bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annual Southeast Asia haze increases respiratory admissions: A 2‐year large single institution experience
Authors: Ming Chew R. , Ban Yu‐Lin Andrea , Abdul Hamid Mohammad F. , Latif Mohd T. , Mohammad Nurashikin , Hassan Tidi 
Published: June 2018

AbstractBackground and objectiveThe Southeast Asia (SEA) haze is an annual problem and at its worst could produce respirable particles of concentrations up to 500 μg/m3 which is five times the level considered as ‘unhealthy’. However, there are limited reports examining the direct clinical impact of the annual haze. This study examines the effects of the SEA haze on respiratory admissions.MethodsData from all respiratory admissions in Universiti Kebangsaan Malaysia Medical Centre (UKMMC) from 1st January 2014 to 31st December 2015 were collected retrospectively from chart and electronic database. A total of 16 weeks of haze period had been formally dated by the Department of Environment using the definition of weather phenomenon leading to atmospheric visibility of less than 10 km. Multivariable regression analyses were performed to estimate rate ratios and 95% CI.ResultsThere were 1968 subjects admitted for respiratory admissions in UKMMC during the study period. Incidence rates per week were significantly different between the two groups with 27.6 ± 9.2 cases per week during the haze versus 15.7 ± 6.7 cases per week during the non‐haze period (P < 0.01). A total of 4% versus 2% was admitted to the intensive care unit in the haze and the non‐haze groups, respectively (P = 0.02). The mean ± SD lengths of stay was 12.1 ± 5.2 days; the haze group had a longer stay (18.2 ± 9.7 days) compared to the non‐haze groups (9.7 ± 3.9) (P < 0.001).ConclusionThe annual SEA haze is associated with increased respiratory admissions.
Bayesian Analysis of Air Emission Violations from Waste Incineration and Coincineration Plants
Authors: Paleologos Evan K. , Elhakeem Mohamed , Amrousi Mohamed El 
Published: June 2018

AbstractWaste incineration and coincineration plants in most European countries have frequently updated their flue gas cleaning systems, surpassing in most cases E.U. air emission standards. At the same time, in most developing countries, cement and other coincineration facilities follow less stringent emission regulations and have a mixed record of protecting air quality. The European Union, the United States, and Canada have established penalties for air emission violations that account for the harm done to the environment and to human health and aiming to remove the economic benefit reaped as a result of noncompliance. Despite their legal completeness, these regulations do not adequately address the probabilistic nature of air pollution. This article recasts the issue of air pollution penalties in a Bayesian decision‐making framework with the aspiration that the assessment of penalties on a rigorous mathematical framework can assist in alleviating the mistrust by sections of the public on the effectiveness of air pollution regulations. Integration of economic analyses into risk assessments of emission violations can help clarify to policymakers the effect of environmental policies. Our analysis indicates that the penalty structure of the United States appears to favor the update of emission systems more often than the corresponding European Commission's penalties. Our study advances the use of the loss function as a risk analysis tool that can be used as a public policy instrument to promote environmentally friendlier air emission choices. A parabolic, compared to a linear, loss function was seen to justify higher expenses in gas cleaning systems.
Multivariate Posterior Inference for Spatial Models with the Integrated Nested Laplace Approximation
Authors: Gómez-Rubio Virgilio , Palmí-Perales Francisco 
Published: June 2018

