bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ammonia loss from urea in grassland and its mitigation by the new urease inhibitor 2-NPT
Authors: SCHRAML M. , GUTSER R. , MAIER H. , SCHMIDHALTER U. 
Published: March 2016

SUMMARYFollowing the surface application of granulated urea to grassland, high ammonia (NH3) losses of up to 30% have been reported. The addition of a urease inhibitor (UI) to urea granules could be a way to abate these losses. Field experiments were conducted at two intensive grassland sites in 2007 and 2008 to evaluate the potential of the new UI N-(2-nitrophenyl) phosphoric triamide (2-NPT; concentrations of 0·75, 1·0 and 1·5 g N/kg) to reduce NH3 emissions resulting from the application of granulated urea. Ammonia losses were continuously measured on plots fertilized with urea, urea + 2-NPT, calcium ammonium nitrate and a control (0N). The measurements were made with a dynamic chamber system. All measurement periods were started after a period of precipitation with a following rainless period being forecasted. Results over measurement periods of 10 days following fertilization are presented. Ammonia losses following the application of granulated urea varied between 4·6 and 11·8 kg N/ha, corresponding to 4·2 up to 14·0% of the applied nitrogen. The addition of 2-NPT to urea granules at three concentrations significantly reduced NH3 losses by 69–100%. Comparable losses of NH3 were observed for urea containing the UI 2-NPT as well as calcium ammonium nitrate, and were not significantly different from the control treatment. No relationships between losses, meteorological factors and soil moisture were observed. The addition of the UI 2-NPT to urea granules applied on grassland effectively reduced NH3 losses.
Geographical distribution ofAngiostrongylus vasorumin foxes (Vulpes vulpes) in the Republic of Ireland
Authors: MCCARTHY G. , FERRAND M. , DE WAAL T. , ZINTL A. , MCGRATH G. , BYRNE W. , O'NEILL E. J. 
Published: March 2016

SUMMARYThe reported incidence of the metastrongylid nematodeAngiostrongylus vasorum, that infects dogs and other canids, is increasing worldwide outside recognized endemic foci. This apparent expansion of the parasite's range is causing concern to veterinary clinicians as the disease caused in dogs can be life threatening and its treatment is not straightforward. The red fox is thought to be a reservoir host for dogs. To investigate the spatial distribution of infection in foxes in Ireland, the hearts and lungs of 542 foxes from all over Ireland were examined. The incidence of infection was found to be 39·9% [95% confidence interval (CI) 35·7–44·1] with positive samples occurring in each of the country's 26 counties. This report confirms that the parasite is endemic in Ireland and the overall prevalence is the second highest in Europe. This is the first survey ofA. vasoruminfection in Irish foxes and highlights the potential exposure of the Irish dog population to high risk of cross-infection. Additionally,Crenosoma vulpiswas found in seven of the foxes, a parasite not previously reported in the Irish fox.
The forgotten role of consonant-like calls in theories of speech evolution
Authors: Lameira Adriano R. 
Published: March 2016

AbstractAckermann et al. provide an informative neurological road-map to primate call communication. However, the proposed model for speech evolution inadequately integrates comparative primate evidence. Critically, great ape voiceless calls are explicitly rendered unimportant, leaving the proposed model deprived of behavioral feedstock and proximate selective drivers capable of triggering the neurological transformations described by the authors in the primate brain.
Cooperative object transportation using parallel line formation with a circular shift
Authors: Eoh Gyuho , Jeon Jae D. , Oh Jung H. , Lee Beom H. 
Published: March 2016

SUMMARYThis paper presents a new cooperative object transportation technique using parallel line formation with a circular shift. Typical areas of research in relation to object transportation are grasping, pushing, and caging techniques, but these require precise grasping behaviors, iterative motion correction according to the object pose, and the real-time acquisition of the object shape, respectively. In this paper, the proposed technique does not need to consider the shape or the pose of objects, and equipped tools are not necessary for object transportation because objects are transported by pushing behavior only. Multiple robots create parallel line formation using a virtual electric dipole field and then push multiple objects into the formation. This parallel line is extended to the goal using cyclic motion by the robots and the objects are transported to the goal by pushing behavior. The above processes are decentralized and activated based on the finite state machine of each robot. Simulations and practical experiments are presented to verify the proposed technique.
Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
Authors: Jewell Talia N M , Karaoz Ulas , Brodie Eoin L , Williams Kenneth H , Beller Harry R 
Published: March 2016

