bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing
Authors: Xie Wan-Ying , Su Jian-Qiang , Zhu Yong-Guan 
Published: November 2014

ABSTRACT

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took
Wolffia australiana
as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of
W. australiana
harbored considerably rich communities of bacteria, with
Proteobacteria
and
Bacteroidetes
as the predominant phyla. The core microbiome in the phyllosphere contained genera such as
Acidovorax
,
Asticcacaulis
,
Methylibium
, and
Methylophilus
. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.
rpoS
-Regulated Core Genes Involved in the Competitive Fitness of Salmonella enterica Serovar Kentucky in the Intestines of Chickens
Authors: Cheng Ying , Pedroso Adriana Ayres , Porwollik Steffen , McClelland Michael , Lee Margie D. , Kwan Tiffany , Zamperini Katherine , Soni Vivek , Sellers Holly S. , Russell Scott M. , Maurer John J. 
Published: November 2014

ABSTRACT

Salmonella enterica
serovar Kentucky has become the most frequently isolated serovar from poultry in the United States over the past decade. Despite its prevalence in poultry, it causes few human illnesses in the United States. The dominance of
S
. Kentucky in poultry does not appear to be due to single introduction of a clonal strain, and its reduced virulence appears to correlate with the absence of virulence genes
grvA
,
sseI
,
sopE
, and
sodC1. S
. Kentucky's prevalence in poultry is possibly attributable to its metabolic adaptation to the chicken cecum. While there were no difference in the growth rate of
S
. Kentucky and
S
. Typhimurium grown microaerophilically in cecal contents,
S
. Kentucky persisted longer when chickens were coinfected with
S
. Typhimurium. The
in vivo
advantage that
S
. Kentucky has over
S
. Typhimurium appears to be due to differential regulation of core
Salmonella
genes via the stationary-phase sigma factor
rpoS
. Microarray analysis of
Salmonella
grown in cecal contents
in vitro
identified several metabolic genes and motility and adherence genes that are differentially activated in
S
. Kentucky. The contributions of four of these operons (
mgl
,
prp
,
nar
, and
csg
) to
Salmonella
colonization in chickens were assessed. Deletion of
mgl
and
csg
reduced
S
. Kentucky persistence in competition studies in chickens infected with wild-type or mutant strains. Subtle mutations affecting differential regulation of core
Salmonella
genes appear to be important in
Salmonella
's adaptation to its animal host and especially for
S
. Kentucky's emergence as the dominant serovar in poultry.
The Cullin-4 Complex DCDC Does Not Require E3 Ubiquitin Ligase Elements To Control Heterochromatin in Neurospora crassa
Authors: Adhvaryu Keyur K. , Gessaman Jordan D. , Honda Shinji , Lewis Zachary A. , Grisafi Paula L. , Selker Eric U. 
Published: November 2014

ABSTRACT

The cullin-4 (CUL4) complex DCDC (
D
IM-5/-7/-9/
C
UL4/
D
DB1
c
omplex) is essential for DNA methylation and heterochromatin formation in
Neurospora crassa
. Cullins form the scaffold of cullin-RING E3 ubiquitin ligases (CRLs) and are modified by the covalent attachment of NEDD8, a ubiquitin-like protein that regulates the stability and activity of CRLs. We report that neddylation is not required for CUL4-dependent DNA methylation or heterochromatin formation but is required for the DNA repair functions. Moreover, the RING domain protein RBX1 and a segment of the CUL4 C terminus that normally interacts with RBX1, the E2 ligase, CAND1, and CSN are dispensable for DNA methylation and heterochromatin formation by DCDC. Our study provides evidence for the noncanonical functions of core CRL components.
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing
Authors: Pang Chao , Hendriksen Dennis , Dijkstra Martijn , van der Velde K Joeri , Kuiper Joel , Hillege Hans L , Swertz Morris A 
Published: November 2014