SummaryThe integrated nested Laplace approximation (INLA) is a convenient way to obtain approximations to the posterior marginals for parameters in Bayesian hierarchical models when the latent effects can be expressed as a Gaussian Markov random field. In addition, its implementation in the R-INLA package for the R statistical software provides an easy way to fit models using the INLA in practice in a fraction of the time that other computer-intensive methods (e.g. Markov chain Monte Carlo methods) take to fit the same model. Although the INLA provides a fast approximation to the marginals of the model parameters, it is difficult to use it with models that are not implemented in R-INLA. It is also difficult to make multivariate posterior inference on the parameters of the model as the INLA focuses on the posterior marginals and not the joint posterior distribution. We describe how to use the INLA within the Metropolis–Hastings algorithm to fit complex spatial models and to estimate the joint posterior distribution of a small number of parameters. We illustrate the benefits of this new method with two examples. In the first, a spatial econometrics model with two auto-correlation parameters (for the response and the error term) is considered. This model is not currently available in R-INLA, and multivariate inference is often required to assess dependence between the two spatial auto-correlation parameters in the model. Furthermore, the estimation of spillover effects is based on the joint posterior distribution of a spatial auto-correlation parameter and a covariate coefficient. In the second example, a multivariate spatial model for several diseases is proposed for disease mapping. This model includes a shared specific spatial effect as well as disease-specific spatial effects. Dependence on the shared spatial effect is modulated via disease-specific weights. By inspecting the joint posterior distribution of these weights it is possible to assess which diseases have a similar spatial pattern.
Field and laboratory comparative evaluation of a LAMP assay for the diagnosis of urogenital schistosomiasis in Cubal, Central Angola
Authors: Gandasegui Javier , Fernández‐Soto Pedro , Dacal Elena , Rodríguez Esperanza , Saugar José María , Yepes Edward , Aznar‐Ruiz‐de‐Alegría María Luisa , Espasa Mateu , Ninda Arlette , Bocanegra Cristina , Salvador Fernando , Sulleiro Elena , Moreno Milagros , Vicente Belén , López‐Abán Julio , Muro Antonio 
Published: June 2018

AbstractObjectiveTo evaluate the performance of Rapid‐Heat LAMPellet assay in field conditions for diagnosis of urogenital schistosomiasis in an endemic area in Cubal, Angola, and to assess the reproducibility in a reference laboratory.MethodsA total of 172 urine samples from school‐age children were tested for microhaematuria, microscopic detection of Schistosoma haematobium eggs and LAMP for DNA detection. Urine samples were stored in a basic equipped laboratory. Field‐LAMP tests were performed with and without prior DNA extraction from urine samples, and the results were read by turbidity and by colour change. When field procedures were finished, samples were sent to a reference laboratory to be reanalysed by LAMP.ResultsA total of 83 of 172 (48.3%) were positive for microhaematuria, 87/172 (50.6%) were microscopy‐positive for S. haematobium eggs detection, and 127/172 (73.8%) showed LAMP‐positive results for detecting S. haematobium using purified DNA and 109/172 (63.4%) without prior DNA extraction. MacNemar's test showed a statistical significant relation between LAMP results and microscopy‐detected S. haematobium infections and microhaematuria (P < 0.001 in both cases), respectively. When samples of purified DNA were reanalysed in a reference laboratory in Spain using the same LAMP methodology, the overall reproducibility achieved 72.1%.ConclusionsThe ease of use, simplicity and feasibility demonstrated by LAMP assay in field conditions together with the acceptable level of reproducibility achieved in a reference laboratory support the use of LAMP assay as an effective test for molecular diagnosis of urogenital schistosomiasis in endemic remote areas.
Impact of prestorage leucoreduction of autologous whole blood on length of hospital stay with a subgroup analysis in bilateral hip arthroplasty
Authors: Sawamura Y. , Ohto H. , Ikeda K. , Kanno T. , Suzuki Y. , Gonda K. , Tasaki T. , Nollet K. E. , Takahashi H. , Aota S. 
Published: June 2018

