bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaic adaptive introgression inTBX15/WARS2
Authors: Racimo Fernando , Gokhman David , Fumagalli Matteo , Ko Amy , Hansen Torben , Moltke Ida , Albrechtsen Anders , Carmel Liran , Huerta-Sánchez Emilia , Nielsen Rasmus 
Published: December 2015

AbstractA recent study conducted the first genome-wide scan for selection in Inuit from Greenland using SNP chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes,WARS2andTBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression ofWARS2andTBX15in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes inTBX15.
A webometric analysis of major keywords and expressions in biochemistry using LexiURL Searcher
Authors: Taram Kobra , Doulani Abbas 
Published: December 2015

Purpose
– The purpose of this paper is to explore webometric analysis of keywords and expressions of the biochemistry field of study via LexiURL Searcher.

Design/methodology/approach
– Interfaces for assisting users with information access have received considerable attention. Along with the extraction of data on Web sites for webometric purposes (e.g. link analysis, ranking of Web sites, etc.), LexiURL Searcher presents some information on the arrangement of links among different Web sites. Such capability enables users to identify one or more Web sites around their intended subject and, accordingly, explore all Web sites linked with their identified Web site(s). LexiURL Searcher has preceded webometric analysis by considering the main expressions and keywords derived from the MeSH database.

Findings
– The worldwide survey indicated that links from countries such as England, Japan, Germany, Australia and Canada were among the Web sites that are most used in biochemistry. Alternatively, other countries such as Singapore, Thailand and Poland had the most advantageous links to the outside world, whereas South Africa, New Zealand and The Netherlands had the least link effect. Biochemistry, being a specialized domain, would benefit greatly from site linking and would provide users the most assistance in information processing.

Originality/value
– Most webometric studies remain on the level of link analysis and Web site statuses; however, this paper gives information on the common thread Web sites based on a standard thesaurus.
An adhesin from hydrogen‐utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen‐producing microorganisms
Authors: Ng Filomena , Kittelmann Sandra , Patchett Mark L. , Attwood Graeme T. , Janssen Peter H. , Rakonjac Jasna , Gagic Dragana 
Published: December 2015

SummarySymbiotic associations are ubiquitous in the microbial world and have a major role in shaping the evolution of both partners. One of the most interesting mutualistic relationships exists between protozoa and methanogenic archaea in the fermentative forestomach (rumen) of ruminant animals. Methanogens reside within and on the surface of protozoa as symbionts, and interspecies hydrogen transfer is speculated to be the main driver for physical associations observed between the two groups. In silico analyses of several rumen methanogen genomes have previously shown that up to 5% of genes encode adhesin‐like proteins, which may be central to rumen interspecies attachment. We hypothesized that adhesin‐like proteins on methanogen cell surfaces facilitate attachment to protozoal hosts. Using phage display technology, we have identified a protein (Mru_1499) from Methanobrevibacter ruminantium M1 as an adhesin that binds to a broad range of rumen protozoa (including the genera Epidinium and Entodinium). This unique adhesin also binds the cell surface of the bacterium Butyrivibrio proteoclasticus, suggesting a broad adhesion spectrum for this protein.
Prediction of small‐for‐gestational‐age status by symphysis–fundus height: a registry‐based population cohort study
Authors: Pay ASD , Frøen JF , Staff AC , Jacobsson B , Gjessing HK 
Published: December 2015

ObjectiveTo develop a chart for risk of small‐for‐gestational‐age (SGA) at birth depending on deviations in symphysis–fundus (SF) height values for gestational age during pregnancy weeks 24–42.DesignRegistry‐based population cohort study.SettingAntenatal clinics, Västra Götaland County, Sweden, 2005–2010.PopulationThe study included 42 018 women with ultrasound‐dated singleton pregnancies who delivered at Sahlgrenska University Hospital. Data (including 282 713 SF height measurements) were extracted from the hospital's computerised obstetric database.MethodsLinear and binary regression analyses were used to derive prediction models with deviations in birthweight (BW) and SF height by gestational age as dependent and independent variables, respectively. Receiver operating characteristic curves were generated to evaluate the predictive value of the model in detecting SGA.Main outcome measuresBirthweight and small‐for‐gestational‐age.ResultsSymphysis–fundus height accounted for 3% of individual BW variance at 24 weeks, increasing gradually to 20% at 40 weeks. Maternal factors explained an additional 10 percentage points of BW variance. Receiver operating characteristic curves confirmed that SF height was a stronger SGA predictor in late than in early pregnancy. Using an SGA relative risk cut‐off limit of ≥2‐fold, the overall sensitivity was 50% and the overall specificity 80%. Only the most recent SF measurement was useful in predicting BW deviation; previous measurements added nothing to the predictive value.ConclusionsThe ability of SF measurements to detect SGA status at birth increases with gestational age. Only the most recent SF measurement has predictive value; a static or falling pattern of SF values did not increase SGA likelihood.Tweetable abstractNew SF curves predict SGA best in late pregnancy; only the most recent SF measurement has predictive value.
Characterization and Quantitation of Triterpenoid Saponins in Raw and Sprouted Chenopodium berlandieri spp. (Huauzontle) Grains Subjected to Germination with or without Selenium Stress Conditions
Authors: Lazo‐Vélez Marco A. , Guajardo‐Flores Daniel , Mata‐Ramírez Daniel , Gutiérrez‐Uribe Janet A. , Serna‐Saldivar Sergio O. 
Published: December 2015