Abstract
Objective Pooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However, searching for desired data elements among the thousands of available elements and harmonizing differences in terminology, data collection, and structure, is arduous and time consuming.
Materials and methods To speed up biobank data pooling we developed BiobankConnect, a system to semi-automatically match desired data elements to available elements by: (1) annotating the desired elements with ontology terms using BioPortal; (2) automatically expanding the query for these elements with synonyms and subclass information using OntoCAT; (3) automatically searching available elements for these expanded terms using Lucene lexical matching; and (4) shortlisting relevant matches sorted by matching score.
Results We evaluated BiobankConnect using human curated matches from EU-BioSHaRE, searching for 32 desired data elements in 7461 available elements from six biobanks. We found 0.75 precision at rank 1 and 0.74 recall at rank 10 compared to a manually curated set of relevant matches. In addition, best matches chosen by BioSHaRE experts ranked first in 63.0% and in the top 10 in 98.4% of cases, indicating that our system has the potential to significantly reduce manual matching work.
Conclusions BiobankConnect provides an easy user interface to significantly speed up the biobank harmonization process. It may also prove useful for other forms of biomedical data integration. All the software can be downloaded as a MOLGENIS open source app from http://www.github.com/molgenis, with a demo available at http://www.biobankconnect.org.
American Medical Society for Sports Medicine recommended sports ultrasound curriculum for sports medicine fellowships
Authors: Finnoff Jonathan T , Berkoff David , Brennan Fred , DiFiori John , Hall Mederic M , Harmon Kimberly , Lavallee Mark , Martin Sean , Smith Jay , Stovak Mark 
Published: November 2014

The American Medical Society for Sports Medicine (AMSSM) developed a musculoskeletal ultrasound curriculum for sports medicine fellowships in 2010. As the use of diagnostic and interventional ultrasound in sports medicine has evolved, it became clear that the curriculum needed to be updated. Furthermore, the name ‘musculoskeletal ultrasound’ was changed to ‘sports ultrasound’ (SPORTS US) to reflect the broad range of diagnostic and interventional applications of ultrasound in sports medicine.This document was created to outline the core competencies of SPORTS US and to provide sports medicine fellowship directors and others interested in SPORTS US education with a guide to create a SPORTS US curriculum. By completing this SPORTS US curriculum, sports medicine fellows and physicians can attain proficiency in the core competencies of SPORTS US required for the practice of sports medicine.
Results from a dietary survey in an Indian T2DM population: a STARCH study
Authors: Joshi Shashank R , Bhansali Anil , Bajaj Sarita , Banzal Subodh S , Dharmalingam Mala , Gupta Shachin , Mukhopadhyay Satinath , Shah Parag R , Sahay Rakesh , Sarkar Swapan , Manjrekar Pravin V , Rathod Rahul T , Joshi Shilpa S 
Published: November 2014

ObjectiveTo assess the dietary total and complex carbohydrate (CHO) contents in type-2 diabetes mellitus (T2DM) participants in India.SettingWe enrolled 796 participants in this cross-sectional, single-visit, multicentre, two-arm, single-country survey. Participants were enrolled from 10 specialty endocrinology/dialectology centres from five regions of India.ParticipantsA total of 796 participants (Asian) were enrolled in this study (385, T2DM and 409, non-T2DM). Key inclusion criteria—male or female ≥18 years, diagnosed with T2DM ≥12 months (T2DM), and not on any diet plan (non-T2DM).Study outcomePrimary outcome was to find out the percentage of total energy intake as simple and complex CHO from total CHO. Secondary outcomes were to find the differences in percentage of total energy intake as simple CHO, complex CHO, proteins and fats between T2DM and non-T2DM groups. The percentage of T2DM participants adhering to diet plan and showing glycaemic controls were also examined.ResultsThe mean (SD) of total calorie intake per day (Kcal) was 1547 (610, 95% CI 1486 to 1608) and 2132 (1892, 95% CI 1948 to 2316), respectively, for T2DM and non-T2DM groups. In the T2DM group (n=385), the mean (SD) percentage of total energy intake as total CHO, complex CHO and simple CHO was 64.1±8.3 (95% CI 63.3 to 64.9), 57.0±11.0 (95% CI 55.9 to 58.1) and 7.1±10.8 (95% CI 6.0 to 8.2), respectively. The mean (SD) percentage of complex CHO intake from total CHO was 89.5±15.3 (95% CI 88.0 to 91.1). The mean (SD) total protein/fat intake per day (g) was 57.1 (74.0)/37.2 (18.6) and 57.9 (27.2)/55.3 (98.2) in T2DM and non-T2DM groups, respectively.ConclusionsOur study shows that CHO constitutes 64.1% of total energy from diet in T2DM participants, higher than that recommended in India. However, our findings need to be confirmed in a larger epidemiological survey.Trial registration numberNCT01450592 & Clinical Trial Registry of India: CTRI/2012/02/002398.
Individualising dual antiplatelet therapy after percutaneous coronary intervention: the IDEAL-PCI registry
Authors: Christ Günter , Siller-Matula Jolanta M , Francesconi Marcel , Dechant Cornelia , Grohs Katharina , Podczeck-Schweighofer Andrea 
Published: November 2014

