II occupancy are more likely to have higher numbers of chromosomal interactions than groups of random genes. We hypothesize that transcription localization occurs around sets of genes with similar transcription rates, and more often around genes that are highly transcribed, in order to produce more efficient transcription. Our analysis cannot discern whether gene co-localization occurs because of similar transcription rates or whether similar transcription rates are a consequence of co-localization.
S Group’s vision for strategic transformation: “Your Own Store”
Authors: Neilimo Kari , Kuusela Hannu , Närvänen Elina , Saarijärvi Hannu 
Published: July 2015

Purpose
– The vision should ignite and facilitate strategic change as well as help a company to transform and reinvent itself in the face of competition. Too often executives use vision as a mere slogan without real relevance. The purpose of this study is to show how the vision guides strategic change.

Design/methodology/approach
– A case study from a successful multi-format, multi-industry service business is used to illustrate the role of vision in strategic change management.

Findings
– The article illustrates how the vision was used in practice in guiding the strategic transformation process of the case organization. The study presents four focal tasks of the vision and concludes with five practical guidelines for executives.

Originality/value
– The article highlights the role of vision as an important tool for managing strategic change.
Body reserves influence allocation to immune responses in capital breeding female northern elephant seals
Authors: Peck Hannah E. , Costa Daniel P. , Crocker Daniel E. 
Published: June 2015

Summary

Mounting an immune response requires substantial energy. Ecological immunology theory predicts allocation trade‐offs between reproductive effort and immune responses under conditions of energy limitation. Little is known about the impact of capital breeding strategies on energy allocation to immune function in mammals.

Northern elephant seals (NES) forage in the marine environment, breed in dense terrestrial colonies and exhibit high rates of energy expenditure for lactation while fasting. Body reserves strongly influence reproductive effort and lactation requires elevation of plasma cortisol for energy mobilization.

We characterized immune response by measuring a suite of immune markers including cytokines, an acute phase protein, and immunoglobulins early and late in breeding and moult haul‐outs in 197 samples from 129 female NES. We explored potential impacts of breeding, body condition and plasma cortisol on immune function.

Immune responses were greater and more varied during breeding. Adiposity had positive associations with innate immune responses across all life‐history stages. Body mass had positive associations with both adaptive and innate immune responses early in fasts. Females with lower fat reserves showed reduced innate immune responses at the end of lactation. Immunoglobulin E, a marker of immune response to parasitic infection, exhibited a significant negative association with cortisol across all life‐history stages.

These data suggest that breeding carries an immune cost and provide evidence for allocation trade‐offs between immune function and breeding effort. These trade‐offs may reflect a compromise between immune costs inherent in colonial breeding and energetic limitations that arise in use of capital breeding strategies. Variation in evidence for immunosuppressive effects of cortisol suggests that decoupling of these effects may be limited to specific aspects of the immune response during terrestrial fasting. Immune responses that are required for survival may be modulated relative to the energetic demands required for successful reproduction.
Structure and functioning of intertidal food webs along an avian flyway: a comparative approach using stable isotopes
Authors: Catry Teresa , Lourenço Pedro M. , Lopes Ricardo J. , Carneiro Camilo , Alves José A. , Costa Joana , Rguibi‐Idrissi Hamid , Bearhop Stuart , Piersma Theunis , Granadeiro José P. 
Published: June 2015

Summary

Food webs and trophic dynamics of coastal systems have been the focus of intense research throughout the world, as they prove to be critical in understanding ecosystem processes and functions. However, very few studies have undertaken a quantitative comparison of entire food webs from a key consumer perspective across a broad geographical area, limiting relevant comparisons among systems with distinct biotic and abiotic components.

We investigate the structure and functioning of food webs in four tidal ecosystems of international importance for migratory shorebirds along the East Atlantic Flyway: Tejo estuary in Portugal, Sidi Moussa in Morocco, Banc d'Arguin in Mauritania and Bijagós archipelago in Guinea‐Bissau. Basal food sources, shorebirds and their prey (benthic invertebrates) were sampled in all areas, and Bayesian stable isotope mixing models and community‐wide metrics were used in a comparative analysis among areas.

