bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery
Authors: Lobréaux Stéphane , Manel Stephanie , Melodelima Christelle 
Published: October 2013

AbstractThe alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next‐generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127 041 single‐nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.
Post‐translocation assortative pairing and social implications for the conservation of an endangered songbird
Authors: Bradley D. W. , Molles L. E. , Waas J. R. 
Published: October 2013

AbstractAnimals translocated for conservation purposes may be sourced from multiple locations which may exhibit inter‐site variability in reproductive behaviours. The influence that these differences may have on the propensity of pair formation, and the ultimate impact this may have on the success of the translocation, is unknown due to the low sample sizes of many translocations. We address this knowledge gap by collating an existing 18‐year data set documenting multisource translocations of the endangered North Island Kōkako, Callaeas wilsoni, a duetting New Zealand species with known population‐specific vocalizations. We found a strong, statistically significant tendency for Kōkako to pair assortatively with respect to source population (like with like) following release. Population‐specific differences in sexually selected behaviours that are important in mate choice decisions, such as bird song, are likely the proximate explanation for such reproductive decisions. Accounting for the tendency to pair assortatively following translocation may be particularly important when managing highly vocal animals like Kōkako that produce vocal duets and cooperatively defend territories as mated pairs. Consequently, careful consideration of behavioural variation between translocated individuals should be made, which will appropriately inform decisions relating to release‐cohort composition. Failure to consider such variation may negatively impact the success of a translocation as the effective population size of the founder group may be lower than intended. Our findings make an important contribution towards understanding the impact that behavioural variation can have on the conservation of endangered species, and highlight the value of combining long‐term data from multiple sources.
Cardiac function and arterial indices in infants born small for gestational age: analysis by speckle tracking
Authors: Sehgal Arvind , Doctor Tejas , Menahem Samuel 
Published: October 2013

AbstractAimTo compare strain indices between small for gestational age (SGA) infants and asymptomatic appropriate for gestational age (AGA) infants and to ascertain correlations with arterial biophysical properties.MethodsIn this prospective observational echocardiographic study, 20 inborn term SGA infants weighing <3rd centile for gestational age were compared with 20 AGA infants. Demographic and echocardiographic data were analysed regarding cardiac strain and strain rate and arterial indices (stiffness, impedance and strain elastic modulus). Correlations between variables were assessed using Pearson's coefficient of correlation.ResultsPonderal index was significantly lower in SGA infants (24.6 ± 2.9 vs. 29.5 ± 2.5). Left ventricular global longitudinal strain (GLS) was noted to be significantly impaired in the SGA infants (−15.9% ± 2.1 vs. −21.3% ± 2.8, p < 0.001). A basal to apical gradient was noted in segmental strain. Arterial biophysical measurements were significantly altered in the SGA infants. Significant correlations were noted between GLS and arterial stiffness (r = −0.4, p = 0.03), weight‐indexed stiffness (r = −0.45, p = 0.02) and pressure–strain elastic modulus (r = −0.49, p = 0.01).ConclusionImpairment in myocardial deformation was noted in the presence of altered arterial biophysical properties in the SGA infants.
Selected family characteristics are associated with adolescents' subjective health complaints
Authors: Petanidou Dimitra , Mihas Constantinos , Dimitrakaki Christine , Kolaitis Gerasimos , Tountas Yannis 
Published: October 2013

AbstractAimThis national study of schoolchildren in Greece investigated the association between adolescents' subjective health complaints (SHC) and a number of family characteristics.MethodsQuestionnaires were completed by a random, school‐based sample of children from 12 to 18 years of age, and one of their parents (76.6% mothers), in 2003. Data from 1041 adolescent–parent pairs were analysed. Multiple linear regression analysis was used to assess the associations between the adolescent's SHC and the following characteristics: parent's marital status, parent's physical and mental health status, parent's worries about their child's SHC, the parent–child relationship, family cohesion, family socio‐economic status and the adolescent's sex and age.ResultsThe analysis showed that the adolescents' SHC were independently and significantly correlated with poor parental subjective mental health status, poor quality parent–child relationships and parental worry. There were also associations between levels of SHC and female and older adolescents.ConclusionCertain family features can be seen as potential contributing factors to SHC in adolescence and should therefore constitute complementary targets for prevention and treatment planning.
Reactive hyperaemia index as a marker of endothelial dysfunction in children with Crohn's disease is significantly lower than healthy controls
Authors: Petr Jehlicka , Michal Huml , Jan Schwarz , Ladislav Trefil , Jiri Kobr , Josef Sykora 
Published: October 2013

