bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of case–control association studies with known risk variants
Authors: Zaitlen Noah , Paşaniuc Bogdan , Patterson Nick , Pollack Samuela , Voight Benjamin , Groop Leif , Altshuler David , Henderson Brian E. , Kolonel Laurence N. , Marchand Loic Le , Waters Kevin , Haiman Christopher A. , Stranger Barbara E. , Dermitzakis Emmanouil T. , Kraft Peter , Price Alkes L. 
Published: May 2012

AbstractMotivation: The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered. Some studies compute a marginal P-value for each Several Nucleotide Polymorphisms independently, ignoring previously discovered variants. Other studies include known variants as covariates in logistic regression, but a weakness of this standard conditioning strategy is that it does not account for disease prevalence and non-random ascertainment, which can induce a correlation structure between candidate variants and known associated variants even if the variants lie on different chromosomes. Here, we propose a new conditioning approach, which is based in part on the classical technique of liability threshold modeling. Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature.Results: We show via simulation and application to empirical datasets that our approach outperforms both the no conditioning strategy and the standard conditioning strategy, with a properly controlled false-positive rate. Furthermore, in multiple data sets involving diseases of low prevalence, standard conditioning produces a severe drop in test statistics whereas our approach generally performs as well or better than no conditioning. Our approach may substantially improve disease gene discovery for diseases with many known risk variants.Availability: LTSOFT software is available online http://www.hsph.harvard.edu/faculty/alkes-price/software/Contact: nzaitlen@hsph.harvard.edu; aprice@hsph.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Reconstructing the population dynamics of sprat (Sprattus sprattus balticus) in the Baltic Sea in the 20th century
Authors: Eero Margit 
Published: May 2012

Abstract
Eero, M. 2012. Reconstructing the population dynamics of sprat (Sprattus sprattus balticus) in the Baltic Sea in the 20th century. – ICES Journal of Marine Science, 69: 1010–1018 . Long time-series of population dynamics are increasingly needed in order to understand human impacts on marine ecosystems and support their sustainable management. In this study, the estimates of sprat (Sprattus sprattus balticus) biomass in the Baltic Sea were extended back from the beginning of ICES stock assessments in 1974 to the early 1900s. The analyses identified peaks in sprat spawner biomass in the beginning of the 1930s, 1960s, and 1970s at ∼900 kt. Only a half of that biomass was estimated for the late 1930s, for the period from the late 1940s to the mid-1950s, and for the mid-1960s. For the 1900s, fisheries landings suggest a relatively high biomass, similar to the early 1930s. The exploitation rate of sprat was low until the development of pelagic fisheries in the 1960s. Spatially resolved analyses from the 1960s onwards demonstrate changes in the distribution of sprat biomass over time. The average body weight of sprat by age in the 1950s to 1970s was higher than at present, but lower than during the 1980s to 1990s. The results of this study facilitate new analyses of the effects of climate, predation, and anthropogenic drivers on sprat, and contribute to setting long-term management strategies for the Baltic Sea.
Brazilian sardine (Sardinella brasiliensis Steindachner, 1879) spawning and nursery habitats: spatial-scale partitioning and multiscale relationships with thermohaline descriptors
Authors: Moraes Luiz Eduardo de Souza , Gherardi Douglas Francisco Marcolino , Katsuragawa Mario , Paes Eduardo Tavares 
Published: May 2012

