bluuebunny/crossref_metadata_2025_split huggingface dataset:
GRASP: Guided Reference-based Assembly of Short Peptides
Authors: Zhong Cuncong , Yang Youngik , Yooseph Shibu 
Published: November 2014

Abstract
Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release.
Does Working from Home Work? Evidence from a Chinese Experiment
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Authors: Bloom Nicholas , Liang James , Roberts John , Ying Zhichun Jenny 
Published: November 2014

Abstract
A rising share of employees now regularly engage in working from home (WFH), but there are concerns this can lead to “shirking from home.” We report the results of a WFH experiment at Ctrip, a 16,000-employee, NASDAQ-listed Chinese travel agency. Call center employees who volunteered to WFH were randomly assigned either to work from home or in the office for nine months. Home working led to a 13% performance increase, of which 9% was from working more minutes per shift (fewer breaks and sick days) and 4% from more calls per minute (attributed to a quieter and more convenient working environment). Home workers also reported improved work satisfaction, and their attrition rate halved, but their promotion rate conditional on performance fell. Due to the success of the experiment, Ctrip rolled out the option to WFH to the whole firm and allowed the experimental employees to reselect between the home and office. Interestingly, over half of them switched, which led to the gains from WFH almost doubling to 22%. This highlights the benefits of learning and selection effects when adopting modern management practices like WFH.
Are earnings quality attributes reflected in financial strength ratings?
Authors: Ames Daniel , S. Hines Chris , Sankara Jomo 
Published: November 2014

Purpose
– The purpose of this paper is to examine whether earnings quality attributes are reflected in AM best's financial strength ratings (FSRs), a measure widely used in the insurance industry to assess financial health.

Design/methodology/approach
– Using a sample of insurance companies during the period 2006-2012, the authors measure the quality of reported earnings using three accounting-based measures: earnings persistence, accrual quality, and earnings smoothness.

Findings
– The authors find that better earnings persistence, higher accrual quality, and less earnings smoothing are reflected in higher FSRs for both public and private insurers, with the magnitude of the effect greater for private insurers.

Originality/value
– This is the first study of which the authors are aware that seeks to understand the impact, if any, of variations in the quality of reported financial information on the perceived financial health of firms by ratings agencies in the insurance industry. The authors also include a novel research design in assessing the determinants of financial health ratings. Users of FSRs should be aware of the impact of ownership structure on ratings agencies’ propensity to incorporate reported earnings attributes in their ratings.
Abiotic constraints on the activity of tropical lizards
Authors: Logan Michael L. , Fernandez Sarah G. , Calsbeek Ryan 
Published: November 2014

Summary

Many tropical ectotherms are considered vulnerable to anthropogenic climate change because they have evolved to become thermal specialists. Indeed, several recent studies have suggested that even small increases in mean operative temperature may lead to a reduction in activity and the subsequent extinction of populations. Within the tropics, lizards are considered particularly vulnerable due to the potential for climate change to directly impact physiology and alter community interactions. However, models usually focus on the effects of mean operative temperature at the expense of other climate variables that may also affect lizard physiology.

We used daily variation in operative temperature, humidity and wind speed to examine how changes in climate influence activity in two species of lizards from the island of Cayo Menor, Honduras. Anolis lemurinus is a forest species, whereas A. allisoni is an open‐habitat species. We conducted daily surveys for active lizards in habitat typical to each species, while simultaneously measuring operative thermal environments with physical models. The effects of the thermal environment were considered in the context of the thermal sensitivity of locomotor performance for each species and compared with the effects of the hydric (humidity) and convective (wind) environments.

When all surveys were combined into a single analysis, the activity of the forest species Anolis lemurinus was positively correlated with wind speed, the spatial heterogeneity of operative temperature, and the mismatch between mean operative temperature and the optimal temperature for sprint performance. Mean operative temperature did significantly affect Anolis lemurinus activity, but only when it was above their thermal optimum. Activity of the open‐habitat species A. allisoni was negatively correlated with wind speed, but was not related to any other climate variable.