ObjectiveTo evaluate the clinical utility of individualising dual antiplatelet therapy (DAPT) after percutaneous coronary intervention (PCI) in an all-comers population, including ST-elevation myocardial infarction (STEMI) patients.SettingTertiary care single centre registry.Participants1008 consecutive PCI patients with stent implantation, without exclusion criteria.InterventionPeri-interventional individualisation of DAPT, guided by multiple electrode aggregometry (MEA), to overcome high on-treatment platelet reactivity (HPR) to ADP-induced (≥50 U) and arachidonic acid (AA)-induced aggregation (>35 U).Outcome measuresThe primary efficacy end point was definite stent thrombosis (ST) at 30 days. The primary safety end point was thrombolysis in myocardial infarction (TIMI) major and minor bleeding. Secondary end points were probable ST, myocardial infarction, cardiovascular death and the combined end point: major cardiac adverse event (MACE).Results53% of patients presented with acute coronary syndrome (9% STEMI, 44% non-ST-elevation). HPR to ADP after 600 mg clopidogrel loading occurred in 30% of patients (73±19 U vs 28±11 U; p<0.001) and was treated by prasugrel or ticagrelor (73%), or clopidogrel (27%) reloading (22±12 U; p<0.001). HPR to ADP after prasugrel loading occurred in 2% of patients (82±26 U vs 19±10 U; p<0.001) and was treated with ticagrelor (34±15 U; p=0.02). HPR to AA occurred in 9% of patients with a significant higher proportion in patients with HPR to ADP (22% vs 4%, p<0.001) and was treated with aspirin reloading. Definite ST occurred in 0.09% of patients (n=1); probable ST, myocardial infarction, cardiovascular death and MACE occurred in 0.19% (n=2), 0.09% (n=1) and 1.8% (n=18) of patients. TIMI major and minor bleeding did not differ between patients without HPR and individualised patients (2.6% for both).ConclusionsIndividualisation of DAPT with MEA minimises early thrombotic events in an all-comers PCI population to an unreported degree without increasing bleeding. A randomised multicentre trial utilising MEA seems warranted.Trial registration numberhttp://www.clinicaltrials.gov;NCT01515345.
Evaluating Midwifery Units (EMU): a prospective cohort study of freestanding midwifery units in New South Wales, Australia
Authors: Monk Amy , Tracy Mark , Foureur Maralyn , Grigg Celia , Tracy Sally 
Published: November 2014

ObjectiveTo compare maternal and neonatal birth outcomes and morbidities associated with the intention to give birth in two freestanding midwifery units and two tertiary-level maternity units in New South Wales, Australia.DesignProspective cohort study.Participants494 women who intended to give birth at freestanding midwifery units and 3157 women who intended to give birth at tertiary-level maternity units. Participants had low risk, singleton pregnancies and were at less than 28+0weeks gestation at the time of booking.Primary and secondary outcome measuresPrimary outcomes were mode of birth, Apgar score of less than 7 at 5 min and admission to the neonatal intensive care unit or special care nursery. Secondary outcomes were onset of labour, analgesia, blood loss, management of third stage of labour, perineal trauma, transfer, neonatal resuscitation, breastfeeding, gestational age at birth, birth weight, severe morbidity and mortality.ResultsWomen who planned to give birth at a freestanding midwifery unit were significantly more likely to have a spontaneous vaginal birth (AOR 1.57; 95% CI 1.20 to 2.06) and significantly less likely to have a caesarean section (AOR 0.65; 95% CI 0.48 to 0.88). There was no significant difference in the AOR of 5 min Apgar scores, however, babies from the freestanding midwifery unit group were significantly less likely to be admitted to neonatal intensive care or special care nursery (AOR 0.60; 95% CI 0.39 to 0.91). Analysis of secondary outcomes indicated that planning to give birth in a freestanding midwifery unit was associated with similar or reduced odds of intrapartum interventions and similar or improved odds of indicators of neonatal well-being.ConclusionsThe results of this study support the provision of care in freestanding midwifery units as an alternative to tertiary-level maternity units for women with low risk pregnancies at the time of booking.
Computerised cognitive behaviour therapy for depression in adolescents: study protocol for a feasibility randomised controlled trial
Authors: Wright Barry , Tindall Lucy , Littlewood Elizabeth , Adamson Joy , Allgar Victoria , Bennett Sophie , Gilbody Simon , Verduyn Chrissie , Alderson-Day Ben , Dyson Lisa , Trépel Dominic , Ali Shehzad 
Published: November 2014