AbstractPseudocereal Chenopodium berlandieri spp. (huauzontle) was evaluated to determine saponin composition. Saponins were evaluated in raw and germinated grains subjected to chemical stress induced by sodium selenite. Analysis by liquid chromatography coupled with ELSD detector revealed the presence of 12 saponins, identified according to compounds previously assayed in Chenopodium quinoa. Saponins found at the highest concentrations in raw grains were derived from oleanolic and phytolaccagenic acids. Total saponin concentration significantly decreased in germinated compared to raw grains due to the significant loss of 90.1% and 95.7% of the phytolaccagenic acid without and with chemical selenium stress, respectively. The most abundant saponin in germinated sprouts decreased during normal germination. Interestingly, the concentration of this particular saponin significantly increased during the Se‐induced stress germination. Chemical stress with selenium salts proved to change the saponin composition in geminated Chenopodium berlandieri spp. grains, therefore affecting their potential use as ingredient in the food industry.
Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA‐seq
Authors: Pérez‐Portela R. , Turon X. , Riesgo A. 
Published: December 2015

AbstractThe sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA‐seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the ‘somatic’ tissues (coelomocytes and digestive tissue) and the ‘reproductive’ tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the ‘reference’ transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186 084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10−5), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30 794 transcripts showed DE (~11.8% of them with blast hit), and 19 567 transcripts did so between testis and ovary (~28.5% of them with blast hit). Major GO‐term categories upregulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated with immune response in coelomocytes. Between reproductive tissues, the major upregulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.
Excessive alcohol consumption increases mortality in later life: a genetic analysis of the health in men cohort study
Authors: Almeida Osvaldo P. , McCaul Kieran , Hankey Graeme J. , Yeap Bu B. , Golledge Jonathan , Flicker Leon 
Published: December 2015

AbstractWe designed this cohort study of men aged 70–89 years to determine if excessive alcohol use increases mortality. They reported history of alcohol use (never, past, ≤ two daily drinks, two to four daily drinks, four to six daily drinks, > six daily drinks) and donated a blood sample in 2001–2004. We determined the ADH1B rs1229984 G>A polymorphism and retrieved mortality data from the Western Australian Data Linkage System. Other study measures included age, education, body mass index, smoking, and history of hypertension, diabetes, chronic respiratory diseases, coronary heart disease and stroke. Of the 3496 participants, 225 (6.4 percent) carried the ADH1B rs1229984 G>A polymorphism. Carriers consumed significantly less alcohol than non‐carriers. The adjusted mortality hazard ratio (MHR, 95 percent confidence interval—95%CI) over 8.0 years (range: 10 weeks to 11.2 years) relative to never drinkers was 1.15 (95%CI = 0.86, 1.55) for past drinkers, 0.98 (95%CI = 0.76, 1.25) for men consuming ≤ two daily drinks, 1.13 (95%CI = 0.85, 1.49) for two to four drinks, 1.18 (95%CI = 0.81, 1.71) for four to six drinks and 1.87 (95%CI = 1.11, 3.12) for those consuming more than six daily drinks on a regular basis. The MHR associated with the ADH1B rs1229984 G>A polymorphism was 0.68 (95%CI = 0.54, 0.87). Excessive alcohol use in later life is associated with increased mortality, and this association is likely to be causal. We found no evidence that light to moderate alcohol use decreases the mortality of older men. Health messages regarding the safe use of alcohol in older age may benefit from taking these findings into account.
Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed
Authors: Schiavo G. , Galimberti G. , Calò D. G. , Samorè A. B. , Bertolini F. , Russo V. , Gallo M. , Buttazzoni L. , Fontanesi L. 
Published: December 2015

SummaryIn this study, we investigated at the genome‐wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.
A randomised comparison of the Ambu® AuraGain™ and the LMA® supreme in infants and children
Authors: Jagannathan N. , Hajduk J. , Sohn L. , Huang A. , Sawardekar A. , Gebhardt E. R. , Johnson K. , De Oliveira G. S. 
Published: December 2015

