bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices
Authors: Peck Vincent , Quiza Liliana , Buffet Jean‐Philippe , Khdhiri Mondher , Durand Audrey‐Anne , Paquette Alain , Thiffault Nelson , Messier Christian , Beaulieu Nadyre , Guertin Claude , Constant Philippe 
Published: February 2016

SummaryThe impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high‐throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment.
pophelper: an R package and web app to analyse and visualize population structure
Authors: Francis R. M. 
Published: February 2016

AbstractThepophelper rpackage and web app are software tools to aid in population structure analyses. They can be used for the analyses and visualization of output generated from population assignment programs such asadmixture,structureandtess. Some of the functions include parsing output run files to tabulate data, estimatingKusing the Evanno method, generating files forclumppand functionality to create barplots. These functions can be streamlined into standardranalysis workflows. The latest version of the package is available ongithub(https://github.com/royfrancis/pophelper). An interactive web version of thepophelperpackage is available which covers the same functionalities as therpackage version with features such as interactive plots, cluster alignment during plotting, sorting individuals and ordering of population groups. The interactive version is available athttp://pophelper.com/.
Direct Versus Video Laryngoscopy Using the C‐MAC for Tracheal Intubation in the Emergency Department, a Randomized Controlled Trial
Authors: Driver Brian E. , Prekker Matthew E. , Moore Johanna C. , Schick Alexandra L. , Reardon Robert F. , Miner James R. 
Published: February 2016

AbstractBackgroundDirect laryngoscopy (DL) has long been the most common approach for emergency endotracheal intubation, although the use of video laryngoscopy (VL) is becoming more widespread. Current observational data suggest that VL has higher first‐pass success, although randomized trials are lacking.ObjectivesThe objective was to compare first‐pass success in patients undergoing emergency intubation with DL or VL using a C‐MAC device.MethodsThis was an open‐label, prospective, randomized, controlled trial in an academic emergency department of patients undergoing emergency intubation with a plan of DL for the first attempt. Patients were randomly assigned in a 1:1 ratio to either DL or VL using a C‐MAC device for the first intubation attempt. The primary outcome was first‐pass success. Secondary outcomes included time to intubation, development of aspiration pneumonia, and hospital length of stay (LOS). The study was registered at Clinicaltrials.gov, number NCT01710891.ResultsA total of 198 patients were enrolled and intubated with either DL (n = 95) or VL (n = 103). First‐attempt success was 86 and 92% for the DL and VL groups, respectively (difference = −5.9%, 95% confidence interval = −14.5% to 2.7%, p = 0.18). Time to intubation, rates of aspiration pneumonia, and hospital LOS were not different between the two groups.ConclusionsIn patients undergoing emergency intubation in whom DL was planned for the first attempt, we did not detect a difference between VL or DL using the C‐MAC device in first‐pass success, duration of intubation attempt, aspiration pneumonia, or hospital LOS.
Cannabinoid receptor 2 augments eosinophil responsiveness and aggravates allergen‐induced pulmonary inflammation in mice
Authors: Frei R. B. , Luschnig P. , Parzmair G. P. , Peinhaupt M. , Schranz S. , Fauland A. , Wheelock C. E. , Heinemann A. , Sturm E. M. 
Published: February 2016

