bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small scale temporal patterns of recruitment and hatching of Atlantic horse mackerel (L.) at a nearshore reef area
Authors: Klein Maria , Beveren Elisabeth Van , Rodrigues Diana , Serrão Ester A. , Caselle Jennifer E. , Gonçalves Emanuel J. , Borges Rita 
Published: April 2018

AbstractAtlantic horse mackerel (Trachurus trachurus, Linnaeus, 1758) is a highly exploited species, common throughout the North‐East Atlantic. As a pelagic‐neritic fish it typically occurs over the shelf from the surface to 200 m deep on sandy bottoms. Most research has focused on distributions of adults or early life stages (eggs and larvae) of this species in offshore waters and only a few studies have reported the occurrence of early stages near the coast. However, these nearshore environments might be important for the early growth and survival of the Atlantic horse mackerel. In addition, little is known on how environmental processes might affect the early stages of this species. Here, we monitored weekly recruitment of horse mackerel to artificial substrates (SMURFS) deployed near the coast at both the surface and near the bottom, and back‐calculated hatching cohorts. The relationship of both recruitment and hatching patterns with environmental factors was investigated. From a total of 2,515 fish, 2,490 (99%) recruited to surface SMURFS. A GAM and GAMM analysis of the recruitment and hatching patterns, respectively, revealed a strong relationship with the lunar cycle and upwelling. Both recruitment and hatching showed lunar periodicity, with peaks near the new moon and revealed to be influenced negatively by upwelling. This study suggests that the nearshore environment might be an important nursery area for post‐larval and early juvenile Atlantic horse mackerel.
Cross‐scale controls on carbon emissions from boreal forest megafires
Authors: Walker Xanthe J. , Rogers Brendan M. , Baltzer Jennifer L. , Cumming Steven G. , Day Nicola J. , Goetz Scott J. , Johnstone Jill F. , Schuur Edward A. G. , Turetsky Merritt R. , Mack Michelle C. 
Published: April 2018

AbstractClimate warming and drying is associated with increased wildfire disturbance and the emergence of megafires in North American boreal forests. Changes to the fire regime are expected to strongly increase combustion emissions of carbon (C) which could alter regional C balance and positively feedback to climate warming. In order to accurately estimate C emissions and thereby better predict future climate feedbacks, there is a need to understand the major sources of heterogeneity that impact C emissions at different scales. Here, we examined 211 field plots in boreal forests dominated by black spruce (Picea mariana) or jack pine (Pinus banksiana) of the Northwest Territories (NWT), Canada after an unprecedentedly large area burned in 2014. We assessed both aboveground and soil organic layer (SOL) combustion, with the goal of determining the major drivers in total C emissions, as well as to develop a high spatial resolution model to scale emissions in a relatively understudied region of the boreal forest. On average, 3.35 kg C m−2 was combusted and almost 90% of this was from SOL combustion. Our results indicate that black spruce stands located at landscape positions with intermediate drainage contribute the most to C emissions. Indices associated with fire weather and date of burn did not impact emissions, which we attribute to the extreme fire weather over a short period of time. Using these results, we estimated a total of 94.3 Tg C emitted from 2.85 Mha of burned area across the entire 2014 NWT fire complex, which offsets almost 50% of mean annual net ecosystem production in terrestrial ecosystems of Canada. Our study also highlights the need for fine‐scale estimates of burned area that represent small water bodies and regionally specific calibrations of combustion that account for spatial heterogeneity in order to accurately model emissions at the continental scale.
Spring phenology at different altitudes is becoming more uniform under global warming in Europe
Authors: Chen Lei , Huang Jian‐Guo , Ma Qianqian , Hänninen Heikki , Rossi Sergio , Piao Shilong , Bergeron Yves 
Published: April 2018