Whereas the mismatch between mean operative temperature and the thermal optimum for performance predicted the activity level of the forest species in ways partially consistent with its use in models for the response of lizards to climate change, the effects of the abiotic environment were habitat dependent. Our results suggest that successfully predicting the biological impacts of climate change will require holistic models that account for more than changes in mean temperature alone.
What can reunification of East and West Germany tell us about the cause of the allergy epidemic?
Authors: Krämer U. , Schmitz R. , Ring J. , Behrendt H. 
Published: November 2014

SummaryThe increase of allergies in East Germany – reaching West German prevalence shortly after the reunification – is considered a model for the allergy epidemic in the western world. Whether such a pattern was observed in all comparison studies and for all allergic manifestations is not known because a complete overview is missing. Hints about possible causal factors for the allergy epidemic could be gained by identifying known risk factors, which explain the observed pattern of allergy development in Germany. Again, an overview about these efforts is missing. We identified 14 cross‐sectional studies conducted after 1989 and calculated prevalence ratios (West/East) for asthma, hayfever, eczema and allergic sensitization. Additionally, a tabular overview about the explanatory power of risk factors hypothesized in the nineties and covering outdoor exposure, indoor factors, early childhood influences, nutrition as well as awareness is given. At the time of the German reunification, the prevalence ratio West/East was largest for hayfever and sensitization to birch pollen, less pronounced for the other phenotypes and even less than one for atopic eczema. Hayfever and sensitization to birch pollen also showed the steepest increase in East Germany afterwards. Single‐room heating with fossil fuels and living as only child in a family were identified as explaining up to 23.5% of the excess trend in East compared to the trend in West. Hayfever as most typical atopic disease showed the difference in allergy pattern between East and West Germany clearest. Risk factors identified for these phenotypes are completely different (single child) or even act in the opposite direction (single‐room heating) from classical risk factors for airway diseases. This might be the most important lesson from the West/East German experience. It already stimulated many other studies focussing on protective factors such as microbial stimulation.
How should a district general hospital immunology service screen for anti-nuclear antibodies? An ‘in-the-field’ audit
Authors: Hira-Kazal R , Shea-Simonds P , Peacock J L , Maher J 
Published: November 2014

Summary
Anti-nuclear antibody (ANA) testing assists in the diagnosis of several immune-mediated disorders. The gold standard method for detection of these antibodies is by indirect immunofluorescence testing on human epidermoid laryngeal carcinoma (HEp-2) cells. However, many laboratories test for these antibodies using solid-phase assays such as enzyme-linked immunosorbent assay (ELISA), which allows for higher throughput testing at reduced cost. In this study, we have audited the performance of a previously established ELISA assay to screen for ANA, making comparison with the gold standard HEp-2 immunofluorescence test. A prospective and unselected sample of 89 consecutive ANA test requests by consultant rheumatologists were evaluated in parallel over a period of 10 months using both tests. ELISA and HEp-2 screening assays yielded 40 (45%) and 72 (81%) positive test results, respectively, demonstrating lack of concordance between test methods. Using standard and clinical samples, it was demonstrated that the ELISA method did not detect several ANA with nucleolar, homogeneous and speckled immunofluorescence patterns. None of these ELISANEG HEp-2POS ANA were reactive with a panel of six extractable nuclear antigens or with double-stranded DNA. Nonetheless, 13 of these samples (15%) originated from patients with recognized ANA-associated disease (n = 7) or Raynaud's phenomenon (n = 6). We conclude that ELISA screening may fail to detect clinically relevant ANA that lack defined specificity for antigen.
Effects of Insulin Resistance on Myocardial Blood Flow and Arterial Peripheral Circulation in Patients with Polycystic Ovary Syndrome
Authors: Aldrighi José M. , Tsutsui Jeane M. , Kowastch Ingrid , Ribeiro Alessandra L. , Scapinelli Alessandro , Tamanaha Sonia , Oliveira Ricardo M. , Mathias Wilson 
Published: November 2014

