bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative approaches for large-scale transcriptome-wide association studies
Authors: Gusev Alexander , Ko Arthur , Shi Huwenbo , Bhatia Gaurav , Chung Wonil , Penninx Brenda W J H , Jansen Rick , de Geus Eco JC , Boomsma Dorret I , Wright Fred A , Sullivan Patrick F , Nikkola Elina , Alvarez Marcus , Civelek Mete , Lusis Aldonis J. , Lehtimäki Terho , Raitoharju Emma , Kähönen Mika , Seppälä Ilkka , Raitakari Olli T. , Kuusisto Johanna , Laakso Markku , Price Alkes L. , Pajukanta Päivi , Pasaniuc Bogdan 
Published: August 2015

AbstractMany genetic variants influence complex traits by modulating gene expression, thus altering the abundance levels of one or multiple proteins. In this work we introduce a powerful strategy that integrates gene expression measurements with large-scale genome-wide association data to identify genes whose cis-regulated expression is associated to complex traits. We use a relatively small reference panel of individuals for which both genetic variation and gene expression have been measured to impute gene expression into large cohorts of individuals and identify expression-trait associations. We extend our methods to allow for indirect imputation of the expression-trait association from summary association statistics of large-scale GWAS1-3. We applied our approaches to expression data from blood and adipose tissue measured in ∼3,000 individuals overall. We then imputed gene expression into GWAS data from over 900,000 phenotype measurements4-6to identify 69 novel genes significantly associated to obesity-related traits (BMI, lipids, and height). Many of the novel genes were associated with relevant phenotypes in the Hybrid Mouse Diversity Panel. Overall our results showcase the power of integrating genotype, gene expression and phenotype to gain insights into the genetic basis of complex traits.
Impact of the X chromosome and sex on regulatory variation
Authors: Kukurba Kimberly R. , Parsana Princy , Smith Kevin S. , Zappala Zachary , Knowles David A. , Favé Marie-Julie , Li Xin , Zhu Xiaowei , Potash James B. , Weissman Myrna M. , Shi Jianxin , Kundaje Anshul , Levinson Douglas F. , Awadalla Philip , Mostafavi Sara , Battle Alexis , Montgomery Stephen B. 
Published: August 2015

AbstractThe X chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. We have conducted an analysis of the impact of both sex and the X chromosome on patterns of gene expression identified through transcriptome sequencing of whole blood from 922 individuals. We identified that genes on the X chromosome are more likely to have sex-specific expression compared to the autosomal genes. Furthermore, we identified a depletion of regulatory variants on the X chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X chromosome. To resolve the molecular mechanisms underlying such effects, we generated and connected sex-specific chromatin accessibility to sex-specific expression and regulatory variation. As sex-specific regulatory variants can inform sex differences in genetic disease prevalence, we have integrated our data with genome-wide association study data for multiple immune traits and to identify traits with significant sex biases. Together, our study provides genome-wide insight into how the X chromosome and sex shape human gene regulation and disease.
Isolation-By-Distance-and-Time in a Stepping-Stone model
Authors: Duforet-Frebourg Nicolas , Slatkin Montgomery 
Published: August 2015

AbstractWith the great advances in ancient DNA extraction, population genetics data are now made of geographically separated individuals from both present and ancient times. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping–stone model, we develop the theory of Isolation by Distance and Time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present in the data, and investigate the impact of edge effects with forward–in–time simulations. We also derive results about coalescent times in circular/toroidal models. As one of the most common way to investigate population structure is to apply principal component analysis, we evaluate the impact of this theory on plots of principal components. Our results demonstrate that time between samples is a non-negligible factor that requires new attention in population genetics.
Social Sciences and Urban Studies: Goodbye to Paradigms?
Authors: Duhau Emilio 
Published: August 2015

AbstractThe development of urban studies during the 1960s and 1970s was an offshoot of mainstream social sciences which, at least in Latin America, were formulated from a critical standpoint based largely on a renovated Marxism and the rise of the structuralisms. Now that this framework's apparently solid base has come under question in the so&#x02010;called ‘paradigm crisis', what is the outlook for urban studies and, in general, for the critical social sciences? This article poses a series of ideas which hopefully will contribute to a discussion on these and other aspects of a theoretical debate which cannot be ignored by urban researchers.
The Erratic Behavior of Lesions in Burnt Bone
Authors: Collini Federica , Amadasi Alberto , Mazzucchi Alessandra , Porta Davide , Regazzola Valeria Luisa , Garofalo Paola , Di Blasio Annalisa , Cattaneo Cristina 
Published: August 2015