Abstract
de Souza Moraes, L. E., Marcolino Gherardi, D. F., Katsuragawa, M., and Tavares Paes, E. 2012. Brazilian sardine (Sardinella brasiliensis Steindachner, 1879) spawning and nursery habitats: spatial-scale partitioning and multiscale relationships with thermohaline descriptors. – ICES Journal of Marine Science, 69: 939–952. We provide a detailed account of the spatial structure of the Brazilian sardine (Sardinella brasiliensis) spawning and nursery habitats, using ichthyoplankton data from nine surveys (1976–1993) covering the Southeastern Brazilian Bight (SBB). The spatial variability of sardine eggs and larvae was partitioned into predefined spatial-scale classes (broad scale, 200–500 km; medium scale, 50–100 km; and local scale, <50 km). The relationship between density distributions at both developmental stages and environmental descriptors (temperature and salinity) was also explored within these spatial scales. Spatial distributions of sardine eggs were mostly structured on medium and local scales, while larvae were characterized by broad- and medium-scale distributions. Broad- and medium-scale surface temperatures were positively correlated with sardine densities, for both developmental stages. Correlations with salinity were predominantly negative and concentrated on a medium scale. Broad-scale structuring might be explained by mesoscale processes, such as pulsing upwelling events and Brazil Current meandering at the northern portion of the SBB, while medium-scale relationships may be associated with local estuarine outflows. The results indicate that processes favouring vertical stability might regulate the spatial extensions of suitable spawning and nursery habitats for the Brazilian sardine.
GB‐to‐TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT
Authors: Goloboff Pablo A. , Catalano Santiago A. 
Published: May 2012

AbstractThis paper presents a pipeline, implemented in an open‐source program called GB→TNT (GenBank‐to‐TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent.© The Willi Hennig Society 2012.
Medicinal Δ9‐tetrahydrocannabinol (dronabinol) impairs on‐the‐road driving performance of occasional and heavy cannabis users but is not detected in Standard Field Sobriety Tests
Authors: Bosker Wendy M. , Kuypers Kim P. C. , Theunissen Eef L. , Surinx Anke , Blankespoor Roos J. , Skopp Gisela , Jeffery Wayne K. , Walls H. Chip , van Leeuwen Cees J. , Ramaekers Johannes G. 
Published: May 2012

AbstractAimsThe acute and chronic effects of dronabinol [medicinal Δ9‐tetrahydrocannabinol (THC)] on actual driving performance and the Standard Field Sobriety Test (SFST) were assessed. It was hypothesized that occasional users would be impaired on these tests and that heavy users would show less impairment due to tolerance.Design, setting and participantsDouble‐blind, placebo‐controlled, randomized, three‐way cross‐over study. Twelve occasional and 12 heavy cannabis users (14 males/10 females) received single doses of placebo, 10 and 20 mg dronabinol.MeasurementsStandard deviation of lateral position (SDLP; i.e. weaving) is the primary measure of road‐tracking control. Time to speed adaptation (TSA) is the primary reaction‐time measure in the car‐following test. Percentage of impaired individuals on the SFST and subjective high on a visual analogue scale were secondary measures.FindingsSuperiority tests showed that SDLP (P = 0.008) and TSA (P = 0.011) increased after dronabinol in occasional users. Equivalence tests demonstrated that dronabinol‐induced increments in SDLP were bigger than impairment associated with BAC of 0.5 mg/ml in occasional and heavy users, although the magnitude of driving impairment was generally less in heavy users. The SFST did not discriminate between conditions. Levels of subjective high were comparable in occasional and heavy users.ConclusionsDronabinol (medicinal tetrahydrocannabinol) impairs driving performance in occasional and heavy users in a dose‐dependent way, but to a lesser degree in heavy users due possibly to tolerance. The Standard Field Sobriety Test is not sensitive to clinically relevant driving impairment caused by oral tetrahydrocannabinol.
Characteristics of Epstein–Barr virus hepatitis among patients with jaundice or acute hepatitis
Authors: Vine L. J. , Shepherd K. , Hunter J. G. , Madden R. , Thornton C. , Ellis V. , Bendall R. P. , Dalton H. R. 
Published: May 2012