AbstractBackgroundAccumulation of activated eosinophils in tissue is a hallmark of allergic inflammation. The endocannabinoid 2‐arachidonoylglycerol (2‐AG) has been proposed to elicit eosinophil migration in a CB2 receptor/Gi/o‐dependent manner. However, it has been claimed recently that this process may also involve other mechanisms such as cytokine priming and the metabolism of 2‐AG into eicosanoids. Here, we explored the direct contribution of specific CB2 receptor activation to human and mouse eosinophil effector function in vitro and in vivo.MethodsIn vitro studies including CB2 expression, adhesion and migratory responsiveness, respiratory burst, degranulation, and calcium mobilization were conducted in human peripheral blood eosinophils and mouse bone marrow‐derived eosinophils. Allergic airway inflammation was assessed in mouse models of acute OVA‐induced asthma and directed eosinophil migration.ResultsCB2 expression was significantly higher in eosinophils from symptomatic allergic donors. The selective CB2 receptor agonist JWH‐133 induced a moderate migratory response in eosinophils. However, short‐term exposure to JWH‐133 potently enhanced chemoattractant‐induced eosinophil shape change, chemotaxis, CD11b surface expression, and adhesion as well as production of reactive oxygen species. Receptor specificity of the observed effects was confirmed in eosinophils from CB2 knockout mice and by using the selective CB2 antagonist SR144528. Of note, systemic application of JWH‐133 clearly primed eosinophil‐directed migration in vivo and aggravated both AHR and eosinophil influx into the airways in a CB2‐specific manner. This effect was completely absent in eosinophil‐deficient ∆dblGATA mice.ConclusionOur data indicate that CB2 may directly contribute to the pathogenesis of eosinophil‐driven diseases. Moreover, we provide new insights into the molecular mechanisms underlying the CB2‐mediated priming of eosinophils. Hence, antagonism of CB2 receptors may represent a novel pharmacological approach for the treatment of allergic inflammation and other eosinophilic disorders.
Efficacy of a therapeutic treatment using gas‐filled microbubble‐associated phospholipase A2 in a mouse model of honeybee venom allergy
Authors: Corthésy B. , Lassus A. , Terrettaz J. , Tranquart F. , Bioley G. 
Published: February 2016

AbstractBackgroundVenom immunotherapy is efficient to desensitize people suffering from insect sting allergies. However, the numerous injections required over several years and important risks of severe side reactions complicate the widespread use of immunotherapy. In the search for novel approaches to blunt the overwhelming pro‐allergic Th2 response, we evaluated the therapeutic efficacy of a treatment based on a denatured form of the major allergen, phospholipase A2, associated with microbubbles (PLA2denat‐MB) in a mouse model of honeybee venom allergy.MethodsAntibodies measured by ELISA, T‐cell responses assessed by CFSE‐based proliferation assays and ELISA, and basophil degranulation were examined after PLA2denat‐MB‐based therapeutic treatment of sensitized mice. Mice were challenged with a lethal dose of PLA2 to evaluate protection against anaphylaxis.ResultsTherapeutic subcutaneous administration of two different PLA2denat‐MB formulations, in contrast to PLA2denat alone, reduced allergic symptoms and protected all mice from anaphylaxis‐mediated death after allergen challenge. At the functional level, the use of PLA2denat decreased IgE‐mediated basophil degranulation as compared to the native form of the allergen. In comparison with PLA2denat alone, both PLA2denat‐MB formulations decreased allergen‐specific Th2 CD4 T‐cell reactivity. At the mechanistic level, PLA2denat‐MB containing 20% palmitic acid and PEG induced PLA2‐specific IgA and increased Foxp3+ Treg frequencies and TGF‐β production, whereas the formulation bearing 80% palmitic acid triggered the production of IFN‐γ, IgG2a, and IgG3.ConclusionsIn contrast to conventional PLA2 subcutaneous immunotherapy, the therapeutic administration of PLA2‐MB treatment to mice that already had established allergy to PLA2 protects all subsequently challenged animals.
The challenge of measuring IL‐33 in serum using commercial ELISA: lessons from asthma
Authors: Ketelaar M. E. , Nawijn M. C. , Shaw D. E. , Koppelman G. H. , Sayers I. 
Published: February 2016

SummaryBackgroundInterleukin‐33 (IL‐33) has been subject of extensive study in the context of inflammatory disorders, particularly in asthma. Many human biological samples, including serum, have been used to determine the protein levels of IL‐33, aiming to investigate its involvement in asthma. Reliable methods are required to study the association of IL‐33 with disease, especially considering the complex nature of serum samples.ObjectiveWe evaluated four IL‐33 ELISA kits, aiming to determine a robust and reproducible approach to quantifying IL‐33 in human serum from asthma patients.MethodsIL‐33 levels were investigated in serum of well‐defined asthma patients by the Quantikine, DuoSet (both R&D systems), ADI‐900‐201 (Enzo Life Sciences), and SKR038 (GenWay Biotech Inc San Diego USA) immunoassays, as well as spiking experiments were performed using recombinant IL‐33 and its soluble receptor IL‐1RL1‐a.ResultsWe show that 1) IL‐33 is difficult to detect by ELISA in human serum, due to lack of sensitivity and specificity of currently available assays; 2) human serum interferes with IL‐33 quantification, in part through IL‐1RL1‐a; and 3) using non‐serum certified kits may lead to spurious findings.Conclusion and Clinical RelevanceIf IL‐33 is to be studied in the serum of asthma patients and other diseases, a more sensitive and specific assay method is required, which will be vital for further understanding and targeting of the IL‐33/IL‐1RL1 axis in human disease.
Acylated and unacylated ghrelin during OGTT in Prader‐Willi syndrome: support for normal response to food intake
Authors: Kuppens R.J. , Delhanty P.J.D. , Huisman T.M. , van der Lely A.J. , Hokken‐Koelega A.C.S. 
Published: February 2016