AbstractUnder current global warming, high‐elevation regions are expected to experience faster warming than low‐elevation regions. However, due to the lack of studies based on long‐term large‐scale data, the relationship between tree spring phenology and the elevation‐dependent warming is unclear. Using 652k records of leaf unfolding of five temperate tree species monitored during 1951–2013 in situ in Europe, we discovered a nonlinear trend in the altitudinal sensitivity (SA, shifted days per 100 m in altitude) in spring phenology. A delayed leaf unfolding (2.7 ± 0.6 days per decade) was observed at high elevations possibly due to decreased spring forcing between 1951 and 1980. The delayed leaf unfolding at high‐elevation regions was companied by a simultaneous advancing of leaf unfolding at low elevations. These divergent trends contributed to a significant increase in the SA (0.36 ± 0.07 days 100/m per decade) during 1951–1980. Since 1980, the SA started to decline with a rate of −0.32 ± 0.07 days 100/m per decade, possibly due to reduced chilling at low elevations and improved efficiency of spring forcing in advancing the leaf unfolding at high elevations, the latter being caused by increased chilling. Our results suggest that due to both different temperature changes at the different altitudes, and the different tree responses to these changes, the tree phenology has shifted at different rates leading to a more uniform phenology at different altitudes during recent decades.
Supervised forecasting of the range expansion of novel non‐indigenous organisms: Alien pest organisms and the 2009 H1N1 flu pandemic
Authors: Koike Fumito , Morimoto Nobuo 
Published: April 2018

AbstractAimWe propose a simple supervised method for forecasting the expansion of the geographical range of non‐indigenous species without any detailed information on the pathway mechanisms. The models currently used, such as metapopulation models, population dynamics [e.g., the susceptible‐infected‐recovered (SIR) model] with diffusion process, and models using individual‐based mechanisms, require specific parameters according to the assumed mechanisms. These parameters are difficult to obtain immediately after the first infestation is detected, although subsequent pandemics of novel pathogens and non‐indigenous pest organisms can be fatal to humans and damage agriculture and native ecosystems.InnovationA simple machine‐learning approach was developed. The future distribution of the target species was predicted by composing the spreading patterns of the previous range expansions of various alien species similar to the target species. A matrix representing the early–late relationship of infestation between regions was used to compare and compose various range expansion patterns. The eigenvector of the composed matrix gives the predicted order of infestation. Spreading speed was considered using the standard deviation of infestation dates, and future infestation dates were calculated by a reduced major axis with the eigenvector. In the feasibility assessment, the study area (Japan) was divided into many small regions (prefectures), and the dates of infestation in these regions were predicted. Our method successfully predicted the infestation dates of various alien species and the novel H1N1 influenza pandemic in 2009.Main conclusionsOur method is less complex and requires simpler information than other methods and is applicable to all organisms. Constructing a database of the range expansions of alien species, including novel pathogens and agricultural and environmental pests, at the global level and with high spatial resolution, such as at the county or city level, will facilitate the prediction of future range expansions of hazardous organisms.
Migraine Burden of Disease: From the Patient's Experience to a Socio‐Economic View
Authors: Agosti Reto 
Published: April 2018

Migraine is one of the most common diseases worldwide and, importantly, a major cause of disability. This translates into a huge clinical and economic burden to individuals and society. Despite existing data on how migraine affects populations, the disease continues to be underdiagnosed and therefore undertreated, so the scale of the public health problem may be underestimated. The impact on the daily lives of patients and their families has also been underappreciated. Clinical and regulatory guidelines are encouraging the use of patient‐reported outcome tools (PROs), as these may help in disease management and facilitate physician–patient interactions. In clinical trials in migraine, PRO data are key to evaluating the effects of new therapies on patients, such as disability assessment, productivity, quality of life, and emotional and physical functioning. Digital technologies have enabled the development of ePRO tools, which may play a growing role in the collection of PRO data in the future.Here, we will consider the current view of the burden imposed by migraine on patients and society, illustrate this with two patient case studies, and examine the initiatives underway to use our knowledge to improve our management approaches for the disease.
Bismuth improves efficacy of proton‐pump inhibitor clarithromycin, metronidazole triple Helicobacter pylori therapy despite a high prevalence of antimicrobial resistance
Authors: Long Xiaohua , Chen Qi , Yu Lou , Liang Xiao , Liu Wenzhong , Lu Hong 
Published: April 2018