SummaryBackgroundAbnormal liver blood tests are common in Epstein–Barr virus (EBV) infection, but symptomatic hepatitis is rare. The demographics, clinical features and outcome of EBV hepatitis are incompletely understood, particularly in the elderly people.AimTo identify the demographics, presenting features and natural history of EBV hepatitis.MethodsRetrospective review of 1995 consecutive patients attending the jaundice hotline clinic over a 13‐year period. Data collected included demographic information, presenting features, clinical and laboratory parameters, radiology imaging and clinical outcome.ResultsSeventeen of 1995 (0.85%) had EBV hepatitis. The median age was 40 years (range 18–68 years). Ten of 17 (59%) patients were aged >30 years, and seven of 17 (41%) patients were aged ≥60 years. Fifteen of 17 (88%) patients presented with clinical/biochemical evidence of jaundice. Seventeen of 17 (100%) patients had a serum lymphocytosis at presentation. 2/17 (12%) patients with EBV hepatitis presented with the classical features of infectious mononucleosis (fever, sore throat and lymphadenopathy). Splenomegaly was present in 15/17 (88%) of patients. Symptoms lasted for a median 8 weeks (range 1–12 weeks). Three of 17 (18%) patients required a brief hospital admission.ConclusionsIn patients presenting with jaundice/hepatitis, EBV hepatitis is an uncommon diagnosis and causes a self‐limiting hepatitis. The diagnosis is suggested by the presence of a lymphocytosis and/or splenomegaly. The majority of patients do not have infectious mononucleosis. Compared with infectious mononucleosis, EBV hepatitis affects an older age group, with nearly half of patients being aged more than 60 years. The diagnosis should be considered in all patients with unexplained hepatitis irrespective of their age.
Two conversational practices for encouraging adults with intellectual disabilities to reflect on their activities
Authors: Antaki C. 
Published: May 2012

AbstractBackground  Staff can encourage adults with intellectual disabilities to reflect on their experiences in a number of ways. Not all are equally successful interactionally.Methods  Conversation Analysis is used to examine c. 30 h of recordings made at two service‐provider agencies.Results  I identify two practices for soliciting reflection: both start with open‐ended ‘test’ questions, but they differ on how these are followed up. A more interrogatory practice is to follow up with alternatives and yes/no questions. A more facilitative practice is to give hints and elaborate the replies.Conclusions  I discuss the differences between the two practices in terms of the institutional agendas that guide the staff's interactional routines. With regard to the more successful one, I note the sensitivity of using ‘hints’ when asking about clients' own experiences.
Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey
Authors: SPICE ERIN K. , GOODMAN DAMON H. , REID STEWART B. , DOCKER MARGARET F. 
Published: May 2012

AbstractMost species with lengthy migrations display some degree of natal homing; some (e.g. migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine microsatellite loci to examine the population structure in 965 Pacific lamprey from 20 locations from central British Columbia to southern California and supplemented this analysis with mitochondrial DNA restriction fragment length polymorphism analysis on a subset of 530 lamprey. Microsatellite analysis revealed (i) relatively low but often statistically significant genetic differentiation among locations (97% pairwise FST values were <0.04 but 73.7% were significant); and (ii) weak but significant isolation by distance (r2 = 0.0565, P = 0.0450) but no geographic clustering of samples. The few moderate FST values involved comparisons with sites that were geographically distant or far upstream. The mtDNA analysis—although providing less resolution among sites (only 4.7%FST values were significant)—was broadly consistent with the microsatellite results: (i) the southernmost site and some sites tributary to the Salish Sea were genetically distinct; and (ii) southern sites showed higher haplotype and private haplotype richness. These results are inconsistent with philopatry, suggesting that anadromous lampreys are unusual among species with long migrations, but suggest that limited dispersal at sea precludes panmixia in this species.
Evolution of TPS20‐related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites
Authors: Gonzales‐Vigil Eliana , Hufnagel David E. , Kim Jeongwoon , Last Robert L. , Barry Cornelius S. 
Published: May 2012