SummaryWe conducted a randomised trial in 100 children in order to compare the clinical performance of the Ambu® AuraGain™ and the LMA® Supreme* for airway maintenance during mechanical ventilation. The primary outcomes were initial and 10‐min airway leak pressures. Ease, time and success rates for device and gastric tube insertion, fibreoptic grades of view, airway quality during anaesthetic maintenance, and complications were also assessed. There were no differences in the initial and ten min airway leak pressures between the Ambu AuraGain and LMA Supreme, median (IQR [range]) initial: 19 (16–22 [10–34]) vs 18 (14–24 [8–40]) cmH2O, p = 0.4; and ten min: 22 (18–26 [11–40]) vs 20 (16–26 [12–40]) cmH2O, p = 0.08, respectively. Ease, time and success rates for device placement, gastric tube insertion and complications were also not significantly different. Children receiving the LMA Supreme required more airway manouevers (7 vs 1 patient, p = 0.06) to maintain a patent airway. Our results suggest that the Ambu AuraGain may be a useful alternative to the LMA Supreme, as demonstrated by comparable overall clinical performance in children.
Use of vaginal estrogen in Danish women: a nationwide cross‐sectional study
Authors: Meaidi Amani , Goukasian Irina , Lidegaard Oejvind 
Published: December 2015

AbstractIntroductionWe know little about the use of vaginal estrogen in perimenopausal and postmenopausal women. We aimed to assess the prevalence of vaginal estrogen use in Denmark.Material and methodsThe study was designed as a nationwide cross‐sectional study of all Danish women aged 40–79 years, living in Denmark during the period 2007–2013. The Danish Prescription Register delivered data permitting us to assess the prevalence, age and regional geographical belonging of women purchasing prescribed vaginal estradiol. The number of women using over‐the‐counter vaginal estriol products was estimated from sale statistics from the same register.ResultsIn 2013, 10.2% of all Danish women between 40 and 79 years of age used vaginal estradiol. The prevalence of women using this type of vaginal estrogen increased from 8.5% in year 2007 to 10.2% in 2013. The use peaked at 16.5% in women aged 60–74 years. The vaginal tablet was purchased more than the vaginal ring. We found no relevant difference in use between the five regions of Denmark. Taking the sale of vaginal estriol into account, the prevalence of vaginal estrogen use in 2013 could be estimated to a total of 12.1%.ConclusionsComparing our result to the prevalence of urogenital atrophy‐related symptoms reported in the literature, our study suggests an under‐diagnosis and under‐treatment of this condition. Teaching women and primary‐care physicians about symptomatic urogenital atrophy and its treatment options may increase the quality of life for many women.
The efficacy and complications of black diaphragm intra‐ocular lens implantation in patients with congenital aniridia
Authors: Qiu Xiaodi , Ji Yinghong , Zheng Tianyu , Lu Yi 
Published: December 2015

AbstractPurposeTo evaluate the efficacy and complications of black diaphragm intra‐ocular (BDI) lens implantation in patients with congenital aniridia.MethodsTwenty patients underwent BDI lens implantation for the treatment of congenital aniridia from January 1999 to December 2012. Fifteen patients (23 eyes) were enrolled in our study, and the mean follow‐up period was 26 months. Patient demographics, clinical evaluations [visual acuity (VA), best‐corrected visual acuity (BCVA), intra‐ocular pressure measurement (IOP), corneal endothelial cell density (ECD) and ultrasound biomicroscopy (UBM)], complications and treatments were analysed for each patient.ResultsSixteen eyes (70.1%) had a BCVA better than 20/200 after BDI lens implantation, and photophobia obviously decreased in all patients. Six eyes (26.09%) developed secondary glaucoma after BDI lens implantation, and one eye underwent glaucoma surgery. Corneal decompensation occurred in two eyes (8.70%), one of which was complicated by glaucoma. Two eyes (8.70%) developed visual axis opacity (VAO) after surgery. One patient (4.35%) had limbal stem cell failure, and another patient (4.35%) had an eccentric BDI lens. Intra‐ocular pressure measurement elevation and ECD reduction were found after BDI lens implantation.ConclusionsBlack diaphragm intra‐ocular lens implantation can effectively improve VA, decrease photophobia and resolve cosmetic issues in most congenital aniridia eyes. Glaucoma, corneal decompensation and VAO were the major long‐term complications of BDI lens implantation in patients with congenital aniridia. All patients should be managed attentively because of high risk of complications and followed long term to achieve favourable outcomes.
Pharmacokinetics and safety of single doses of tabalumab in subjects with rheumatoid arthritis or systemic lupus erythematosus
Authors: Witcher Jennifer , Fleischmann Roy , Chindalore Vishala L. , Hansen Ryan J. , Hu Leijun , Radtke David , Voelker James , Gomez Elisa , McColm Juliet 
Published: December 2015