SummaryBackgroundPrader‐Willi syndrome (PWS) is characterized by hyperphagia with impaired satiety. PWS patients have very high acylated ghrelin (AG) with normal unacylated ghrelin (UAG) levels, resulting in an elevated AG/UAG ratio, suggesting an intrinsic defect in the ghrelin regulation. Normally, food intake induces satiety and a drop in AG and UAG levels, but it is unknown if these levels also decline in PWS.ObjectiveTo evaluate whether the high AG levels in PWS decline in response to glucose intake during an oral glucose tolerance test (OGTT), and to investigate the effects of growth hormone (GH) treatment on this response.MethodSerum levels of AG, UAG and AG/UAG ratio during an OGTT were determined in 24 GH‐treated patients with PWS (median age 19·0, range 14·2–25·9 years) and in 10 GH‐stop patients (of whom five were in GH‐treated group; 18·5, 14·5–20·3 years).ResultsIn GH‐treated and GH‐stop young adults with PWS, there was a sharp decline of AG levels and a decrease of UAG levels in the first 30 min after the glucose load, which resulted in a lower AG/UAG ratio. GH‐treated patients had significantly lower AG levels than GH‐stop patients at baseline and during the OGTT. All UAG levels and AG/UAG ratios were lower in the GH‐treated patients, although not significantly.ConclusionsIn young adults with PWS, an oral glucose load significantly reduces AG and UAG levels, suggesting normal regulation of the ghrelin axis by food intake. GH treatment results in lower AG levels at baseline and during OGTT, suggesting a more favourable metabolic profile. Our findings might suggest that the impaired satiety is not the result of an abnormal response of the orexigenic ghrelin to food intake.
Serum thyroglobulin as a biomarker of iodine deficiency in adult populations
Authors: Krejbjerg Anne , Bjergved Lena , Bülow Pedersen Inge , Carlé Allan , Knudsen Nils , Perrild Hans , Ovesen Lars , Banke Rasmussen Lone , Laurberg Peter 
Published: February 2016

SummaryObjectiveTo clarify which factors may influence the serum Tg level in an adult population and how this may affect Tg as a biomarker of iodine deficiency (ID).Design and methodsTwo identical cross‐sectional studies were performed before (C1a: 1997–98, n = 4649) and after (C2: 2004–05, n = 3570) the Danish mandatory iodine fortification (IF) of salt (2000). Additionally, a follow‐up study of C1a was performed after IF (C1b: 2008–10, n = 2465). The studies took place in two regions with mild (Copenhagen) and moderate (Aalborg) ID before IF. Serum Tg was measured by immunoradiometric method and investigated as outcome variable in multivariate models.ResultsMultiple factors were associated with serum Tg. Some were directly related to iodine intake (cohort, urinary iodine concentration (UIC) level and region), and some were likely mediators of iodine intake effects on Tg (thyroid nodularity, thyroid size and autonomy with low TSH). Others were caused by Tg assay interference (Tg‐Ab positivity), aggravation of ID (childbirths and smoking) or TSH stimulation of the thyroid. Estimated 24‐h urinary iodine excretion was a more sensitive predictor of Tg than UIC. Iodine supplement users had low median Tg values compared with nonusers both before and after IF.ConclusionsMultiple factors should be taken into consideration when evaluating Tg as a marker of ID in adult populations, and the Tg results may depend on the assay used. Still, Tg is a sensitive marker of ID. We suggest including a reference population with known sufficient iodine intake when Tg is used to evaluate ID.
Survival following salvage abdominoperineal resection for persistent and recurrent squamous cell carcinoma of the anus: do these disease categories affect survival?
Authors: Severino N. P. , Chadi S. A. , Rosen L. , Coiro S. , Choman E. , Berho M. , Wexner S. D. 
Published: February 2016