AbstractAimPatients with inflammatory bowel disease (IBD) are prone to cardiovascular disorders, although there is little research to support this assertion, and other data are controversial in children. We aimed to determine the extent of premature atherosclerosis in Crohn's disease (CD) by measuring reactive hyperaemia index (RHI) as a functional marker of endothelial dysfunction (ED).MethodsTwenty‐one patients with CD and twelve healthy matched subjects were enrolled in the study. Diagnosis was based on the standard clinical, endoscopic and histological criteria, including the Paediatric Crohn's disease Activity Index. ED was assessed using the plethysmographic RHI, combined with specific biochemical markers of ED.ResultRHI values were significantly lower in the patients with CD than the controls (p < 0.05). E‐selectin (p < 0.05), asymmetric dimethylarginine (p < 0.01) and high‐sensitive CRP (p < 0.05), but not vascular cells adhesive molecule‐1 values, were significantly increased in the CD subjects compared with the control group.ConclusionSignificantly decreased RHI and elevated plasma levels of specific biochemical parameters seems to be related to systemic inflammation and ED in children with CD. Our results support the hypothesis regarding RHI and ED in paediatric CD. This combined method assessment might be a useful tool for detection of ED and stratification of cardiovascular risk in patients with CD.
The 2014 Danish references from birth to 20 years for height, weight and body mass index
Authors: Tinggaard Jeanette , Aksglaede Lise , Sørensen Kaspar , Mouritsen Annette , Wohlfahrt‐Veje Christine , Hagen Casper P , Mieritz Mikkel G , Jørgensen Niels , Wolthers Ole D , Heuck Carsten , Petersen Jørgen Holm , Main Katharina M , Juul Anders 
Published: October 2013

AbstractAimTo construct new Danish growth charts for 0‐ to 20‐year‐olds and to compare them with Danish references from 1982 and with World Health Organization (WHO) standards for children aged 0–5 years from 2006, by applying similar inclusion and exclusion criteria.MethodsAnthropometric data from three contemporary Danish population‐based studies were combined. References for height were based on healthy Caucasian children born at term. A total of 12 671 height measurements (8055 in boys and 4616 in girls) were included. Reference charts were developed using the generalised additive models for location, scale and shape.ResultsFrom prepubertal ages, a secular increase in height was observed for both genders. The differences were most pronounced in puberty, and final heights were increased by 1.4 cm in boys and 2.9 cm in girls compared to 1982 references. In boys, but not girls an upward shift in body mass index (BMI) above median levels was found. Reference curves for height were superimposable with standard curves based on the selective WHO criteria. Danish children were longer/taller and heavier and they had larger head circumferences than those reported in the recent multiethnic WHO standards.ConclusionWe recommend national implementation of these contemporary 2014 Danish references for anthropometric measurements.
Benefits of simultaneous laparoscopic resection of primary colorectal cancer and liver metastases
Authors: Takasu Chie , Shimada Mitsuo , Sato Hirohiko , Miyatani Tomohiko , Imura Satoru , Morine Yuji , Ikemoto Tetsuya , Kanamoto Mami , Kurita Nobuhiro , Eto Shohei , Utsunomiya Tohru 
Published: October 2013