Abstract
Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.
A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals
Authors: Shapiro Orr H. , Kramarsky-Winter Esti , Gavish Assaf R. , Stocker Roman , Vardi Assaf 
Published: March 2016

AbstractCoral reefs, and the unique ecosystems they support, are facing severe threats by human activities and climate change. Our understanding of these threats is hampered by the lack of robust approaches for studying the micro-scale interactions between corals and their environment. Here we present an experimental platform, coral-on-a-chip, combining micropropagation and microfluidics to allow direct microscopic study of live coral polyps. The small and transparent coral micropropagates are ideally suited for live-imaging microscopy, while the microfluidic platform facilitates long-term visualization under controlled environmental conditions. We demonstrate the usefulness of this approach by imaging coral micropropagates at previously unattainable spatio-temporal resolutions, providing new insights into several micro-scale processes including coral calcification, coral–pathogen interaction and the loss of algal symbionts (coral bleaching). Coral-on-a-chip thus provides a powerful method for studying coral physiology in vivo at the micro-scale, opening new vistas in coral biology.
Metabolite Modulation in Human Plasma in the Early Phase of Acclimatization to Hypobaric Hypoxia
Authors: Liao Wen-Ting , Liu Bao , Chen Jian , Cui Jian-Hua , Gao Yi-Xing , Liu Fu-Yu , Xu Gang , Sun Bing-Da , Zhang Er-Long , Yuan Zhi-Bin , Zhang Gang , Gao Yu-Qi 
Published: March 2016

AbstractThe exposure of healthy subjects to high altitude represents a model to explore the pathophysiology of diseases related to tissue hypoxia. We explored a plasma metabolomics approach to detect alterations induced by the exposure of subjects to high altitude. Plasma samples were collected from 60 subjects both on plain and at high altitude (5300 m). Metabolite profiling was performed by gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS) in conjunction with univariate and multivariate statistical analyses. ELISA assays were further employed to measure the levels of several relevant enzymes together with perturbed metabolic pathways. The results showed that hypobaric hypoxia caused significant and comprehensive metabolic changes, as represented by significant changes of 44 metabolites and 4 relevant enzymes. Using MetaboAnalyst 3.0, it was found that several key metabolic pathways were acutely perturbed. In addition, 5 differentially expressed metabolites in pre-exposure samples from the acute mountain sickness-susceptible (AMS-S) group compared with those from the AMS-resistant (AMS-R) group are identified, which warrant further validation as potential predictive biomarkers for AMS-S individuals. These results provide new insights for further understanding the pathophysiological mechanism of early acclimatization to hypobaric hypoxia and other diseases correlated to tissue hypoxia.
Assembly scaffolding with PE-contaminated mate-pair libraries
Authors: Sahlin Kristoffer , Chikhi Rayan , Arvestad Lars 
Published: March 2016

Abstract
Motivation: Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-end libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problems is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed before, in relation to integrated scaffolders, but solutions rely on the orientation being observable, e.g. by finding the junction adapter sequence in the reads. This is not always possible, making orientation and insert size of a read pair stochastic. To our knowledge, there is neither previous work on modeling PE-contamination, nor a study on the effect PE-contamination has on scaffolding quality.
Results: We have addressed PE-contamination in an update to our scaffolder BESST. We formulate the problem as an integer linear program which is solved using an efficient heuristic. The new method shows significant improvement over both integrated and stand-alone scaffolders in our experiments. The impact of modeling PE-contamination is quantified by comparing with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in an increased number of misassemblies, more conservative scaffolding and inflated assembly sizes.
Availability and implementation: The model is implemented in BESST. Source code and usage instructions are found at https://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.
Contact: ksahlin@kth.se
Supplementary information: Supplementary data are available at Bioinformatics online.
An exploratory analysis of managerial perceptions of social and environmental reporting in China
Authors: Zhao Na , Patten Dennis M 
Published: March 2016

Purpose
– This paper aims to determine the perceptions of managers in China with respect to the pressures for, and the purposes of, social and environmental reporting (SER) in the Chinese context.