IntroductionThe 1 year prevalence of depression in adolescents is about 2%. Treatment with antidepressant medication is not recommended for initial treatment in young people due to concerns over high side effects, poor efficacy and addictive potential. Evidence suggests that cognitive behaviour therapy (CBT) is an effective treatment for depression and is currently one of the main treatment options recommended in adolescents. Given the affinity young people have with information technology they may be treated effectively, more widely and earlier in their illness evolution using computer-administered CBT (CCBT). Currently little is known about the clinical and resource implications of implementing CCBT within the National Health Service for adolescents with low mood/depression. We aim to establish the feasibility of running a fully powered randomised controlled trial (RCT).Methods and analysisAdolescents aged 12–18 with low mood/depression, (scoring ≥20 on the Mood and Feelings Questionnaire (MFQ)), will be approached to participate. Consenting participants will be randomised to either a CCBT programme (Stressbusters) or accessing selected websites providing information about low mood/depression. The primary outcome measure will be the Beck Depression Inventory (BDI). Participants will also complete generic health measures (EQ5D-Y, HUI2) and resource use questionnaires to examine the feasibility of cost-effectiveness analysis. Questionnaires will be completed at baseline, 4 and 12-month follow-ups. Progress and risk will be monitored via the MFQ administered at each treatment session. The acceptability of a CCBT programme to adolescents; and the willingness of clinicians to recruit participants and of participants to be randomised, recruitment rates, attrition rates and questionnaire completion rates will be collected for feasibility analysis. We will estimate ‘numbers needed’ to plan a fully powered RCT of clinical and cost-effectiveness.Ethics and disseminationThe current trial protocol received a favourable ethical opinion from Leeds (West) Research and Ethics Committee. (Reference: 10/H1307/137).Trial registration numberISRCTN31219579.
Abdominal ultrasound features and reference values in 21 healthy rabbits
Authors: Banzato T. , Bellini L. , Contiero B. , Selleri P. , Zotti A. 
Published: November 2014

This study aimed to determine the ultrasonographic features and reference values of the abdominal anatomy in mixed‐breed dwarf rabbits. Complete abdominal ultrasonographic examination was performed in 21 mixed‐breed rabbits (12 males and 9 females) referred for examination to the Department of Animal Medicine, Production and Health, University of Padua, Italy. All animals were sedated during the procedure. The ultrasonographic anatomy of the abdomen was determined, including measurement (mean±SD) of the right kidney (length 2.87±0.34 mm; width 1.62±0.17 mm; height 1.66±0.14 mm) and left kidney (length 2.86±0.33 mm; width 1.72±0.19; height 1.58±0.15 mm), left adrenal gland (width 0.38±0.11 mm; length 0.71±0.14), right adrenal gland (width 0.34±0.08 mm; length 0.73±0.15 mm) and thickness of the walls of the stomach (0.10±0.01 mm), pylorus (0.28±0.04 mm), duodenum (0.19±0.04 mm), sacculus rotundus (0.22±0.06 mm), caecum (0.08±0.01 mm), appendix (0.19±0.04 mm), spiral loop of the ascending colon (0.14±0.04 mm) and distal colon (0.10±0.02 mm). A significant positive correlation between bodyweight and kidney size, adrenal gland length, stomach wall and sacculus rotundus wall was detected.
Mutant KRAS–Induced Expression of ICAM-1 in Pancreatic Acinar Cells Causes Attraction of Macrophages to Expedite the Formation of Precancerous Lesions
Authors: Liou Geou-Yarh , Döppler Heike , Necela Brian , Edenfield Brandy , Zhang Lizhi , Dawson David W. , Storz Peter 
Published: November 2014