AbstractIntroductionRecently, consensus on the optimal strategy for resectable synchronous colorectal liver metastases (LM) seems to have shifted toward simultaneous resection. However, there are still relatively few reports about simultaneous laparoscopic resection. The aim of this study is to evaluate the outcomes of patients who underwent simultaneous laparoscopic resection.MethodsWe evaluated 14 patients who underwent simultaneous resection of primary colorectal cancer and LM in our hospital from 2004 to 2012. Patients were selected by matched pair analysis based on the number of LM (≤4) and tumor size (≤5 cm). We divided them into two groups: the simultaneous laparoscopic resection of primary colorectal cancer and LM (Lap‐S) group (n = 7) and the simultaneous open resection of primary colorectal cancer and LM (Open‐S) group (n = 7). Clinical and oncologic outcomes were compared between the groups.ResultsThe Lap‐S patients were significantly older than the Open‐S patients. The mean operative times of Lap‐S and Open‐S were 472 min and 466 min, respectively. The mean blood loss was significantly smaller in the Lap‐S group (153 mL) than in the Open‐S group (496 mL). There was no surgical mortality in either group. The incidence of postoperative complications in the Lap‐S and Open‐S groups was 12.3% and 33.0%, respectively. The mean postoperative hospital stay was significantly shorter in the Lap‐S group (16 days) than in the Open‐S group (36 days). There was no significant difference in long‐term survival between the two groups.ConclusionLap‐S patients had equivalent long‐term outcomes to Open‐S patients. Therefore, given its technical feasibility and safety, Lap‐S may be one of the most promising options in selected patients.
Evaluation of effects of multiple candidate genes (LEP, LEPR, MC4R, PIK3C3, and VRTN) on production traits in Duroc pigs
Authors: Hirose Kensuke , Ito Tetsuya , Fukawa Kazuo , Arakawa Aisaku , Mikawa Satoshi , Hayashi Yoichi , Tanaka Kazuaki 
Published: October 2013

AbstractWe evaluated multiple effects of genetic variations of five candidate loci (LEP, LEPR, MC4R, PIK3C3 and VRTN) on four production traits (average daily weight gain (ADG); backfat thickness (BFT); loin eye muscle area (EMA); and intramuscular fat content (IMF)) in a closed nucleus herd of pure Duroc pigs. Polymorphisms in LEPR, MC4R and PIK3C3 had significant single gene effects on ADG and BFT. The additive genetic variance in ADG and BFT (16.99% and 22.51%, respectively) was explained by genetic effects of these three loci. No correlations were observed between the LEP genotype and production traits in this study. Although we detected marginally epistatic interactions between LEPR and PIK3C3 on the eye muscle area, there were no significant epistatic effects on any traits among all loci pairs. These results suggest that LEPR, MC4R, PIK3C3 and VRTN may independently influence growth rate and fat deposition. Furthermore, the statistical models for predicting the breeding values of each trait had the lowest Akaike's information criterion values when considering the effect of the MC4R, LEPR, PIK3C3 and VRTN genotype simultaneously. These results suggest that LEPR, MC4R, PIK3C3 and VRTN are useful markers for accurately predicting breeding values in Duroc pigs.
A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis
Authors: Xia Fan , Chen Jun , Fung Wing Kam , Li Hongzhe 
Published: October 2013

SummaryChanges in human microbiome are associated with many human diseases. Next generation sequencing technologies make it possible to quantify the microbial composition without the need for laboratory cultivation. One important problem of microbiome data analysis is to identify the environmental/biological covariates that are associated with different bacterial taxa. Taxa count data in microbiome studies are often over-dispersed and include many zeros. To account for such an over-dispersion, we propose to use an additive logistic normal multinomial regression model to associate the covariates to bacterial composition. The model can naturally account for sampling variabilities and zero observations and also allow for a flexible covariance structure among the bacterial taxa. In order to select the relevant covariates and to estimate the corresponding regression coefficients, we propose a group penalized likelihood estimation method for variable selection and estimation. We develop a Monte Carlo expectation-maximization algorithm to implement the penalized likelihood estimation. Our simulation results show that the proposed method outperforms the group penalized multinomial logistic regression and the Dirichlet multinomial regression models in variable selection. We demonstrate the methods using a data set that links human gut microbiome to micro-nutrients in order to identify the nutrients that are associated with the human gut microbiome enterotype.
Are Unions Good or Bad for Organizations? The Moderating Role of Management's Response
Authors: Pohler Dionne , Luchak Andrew 
Published: October 2013