AbstractAimThis study aimed to investigate the results of salvage abdominoperineal excision (APR) in patients with persistent or recurrent squamous cell carcinoma of the anus (SCCA).MethodPatients with anal neoplasia were identified from a prospective database. Patients with invasive SCCA with demonstrated failure of chemoradiation therapy (CRT) who underwent salvage APR for one of three disease categories (persistent, < 6 months post‐CRT; early recurrent, 6–24 months post‐CRT; late recurrent, > 24 months post‐CRT) were included. The primary outcome was overall survival after salvage APR. Tumour size, metastatic lymph nodes (LN), circumferential resection margin positivity (CRM) and neurolymphovascular invasion (NLVI) were correlated with the outcome.ResultsThirty‐six patients with a median 3‐year overall survival of 46% (median follow‐up 24 months) underwent salvage APR due to persistent or recurrent SCCA (14 men, mean age 59 years). Eleven (31%) patients were diagnosed with persistent disease, 17 (47%) with early and 8 (22%) with late recurrence. Two‐year overall survival of Stage 0/I/II and III/IV disease was 81.5% and 33.74%, respectively (P = 0.022). Overall disease stage was associated with disease categorization (P = 0.009): patients with persistent disease or early recurrence had a significantly higher disease stage than patients with late recurrence (OR = 20.9 and 17.2). Despite apparently improved survival in patients with late disease recurrence on live table analysis, no significant difference was identified in overall survival when stratified by disease category on log‐rank test analysis.ConclusionPersistent and recurrent disease does not show any significant difference in survival, but patients with late recurrence may have a better prognosis.
Differences in screening vs non‐screening colonoscopy: scope for improvement?
Authors: Ahmed S. , Naumann D. N. , Karandikar S. 
Published: February 2016

AbstractAimColonoscopy performed as part of the NHS Bowel Cancer Screening Programme (BCSP) is of high standard as measured using global rating scale (GRS) criteria. Screening practitioners also provide a non‐screening colonoscopy service. The current study compares colonoscopy quality indicators between screening and non‐screening groups performed by a single practitioner using the GRS.MethodPatient details were obtained for all consecutive colonoscopies between 2007 and 2014 performed by a single screening practitioner. Data were collected retrospectively from electronic patient records; BCSP Exeter database and non‐screening colonoscopies were compared. Data included patient demographics (age, gender), sedation, and the GRS data including caecal intubation, adenoma and neoplasia detection rates.ResultsIn all, 1961 colonoscopy procedures (1067 screening and 894 non‐screening) were identified; 57% were men. Mean (SD) age for all patients was 64 (± 10.4) years. Non‐screening patients were younger [62 (± 14) vs 66 (± 4.8) years; P < 0.05] and were less likely to be men (51.5% vs 61.9%; P < 0.05) than their screening counterparts. Caecal intubation was more successful in screening patients [1027/1067 (96.3%)] than non‐screening patients [805/894 (90%)]; P < 0.05. Adenoma detection rate was higher in the screening (46.8 ± 4.4) than non‐screening (26.3 ± 11.8) group; P < 0.05. There were no differences in neoplasia detection. Polypectomy was more likely (55.5% vs 30.2%) and polyp retrieval more successful (97.5% vs 86.7%) in the screening group.ConclusionScreening and non‐screening colonoscopy differ in the GRS domains of completion and pathology detection. These differences need to be acknowledged when comparing screeners and non‐screeners using GRS within units.
Transanal completion proctectomy after total colectomy and ileal pouch‐anal anastomosis for ulcerative colitis: a modified single stapled technique
Authors: de Buck van Overstraeten A. , Wolthuis A. M. , D'Hoore A. 
Published: February 2016