AbstractDesmoplasia and an inflammatory environment are defining features of pancreatic cancer. Unclear is how pancreatic cells that undergo oncogenic transformation can cross-talk with immune cells and how this contributes to the development of pancreatic lesions. Here, we demonstrate that pancreatic acinar cells expressing mutant KRAS can expedite their transformation to a duct-like phenotype by inducing local inflammation. Specifically, we show that KRASG12D induces the expression of intercellular adhesion molecule-1 (ICAM-1), which serves as chemoattractant for macrophages. Infiltrating macrophages amplify the formation of KRASG12D-caused abnormal pancreatic structures by remodeling the extracellular matrix and providing cytokines such as TNF. Depletion of macrophages or treatment with a neutralizing antibody for ICAM-1 in mice expressing oncogenic Kras under an acinar cell–specific promoter resulted in both a decreased formation of abnormal structures and decreased progression of acinar-to-ductal metaplasia to pancreatic intraepithelial neoplastic lesions.Significance: We here show that oncogenic KRAS in pancreatic acinar cells upregulates the expression of ICAM-1 to attract macrophages. Hence, our results reveal a direct cooperative mechanism between oncogenic Kras mutations and the inflammatory environment to drive the initiation of pancreatic cancer. Cancer Discov; 5(1); 52–63. ©2014 AACR.This article is highlighted in the In This Issue feature, p. 1
Familial Clustering of Mitral Valve Prolapse in the Community
Authors: Delling Francesca N. , Rong Jian , Larson Martin G. , Lehman Birgitta , Osypiuk Ewa , Stantchev Plamen , Slaugenhaupt Susan A. , Benjamin Emelia J. , Levine Robert A. , Vasan Ramachandran S. 
Published: November 2014

Background—
Knowledge of mitral valve prolapse (MVP) inheritance is based on pedigree observation and M-mode echocardiography. The extent of familial clustering of MVP among unselected individuals in the community using current, more specific echocardiographic criteria is unknown. In addition, the importance of nondiagnostic MVP morphologies (NDMs; first described in large pedigrees) has not been investigated in the general population. We hypothesized that parental MVP and NDMs increase the risk of offspring MVP.

Methods and Results—

Study participants were 3679 Generation 3 individuals with available parental data in the Offspring or the New Offspring Spouse cohorts. MVP and NDMs were distinguished by leaflet displacement >2 versus ≤2 mm beyond the mitral annulus, respectively. We compared MVP prevalence in Generation 3 participants with at least 1 parent with MVP (n=186) with that in individuals without parental MVP (n=3493). Among 3679 participants (53% women; mean age, 40±9 years), 49 (1%) had MVP. Parental MVP was associated with a higher prevalence of MVP in Generation 3 participants (10 of 186, 5.4%) compared with no parental MVP (39 of 3493, 1.1%; adjusted odds ratio, 4.51; 95% confidence interval, 2.13–9.54;
P
<0.0001). When parental NDMs were examined alone, the prevalence of Generation 3 MVP remained higher (12 of 484, 2.5%) compared with those without parental MVP or NDMs (27 of 3009, 0.9%; adjusted odds ratio, 2.52; 95% confidence interval, 1.25–5.10;
P
=0.01).

Conclusions—
Parental MVP and NDMs are associated with increased prevalence of offspring MVP, highlighting the genetic substrate of MVP and the potential clinical significance of NDMs in the community.
Temporal artery biopsies: do they make the cut?
Authors: McMurran AEL , Boom SJ 
Published: November 2014

Background and Aims Temporal artery biopsy is the gold standard investigation for giant cell arteritis. Guidelines recommend that specimens should measure no less than 1 cm and ideally more than 2 cm in length, as this influences the likelihood of biopsy positivity. This audit investigates the extent to which temporal artery biopsies acquired in our hospital meet these guidelines. Methods Histopathology reports for all temporal artery biopsies performed at University Hospital Ayr between January 2011 and June 2013 were examined. Results Fifty-six temporal artery biopsy specimens showed a range in length from 0.5 cm to 3.1 cm, with a mean of 1.4 cm. Thirty-seven biopsies measured ≥1 cm (66%) and 13 were ≥2 cm (23%). Therefore, 19 samples (34%) did not meet the recommended standard. Just seven biopsies showed features of giant cell arteritis, with six of these measuring ≥1 cm in length (86%). Conclusion The guidelines for temporal artery specimens are not being met at our centre. Furthermore, biopsies measuring ≥1 cm are much more common in the small group of positive results. This validates the minimum recommended biopsy length and displays the importance of achieving this standard. We suggest changes to increase the number of biopsies meeting these guidelines, improving the accuracy of this invasive test.