AbstractUnion impact research has been hindered by an underdeveloped conceptualization of management response, contributing to inconclusive empirical findings. Integrating the collective voice/institutional response model with the appropriateness framework, we propose that an employee‐focused business strategy is a critical moderating variable in the relationship between union density and organizational outcomes that mitigates the negative effects of unions and enhances the positive effects by sending a clear signal of management's intentions to co‐operate. Using a panel dataset of Canadian organizations over six years, we provide empirical evidence to support our arguments. Implications for theory and practice are discussed.
Metaplastic conditions of the bladder
Authors: Clouston David , Lawrentschuk Nathan 
Published: October 2013

What's known on the subject? and What does the study add?
Urologists are often confronted with cystoscopic appearances that at times are abnormal but non‐specific, may mimic urothelial carcinoma or in some instances are quite bizarre given the clinical scenarios in which they occur (e.g. changes associated with a catheter will be more obvious than a de‐novo presentation of cystitis cystica). Metaplasias of the bladder urothelium make up the majority of such cases. Furthermore, when confronted with a pathological diagnosis of a metaplasia within the bladder‐ what are the implications for the patient and how should they be followed‐up?
This review provides a concise summary of the pathological features of the various metaplasias that occur in the bladder and briefly describes their current treatment and requirement for follow‐up.
Metaplasia of the bladder urothelium occurs commonly in response to local injury. Usually the changes are reversible, but some conditions may be premalignant. This review describes the different metaplastic entities and their clinical significance. Most importantly, keratinising squamous metaplasia is a precursor to the development of bladder cancer, and requires treatment and long term follow up. The role of intestinal metaplasia in the development of cancer is uncertain, and these patients require follow‐up until further evidence is obtained on the outcome of this entity.
The role of magnetic resonance imaging in the diagnosis and management of prostate cancer
Authors: Thompson James , Lawrentschuk Nathan , Frydenberg Mark , Thompson Les , Stricker Phillip ,   USANZ
Published: October 2013

Background
The diagnosis of prostate cancer has long been plagued by the absence of an imaging tool that reliably detects and localises significant tumours. Recent evidence suggests that multi‐parametric MRI could improve the accuracy of diagnostic assessment in prostate cancer. This review serves as a background to a recent USANZ position statement. It aims to provide an overview of MRI techniques and to critically review the published literature on the clinical application of MRI in prostate cancer.
Technical Aspects
The combination of anatomical (T2‐weighted) MRI with at least two of the three functional MRI parameters – which include diffusion‐weighted imaging, dynamic contrast‐enhanced imaging and spectroscopy – will detect greater than 90% of significant (moderate to high risk) tumours; however MRI is less reliable at detecting tumours that are small (<0.5 cc), low grade (Gleason score 6) or in the transitional zone. The higher anatomical resolution provided by 3‐Tesla magnets and endorectal coils may improve the accuracy, particularly in primary tumour staging.
Screening
The use of mpMRI to determine which men with an elevated PSA should undergo biopsy is currently the subject of two large clinical trials in Australia. MRI should be used with caution in this setting and then only in centres with established uro‐radiological expertise and quality control mechanisms in place. There is sufficient evidence to justify using MRI to determine the need for repeat biopsy and to guide areas in which to focus repeat biopsy.
Image‐Directed Biopsy
MRI‐directed biopsy is an exciting concept supported by promising early results, but none of the three proposed techniques have so far been proven superior to standard biopsy protocols. Further evidence of superior accuracy and core‐efficiency over standard biopsy is required, before their costs and complexities in use can be justified.
Treatment Selection and Planning
When used for primary‐tumour staging (T‐staging), MRI has limited sensitivity for T3 disease, but its specificity of greater than 95% may be useful in men with intermediate‐high risk disease to identify those with advanced T3 disease not suitable for nerve sparing or for surgery at all. MRI appears to be of value in planning dosimetry in men undergoing radiotherapy, and in guiding selection for and monitoring on active surveillance.
Changes in upper urinary tract stone composition in Australia over the past 30 years
Authors: Lee Ming‐Chak , Bariol Simon Virgil 
Published: October 2013