ObjectivePolycystic ovary syndrome (PCOS) is associated with increased risk for cardiovascular disease. We sought to evaluate the effects of insulin resistance (IR) on myocardial microcirculation and peripheral artery function in patients with PCOS.MethodsWe studied 55 women (28 with PCOS without IR, 18 with PCOS and IR and 11 normal controls) who underwent laboratorial analysis, high‐resolution vascular ultrasound and real time myocardial contrast echocardiography (RTMCE). Intima–media thickness (IMT) and brachial artery flow‐mediated dilation (FMD) were evaluated by vascular ultrasound. The replenishment velocity (β), plateau of acoustic intensity (A) and myocardial blood flow reserve (MBFR) were determined by quantitative dipyridamole stress RTMCE.Resultsβ reserve in group PCOS + IR was lower than control (2.34 ± 0.55 vs. 3.60 ± 0.6; P < 0.001) and than PCOS without IR (2.34 ± 0.55 vs. 3.17 ± 0.65; P < 0.001). MBFR in patients with PCOS without IR did not differ from those of control (4.59 ± 1.59 vs. 5.30 ± 1.64; P = 0.22) or from patients with PCOS + IR (4.59 ± 1.59 vs. 3.70 ± 1.47; P = 0.07). When comparing with control group, patients with PCOS + IR had lower MBFR (5.30 ± 1.64 vs. 3.70 ± 1.47; P = 0.01). No significant differences were found between control, PCOS without IR and PCOS + IR for FMD (0.18 ± 0.05, 0.15 ± 0.04 and 0.13 ± 0.07; P =NS) or IMT (0.48 ± 0.05, 0.47 ± 0.05 and 0.49 ± 0.07; P = NS).ConclusionWomen with PCOS and IR had depressed β and MBFR as demonstrated by quantitative RTMCE, but no alteration in endothelial dysfunction or IMT. PCOS without IR showed isolated depression in β reserve, probably an earlier marker of myocardial flow abnormality.
Migratory fish excretion as a nutrient subsidy to recipient stream ecosystems
Authors: Wheeler Kit , Miller Scott W. , Crowl Todd A. 
Published: November 2014

Summary

Consumer excretion can be an important component of nutrient cycling in aquatic ecosystems. Uncertainty concerning the functional role of many freshwater organisms remains, including those with migratory life‐history strategies that may introduce nutrients to recipient systems.

We quantified the magnitude, variability and importance of excretion by migratory fish in the context of stream nutrient cycling. In 2011–12, we collected data from tributaries of a central Utah reservoir used by two potamodromous fishes (Bonneville cut‐throat trout – BCT, Oncorhynchus clarkii utah; kokanee salmon – KOK, Oncorhynchus nerka) with temporally separated spawning migrations. To quantify the contribution of the two migratory freshwater fishes to nutrient cycling, we extrapolated measurements of per capita nitrogen (N) and phosphorus (P) excretion rates to the population level within the local environmental context of two tributaries.

We observed differences in excretion subsidies between species and tributaries. BCT excretion rates and ratios were significantly greater than those for KOK. Estimates of the ratio of population‐level migrant excretion to tributary nutrient export were highly variable through time and between tributaries. These estimates were influenced by spatiotemporal hydrologic variation and positively related to ratios of migrant biomass to discharge. During migrations, daily migrant excretion loading comprised a maximum of 6–859% and 1–388% of tributary NH4‐N and soluble reactive phosphorus (SRP) export, respectively.

Measurements of nutrient uptake suggested that migrant excretion could meet a substantial portion of ecosystem nutrient demand. Migrant excretion fluxes comprised 46–188% of ecosystem NH4‐N demand and varied between streams and species. In contrast, the proportion of SRP demand supplied by migrant excretion (34–37%) was relatively invariant.