Design/methodology/approach
– The authors interviewed 14 managers from nine different state-owned enterprises, all headquartered in Beijing. Interviews were conducted during 2009, the height of the period of growth in standalone corporate social responsibility (CSR) reporting in China. The authors assess the perceptions of the managers from a neo-institutional perspective.

Findings
– The findings indicate that, similar to reporting in more Western economies, managers perceive that a variety of coercive, normative and mimetic pressures interplay to influence SER in the Chinese context. The managers perceive peer institutions as exerting the greatest pressures for reporting and, surprisingly, indicate that the government, rather than exerting coercive pressures for SER, instead is seen as playing a facilitating role. The findings also reveal that the managers almost uniformly see the purpose of the reporting as a tool of image enhancement, particularly with respect to the general public. However, in contrast to studies of organizational response to institutional change in other settings, the authors find little non-conformity.

Research limitations/implications
– The findings suggest neo-institutional arguments for CSR reporting appear to hold, even in China’s socialist market economy.

Practical implications
– The finding that managers see CSR reporting as being largely about image enhancement may help to explain the low quality of disclosure documented in other studies.

Social implications
– Improving CSR disclosure in China would appear to require more mandated pressure from, particularly, governmental powers.

Originality/value
– This is the first study to explore via in-depth interviews the perceptions of managers in China to the evolving practice of standalone CSR reporting.
CSR disclosure in response to major airline accidents: a legitimacy-based exploration
Authors: Vourvachis Petros , Woodward Thérèse , Woodward David G. , Patten Dennis M 
Published: March 2016

Purpose
– The purpose of this paper is to contribute to the literature investigating disclosure reactions to legitimacy threats by analyzing the corporate social responsibility (CSR) disclosure reactions to catastrophic accidents suffered by major airlines.

Design/methodology/approach
– The authors use content analysis to examine changes in annual report disclosure in response to four separate airline disasters. The authors adopt two classification schemes and two measurement approaches to explore these changes.

Findings
– The authors find that for three events the organizations appear to have responded with considerable increases in CSR disclosure that are consistent with attempts of legitimation. For one of the events examined, the authors find no disclosure response and suggest that this could be due to the company’s unwillingness to accept responsibility.

Research limitations/implications
– The study’s focus on major airlines that have suffered an accident with available annual reports in English meant that other companies had to be excluded from the analysis.

Practical implications
– The findings demonstrate the use of the annual report as a legitimation tool and further highlight the need for greater transparency and comparability across publications.

Originality/value
– The paper adds to the scarce literature examining corporate disclosure reactions following threats to their social legitimacy.
Draft Genome Sequence of Goose Dicistrovirus
Authors: Greninger Alexander L. , Jerome Keith R. 
Published: March 2016

ABSTRACTWe report the draft genome sequence of goose dicistrovirus assembled from the filtered feces of a Canadian goose from South Lake Union in Seattle, Washington. The 9.1-kb dicistronic RNA virus falls within the familyDicistroviridae; however, it shares <33% translated amino acid sequence within the nonstructural open reading frame (ORF) from aparavirus or cripavirus.
Association of cannabis use with hospital admission and antipsychotic treatment failure in first episode psychosis: an observational study
Authors: Patel Rashmi , Wilson Robin , Jackson Richard , Ball Michael , Shetty Hitesh , Broadbent Matthew , Stewart Robert , McGuire Philip , Bhattacharyya Sagnik 
Published: March 2016