Objectives
To investigate upper urinary tract stone composition rates in Australia
To investigate changes in stone composition in Australia over the past 30 years
Patients and Methods
The Institute for Clinical Pathology and Medical Research (ICPMR) database was used to obtain – stone composition statistics from 2009–2011
Historical comparisons of stone composition rates were obtained from previous Australian studies; Rofe; 1981, and Baker; 1993 for epidemiological data from the 1970s and 1980s respectively.
Stone composition data was separated into gender and age‐groups
Results
From the 791 stones analysed between 2009 and 2011, calcium oxalate remains the dominant type accounting for 64% of stones in our dataset, which compares to 68% from both the 1970s and 1980s.
Uric acid stones contributed 16% of contemporary stone compositions, comparable to 16% in the 1970s and 17% in the 1980s.
Struvite stones showed a decreasing trend from 14% in the 1970s, to 12% in the 1980s and 7% in the current data.
For struvite stones, while the female 21–30 age‐group was the most prolific for struvite stone formation in the 1980s, the peak group in contemporaneous records is 61–70 year‐old men.
Conclusion
Stone composition in Australia has remained relatively static over the past 30 years. Modifications in diet and body habitus have not resulted in significant changes in the proportion of uric acid and calcium oxalate stones detected.
The decreasing trend in the proportion of struvite stones most likely reflects improved management of urinary tract infections within the Australian population.
USANZ: Time‐trends in use and impact on outcomes of perioperative chemotherapy in patients treated with radical cystectomy for urothelial bladder cancer
Authors: Liew Mun Sem , Azad Arun , Tafreshi Ali , Eapen Renu , Bolton Damien , Davis Ian D. , Sengupta Shomik 
Published: October 2013

Objective
To review time‐trends in the use of perioperative chemotherapy and its impact on oncological outcomes in patients with bladder urothelial cancer (UC) at a single tertiary institution.
Patients and Methods
Using electronic and paper medical records, 89 patients were identified who underwent radical cystectomy with or without perioperative chemotherapy between 2004 and 2011 at Austin Health in Melbourne, Australia.
Patient demographics, clinico‐pathological characteristics and details of recurrence and death were assessed by retrospective chart review.
Survival analysis was carried out using the Kaplan Meier method, with the impact of predictors assessed using Cox proportional hazard models.
Results
The median (range) age of this cohort was 65 (37–84) years, and 66 (74%) patients were male. Pathologic features included 68 (76%) pure UC, 21 (24%) mixed UC and 84 (94%) high grade tumours.
On clinical staging, 63 (71%) patients had muscle‐invasive bladder cancer (cT‐stage ≥T2), of whom 11 (17%) received neoadjuvant chemotherapy, with an increasing trend in use over time.
Following radical cystectomy, pT‐stage ≥T3 and/or node positive were identified in 35 (39%) patients, of whom 16 (46%) received adjuvant chemotherapy. In addition, five patients with stage pT2 received adjuvant chemotherapy.
Of the total cohort of patients, 31 (35%) suffered recurrences, and 33 died, 27 from urothelial carcinoma.
On multivariate analysis, after adjusting for age, pT‐stage and pN‐stage, perioperative chemotherapy was associated with a significantly lower risk of recurrence [relative risk (RR) 0.41, p < 0.05], but not death from cancer or all causes.
Conclusions
Perioperative chemotherapy, and in particular neoadjuvant chemotherapy, remains relatively under‐utilised at our institution despite recent increases.
The significant reduction in the risk of recurrence following treatment with perioperative chemotherapy with radical cystectomy highlights the importance of multi‐modality treatment in bladder UC.
Identifying barriers to more widespread implementation of perioperative chemotherapy is critical for enhancing outcomes in patients with bladder UC.