AimsTwo phase 1 studies evaluated the pharmacokinetics (PK), safety and biological activity of tabalumab, a human monoclonal antibody against B‐cell activating factor (BAFF), administered intravenously (i.v.) or subcutaneously (s.c.) in subjects with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE).MethodsIn study A, subjects with RA (n = 23) or SLE (n = 6) received a single i.v. dose of tabalumab (RA 0.01, 0.04, 0.125, 0.5, 2.0, and 8.0 mg kg–1 and SLE 0.125 or 2.0 mg kg–1) or placebo. In study B, subjects with RA received a single tabalumab dose i.v. (10 mg) (n = 12) or s.c. (20 mg) (n = 12). Serum tabalumab and CD20+ B cells were evaluated and safety was assessed throughout both studies.ResultsTabalumab PK were non‐linear across the 0.01 to 8.0 mg kg–1 dose range. Clearance (CL) decreased from 2.9 to 0.1 l day–1 and terminal half‐life (t1/2) increased from about 1.6 to 25 days. Subjects with RA or SLE had similar PK. After s.c. dosing, tabalumab time to maximal concentration (tmax) was 5.5 days. Absolute bioavailability (F) was approximately 62%. Following tabalumab dosing, CD20+ B cells transiently increased from baseline followed by a progressive decrease below baseline.ConclusionA single tabalumab dose administered i.v. or s.c. was well tolerated and had non‐linear CL over the dose range investigated in subjects with RA and SLE. The non‐linearity likely reflects target‐mediated CL due to binding to BAFF. Tabalumab showed biological activity based on changes in peripheral CD20+ lymphocyte numbers in both subjects with RA and SLE.
Integrative Bioethics: A Conceptually Inconsistent Project
Authors: Ivanković Viktor , Savić Lovro 
Published: December 2015

ABSTRACTThis article provides a critical evaluation of the central components of Integrative Bioethics, a project aiming at a bioethical framework reconceptualization. Its proponents claim that this new system of thought has developed a better bioethical methodology than mainstream Western bioethics, a claim that we criticize here. We deal especially with the buzz words of Integrative Bioethics – pluriperspectivism, integrativity, orientational knowledge, as well as with its underlying theory of moral truth. The first part of the paper looks at what the claims of a superior methodology consist in. The second reveals pluriperspectivism and integrativity to be underdeveloped, hazy terms, but which seem to be underpinned by two theses – the incommensurability and the inclusiveness theses. These theses we critically scrutinize. We then consider strategies the project's proponents might apply to curb these theses in order to acquire minimal consistency for their framework. This part of the article also deals with the conception of moral truth that drives the theory, a position equally burdened with inconsistencies. In the last part of the article, we observe the concept of orientational knowledge, and develop two interpretations of its possible meaning. We claim that, following the first interpretation, Integrative Bioethics is completely descriptive, in which case it is informative and important, but hardly bioethics; if it is normative, following the second interpretation, it is bioethics as we already know it, but merely clad in rhetorical embellishments. We conclude that there is nothing new about this project, and that its inconsistencies are reason enough for its abandonment.
Pregnancy Outcome in Women with Decreased Sensation of Fetal Movements at Term According to Parity
Authors: Aviram Amir , Shmueli Anat , Hiersch Liran , Ashwal Eran , Wiznitzer Arnon , Yogev Yariv , Hadar Eran 
Published: December 2015

AbstractBackgroundDecreased sensation of fetal movements (DFM) is a common maternal complaint. Thus, we aimed to evaluate the association between DFM and pregnancy outcome in singleton gestation at term according to parity.MethodsA retrospective cohort study of singleton pregnancies at term between 2008 and 2013. Eligibility was limited to women carrying a fetus with no known structural or chromosomal anomalies, at 37+0/7 to 42+0/7 weeks of gestation. Women presenting to the delivery ward with DFM were compared with women without similar complaints.ResultsOverall, 12,564 nulliparous women and 25,292 multiparous women gave birth during the study period; of them, 300 nulliparous women (2.4%) and 525 multiparous women (2.1%) complained of DFM. For nulliparous women, after adjusting for potential confounders, DFM was associated with antepartum fetal death (aOR 4.6 [95% CI 1.1–19.8]), cesarean delivery (CD) (aOR 1.3 [95% CI 1.01–1.8]), 1‐minute Apgar score less than 7 (aOR 2.3 [95% CI 1.5–3.5]) and neonatal seizures (aOR 3.2 [95% CI 1.3–8.2]). For multiparous women, DFM was associated with unscheduled CD (aOR 2.7 [95% CI 1.6–4.6]) and CD indicated by intermediate/abnormal fetal heart rate tracing (aOR 4.8 [95% CI 2.8–8.4]).ConclusionsDFM carries different outcomes according to parity. Although for nulliparous women, DFM is associated with increased risk of CD and immediate adverse perinatal outcome, for multiparous women it is associated with increased risk for CD, with no immediate increased risk for adverse perinatal outcome.