bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family
Authors: Malé Pierre‐Jean G. , Bardon Léa , Besnard Guillaume , Coissac Eric , Delsuc Frédéric , Engel Julien , Lhuillier Emeline , Scotti‐Saintagne Caroline , Tinaut Alexandra , Chave Jérôme 
Published: March 2014

AbstractWhole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high‐copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost‐effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under‐studied groups.
Epigenetic estimation of age in humpback whales
Authors: Polanowski Andrea M. , Robbins Jooke , Chandler David , Jarman Simon N. 
Published: March 2014

AbstractAge is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age‐induced changes in DNA methylation of specific genes. We used information on age‐associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age‐related profiles. The three most age‐informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R2 of 0.787 (P = 3.04e−16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent–offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms.
Genome‐wide association analysis for growth, muscularity and meat quality in Piétrain pigs
Authors: Stratz P. , Wellmann R. , Preuss S. , Wimmers K. , Bennewitz J. 
Published: March 2014

SummaryImprovement in growth and meat quality is one of the main objectives in sire line pig breeding programmes. Mapping quantitative trait loci for these traits using experimental crosses and a linkage‐based approach has been performed frequently in the past. The Piétrain breed often was involved as a founder breed to establish the experimental crosses. This breed was selected for muscularity and leanness but shows relatively poor meat quality. It is frequently used as a sire line breed. With the advent of genome‐wide and dense SNP chips in pig genomic research, it is possible to also conduct genome‐wide association studies within the Piétrain breed. In this study, around 500 progeny‐tested sires were genotyped with 60k SNPs. Data filtering showed that around 48k SNPs were useable in this sample. These SNPs were used to conduct a genome‐wide association study for growth, muscularity and meat quality traits. Because it is known that a mutation in the RYR1 gene located on chromosome 6 shows a major effect on meat quality, this mutation was included in the models. Single‐marker and multimarker association analyses were performed. The results revealed between zero and eight significant associations per trait with P < 5 × 10−5. Of special interest are SNPs located on SSC6, SSC10 and SSC15.
Delivery room management of extremely low birthweight infants shows marked geographical variations in Italy
Authors: Trevisanuto Daniele , Satariano Irene , Doglioni Nicoletta , Criscoli Giulio , Cavallin Francesco , Gizzi Camilla , Martano Claudio , Ciralli Fabrizio , Torielli Flaminia , Villani Paolo E. , Di Fabio Sandra , Quartulli Lorenzo , Giannini Luigi ,   Neonatal Resuscitation Study Group, Italian Society of Neonatology
Published: March 2014

AbstractAimTo evaluate any geographical variations in practice and adherence to international guidelines for early delivery room management of extremely low birthweight (ELBW) infants in the North, Centre and South of Italy.MethodsA questionnaire was sent to all 107 directors of Italian level III centres between April and August 2012.ResultsThere was a 92% (n = 98) response rate. A polyethylene bag/wrap was used by 54 centres (55.1%), with the highest rate in Northern Italy (77.5%) and the lowest rate in Southern (37.7%) areas. In Northern regions, one centre (2.5%) said it used oxygen concentrations >40% to initiate positive pressure ventilation in ELBW infants. These proportions were higher in the Central (14.3%) and Southern (16.2%) areas. A T‐piece device for positive pressure ventilation was more frequently available in the Northern (95%) units than in those in the Central (66.7%) and Southern (69.4%) regions. A median of 13% (IQR: 5%–30%) of ELBW infants received chest compressions at birth in Italy: 5%, 18% and 22% in Northern, Central and Southern units, respectively.ConclusionIn Italy, delivery room management of ELBW infants showed marked geographical variations. Implementation of national training programmes could increase adherence to the guidelines and reduce such discordance.
Cholesteatoma has a high prevalence in Turner syndrome, highlighting the need for earlier diagnosis and the potential benefits of otoscopy training for paediatricians
Authors: Lim DBN , Gault EJ , Kubba H , Morrissey MSC , Wynne DM , Donaldson MDC 
Published: March 2014