SummaryA systematic screen of volatile terpene production in the glandular trichomes of 79 accessions of Solanum habrochaites was conducted and revealed the presence of 21 mono‐ and sesquiterpenes that exhibit a range of qualitative and quantitative variation. Hierarchical clustering identified distinct terpene phenotypic modules with shared patterns of terpene accumulation across accessions. Several terpene modules could be assigned to previously identified terpene synthase (TPS) activities that included members of the TPS‐e/f subfamily that utilize the unusual cis‐prenyl diphosphate substrates neryl diphosphate and 2z,6z‐farnesyl diphosphate. DNA sequencing and in vitro enzyme activity analysis of TPS‐e/f members from S. habrochaites identified three previously unassigned enzyme activities that utilize these cisoid substrates. These produce either the monoterpenes α‐pinene and limonene, or the sesquiterpene 7‐epizingiberene, with the in vitro analyses that recapitulated the trichome chemistry found in planta. Comparison of the distribution of S. habrochaites accessions with terpene content revealed a strong preference for the presence of particular TPS20 alleles at distinct geographic locations. This study reveals that the unusually high intra‐specific variation of volatile terpene synthesis in glandular trichomes of S. habrochaites is due at least in part to evolution at the TPS20 locus.
A new quality of life scale for teenagers with food hypersensitivity
Authors: MacKenzie Heather , Roberts Graham , Van Laar Darren , Dean Taraneh 
Published: May 2012

To cite this article: MacKenzie H, Roberts G, Van Laar D, Dean T. A new quality of life scale for teenagers with food hypersensitivity. Pediatr Allergy Immunol 2012: 23: 404–411.AbstractBackground:  A disease‐specific health‐related quality of life (HRQL) scale enables the impact of current and new interventions on the HRQL of teenagers with food hypersensitivity (FHS) to be evaluated. No such scale exists for teenagers with FHS living in the UK. This research aimed to develop and validate a disease‐specific HRQL scale for this group, thus facilitating HRQL measurement in this population.Methods:  A preliminary 51‐item questionnaire was generated from interviews with 21 teenagers with FHS, the coverage and acceptability of which was refined in pre‐ and pilot testing (N = 102). On the basis of the field test data (N = 299), principal components analysis identified those items best measuring HRQL.Results:  The final 34‐item You and Your Food Allergy scale covered five domains: social well‐being and independence, support, day‐to‐day activities, family relations and emotional well‐being. The whole scale displayed excellent internal consistency (Cronbach’s α = 0.92) and test–retest reliability (ICC = 0.87). The scale correlated as hypothesised with a generic HRQL scale (PedsQL) and discriminated by disease severity, providing evidence for its construct validity.Conclusions:  The You and Your Food Allergy scale is the first HRQL scale to have been developed and validated with UK teenagers with FHS. Subject to further evaluation of its psychometric properties, its development has important applications in future research into the HRQL of teenagers with FHS. Short and easy‐to‐complete, the scale has been designed to appeal to teenagers and is likely to be useful to facilitate discussion of HRQL issues.
Depletion of alloreactive T cells for tolerance induction in a recipient of kidney and hematopoietic stem cell transplantations
Authors: Tangnararatchakit Kanchana , Tirapanich Wiwat , Anurathapan Usanarat , Tapaneya‐Olarn Wiwat , Pakakasama Samart , Jootar Saengsuree , Slavin Shimon , Hongeng Suradej 
Published: May 2012