Significant differences among study areas were found in the structure of food webs, as well as in the relative importance of basal resource pools supporting each food web. Overall, the food web of Banc d'Arguin was characterized by lower trophic diversity and higher functional redundancy than the other sites. This result might be explained by the low number of trophic pathways of organic matter transfer in this seagrass‐dominated system which, as a fossil estuary, lacks inputs from both freshwater and nutrient‐rich offshore oceanic waters.

Structure of shorebird communities was consistent with the main organizational patterns found for each food web, highlighting the less diverse character of the community of Banc d'Arguin. At Banc d'Arguin and Bijagós archipelago, which displayed the smallest and largest isotopic niche widths in bird assemblage, respectively, mean niche overlap among species was low, suggesting high interspecific partitioning in resource use. Tropical systems typically offer comparatively lower harvestable prey biomass for shorebirds and might thus strengthen interspecific competition, leading to low niche overlap among species.

Our study reveals relevant differences in the structure of food webs and shorebird communities in coastal areas along an avian flyway. While differences in trophic redundancy of food webs point to distinct levels of ecosystem resilience, contrasts in the organization of shorebird communities highlight the plasticity in the foraging behaviour of species inhabiting areas with distinct environmental conditions.
Scale‐dependent responses of pollination and seed dispersal mutualisms in a habitat transformation scenario
Authors: Fontúrbel Francisco E. , Jordano Pedro , Medel Rodrigo 
Published: June 2015

Summary

Transformed habitats are the result of deliberate replacement of native species by an exotic monoculture, involving changes in biotic and abiotic conditions. Despite the fact that transformed habitats are becoming more common and constitute a major biodiversity change driver, little is known about the scale‐dependent responses of plant–animal mutualisms.

Aiming to test the multiscale responses of pollination and seed dispersal in a habitat transformation scenario, we examined a gradient of native and transformed habitats at three spatial scales (0–50, 50–100 and 100–250 m) and focused on a highly specialized mutualistic system composed of a hemiparasitic mistletoe (Tristerix corymbosus) that is almost exclusively pollinated by a hummingbird (Sephanoides sephaniodes) and dispersed by an arboreal marsupial (Dromiciops gliroides).

Even though mistletoes were found along the gradient, they were more abundant and more densely aggregated when the transformed habitat was dominant. Disperser and pollinator activity also increased as the transformed habitat becomes dominant, at the scale of 0–50 and 50–100 m, respectively. Furthermore, crop size and disperser activity covaried at broad and intermediate scales, whereas recruitment covaried at intermediate and fine scales. Moreover, disperser activity and the number of seedlings were spatially associated, stressing D. gliroides’ role in the recruitment of the mistletoe.

Synthesis. This highly specialized mutualistic system seems to be responding positively to the habitat structure modifications associated with Eucalyptus plantations. However, the actual costs (e.g. reduced gene flow, increased herbivory) in these transformed habitats are yet to be assessed.
Barriers and Facilitators for Sustainability of Tele‐Homecare Programs: A Systematic Review
Authors: Radhakrishnan Kavita , Xie Bo , Berkley Amy , Kim Miyong 
Published: June 2015

ObjectiveTo identify the barriers and facilitators for sustainability of tele‐homecare programs implemented by home health nursing agencies for chronic disease management.Data SourcesEnglish‐language articles on home telehealth in the CINAHL, PubMed/MEDLINE, PsychInfo, Web of Science, and Cochrane Reviews databases published from January 1996 to December 2013.Study DesignWe performed a systematic literature review. Data extraction using PRISMA guidelines and quality appraisal using the Mixed Methods Appraisal Tool (MMAT) were conducted on relevant empirical studies. Thematic analysis across the studies and narrative summaries were used to synthesize the findings from the included studies.Principal FindingsOf the initial 3,920 citations, we identified 16 articles of moderate quality meeting our inclusion criteria. Perceptions on effectiveness of tele‐homecare programs for achieving intended outcomes; tailoring of tele‐homecare programs to patient characteristics and needs; relationship and communication between patient, nurse, and other health care professional users of tele‐homecare; home health organizational process and culture; and technology quality, capability, and usability impacted the sustainability of tele‐homecare programs.ConclusionsThe findings of this systematic review provide implications for sustained usage of tele‐homecare programs by home health nursing agencies and can help such programs realize their potential for chronic disease management.
Accuracy of Self‐Reported Health Care Use in a Population‐Based Sample of Homeless Adults
Authors: Hwang Stephen W. , Chambers Catharine , Katic Marko 
Published: June 2015