AbstractBackgroundHelicobacter pylori (H. pylori) eradication has become increasingly difficult especially for penicillin allergy patients.AimsTo evaluate the efficacy of adding bismuth or high‐dose metronidazole to an H. pylori eradication regimen containing a proton‐pump inhibitor, clarithromycin, and metronidazole in patients allergic to penicillin.MethodsPilot study in which penicillin‐allergic, treatment‐naive subjects were randomized (1:1) to 14‐day esomeprazole (20 mg q12h), clarithromycin (500 mg q12h), and high dose of metronidazole (400 mg q6h) with (BECM group) or without (ECM group) bismuth (600 mg q12h). Eradication was confirmed by 13C‐urea breath test 6 weeks after therapy. Antimicrobial susceptibility was assessed by the agar dilution method. Adverse events were recorded.ResultsSixty‐six subjects were randomized, four were lost to follow‐up and eight violated the protocol. The eradication rates were 63.6% (95% CI: 47.2%‐80.0%) for ECM vs 84.8% (95% CI 72.6%‐97.1%) (p = .049) for BECM by intention‐to‐treat, 67.7% (95% CI 51.3%‐84.2%) vs 90.3% (95% CI 79.9%‐100%) (p = .029) by modified ITT, and 70% (95% CI 53.6%‐86.4%) vs 96% (95% CI 88.3%‐100%) (P = .033) by per‐protocol. Metronidazole, clarithromycin, and dual‐resistant rates were 74.2%, 24.2%, and 18.2%, respectively. The cure rates were significantly improved by the addition of bismuth for both clarithromycin‐resistant isolates (100% vs 25%, P = .024) and metronidazole‐resistant isolates (94.7% vs 63.6%, P = .043). Adverse events were reported by 45.5% of subjects in ECM group and 48.5% in the BECM group (P = .805).ConclusionsThis prospective trial demonstrated that while high‐dose metronidazole could not completely overcome metronidazole resistance, bismuth was additive and improved the overall cure rates by 21%‐26%.
Pediatric Helicobacter pylori gastropathy demonstrates a unique pattern of gastric foveolar hyperplasia
Authors: Saghier Sadaf , Schwarz Steven M. , Anderson Virginia , Gupta Raavi , Heidarian Amin , Rabinowitz Simon S. 
Published: April 2018

AbstractObjectivesHelicobacter pylori (Hp) are the most common agents causing gastric mucosal injury worldwide. Foveolar hyperplasia is a key component of the stomach's reaction to injury. This study examines histopathologic characteristics associated with Helicobacter pylori and with non‐ Helicobacter pylori‐associated gastropathy in children and adolescents, and compares the prevalence of foveolar hyperplasia among these disease subgroups and normal control subjects.MethodsEighty‐one gastric antral and corpus biopsies from subjects 2‐19 years of age were studied. Twenty‐two subjects with Helicobacter pylori gastritis were compared to 23 with non‐Helicobacter pylori gastropathy and to 36 controls (normal biopsies). Foveolar length, full mucosal thickness, and the foveolar length: full mucosal thickness ratio were derived by a morphometric technique previously developed to analyze adult gastric tissue.ResultsCompared to controls, Helicobacter pylori gastritis demonstrated significant increases in antral foveolar length (P < .0001), full mucosal thickness (P < .0001), as well as corpus foveolar length (P < .05) and corpus full mucosal thickness (P < .05). Non‐Helicobacter pylori‐associated gastropathy also was characterized by increased antral foveolar length (P < .0001) and full mucosal thickness (P < .001) but corresponding corpus measurements did not differ from controls. Antral foveolar length in non‐Helicobacter pylori gastropathy was increased, when compared to Helicobacter pylori gastritis (P < .05), while corpus values were not. The non‐Helicobacter pylori gastropathy group demonstrated increased antral foveolar length: full mucosal thickness ratios, compared with Helicobacter pylori gastritis (P < .001) and with normal controls (P < .0001).DiscussionAn objective, quantitative approach to measuring foveolar hyperplasia in adults was successfully applied to pediatric biopsies and yielded a richer characterization of gastric pathology in children. Foveolar hyperplasia appears to be a generalized phenomenon in the presence of pediatric Helicobacter pylori gastritis but is limited to the antrum in non‐Helicobacter pylori gastropathy.
Acid‐regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Authors: Marcus Elizabeth A. , Sachs George , Scott David R. 
Published: April 2018