AbstractThis study analyses depressed fractures (by blunt force trauma) and circular full‐thickness injuries (drill injuries and gunshot wounds) in charred bones. Fifty bovine ribs (total 104 lesions) were divided into three groups. The first group consisted in 20 depressed hammer‐produced fractures; in the second one, 60 round drill‐holes were produced (30 circular, 30 semicircular); in the third group, 12 fleshed and 12 skeletonized ribs were hit by 9‐mm bullets. Each specimen was carbonized in an electric oven up to 800°C. Morphological and metric analyses were performed before and after: morphological features were preserved, but depressed fractures showed an increase in their dimensions (p‐value < 0.05); the drilled holes shrunk (p‐value < 0.01); the charring cycle increased the number of fractures in samples with gunshot wounds differently in fleshed and defleshed ribs. This study showed the complex behavior of charred bone, for what concerns the interpretation of trauma and how caution should be applied.
The missing vitamin alphabet
Authors: Williams Peter 
Published: August 2015

AbstractAimThe aims of this paper were to catalogue a complete list of all the alphabetical names for vitamins that have appeared in the scientific literature, provide the citations of their first use and seek explanations for any apparent gaps in the naming system.MethodsThe names of known vitamins and pseudo‐vitamins were identified from standard nutrition textbooks, historical monographs and several review articles. If the first citation for the alphabetical vitamin name was not found in these sources, additional searches were conducted in the Scopus and Medline databases, in Google and Google Scholar, using the names of vitamins as search terms.ResultsSixty‐seven different alphabet‐based vitamin names were tabulated, including where possible the scientific and alternative names, a description of the source substance, physiological roles and the first citation of the alphabetical name. The results show that all the letters of the alphabet have been used to describe putative vitamin compounds. The simple alphabetical naming system proposed by Drummond in 1920 lasted for less than a decade. A number of other systems have been used based on the name of the discoverer, the source of the material or its physiological function.ConclusionsUsing simplified alphabetical names may assist in nutrition communication and education of the general public, but dietitians need to be careful to maintain a clear understanding of the proper biochemical distinctions and nomenclatures of the known vitamins, especially when writing for academic publication.
Characterization and Comparison of the Pungent Components in Commercial Zanthoxylum bungeanum Oil and Zanthoxylum schinifolium Oil
Authors: Zhao Zhi‐Feng , Zhu Rui‐Xue , Zhong Kai , He Qiang , Luo Ai‐Min , Gao Hong 
Published: August 2015

AbstractIn the present study, the characterization and comparison of the pungent components in commercial Z. bungeanum oils and Z. schinifolium oils were investigated. By high‐performance liquid chromatography (HPLC)‐mass spectrometry (MS/MS) analysis, the major alkylamides in Z. bungeanum and Z. schinifolium oils were identified as hydroxy‐ε‐sanshool, hydroxy‐α‐sanshool, hydroxy‐β‐sanshool, hydroxy‐γ‐sanshool, hydroxy‐γ‐isosanshool, bungeanool, isobungeanool, and tetrahydrobungeanool, respectively. Hydroxy‐α‐sanshool was found to be the most abundant alkylamide in all oils. The levels of hydroxy‐ε‐sanshool and hydroxy‐β‐sanshool in Z. bungeanum oils were comparable to that in Z. schinifolium oils, whereas Z. bungeanum oils contained significantly (P less than 0.05) higher levels of hydroxy‐γ‐isosanshool, bungeanool, isobungeanool, and tetrahydrobungeanool, compared with Z. schinifolium oils. Furthermore, principal component analysis (PCA) indicated that Z. bungeanum oil and Z. schinifolium oil were clearly classified by HPLC fingerprinting profiles and concentrations of alkylamides. In addition, the results of PCA suggested that alkylamides, such as hydroxy‐γ‐sanshool and bungeanool, could be potential markers to distinguish Z. bungeanum oil and Z. schinifolium oil. The results from this study could be used to discriminate the different flavor characterization and control the quality of commercial Z. bungeanum oil and Z. schinifolium oil.
Challenges to Providing Fetal Anomaly Testing in a Cross‐Cultural Environment: Experiences of Practitioners Caring for Aboriginal Women
Authors: Rumbold Alice R. , Wild Kayli J. , Maypilama Elaine Lawurrpa , Kildea Sue V. , Barclay Lesley , Wallace Euan M. , Boyle Jacqueline A. 
Published: August 2015