ObjectiveTo assess the accuracy of self‐reported ambulatory care visits, emergency department (ED) encounters, and overnight hospitalizations in a population‐based sample of homeless adults.Data SourceSelf‐report survey data and administrative health care utilization databases.Study DesignSelf‐reported health care use in the past 12 months was compared to administrative encounter records among 1,163 homeless adults recruited in 2004–2005 from shelters and meal programs in Toronto, Ontario.Data Extraction MethodsSelf‐reported health care use was assessed using a structured face‐to‐face survey. Each participant was linked to administrative databases using a unique personal health number or their first name, last name, sex, and date of birth.Principal FindingsThe sensitivity of self‐report for ambulatory care visits, ED encounters, and overnight hospitalizations was 89, 80, and 73 percent, respectively; specificity was 37, 83, and 91 percent. The mean difference between self‐reported and documented number of encounters in the past 12 months was +1.6 for ambulatory care visits (95 percent CI = 0.4, 2.8), −0.6 for ED encounters (95 percent CI = −0.8, −0.4), and 0.0 for hospitalizations (95 percent CI = 0.0, 0.1).ConclusionsAdults experiencing homelessness are quite accurate reporters of their use of health care, especially for ED encounters and hospitalizations.
Impacts of New Zealand's lowered minimum purchase age on context‐specific drinking and related risks
Authors: Gruenewald Paul J. , Treno Andrew J. , Ponicki William R. , Huckle Taisia , Yeh Li‐Chia , Casswell Sally 
Published: June 2015

AbstractAimsThe minimum purchase age (MPA) for alcohol in New Zealand (NZ) was reduced from 20 to 18 years in 1999. We assessed the degree to which this change was associated with alterations in uses of drinking contexts, drinking and related problems.MethodsNZ National Alcohol Surveys among people 14+ years of age provided demographics, frequencies and amounts consumed in drinking places, and problem measures for 1995, 2000 and 2004. Censored regression estimates of parameters of a context‐specific dose–response model identified MPA‐associated changes in drinking and problems.ResultsThe lowered MPA was associated with more frequent drinking at pubs/nightclubs among the newly of‐age 18–19‐year‐olds (b = 15.26, P = 0.009), moderated drinking quantities at these places (b = –0.94, P = 0.034) and greater quantities consumed at home (b = 1.01, P = 0.010) and others’ homes (b = 0.87; P = 0.029). Drinking frequency and quantity in the 16–17‐year age group increased at home (b = 22.11, P = 0.040 and b = 1.22, P = 0.002) and others’ homes (b = 11.65, P = 0.002 and b = 0.91, P = 0.021). Problems associated with drinking contexts changed post‐MPA (G2 ≥ 27.45, P ≤ 0.002), specifically increased association with drinking in pubs/nightclubs (b = 0.09, P < 0.001) across both age groups.ConclusionsThe 1999 change in New Zealand's minimum purchase age for alcohol from 20 to 18 years appears to have been associated with substantive changes in uses of drinking contexts, drinking and associated drinking problems among 16–19‐year‐olds.
eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS‐identified asthma genes
Authors: Li X. , Hastie A. T. , Hawkins G. A. , Moore W. C. , Ampleford E. J. , Milosevic J. , Li H. , Busse W. W. , Erzurum S. C. , Kaminski N. , Wenzel S. E. , Meyers D. A. , Bleecker E. R. 
Published: June 2015