Tangnararatchakit K, Tirapanich W, Anurathapan U, Tapaneya‐Olarn W, Pakakasama S, Jootar S, Slavin S, Hongeng S. Depletion of alloreactive T cells for tolerance induction in a recipient of kidney and hematopoietic stem cell transplantations.Abstract:  The present case report represents a successful attempt to induce transplantation tolerance to organ allograft by combined administration of donor hematopoietic cells and kidney based on in vivo deletion of alloreactive host‐vs‐graft and graft‐vs‐host alloreactive T cells following non‐myeloablative conditioning. We were able to induce mixed and eventually full donor chimerism and tolerance of kidney allograft in a 15‐yr‐old male with ESRD after cisplatin treatment and autologous HSCT for mediastinal germ cell tumor. Our approach to induce tolerance was based on preferential depletion of alloreactive T cells induced by exposure to donor’s alloantigens and administration of cyclophosphamide at day 2 and day 3 after stem cell infusion. Additional non‐specific immunosuppression as part of the conditioning included exposure to two fractions of TLI, treatment with alemtuzumab (monoclonal anti‐CD52) and short‐term conventional IS treatment to avoid early graft loss, because of request of IRB. Using this approach, with rapid tapering of all conventional IS treatment, the patient maintains good renal functions without evidence of both acute and chronic rejection for 32 months off all medications.
Graft rejection in pediatric liver transplant patients with Epstein‐Barr viremia and post‐transplant lymphoproliferative disease
Authors: Weiner Chana , Weintraub Lauren , Wistinghausen Birte , Tomaino Juli , Arnon Ronen , Kerkar Nanda , Miloh Tamir 
Published: May 2012

Weiner C, Weintraub L, Wistinghausen B, Tomaino J, Arnon R, Kerkar N, Miloh T. Graft rejection in pediatric liver transplant patients with Epstein‐Barr viremia and post‐transplant lymphoproliferative disease.Abstract:  Treatment of primary EV and PTLD in pediatric LT recipients (pLT) involves IS reduction/cessation. Retrospective review of pLT at our institution from 2001–2009 was conducted to characterize risk factors for GR after EV/ PTLD. Of 184 pLT, EV occurred in 61 (33%) at mean 16.5 m (0–82) and PTLD in 18 (9.8%) at mean 17.7 m (3–78) post‐LT. Median age at pLT was 11 m (1–245 m) and follow‐up six yr. For EV, 86% underwent IS reduction and 51% received antivirals. GR occurred in 12 (27.9%) with EV and 15 (83.3%) after PTLD diagnosis (relative risk of GR for PTLD 2.98). GR treated with methylprednisolone bolus in half and/or oral IS in half. Following GR therapy, four had PTLD relapses, no graft loss and one EV patient required re‐transplantation. GR history before EV was a risk factor for GR after EV (p = 0.024). GR at any point after pLT was a risk factor for PTLD (p = 0.001). Children with EV and GR prior to EV should be monitored closely for GR after IS reduction and GR is a significant risk factor for PTLD. Most children with PTLD eventually developed GR.
Double balloon enteroscopy for pediatric inflammatory bowel disease
Authors: Uchida Keiichi , Yoshiyama Shigeyuki , Inoue Mikihiro , Koike Yuki , Yasuda Hiromi , Fujikawa Hiroyuki , Okita Yoshiki , Araki Toshimitsu , Tanaka Kouji , Kusunoki Masato 
Published: May 2012

AbstractBackground:  The aim of the present study was to evaluate the efficacy and safety of double balloon enteroscopy (DBE) in children with inflammatory bowel disease (IBD).Methods:  A total of 106 DBE procedures in 67 patients were performed at Mie University Hospital from January 2008 to June 2011. Of these, 17 procedures in 12 children and adolescents with established or suspected Crohn's disease (CD) were included in the present study. The procedure, sedation, efficacy, and safety of DBE were evaluated.Results:  Mean patient age was 12.9 years (range, 3–19 years). Patients ≤15 years old had general anesthesia. The procedures included the oral approach (n= 9), the anal approach (n= 4), and the ileostomal approach (n= 4). The mean procedure duration was 60 min. Accurate diagnosis was obtained in 7/8 cases (88%) of suspected CD. Only one case was diagnosed as indeterminate colitis, although the total small and large bowel was examined on DBE and pathology. Procedure tolerance was acceptable and recovery was uneventful in all cases. No serious complications were encountered.Conclusions:  With regard to the present limited IBD pediatric case series, DBE is a safe and effective procedure.