BackgroundAlthough prestorage leucoreduction (LR) of blood components for transfusion has gained favour around the world, evidence of its beneficial clinical effects is ambiguous.Study design and methodsTo reveal whether leucocytes and/or platelets in transfused blood are related to transfusion‐related adverse effects, a prospective randomized crossover study was performed on patients who donated autologous blood prior to elective surgery. Among 1487 primary enrolees, a total of 192 patients undergoing two‐stage, bilateral total hip arthroplasty were randomized to receive autologous blood that was either prestorage leucoreduced, or not, for the first procedure. For the second procedure, each patient was crossed over to receive alternatively processed autologous blood. Length of hospital stay served as a primary end‐point, with perioperative infectious/thrombotic complications, pre‐ and postoperative laboratory values, and body temperature serving as secondary endpoints.ResultsNo significant differences emerged between prestorage LR and non‐LR cohorts in length of hospital stay, as well as perioperative infectious/thrombotic complications, postoperative body temperature and duration of fever. Postoperative laboratory values including white blood cell counts and C‐reactive protein levels had no significant differences.ConclusionThis study could not prove any superiority of prestorage LR over non‐LR for autologous whole blood among patients who underwent total hip arthroplasty.
Modelling the sprouting capacity from underground buds of the perennial weed Sonchus arvensis
Authors: Taab A , Andersson L , Boström U 
Published: June 2018

SummarySonchus arvensis is a problematic perennial weed species causing problems in many crops. Control measures often rely on soil tillage or mowing; both methods are used to exhaust the root system. This approach fails during periods of restrictions in sprouting capacity or shoot regrowth. The aim of this study was to develop a simulation model for prediction of shoot sprouting capacity in underground buds of S. arvensis. We hypothesised restricted regrowth to be induced as a function of photoperiod and temperature sum and released as a function of cold temperature sum. The model was parameterised and calibrated against observations of shoot regrowth from an experiment on intact roots of S. arvensis. Subsequently, it was validated against observations of regrowth from another experiment on intact roots and sprouting from fragmented roots from a third experiment. Restriction in regrowth was attributed to reduction in the photoperiod, observed when the day length decreased below a threshold of 16.5 h, but also to a daily mean temperature below 16.8°C. Resumed regrowth occurred in late autumn at a daily mean temperature threshold of 4.7°C. The pattern of changes over time in shoot regrowth from an intact root system was well predicted by the model. The temporal change in sprouting capacity from buds on fragmented roots followed the same pattern, but with a quantitative difference between the model prediction and the observed sprouting capacity. We conclude that the model can be used to predict the pattern over time of sprouting capacity in intact roots of S. arvensis.
You cannot fight fire with fire: a demographic model suggests alternative approaches to manage multiple herbicide‐resistant Avena fatua
Authors: Burns E E , Lehnhoff E A , Mckenzie S C , Maxwell B D , Dyer W E , Menalled F D 
Published: June 2018

SummaryMultiple herbicide‐resistant (MHR) weed populations pose significant agronomic and economic threats and demand the development and implementation of ecologically based tactics for sustainable management. We investigated the influence of nitrogen fertiliser rate (56, 112, 168, or 224 kg N ha−1) and spring wheat seeding density (67.3 kg ha−1 or 101 kg ha−1) on the demography of one herbicide susceptible and two MHR Avena fatua populations under two cropping systems (continuous cropping and crop‐fallow rotation). To represent a wide range of environmental conditions, data were obtained in field conditions over 3 years (2013–2015). A stochastic density‐dependent population dynamics model was constructed using the demographic data to project A. fatua populations. Elasticity analysis was used to identify demographic processes with negative impacts on population growth. In both cropping systems, MHR seedbank densities were negatively impacted by increasing nitrogen fertilisation rate and wheat density. Overall, MHR seedbank densities were larger in the wheat‐fallow compared with the continuous wheat cropping system and seedbank densities stabilised near zero in the high nitrogen and high spring wheat seeding rate treatment. In both cropping systems, density‐dependent seed production was the most influential parameter impacting population growth rate. This study demonstrated that while the short‐term impact of weed management tactics can be investigated by field experiments, evaluation of long‐term consequences requires the use of population dynamics models. Demographic models, such as the one constructed here, will aid in selecting ecologically based weed management tactics, such as appropriate resource availability and modification to crop competitive ability to reduce the impact of MHR.
Draft Genome Sequence of Serratia sp. Strain S1B, Isolated from Mercury-Contaminated Soil
Authors: Pathak Ashish , Jaswal Rajneesh , Xu Xiaoyu , Chauhan Ashvini 
Published: June 2018