AbstractAimMinimally invasive surgery has proved its efficacy for the surgical treatment of ulcerative colitis (UC). The recent evolution in single port (SP) surgery together with transanal rectal surgery could further facilitate minimally invasive surgery in UC patients. This technical note describes a technical modification for single stapled anastomoses in patients undergoing transanal completion proctectomy and ileal pouch‐anal anastomosis (ta‐IPAA) for UC.MethodsA step‐by‐step approach of the ta‐IPAA in UC is described, including pictures and a video illustration.ResultsWe describe a ta‐IPAA with SP laparoscopy at the ileostomy site. All patients underwent a total colectomy with end‐ileostomy for therapy refractory UC in a first step. Colectomy was done by multiport laparoscopy in six patients, while the ileostomy site was used as single port access in five patients. In all 11 patients the stoma site was used for SP mobilization of the mesenteric root and fashioning of the J‐pouch. Completion proctectomy was done using a transanal approach. A single stapled anastomosis was performed in all patients. An 18 French catheter was used to approximate the pouch to the rectal cuff.ConclusionA technical modification of the single stapled anastomosis facilitates the formation of the ta‐IPAA, further reducing invasiveness in UC patients.
Impact of EGF,IL28B, and PNPLA3 polymorphisms on the outcome of allograft hepatitis C: a multicenter study
Authors: Mueller Jessica L. , King Lindsay Y. , Johnson Kara B. , Gao Tian , Nephew Lauren D. , Kothari Darshan , Simpson Mary Ann , Zheng Hui , Wei Lan , Corey Kathleen E. , Misdraji Joseph , Lee Joon Hyoek , Lin M. Valerie , Gogela Neliswa A. , Fuchs Bryan C. , Tanabe Kenneth K. , Gordon Fredric D. , Curry Michael P. , Chung Raymond T. 
Published: February 2016

AbstractHepatitis C virus (HCV) infection is accelerated following liver transplantation (LT). Single nucleotide polymorphisms (SNPs) near the epidermal growth factor (EGF) (rs4444903), IL28B (rs12979860), and PNPLA3 (rs738409) loci are associated with treatment response, fibrosis, and hepatocellular carcinoma in non‐transplant hepatitis C, but allograft population data are limited. We sought to determine the role of these SNPs in 264 patients with HCV who underwent LT between 1990 and 2008. Genotypes were determined from donor wedge/allograft biopsies and recipient explants. Cox proportional hazards model was used to assess time to cirrhosis, liver‐related death, and retransplantation, adjusting for donor age and sustained virological response (SVR). Over a median follow‐up of 6.3 yr, a trend toward increased progression to graft cirrhosis was observed among recipients of an EGF non‐AA vs. AA donor liver (adjusted HR 2.01; 95% CI 0.93–4.34; p = 0.08). No other genotypes predicted cirrhosis development or graft survival. The CC IL28B variant in both recipients and donors was associated with increased rate of SVR (R‐CC/D‐CC 8/12[67%], R‐non‐CC/D‐CC or R‐CC/D‐non‐CC 23/52[44%], R‐non‐CC/D‐non‐CC 12/45[27%], p linear trend = 0.009). Recipient EGF, IL28B, and PNPLA3, and donor IL28B and PNPLA3 genotypes do not predict adverse outcomes in HCV LT recipients. A potential association exists between donor EGF genotype and cirrhosis.
Fatal outcome of human coronavirus NL63 infection despite successful viral elimination by IFN‐alpha in a patient with newly diagnosed ALL
Authors: Mayer Karin , Nellessen Cordula , Hahn‐Ast Corinna , Schumacher Martin , Pietzonka Sandra , Eis‐Hübinger Anna M. , Drosten Christian , Brossart Peter , Wolf Dominik 
Published: February 2016

AbstractIntroductionHuman coronavirus NL63 (HCoV‐NL63) is one of four common human respiratory coronaviruses. Despite high incidence, HCoV infections are grossly understudied. We here report a case of HCoV infection in a leukemia patient with fatal ARDS despite successful virus elimination by pegylated interferon‐alpha (PEG‐IFN‐α).CaseThe 27‐year‐old female pre‐T‐ALL patient was treated according to the German‐Multicenter Trial for Adult ALL protocol. No relevant infectious complications were seen until day 35 when the neutropenic patient developed fever without any clinical focus. Antibiotic prophylaxis was switched to meropenem. The patient deteriorated rapidly with respiratory failure due to ARDS. Anti‐infectious therapy was escalated to additional linezolid and liposomal amphotericine‐B. BAL revealed a significant viral load of HCoV‐NL63. Based on successful application of PEG‐IFN against the related SARS coronavirus in animal experiments, a single injection of 180 μg PEG‐IFN‐α2b was applied. Despite immediate initiation of treatment and elimination of virus in subsequent tests, the progressive lung failure led to death 7 d after onset of fever with massive lung bleeding as a consequence of diffuse alveolar hemorrhage.ConclusionThis report emphasizes the fatal consequences of common respiratory virus infections in immunocompromised patients. HCoV‐NL63 replication can be reduced by treatment with peg‐IFN if diagnosed early.