AbstractAimGirls with Turner syndrome are prone to cholesteatoma, a serious suppurative middle ear disease. We aimed to confirm its high prevalence in Turner syndrome, identify risk factors and suggest possible strategies for earlier detection.MethodsWe reviewed 179 girls with Turner syndrome between 1989 and 2012 to identify cases of cholesteatoma.ResultsSeven girls (3.9%) had cholesteatoma (index girls) and each was compared with three age‐matched girls without cholesteatoma (comparison girls). All the index girls had either the 45,X or 45,X/46X,i(Xq) karyotypes. Nine ears were initially affected, with three recurrences in two girls. Median age at first cholesteatoma presentation was 11.9 years (range: 7.5–15.2), with otorrhoea for three (range: one to seven) months in all 12 affected ears. Index girls had a significantly higher proportion of previous recurrent acute (p = 0.007) and chronic otitis media (p = 0.008), chronic perforation (p = 0.038) aural polyps (p < 0.0001) and tympanic membrane retraction (p = 0.0001) than comparison girls.ConclusionCholesteatoma has a high prevalence in Turner syndrome. Risk factors include 45,X and 46,XiXq karyotypes; a history of chronic otitis media, tympanic membrane retraction and persistent otorrhoea; and older age. Earlier recognition of ear disease is needed and otoscopy training for paediatricians caring for Turner syndrome patients may be beneficial.
Viral aetiology and clinical outcomes in hospitalised infants presenting with respiratory distress
Authors: Falkenstein‐Hagander Kathy , Månsson Ann‐Sofie , Redmo Johan , Nilsson Wimar Percy , Widell Anders 
Published: March 2014

AbstractAimTo determine the prevalence of various types of viruses in infants hospitalised due to respiratory distress, compare molecular diagnostic tests and evaluate symptom severity.MethodsAll 136 nasopharyngeal aspirates from infants hospitalised for respiratory distress over a 9‐month period were analysed for virus type by in‐house respiratory syncytial virus (RSV) polymerase chain reaction (PCR) microarray‐based and/or Luminex‐based multiplex molecular tests. Medical records were reviewed retrospectively for clinical data.ResultsViral aetiology was confirmed in 126 subjects (92.6%) with 26 infected by more than one virus. RSVA/B was the most common (50.9%), followed by entero/rhinovirus (21.6%), human metapneumovirus (10.5%), parainfluenza virus (5.9%) and influenza (3.3%). RSV‐infected infants had significantly lower saturation levels (89% versus 92%, p < 0.001), higher demand for oxygen (42.7% versus 21.6%, p = 0.021) and fluids (28% versus 9.8%; p = 0.014) and longer hospital stays (4 versus 3 days, <0.001) than other viruses. Luminex assays gave repeatable, slightly less sensitive results than in‐house RSV PCR. Microarray‐based assays were more sensitive, however, producing some unrepeatable results.ConclusionRespiratory syncytial virus dominates as the viral cause in hospitalised infants with respiratory distress in Sweden during the winter season, resulting in a clinical course that is significantly more severe. The multiplex assays produced reasonably concordant results.
Influence of age on leptin induced skeletal muscle signalling
Authors: Guadalupe‐Grau A. , Larsen S. , Guerra B. , Calbet J. A. L. , Dela F. , Helge J. W. 
Published: March 2014

AbstractAimAge associated fat mass accumulation could be because of dysregulation of leptin signalling in skeletal muscle. Thus, we investigated total protein expression and phosphorylation levels of the long isoform of the leptin receptor (OB‐Rb), and leptin signalling through janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3), insulin receptor substrate 1 (IRS‐1), AMP‐activated protein kinase (AMPK) and acetyl‐coenzyme A carboxylase (ACC), combined with the leptin signalling inhibitors suppressor of cytokine signalling 3 (SOCS3) and protein tyrosine phosphatase 1B (PTP1B) in human skeletal muscle of different age.MethodsVastus lateralis muscle biopsies were obtained from 39 men matched for BMI < 30 kg m−2 and separated into three groups: 13 young (Y, 24 ± 4 years); 14 middle aged (MA, 44 ± 5 years) and 12 aged (A, 58 ± 8 years) subjects.ResultsWhole body fat percentage and plasma leptin were higher (P < 0.05), whereas lean mass, plasma free testosterone and total testosterone were lower (P < 0.05) in A compared to Y. Skeletal muscle OB‐Rb (170 KDa) protein expression and pTyr1141‐OB‐R170 were comparable between groups, whereas pTyr985‐OB‐R170 was lower in A compared to Y (P < 0.05). pSTAT3 levels tended (P = 0.09) to be lower (50%) in A compared to Y. In A, muscle PTP1B was greater and IRS‐1 lower than Y and MA respectively (P < 0.05). PTyr612‐IRS‐1 tended to be lower in A than in Y (P = 0.09). Suppressor of cytokine signalling 3 (SOCS3) protein expression, pJAK2, pSer1101‐IRS‐1, pAMPKα and pACCβ were similar between groups.ConclusionAge is associated with dysregulation of the leptin signalling and increased PTP1B protein expression in skeletal muscle.
In silico Characterization of an Atypical MAPK Phosphatase of Plasmodium falciparum as a Suitable Target for Drug Discovery
Authors: Campbell Christopher O. , Santiago Daniel N. , Guida Wayne C. , Manetsch Roman , Adams John H. 
Published: March 2014