ABSTRACT

We report here the draft genome sequence of
Serratia
sp. strain S1B, comprising 7,710,841 bases, 7,075 coding sequences, a G+C content of 45.9%, and 138 RNAs. Notably, a repertoire of biodegradative genes, several occurring on genomic islands, was also identified, which enhances our understanding of the environmental relevance of
Serratia
spp.
Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces
Authors: Albert Korin , Sela David A. 
Published: June 2018

ABSTRACT

The draft genome sequence of an isolate identified as
Bifidobacterium longum
is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this
Bifidobacterium longum
isolate is 2.39 Mb in length, with a G+C content of 60.1%.
Bacterial Small RNAs in Mixed Regulatory Networks
Authors: Brosse Anaïs , Guillier Maude 
Published: June 2018

ABSTRACT
Small regulatory RNAs are now recognized as key regulators of gene expression in bacteria. They accumulate under specific conditions, most often because their synthesis is directly controlled by transcriptional regulators, including but not limited to alternative sigma factors and response regulators of two-component systems. In turn, small RNAs regulate, mostly at the posttranscriptional level, expression of multiple genes, among which are genes encoding transcriptional regulators. Small RNAs are thus embedded in mixed regulatory circuits combining transcriptional and posttranscriptional controls, and whose properties are discussed here.
Detailed genetic characteristics of an international large cohort of patients with Stargardt disease: ProgStar study report 8
Authors: Fujinami Kaoru , Strauss Rupert W , Chiang John (Pei-Wen) , Audo Isabelle S , Bernstein Paul S , Birch David G , Bomotti Samantha M , Cideciyan Artur V , Ervin Ann-Margret , Marino Meghan J , Sahel José-Alain , Mohand-Said Saddek , Sunness Janet S , Traboulsi Elias I , West Sheila , Wojciechowski Robert , Zrenner Eberhart , Michaelides Michel , Scholl Hendrik P N ,   ProgStar Study Group
Published: June 2018

Background/aims
To describe the genetic characteristics of the cohort enrolled in the international multicentre progression of Stargardt disease 1 (STGD1) studies (ProgStar) and to determine geographic differences based on the allele frequency.

Methods

345 participants with a clinical diagnosis of STGD1 and harbouring at least one disease-causing ABCA4 variant were enrolled from 9 centres in the USA and Europe. All variants were reviewed and
in silico
analysis was performed including allele frequency in public databases and pathogenicity predictions. Participants with multiple likely pathogenic variants were classified into four national subgroups (USA, UK, France, Germany), with subsequent comparison analysis of the allele frequency for each prevalent allele.

Results
211 likely pathogenic variants were identified in the total cohort, including missense (63%), splice site alteration (18%), stop (9%) and others. 50 variants were novel. Exclusively missense variants were detected in 139 (50%) of 279 patients with multiple pathogenic variants. The three most prevalent variants of these patients with multiple pathogenic variants were p.G1961E (15%), p.G863A (7%) and c.5461-10 T>C (5%). Subgroup analysis revealed a statistically significant difference between the four recruiting nations in the allele frequency of nine variants.

Conclusions
There is a large spectrum of ABCA4 sequence variants, including 50 novel variants, in a well-characterised cohort thereby further adding to the unique allelic heterogeneity in STGD1. Approximately half of the cohort harbours missense variants only, indicating a relatively mild phenotype of the ProgStar cohort. There are significant differences in allele frequencies between nations, although the three most prevalent variants are shared as frequent variants.
Comparison of the efficacy and acceptability of Chinese herbal medicine in adult patients with heart failure and reduced ejection fraction: study protocol for a systematic review and network meta-analysis
Authors: Liu Jing , Lu Jin-Jin , Zhou Kun , Wan Jie , Li Yan , Cui Xiao-Yun , Gao Qun , Huang Yan-Chao , Li Si-Nai , Dong Qiao-Zhi , Lin Qian 
Published: June 2018