These results demonstrate an important role for potamodromous fishes as nutrient sources in recipient ecosystems. Furthermore, our data support predictions about when and where effects of fish‐derived nutrients will be strongest, thereby advancing the understanding of context‐dependent migratory fish effects in riverine ecosystems. Although widespread and common, potamodromous fishes are overlooked but important organisms capable of substantially affecting stream nutrient cycling.
Biogeochemical hotspots: temporal and spatial scaling of the impact of freshwater mussels on ecosystem function
Authors: Atkinson Carla L. , Vaughn Caryn C. 
Published: November 2014

Summary

In streams, the creation of nutrient‐transformation hotspots by aggregated organisms may have heterogeneous and strong cumulative influences on stream nutrient dynamics. Here, we examine the potential for aggregations of freshwater mussels to create such hotspots.

We measured nitrogen (N) and phosphorus (P) excretion rates of six mussel species and body tissue composition of eight. We combined these data with population densities of surveyed mussel beds in the Kiamichi River, OK, to estimate reach‐scale and stream‐scale nutrient recycling and storage. Additionally, we estimated the temporal variability in the magnitude of mussel nutrient recycling combining volumetric excretion at a reach scale with discharge and temperature data.

Mussel beds constituted 1.45% of the area of the Kiamichi River. Mussel nutrient remineralisation varied greatly across beds (11.1–699.5 μmol N m−2 h−1 and 0.8–53.0 μmol P m−2 h−1), because of varying mussel densities. The community‐wide average excretion N:P (molar) of the mussel communities was 29.57, with higher excretion N:P significantly associated with higher abundances of Actinonaias ligamentina. Total nutrient storage per bed varied two orders of magnitude (6.3–631.7 kg N and 2.3–227.5 kg P) between mussel beds. Moreover, areal nutrient storage varied among the beds (11.2–133.7 mg N m−2, 4.1–48.9 mg P m−2) with the majority of nutrient storage in a long‐term store, shell (c. 87% of total N storage, c. 95% of total P storage).

Freshwater mussels can be important to nutrient dynamics through nutrient regeneration and the creation of storage hotspots. However, the importance of nutrient remineralisation varies dramatically in response to organism patchiness, flow conditions and background nutrient concentrations.
The Place of Rus' in Medieval Europe
Authors: Raffensperger Christian 
Published: November 2014

AbstractRus', the medieval kingdom that was the progenitor of modern Russia, Ukraine, and Belarus, has had a complicated historiography due to modern political trends. The chief problem that has shaped scholarship on medieval Rus' is what to do with it. Where does it belong? Over the last century alone, scholars have suggested that Rus' should be studied on its own, either as an autochthonous entity or otherwise; that Rus' was the mid‐point on a thousand mile trek from the Varangians (in Scandinavia) to the Greeks (Byzantines) and Muslims; that Rus' existed as part of a Byzantine Commonwealth and thus should be studied in that context and separate from others; and the idea that Rus' was part of medieval Europe and should be studied as such. These various mindsets have been shaped by modern political developments and have created scholarly frames into which the evidence for Rus', and Rus' itself, has been placed. This article highlights these trends over the last one hundred years in largely Anglophone scholarship, demonstrating the current historical understanding of the place of Rus' in medieval Europe.
Immunoexpression of NF‐ĸB and their inhibitory subunits IĸBα and IĸBβ in giant cell lesions of the jaws: implications for their clinical behavior
Authors: Tobón‐Arroyave Sergio Iván , Hurtado‐García Paulina , García‐Quintero Oscar Darío , Isaza‐Guzmán Diana María , Flórez‐Moreno Gloria Amparo 
Published: November 2014