ObjectiveTo investigate whether cannabis use is associated with increased risk of relapse, as indexed by number of hospital admissions, and whether antipsychotic treatment failure, as indexed by number of unique antipsychotics prescribed, may mediate this effect in a large data set of patients with first episode psychosis (FEP).DesignObservational study with exploratory mediation analysis.SettingAnonymised electronic mental health record data from the South London and Maudsley NHS Foundation Trust.Participants2026 people presenting to early intervention services with FEP.ExposureCannabis use at presentation, identified using natural language processing.Main outcome measuresadmission to psychiatric hospital and clozapine prescription up to 5 years following presentation.MediatorNumber of unique antipsychotics prescribed.ResultsCannabis use was present in 46.3% of the sample at first presentation and was particularly common in patients who were 16–25, male and single. It was associated with increased frequency of hospital admission (incidence rate ratio 1.50, 95% CI 1.25 to 1.80), increased likelihood of compulsory admission (OR 1.55, 1.16 to 2.08) and greater number of days spent in hospital (β coefficient 35.1 days, 12.1 to 58.1). The number of unique antipsychotics prescribed, mediated increased frequency of hospital admission (natural indirect effect 1.09, 95% CI 1.01 to 1.18; total effect 1.50, 1.21 to 1.87), increased likelihood of compulsory admission (natural indirect effect (NIE) 1.27, 1.03 to 1.58; total effect (TE) 1.76, 0.81 to 3.84) and greater number of days spent in hospital (NIE 17.9, 2.4 to 33.4; TE 34.8, 11.6 to 58.1).ConclusionsCannabis use in patients with FEP was associated with an increased likelihood of hospital admission. This was linked to the prescription of several different antipsychotic drugs, indicating clinical judgement of antipsychotic treatment failure. Together, this suggests that cannabis use might be associated with worse clinical outcomes in psychosis by contributing towards failure of antipsychotic treatment.
Language spoken at home and the association between ethnicity and doctor–patient communication in primary care: analysis of survey data for South Asian and White British patients
Authors: Brodie Kara , Abel Gary , Burt Jenni 
Published: March 2016

ObjectivesTo investigate if language spoken at home mediates the relationship between ethnicity and doctor–patient communication for South Asian and White British patients.MethodsWe conducted secondary analysis of patient experience survey data collected from 5870 patients across 25 English general practices. Mixed effect linear regression estimated the difference in composite general practitioner–patient communication scores between White British and South Asian patients, controlling for practice, patient demographics and patient language.ResultsThere was strong evidence of an association between doctor–patient communication scores and ethnicity. South Asian patients reported scores averaging 3.0 percentage points lower (scale of 0–100) than White British patients (95% CI −4.9 to −1.1, p=0.002). This difference reduced to 1.4 points (95% CI −3.1 to 0.4) after accounting for speaking a non-English language at home; respondents who spoke a non-English language at home reported lower scores than English-speakers (adjusted difference 3.3 points, 95% CI −6.4 to −0.2).ConclusionsSouth Asian patients rate communication lower than White British patients within the same practices and with similar demographics. Our analysis further shows that this disparity is largely mediated by language.
Lenticulostriate infarctions after successful mechanical thrombectomy in middle cerebral artery occlusion
Authors: Kleine Justus F , Beller Ebba , Zimmer Claus , Kaesmacher Johannes 
Published: March 2016

BackgroundIn stroke due to middle cerebral artery (MCA) occlusion, collaterals may sustain tissue in the peripheral MCA territory, extending the time window for recanalizing therapies. However, MCA occlusions often block some or all of the ‘lenticulostriate’ (LS) arteries originating from the M1 segment, eliminating blood flow to dependent territories in the striatum, which have no collateral supply. This study examines whether mechanical thrombectomy (MTE) can avert imminent striatal infarction in patients with acute MCA occlusion.Methods279 patients with isolated MCA occlusion subjected to MTE were included. Actual LS occlusions and infarctions were assigned to predefined ‘LS occlusion’ and ‘LS infarct’ patterns derived from known LS vascular anatomy. The predictive performance of LS occlusion patterns regarding ensuing infarction in striatal subterritories was assessed by standard statistical measures.ResultsLS occlusion patterns predicted infarction in associated striatal subterritories with a positive predictive value (PPV) of 91% and a negative predictive value of 81%. In 15 of the 22 patients who did not develop the predicted striatal infarctions, reassessment of angiographies revealed LS vascular supply variants that explained these ‘false positive’ LS occlusion patterns, raising the PPV to 96%. Symptom onset to recanalization times were relatively short, but this alone could not account for the false positive LS occlusion patterns in the remaining seven of these patients.ConclusionsWith currently achievable symptom onset to recanalization times, striatal infarctions are determined by MCA occlusion sites and individual vascular anatomy, and cannot normally be averted by MTE, but there are exceptions. Further study of such exceptional cases may yield important insights into the determinants of infarct growth in the hyperacute phase of infarct evolution.