IntroductionHeart failure with reduced ejection fraction (HFrEF) is defined as the clinical diagnosis of heart failure (HF) and ejection fraction (EF) ≤40%, which is a severe public healthcare issue and brings a heavy social and economic burden for patients with HFrEF. Chinese herbal medicine (CHM) has a long history in treating HF. Questions concerning the efficacy and acceptability of CHM-related interventions in adult patients with HFrEF led us to use the method of systematic review and network meta-analysis to integrate direct and indirect evidence to create hierarchies for all CHM.Methods and analysisNine medical databases, including PubMed, EMBASE (OVID), the Cochrane Library, Google Scholar, Web of Science, CNKI, VIP, Wanfang Database and CBM will be searched from the date of database inception to June 2015 (updated to March 2017) without language and publication status restriction. Completely randomised controlled trials (RCTs) comparing CHM or CHM plus routine treatment with CHM, CHM plus routine treatment, routine treatment, no treatment or placebo for adults with HFrEF will be examined. Our primary outcomes will include all-cause mortality, HF-related death, all-cause rehospitalisation, HF-related rehospitalisation and acceptability (discontinuation due to any adverse events during treatment). Secondary outcomes will include response rate, mean value or mean difference from baseline of surrogate indexes. We will perform the Bayesian network meta-analyses (NMA) for the most frequently reported primary or secondary outcome and the acceptability outcome, if available. Meta-regression, subgroup analyses and sensitivity analyses will be conducted based on prespecified effect modifiers to assess the robustness of the findings.DisseminationThe results of this NMA will provide useful information about the effectiveness and acceptability of CHM in adults with HFrEF, which will also have implications for clinical practice and further research. Findings will be disseminated through peer-reviewed journal publication and conference presentations.PROSPERO registration numberCRD42016053854.
Validation of discharge diagnosis codes to identify serious infections among middle age and older adults
Authors: Wiese Andrew D , Griffin Marie R , Stein C Michael , Schaffner William , Greevy Robert A , Mitchel Jr Edward F , Grijalva Carlos G 
Published: June 2018

ObjectivesHospitalisations for serious infections are common among middle age and older adults and frequently used as study outcomes. Yet, few studies have evaluated the performance of diagnosis codes to identify serious infections in this population. We sought to determine the positive predictive value (PPV) of diagnosis codes for identifying hospitalisations due to serious infections among middle age and older adults.Setting and participantsWe identified hospitalisations for possible infection among adults >=50 years enrolled in the Tennessee Medicaid healthcare programme (2008–2012) using International Classifications of Diseases, Ninth Revision diagnosis codes for pneumonia, meningitis/encephalitis, bacteraemia/sepsis, cellulitis/soft-tissue infections, endocarditis, pyelonephritis and septic arthritis/osteomyelitis.DesignMedical records were systematically obtained from hospitals randomly selected from a stratified sampling framework based on geographical region and hospital discharge volume.MeasuresTwo trained clinical reviewers used a standardised extraction form to abstract information from medical records. Predefined algorithms served as reference to adjudicate confirmed infection-specific hospitalisations. We calculated the PPV of diagnosis codes using confirmed hospitalisations as reference. Sensitivity analyses determined the robustness of the PPV to definitions that required radiological or microbiological confirmation. We also determined inter-rater reliability between reviewers.ResultsThe PPV of diagnosis codes for hospitalisations for infection (n=716) was 90.2% (95% CI 87.8% to 92.2%). The PPV was highest for pneumonia (96.5% (95% CI 93.9% to 98.0%)) and cellulitis (91.1% (95% CI 84.7% to 94.9%)), and lowest for meningitis/encephalitis (50.0% (95% CI 23.7% to 76.3%)). The adjudication reliability was excellent (92.7% agreement; first agreement coefficient: 0.91). The overall PPV was lower when requiring microbiological confirmation (45%) and when requiring radiological confirmation for pneumonia (79%).ConclusionsDischarge diagnosis codes have a high PPV for identifying hospitalisations for common, serious infections among middle age and older adults. PPV estimates for rare infections were imprecise.