AbstractBackgroundThe pathogen Helicobacter pylori encounters many stressors as it transits to and infects the gastric epithelium. Gastric acidity is the predominate stressor encountered by the bacterium during initial infection and establishment of persistent infection. H. pylori initiates a rapid response to acid to maintain intracellular pH and proton motive force appropriate for a neutralophile. However, acid sensing by H. pylori may also serve as a transcriptional trigger to increase the levels of other pathogenic factors needed to subvert host defenses such as acid acclimation, antioxidants, flagellar synthesis and assembly, and CagA secretion.Materials and MethodsHelicobacter pylori were acid challenged at pH 3.0, 4.5, 6.0 vs nonacidic pH for 4 hours in the presence of urea, followed by RNA‐seq analysis and qPCR. Cytoplasmic pH was monitored under the same conditions.ResultsAbout 250 genes were induced, and an equal number were repressed at acidic pHs. Genes encoding for antioxidant proteins, flagellar structural proteins, particularly class 2 genes, T4SS/Cag‐PAI, FoF1‐ATPase, and proteins involved in acid acclimation were highly expressed at acidic pH. Cytoplasmic pH decreased from 7.8 at pHout of 8.0 to 6.0 at pHout of 3.0.ConclusionsThese results suggest that increasing extracellular or intracellular acidity or both are detected by the bacterium and serve as a signal to initiate increased production of protective and pathogenic factors needed to counter host defenses for persistent infection. These changes are dependent on degree of acidity and time of acid exposure, triggering a coordinated response to the environment required for colonization.
Using the Public Involvement Impact Assessment Framework to assess the impact of public involvement in a mental health research context: A reflective case study
Authors: Collins Michelle , Long Rita , Page Anthony , Popay Jennie , Lobban Fiona 
Published: April 2018

AbstractBackgroundWe assess the utility of the Public Involvement Impact Assessment Framework (PiiAF) as a resource to support research teams in assessing the impact of Public Involvement across diverse research and public involvement (PI) contexts. PiiAF was developed in response to a well‐documented growth in Public Involvement in health research in the United Kingdom that demands a more sophisticated evidence base to demonstrate its impact.DesignWe used a reflective case study approach drawing on contemporaneous meeting notes, PiiAF website resources and retrospective reflections to describe how PiiAF helped us to develop an impact assessment plan of the PI in a university‐based mental health research centre.DiscussionWe consider key aspects of our experiences of using PiiAF as a tool to help us design an impact assessment of PI, interpret these experiences with reference to relevant theory and research and share insights that may be useful to other teams considering using PiiAF.ConclusionThese insights include understanding the commitment of time and effort required to develop effective PI impact assessment plans; the flexibility of PiiAF and its ability to be used in a range of research and PI contexts; and the advantages of involving all stakeholders (including the public) in the development of an PI assessment plan.
Health Disorder of Climate Migrants in Khulna City: An Urban Slum Perspective
Authors: Rahaman Muhammad Abdur , Rahman Mohammad Mahbubur , Bahauddin Khalid Md. , Khan Shakil , Hassan Shareful 
Published: April 2018

AbstractAs the most vulnerable climatic region in the country, Khulna City is increasingly experiencing climate‐change‐induced urban problems. For instance, occupancy by climate migrants (delete the term “illegal migrant”), drainage congestion, water logging and reduced fresh water availability are all increasing problems. In the last decade, the population in the city increased by more than 20 per cent due to migration from nearby climate vulnerable districts. This study explores the health disorders of climate migrants occupying the urban slums and squats of the Khulna City area. This study found that these climate migrants settled in the urban slums and squats and, as such, they do not have access to urban amenities such as clean drinking water, hygiene services, and health facilities. This study noted that these displaced people are at increased risk of health issues from unhygienic and overcrowded living conditions and from water and sanitation problems. They often suffer from different waterborne diseases, under‐nutrition and micronutrient deficiencies. This study suggests that there is a need for better planning, preparation and training in Bangladesh to which migrants move, including better training in health and related services on how to recognize and respond to health problems that may be slow to manifest. Education and training also need to be provided for the migrants themselves, to help them adapt culturally and to enhance their skills and potential for employment.
Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle
Authors: Miao J. , Wang X. , Bao J. , Jin S. , Chang T. , Xia J. , Yang L. , Zhu B. , Xu L. , Zhang L. , Gao X. , Chen Y. , Li J. , Gao H. 
Published: April 2018