AbstractBackgroundAcross Australia there are substantial disparities in uptake of antenatal testing for fetal anomalies, with very low uptake observed among Aboriginal women. The reasons behind these disparities are unclear, although poorer access to testing has been reported in some communities. We interviewed health care practitioners to explore the perceived barriers to providing fetal anomaly screening to Aboriginal women.MethodsIn 2009 and 2010, in‐depth interviews were undertaken with 59 practitioners in five urban and remote sites across the Northern Territory (NT) of Australia. Data were analyzed thematically. Maximum variation sampling, independent review of findings by multiple analysts, and participant feedback were undertaken to strengthen the validity of findings.ResultsParticipants included midwives (47%), Aboriginal health practitioners (AHP) (32%), general practitioners (12%), and obstetricians (9%); almost all (95%) were female. Participants consistently reported difficulties counseling women. Explaining the concept of “risk” (of abnormalities and the screening test result) was identified as particularly challenging, because of a perceived lack of an equivalent concept in Aboriginal languages. While AHPs could assist with overcoming language barriers, they are underutilized. Participants also identified impediments to organizing testing including difficulties establishing gestational age, late presentation for care, and a lack of standardized information and training.DiscussionThe availability of fetal anomaly testing is challenged by communication difficulties, including a focus on culturally specific biomedical concepts, and organizational barriers to arranging testing. Developing educational activities that address the technical aspects of screening and communication skills will assist in improving access. These activities must include AHPs.
Provenance of Palaeo‐Rhine sediments from zircon thermochronology, geochemistry, U/Pb dating and heavy mineral assemblages
Authors: Tatzel Michael , Dunkl István , von Eynatten Hilmar 
Published: August 2015

AbstractSediments deposited in the Late Cenozoic basins of the Central European Rift System, including the Upper Rhine Graben (URG) and the Lower Rhine Embayment (LRE), document the drastic extension of the Rhine's catchment towards the Central Alps in the Late Pliocene by distinct heavy mineral assemblages. This outstanding change in principal sediment sources should be accompanied by a change towards distinctly younger (i.e. Tertiary) detrital mineral cooling ages. Therefore, it provides a particularly well‐suited framework to explore the thermochronological provenance record in relation to heavy mineral assemblages. In this multi‐proxy approach we (i) exploit and elaborate detrital zircon (U–Th)/He thermochronology (ZHe) for sediment provenance surveys, (ii) document shortcomings if only a single geochronological method is employed, and (iii) obtain tighter constraints on the sources of Paleo‐Rhine sediments. Our results are based on Pliocene and Pleistocene sediment samples from the northern URG (drill core Ludwigshafen P36) and the LRE (lignite mine Hambach). In a Late Pliocene URG sample, Variscan and Permo‐Triassic cooling ages dominate the age spectra of the ZHe and Zircon fission track (ZFT) thermochronometers. The youngest ages are Late Cretaceous and these zircons show rare earth element signatures that suggest derivation from hydrothermally affected basement rocks of the URG margins. In contrast, a Lower Pleistocene URG sample contains significant Tertiary age components that unequivocally indicate Alpine sources. This cardinal difference coincides well with a significant change in the heavy mineral assemblage. The extension of the catchment of the Rhine towards the Central Alps is considered to occur no earlier than the latest Pliocene (i.e. after ~3.0 Ma). Despite strongly contrasting heavy mineral compositions, the Pliocene and Pleistocene samples from the LRE show largely similar ZHe and ZFT age distributions dominated by Permo‐Triassic and Variscan ages. Admixture of zircon‐dominated, but overall heavy mineral‐poor sediment derived from local drainages of the Rhenish Massif likely explains this apparent contradiction in sediment provenance proxies. Tertiary cooling ages occur in both Pliocene and Pleistocene LRE samples. Zircon Th/U ratios and U/Pb ages reveal that the young age component in Late Pliocene sediments from the LRE is not derived from the Alps but from Oligocene trachytic members of the Central European volcanic centres of the Vogelsberg, Westerwald, and/or Siebengebirge. The integration of ZHe and ZFT techniques with zircon geochemistry and U/Pb geochronology adds the respective advantages of each method and allows for a very detailed picture of detrital zircon provenance.
Multi‐scale constraints of sediment source to sink systems in frontier basins: a forward stratigraphic modelling case study of the Levant region
Authors: Hawie Nicolas , Deschamps Remy , Granjeon Didier , Nader Fadi H. , Gorini Christian , Müller Carla , Montadert Lucien , Baudin François 
Published: August 2015