BackgroundThe unpredictable behavior of giant cell lesions (GCLs) of the jaws parallels its controversial histogenesis. This study evaluated a possible association between the immunohistochemical expression of NF‐ĸB, the inhibitory subunits IĸBα/IĸBβ, and clinicopathological variables with the behavior of central and peripheral GCLs of the jaws.Materials and MethodsParaffin‐embedded samples of GCLs of the jaws (n = 68) were prepared for histological/immunohistochemical assessment. Demographic and clinicopathological parameters were assessed to determine the behavior of the lesions. A staining–intensity–distribution (SID) score was used to assess the immunomarkers reactivity. The association between significant candidate immunohistochemical predictor variables regarding clinical behavior was analyzed individually and adjusted for confounding using a binary logistic regression model.ResultsWhile univariate analysis revealed a positive association of NF‐ĸB SID score, NF‐ĸB nuclear expression, IĸBα SID score, and NF‐ĸB to inhibitors average ratio with the aggressive status of GCLs, after bivariate logistic regression analysis, only NF‐ĸB nuclear expression, IĸBα SID score, and NF‐ĸB to inhibitors average ratio remained as robust predictors of aggressiveness. Confounding and interaction effects regarding clinicopathological candidate predictor variables were also noted.ConclusionIt looks that clinical behavior of GCLs of the jaws may be strong/independently linked to the increased nuclear expression of NF‐ĸB, higher NF‐ĸB to inhibitors average ratio, and decreased IĸBα SID score. Notwithstanding, there are simultaneously synergistic and opposing interactive effects with respect to age stratum, growth rate, multinucleated giant cells count, and mononuclear stromal cells density in the susceptible host that may increase the tissue destruction observed in aggressive GCLs.
Studies on a suitable antibiotic therapy for treating swine brucellosis
Authors: Dieste‐Pérez L. , Fraile L. , de Miguel M. J. , Barberán M. , Blasco J. M. , Muñoz P. M. 
Published: November 2014

The aim of this work was developing effective treatments against Brucella suis biovar 2, responsible for swine brucellosis in Europe. MICs for antibiotics used classically in brucellosis and two new macrolides (tulathromycin and tildipirosin) were determined for 33 B. suis biovar 2 field and B. suis reference strains. MIC90 values ranged from 0.01 to 0.25 μg/mL. The best candidates, given alone or combined, were then evaluated in mice. Ten groups (n = 7) of BALB/c mice were inoculated (1 × 105 CFU/mouse) with a virulent B. suis biovar 2 field strain. All groups, excepting untreated control, were treated for 14 days with, respectively, doxycycline, dihydrostreptomycin, tulathromycin (one or two doses), or tildipirosin (one or two doses) given alone, and doxycycline combined with dihydrostreptomycin, tulathromycin, or tildipirosin. Combined tildipirosin treatment was the most effective, then selected for pig studies. Sixteen B. suis biovar 2 naturally infected sows were treated with oxytetracycline (20 mg/kg BW/daily) for 21 days. The half of these received also tildipirosin (4 mg/kg BW) in two doses with a 10‐day interval. An extensive bacteriological study conducted ten days after ceasing treatments proved the efficacy of this combined oxytetracycline/tildipirosin treatment.
Successful treatment of idiopathic colitis related to XIAP deficiency with allo‐HSCT using reduced‐intensity conditioning
Authors: Tsuma Yusuke , Imamura Toshihiko , Ichise Eisuke , Sakamoto Kenichi , Ouchi Kazutaka , Osone Shinya , Ishida Hiroyuki , Wada Taizo , Hosoi Hajime 
Published: November 2014

AbstractRecently, it has been reported that Crohn's‐like intractable colitis occurred in approximately 20% of the patients with XIAP deficiency, also known as X‐linked lymphoproliferative disease type 2. Because treatment used for Crohn's disease is not always effective for Crohn's‐like colitis related to XIAP deficiency, more effective treatment should be established. Although several studies reported allo‐HSCT might be promising even for Crohn's‐like colitis related to XIAP deficiency, the outcome of allo‐HSCT using MAC for XIAP deficiency is extremely poor due to frequent TRM. In addition, there is little information about the outcome of allo‐HSCT for intractable colitis related to XIAP deficiency. Herein, we describe a patient with intractable colitis related to XIAP deficiency who was successfully treated with allo‐HSCT using a reduced‐intensity conditioning regimen. Although allo‐HSCT using the RIC regimen might be a curative therapeutic option for intractable colitis with XIAP deficiency, the prognostic factors that will determine the success of allo‐HSCT require further clinical information of more patients.