SummaryBone weight, defined as the total weight of the bones in all the forequarter and hindquarter joints, can reflect somebody conformation traits and skeletal diseases. To gain a better understanding of the genetic determinants of bone weight, we used a composite strategy including multimarker and rare‐marker association to perform genomewide association studies (GWAS) for that character in Simmental cattle. Our strategy consisted of three models: (i) A traditional linear mixed model (LMM) was applied (Q+K‐LMM); (ii) single nucleotide polymorphisms (SNPs) withp‐values less than .05 from theLMMwere selected to undergo the least absolute shrinkage and selector operator (Lasso) in the second stage (LMM‐Lasso); (iii) genes containing two or more rareSNPs were examined by performing the sequence kernel association test (gene‐basedSKAT). A total of 1,225 cattle were genotyped with an Illumina BovineHDBeadChip containing 770,000SNPs. After the quality‐control procedures, 1,217 individuals with 608,696 commonSNPs and 105,787 rareSNPs (with 0.001 < minor allele frequency [MAF] <0.05) remained in the sample for analysis. A traditionalLMMsuccessfully mapped three genes associated with bone weight, whileLMM‐Lasso identified nine genes, which included all genes found by traditionalLMM. Only a single gene,EPHB3, surpassed the significance threshold after Bonferroni correction in gene‐basedSKAT. In conclusion, based on functional annotation and results from previous endeavours, we believe thatLCORL,RIMS2,LAP3,PRKAR2B,CHSY1,MAP2K6andEPHB3are candidate genes for bone weight. In general, such a comprehensive strategy forGWASmay be useful for researchers seeking to probe the full genetic architecture underlying economic traits in livestock.
Safety and efficacy of antibiotics among acutely decompensated cirrhosis patients
Authors: Habib Shahid , Patel Nehali , Yarlagadda Sandeep , Hsu Chiu‐Hsieh , Patel Sarah , Schader Lindsey , Walker Courtney , Twesigye Innocent 
Published: April 2018

AbstractBackground and AimInfection is a leading precipitant of acute‐on‐chronic liver failure. This study aims to determine the safety and efficacy of antibiotics within acute‐on‐chronic liver failure.MethodsRetrospective study of 457 acute‐on‐chronic liver failure patients admitted to the University of Arizona Health Network between January 1 and December 31, 2014. Eligibility criteria were as follows: at least 18 years of age and 6 months follow‐up, data available to calculate systemic inflammatory response syndrome (SIRS), and acute‐on‐chronic liver failure. This study collected patient's clinical features and historical data. Key data points were infection, antibiotic use, and SIRS. This study used Cox proportional hazards to model the effects of clinical factors on risk of death.ResultsA total of 521 of 1243 met the inclusion criteria, and 64 had missing data, leaving 457 patients. Infection resulted in higher hazard (hazard ratio [HR] = 1.6, confidence interval [CI]: 1.1–1.3, P = 0.01). Patients with infections and antibiotics, compared with non‐infected patients without antibiotics, had higher hazard (HR = 1.633, CI: 1.022–2.609, P = .04). Of those infected patients with antibiotics, SIRS patients experienced higher hazard (HR = 1.9, CI: 1.1–3.0, P = .007). Multivariable Cox proportional hazards associated the following with higher hazard: SIRS (HR = 1.866, CI: 1.242–2.804, P = 0.003), vancomycin (HR = 1.640, CI: 1.119–2.405, P = 0.011), Model for End‐Stage Liver Disease (HR = 1.051, CI: 1.030–1.073, P < 0.001), gastrointestinal bleeding (HR = 1.727, CI: 1.180–2.527, P = 0.005), and hepatic encephalopathy (HR = 1.807, CI: 1.247–2.618, P = 0.002).ConclusionOverall, treatment of infection with antibiotics did not improve survival; however, patients not meeting SIRS criteria had better outcomes, and vancomycin was associated with poorer survival among acute‐on‐chronic liver failure patients.