AbstractBackgroundGenome‐wide association studies (GWASs) have identified various genes associated with asthma, yet, causal genes or single nucleotide polymorphisms (SNPs) remain elusive. We sought to dissect functional genes/SNPs for asthma by combining expression quantitative trait loci (eQTLs) and GWASs.MethodsCis‐eQTL analyses of 34 asthma genes were performed in cells from human bronchial epithelial biopsy (BEC, n = 107) and from bronchial alveolar lavage (BAL, n = 94).ResultsFor TSLP‐WDR36 region, rs3806932 (G allele protective against eosinophilic esophagitis) and rs2416257 (A allele associated with lower eosinophil counts and protective against asthma) were correlated with decreased expression of TSLP in BAL (P = 7.9 × 10−11 and 5.4 × 10−4, respectively) and BEC, but not WDR36. Surprisingly, rs1837253 (consistently associated with asthma) showed no correlation with TSLP expression levels. For ORMDL3‐GSDMB region, rs8067378 (G allele protective against asthma) was correlated with decreased expression of GSDMB in BEC and BAL (P = 1.3 × 10−4 and 0.04) but not ORMDL3. rs992969 in the promoter region of IL33 (A allele associated with higher eosinophil counts and risk for asthma) was correlated with increased expression of IL33 in BEC (P = 1.3 × 10−6) but not in BAL.ConclusionsOur study illustrates cell‐type‐specific regulation of the expression of asthma‐related genes documenting SNPs in TSLP, GSDMB, IL33, HLA‐DQB1, C11orf30, DEXI, CDHR3, and ZBTB10 affect asthma risk through cis‐regulation of its gene expression. Whenever possible, disease‐relevant tissues should be used for transcription analysis. SNPs in TSLP may affect asthma risk through up‐regulating TSLP mRNA expression or protein secretion. Further functional studies are warranted.
The comparative effectiveness of biologics among older adults and disabled rheumatoid arthritis patients in the Medicare population
Authors: Yun Huifeng , Xie Fenglong , Delzell Elizabeth , Chen Lang , Yang Shuo , Saag Kenneth G. , Joseph George , Harrison David , Curtis Jeffrey R. 
Published: July 2015

AimsOlder and disabled rheumatoid arthritis (RA) patients are often not present in large numbers in clinical trials or registries. A novel, claims‐based clinical effectiveness algorithm provides the potential to compare the effectiveness of different biologics among this population using large administrative databases.MethodUsing Medicare 2006–2010 data for 100% of patients with RA, we identified biologic naïve users of abatacept, adalimumab, etanercept and infliximab, defined as no biologic use during the 12 months before the biologic initiation. The effectiveness was evaluated at 365 days after biologic initiation, determined using a validated claims‐based algorithm. We compared the proportion meeting effectiveness criteria for each biologic using robust Poisson regression to compute risk ratios (RRs) adjusted for potential confounders. One year cost per effectively treated patient was calculated by different biologics.ResultsThe study included biologic naïve users of abatacept (n = 2129), adalimumab (n = 2944), etanercept (n = 3517) and infliximab (n = 5654). The algorithm classified the medications as 26% effective for abatacept, 24% for adalimumab, 28% for etanercept and 23% for infliximab, indicating comparable effectiveness. However, after adjustment and compared with infliximab, the RRs for effectiveness were 1.17 (95% CI 1.06, 1.30) for abatacept, 1.11 (95% CI 1.02, 1.23) for adalimumab and 1.27 (95% CI 1.17, 1.39) for etanercept. Older patients had a higher effectiveness than patients who were disabled (RR = 1.18, 95% CI 1.08, 1.28). Infliximab had highest cost per effectively treated patient.ConclusionAbatacept, adalimumab and etanercept are more effective than infliximab among RA patients initiating biologics. Effectiveness was significantly higher among older patients compared with disabled RA Medicare patients.
Morphine Analgesia Modification in Normotensive and Hypertensive Female Rats after Repeated Fluoxetine Administration
Authors: Kosiorek‐Witek Anna , Makulska‐Nowak Helena Elżbieta 
Published: July 2015

AbstractThe purpose of this investigation was to determine through the use of fluoxetine the effect of administering a serotonin reuptake inhibitor over several days on the antinociceptive action of μ‐morphine type opioid receptor agonist. Investigations were performed on rats of both sexes, both the WKY normotensive strains as well as on the SHR genetically conditioned hypertensive strains. Results showed that the efficacy of morphine analgesia is higher in the SHR strain compared to normotensive rats (WKY). Surprisingly, repeated administration of fluoxetine reduced morphine analgesia, with the weakening of opioid antinociceptive action comparable to the duration of serotonin reuptake inhibitor administration. It was also concluded that the antinociceptive action of morphine in female rats and the alteration of its efficacy as a result of fluoxetine premedication for several days depend on oestrus cycle phase. The highest sensitivity of female rats to morphine was reported in the dioestrus and oestrus phases; much lower values were reported for the metoestrus phase.