AbstractRecent scientific work has highlighted the presence of an up to 12 km thick Cenozoic siliclastic and carbonate infill in the Levant Basin. Since the Late Eocene, several regional geodynamic events affecting Afro‐Arabia and Eurasia (collision and strike slip deformation) induced marginal uplifts. The initiation of local and long‐lived regional drainage systems in the Oligo‐Miocene period (e.g., Lebanon, Arabia and Nile) provoked a change in the depositional pattern along the Levant region from carbonate‐dominated to mixed clastic‐rich systems. Herein, we explore the importance of multi‐scale constraints (i.e., seismic, well and field data) in the quantification of subsidence history, sediment transport and deposition of a Middle to Upper Miocene “multi‐source” to sink system along the northern Levant frontier region. Through a comprehensive 4D forward stratigraphic modelling workflow, we suggest that the contribution to basin infill is split between proximal and more distal clastic sources as well asin situcarbonate and hemipelagic deposition. The results show that single‐source scenarios could not reasonably satisfy the basin‐scale constraints. The worldwide application of such new multi‐disciplinary workflows in frontier regions highlights the additional data constraints that are needed to de‐risk highly uncertain geological models in the hydrocarbon exploration phase.
Challenges and Prospects for Scaling‐up Ecological Restoration to Meet International Commitments: Colombia as a Case Study
Authors: Murcia Carolina , Guariguata Manuel R. , Andrade Ángela , Andrade Germán Ignacio , Aronson James , Escobar Elsa Matilde , Etter Andrés , Moreno Flavio H. , Ramírez Wilson , Montes Elena 
Published: August 2015

AbstractThe field of ecological restoration (ER) is now challenged by the need to achieve recovery at large spatial scales. Such scaling up requires technological expertise, inclusiveness and clarity of goals, and correct governance schemes and monitoring protocols, which are often absent from ER projects in most countries. We analyze the case of Colombia by assessing the planning, governance, and monitoring practices of 119 ER projects, and discuss them in the context of scaling up efforts to meet international commitments. In a top‐down approach, Colombia´s government is the biggest ER driver: setting up the necessary policy framework to promote ER, and initiating 64% and fully financing 78% of the projects in the country. However, projects lack depth in participatory governance and adequate planning and monitoring, limiting their potential for sustainability and knowledge sharing, both of which are necessary for scaling up. We propose three areas for improvement in order to scale‐up and meet international ER targets in Colombia, as well as in other Latin American countries, such as Mexico, Chile, and Argentina, which are also in the process of consolidating a large‐scale ER vision. The benefits of some of those improvements have already been demonstrated in Brazil.
A prospective analysis of factors associated with decreased physical activity in patients with cirrhosis undergoing transplant evaluation
Authors: Dela Cruz Anna Christina , Vilchez Valery , Kim Sooyeon , Barnes Benjamin , Ravinuthala Abhishek , Zanni Anthony , Galuppo Roberto , Sourianarayanane Achuthan , Patel Trushar , Maynard Erin , Shah Malay B. , Daily Michael F. , Uhl Timothy , Esser Karyn , Gedaly Roberto 
Published: August 2015