Plasmodium falciparum, the causative agent of malaria, contributes to significant morbidity and mortality worldwide. Forward genetic analysis of the blood‐stage asexual cycle identified the putative phosphatase from PF3D7_1305500 as an important element of intraerythrocytic development expressed throughout the life cycle. Our preliminary evaluation identified it as an atypical mitogen‐activated protein kinase phosphatase. Additional bioinformatic analysis delineated a conserved signature motif and three residues with potential importance to functional activity of the atypical dual‐specificity phosphatase domain. A homology model of the dual‐specificity phosphatase domain was developed for use in high‐throughput in silico screening of the available library of antimalarial compounds from ChEMBL‐NTD. Seven compounds from this set with predicted affinity to the active site were tested against in vitro cultures, and three had reduced activity against a ∆PF3D7_1305500 parasite, suggesting PF3D7_1305500 is a potential target of the selected compounds. Identification of these compounds provides a novel starting point for a structure‐based drug discovery strategy that moves us closer toward the discovery of new classes of clinical antimalarial drugs. These data suggest that mitogen‐activated protein kinase phosphatases represent a potentially new class of P. falciparum drug target.
Response Variables for Evaluation of the Effectiveness of Conservation Corridors
Authors: GREGORY ANDREW J. , BEIER PAUL 
Published: March 2014

AbstractMany studies have evaluated effectiveness of corridors by measuring species presence in and movement through small structural corridors. However, few studies have assessed whether these response variables are adequate for assessing whether the conservation goals of the corridors have been achieved or considered the costs or lag times involved in measuring the response variables. We examined 4 response variables—presence of the focal species in the corridor, interpatch movement via the corridor, gene flow, and patch occupancy—with respect to 3 criteria—relevance to conservation goals, lag time (fewest generations at which a positive response to the corridor might be evident with a particular variable), and the cost of a study when applying a particular variable. The presence variable had the least relevance to conservation goals, no lag time advantage compared with interpatch movement, and only a moderate cost advantage over interpatch movement or gene flow. Movement of individual animals between patches was the most appropriate response variable for a corridor intended to provide seasonal migration, but it was not an appropriate response variable for corridor dwellers, and for passage species it was only moderately relevant to the goals of gene flow, demographic rescue, and recolonization. Response variables related to gene flow provided a good trade‐off among cost, relevance to conservation goals, and lag time. Nonetheless, the lag time of 10–20 generations means that evaluation of conservation corridors cannot occur until a few decades after a corridor has been established. Response variables related to occupancy were most relevant to conservation goals, but the lag time and costs to detect corridor effects on occupancy were much greater than the lag time and costs to detect corridor effects on gene flow.Variables de Respuesta para la Evaluación de la Efectividad de los Corredores de Conservación
Understanding Publication Bias in Reintroduction Biology by Assessing Translocations of New Zealand's Herpetofauna
Authors: MILLER KIMBERLY A. , BELL TRENT P. , GERMANO JENNIFER M. 
Published: March 2014

AbstractThe intentional translocation of animals is an important tool for species conservation and ecosystem restoration, but reported success rates are low, particularly for threatened and endangered species. Publication bias further distorts success rates because the results of successful translocations may be more likely to be published than failed translocations. We conducted the first comprehensive review of all published and unpublished translocations of herpetofauna in New Zealand to assess publication bias. Of 74 translocations of 29 species in 25 years, 35 have been reported in the published literature, and the outcomes of 12 have been published. Using a traditional definition of success, publication bias resulted in a gross overestimate of translocation success rates (41.7% and 8.1% for published and all translocations, respectively), but bias against failed translocations was minimal (8.3% and 6.8%, respectively). Publication bias against translocations with uncertain outcomes, the vast majority of projects, was also strong (50.0% and 85.1% for published and all translocations, respectively). Recent translocations were less likely to be published than older translocations. The reasons behind translocations were related to publication. A greater percentage of translocations for conservation and research were published (63.3% and 40.0%, respectively) than translocations for mitigation during land development (10.0%). Translocations conducted in collaboration with a university were more frequently published (82.7% and 24.4%, respectively). To account for some of this publication bias, we reassessed the outcome of each translocation using a standardized definition of success, which takes into consideration the species’ life history and the time since release. Our standardized definition of translocation success provided a more accurate summary of success rates and allows for a more rigorous evaluation of the causes of translocation success and failure in large‐scale reviews.Entendiendo el Sesgo de Publicaciones en la Biología de la Reintroducción Mediante el Estudio de Traslocaciones de la Herpetofauna de Nueva Zelanda
The confusing tale of depression and distress in patients with diabetes: a call for greater clarity and precision
Authors: Fisher L. , Gonzalez J. S. , Polonsky W. H. 
Published: March 2014