AbstractBackgroundPhysical activity (PA) has been associated with improved recovery time after transplantation. Handgrip strength has been related to post‐transplant outcomes.AimTo evaluate predictors of PA and grip strength in patients with cirrhosis undergoing liver transplant evaluation.MethodsSingle‐center, prospective analysis.ResultsOne hundred patients were evaluated (54% male, mean age 53 ± 9). Common etiologies of liver disease were non‐alcoholic steatohepatitis (27%), hepatitis C (22%) and alcoholic liver disease (21%). Mean model of end‐stage liver disease (MELD) score was 13.5. Forty‐one percent had a history of smoking. Ninety‐three patients completed the International Physical Activity Questionnaire (IPAQ). The median total PA score was 33 metabolic equivalent (MET)‐min/wk. The mean total grip strength was 62.1 ± 22 lb. Total grip strength was found to be an independent predictor of low–moderate PA (OR 4.7, 95% CI 1.4–16.2, p = 0.038), and smoking was the only significant factor associated with reduced grip strength (OR 3.4, 95% CI 1.4–8, p = 0.005).ConclusionsPatients with end‐stage liver disease undergoing liver transplant evaluation have reduced total PA by IPAQ. Total grip strength was found to be a significant predictor of low–moderate PA in patients with cirrhosis. Smoking is a risk factor for reduced grip strength, an important indicator of muscle wasting in cirrhotics.
Primitive follicular induction in molluscum contagiosum
Authors: Molina‐Ruiz Ana María , Bernárdez Claudia , Requena Luis , Schärer Leo 
Published: August 2015

BackgroundMolluscum contagiosum (MC) is the commonest human poxvirus infection. Follicular induction has rarely been observed in the epidermis surrounding lesions of MC. A virus‐induced localized proliferation of germinative/stem cells of the folliculosebaceous‐apocrine unit has been suggested as the underlying cause, however few reports of this peculiar phenomenon exist in the literature and the mechanisms involved in this proliferation require further study.MethodsWe prospectively collected MC cases showing multifocal areas of primitive follicular induction involving the adjacent undersurface epidermis. Immunohistochemical expression of BerEP4, PHLDA1 and cytokeratin 20 (CK20) was evaluated in the basaloid germs surrounding the lesions. For PHLDA1, we used epidermal melanocytes as a positive internal control. For BerEP4, we employed a basal cell carcinoma (BCC) and for CK20, colon as positive external controls. An incubation without the primary antibody functioned as an external negative control.ResultsAll the cases studied showed an intense positive staining of the basaloid buds with BerEP4 and weaker stain for PHLDA1. CK20 showed the presence of scattered Merkel cells within the induced epidermal basaloid proliferations favoring their reactive origin.DiscussionThe pathogenetic mechanisms behind the development of these microscopic features and the link between follicular induction and poxvirus infection are explored. Awareness of this unusual phenomenon by dermatopathologists will be helpful in avoiding a misdiagnosis of a superficial BCC in such cases.ConclusionsBerEP4 and PHLDA1 were consistently expressed in the areas of primitive follicular induction surrounding lesions of MC. CK 20 stained the Merkel cells present in the basaloid buds. All these findings support the reactive origin of this phenomenon, which we believe is most probably viral‐induced.
Lipid parameters in patients with acute coronary syndromes versus stable coronary artery disease
Authors: Vonbank Alexander , Saely Christoph H. , Rein Philipp , Drexel Heinz 
Published: August 2015

AbstractBackgroundDifferences in lipid parameters between patients with acute coronary syndromes (ACS) and patients with stable coronary artery disease (CAD) are unclear and are addressed in this study.MethodsWe enrolled 582 patients with angiographically proven stable CAD (of whom 26·9% had diabetes mellitus type 2 (T2DM)) and 182 patients with ACS (of whom 35·8% had T2DM).ResultsHDL cholesterol and apolipoprotein A1 levels were significantly lower in patients with ACS than in patients with CAD (46 ± 16 mg/dL vs. 50 ± 16 mg/dL, P < 0·001, and 139 ± 30 mg/dL vs. 155 ± 31 mg/dL, P < 0·001, respectively). Analysis of covariance (ancova) adjusting for age, gender, smoking, BMI, statin therapy, alcohol use, hypertension and diabetic state confirmed an independent impact of ACS on HDL cholesterol and apolipoprotein A1 levels (F = 24·1; P < 0·001). In contrast, total cholesterol, LDL cholesterol, non‐HDL cholesterol and apolipoprotein B levels did not differ significantly between patients with ACS and patients with stable CAD.ConclusionHDL cholesterol and apolipoprotein A1 levels are lower in patients with ACS than in patients with stable CAD.