AbstractStudies have identified significant linkages between depression and diabetes, with depression associated with poor self‐management behaviour, poor clinical outcomes and high rates of mortality. However, findings are not consistent across studies, yielding confusing and contradictory results about these relationships. We suggest that there has been a failure to define and measure ‘depression’ in a consistent manner. Because the diagnosis of depression is symptom‐based only, without reference to source or content, the context of diabetes is not considered when addressing the emotional distress experienced by individuals struggling with diabetes. To reduce this confusion, we suggest that an underlying construct of ‘emotional distress’ be considered as a core construct to link diabetes‐related distress, subclinical depression, elevated depression symptoms and major depressive disorder (MDD). We view emotional distress as a single, continuous dimension that has two primary characteristics: content and severity; that the primary content of emotional distress among these individuals include diabetes and its management, other life stresses and other contributors; and that both the content and severity of distress be addressed directly in clinical care. We suggest further that all patients, even those whose emotional distress rises to the level of MDD or anxiety disorders, can benefit from consideration of the content of distress to direct care effectively, and we suggest strategies for integrating the emotional side of diabetes into regular diabetes care. This approach can reduce confusion between depression and distress so that appropriate and targeted patient‐centred interventions can occur.
Serum selenium in relation to measures of glucose metabolism and incidence of Type 2 diabetes in an older Swedish population
Authors: Gao H. , Hägg S. , Sjögren P. , Lambert P. C. , Ingelsson E. , van Dam R. M. 
Published: March 2014

AbstractAimsThe relation between selenium status and risk of Type 2 diabetes is controversial. We aimed to evaluate associations of serum selenium, a marker of dietary selenium, with measures of glucose metabolism and risk of diabetes.MethodsWe used data from a population‐based, longitudinal cohort of 1925 Swedish men who were 50 years old and did not have diabetes at baseline in the 1970s. At baseline, an intravenous glucose tolerance test was performed and, at a follow‐up examination after 20 years, an oral glucose tolerance test and a hyperinsulinaemic euglycaemic clamp for the assessment of insulin sensitivity were conducted.ResultsAt baseline, the mean (standard deviation) selenium concentration was 75.6 (14.3) μg/l. During 20 years of follow‐up, 88 incident cases of diabetes occurred in 1024 participants with follow‐up data. Baseline serum selenium levels were not associated with risk of diabetes (odds ratio 1.06; 95% CI 0.83–1.38). Higher selenium levels were associated with lower early insulin response (standardized β –0.08; 95% CI –0.14 to –0.03) at baseline after adjusting for potential confounders, but not with any other measures of β‐cell function or insulin sensitivity at baseline or follow‐up. The association with early insulin response was non‐significant after taking multiple testing into account.ConclusionsOur results do not support a role of dietary selenium in the development of disturbances in glucose metabolism or diabetes in older individuals.
Type 2 diabetes mellitus and obesity in young adults: the extreme phenotype with early cardiovascular dysfunction
Authors: Wilmot E. G. , Leggate M. , Khan J. N. , Yates T. , Gorely T. , Bodicoat D. H. , Khunti K. , Kuijer J. P. A. , Gray L. J. , Singh A. , Clarysse P. , Croisille P. , Nimmo M. A. , McCann G. P. , Davies M. J. 
Published: March 2014

AbstractAimA pilot study to phenotype young adults (< 40 years) with Type 2 diabetes mellitus.MethodsTwenty people with Type 2 diabetes (aged 18–40 years), 10 lean and 10 obese control subjects underwent detailed assessment, including tagged cardiac magnetic resonance imaging, inflammatory proteins, lipids, vitamin D and maximal oxygen uptake. Outcomes were compared between the group with Type 2 diabetes and the control group.ResultsMean (standard deviation) age, Type 2 diabetes duration and BMI in the group with Type 2 diabetes were 31.8 (6.6) years, 4.7 (4.0) years and 33.9 (5.8) kg/m2 respectively. Compared with lean control subjects, those with Type 2 diabetes had more deleterious profiles of hyperlipidaemia, vitamin D deficiency, inflammation and maximal oxygen uptake relative to body mass. However, there was no difference between the group with Type 2 diabetes and the obese control group. The group with Type 2 diabetes had a higher left ventricular mass and a trend towards concentric remodelling compared with the lean control group (P = 0.002, P = 0.052) but not the obese control group (P > 0.05). Peak early diastolic strain rate was reduced in the group with Type 2 diabetes [1.51 (0.24)/s] compared with the lean control [1.97 (0.34)/s, P = 0.001] and obese control [1.78 (0.39)/s, P = 0.042] group.ConclusionsYoung adults with Type 2 diabetes and those with obesity have similar adverse cardiovascular risk profiles, higher left ventricular mass and a trend towards left ventricular concentric remodelling. In addition, those with Type 2 diabetes demonstrate diastolic dysfunction, a known risk marker for future heart failure and mortality.