bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical presentation, endoscopic features, treatment and prognosis of synchronous upper gastrointestinal malignancies
Authors: BAI Yu , ZOU Duo Wu , LI Zhao Shen 
Published: October 2011

OBJECTIVE:  To study the clinical presentation, endoscopic features and prognosis of patients with synchronous upper gastrointestinal (GI) cancers.METHODS:  A prospective database review of consecutive patients with synchronous upper GI malignancies was performed in a tertiary university hospital endoscopy unit. Gender, age, symptoms and cancer sites, endoscopic and pathological findings, as well as the long‐term survival of these patients were analyzed.RESULTS:  A total of 64 patients with a median age of 56 years were included, in which 81.3% were male, 71.9% presented with notable features, 68.8% had familial history of cancer, 56.3% of gastric cancers were at the gastric body, 92.9% of the duodenal malignancies at the duodenal bulb, all esophageal cancers at the middle and lower part of esophagus and a significant proportion of tumors in the synchronous malignancies group were poorly differentiated. In all patients, 20 underwent curative surgical treatment and the 5‐year survival rate was only 20%.CONCLUSIONS:  Patients with synchronous upper GI cancers are mainly male and present with different anatomic distribution and endoscopic features. They carry a poor prognosis as compared with single primary cancer patients. This case series describes the clinical profiles and emphasizes the necessity of a thorough examination for additional cancers before treatment of upper GI cancer.
Down in the flood? How moth communities are shaped in temperate floodplain forests
Authors: TRUXA CHRISTINE , FIEDLER KONRAD 
Published: October 2011

Abstract.  1. We investigated moth communities in relation to flood regime across three riparian regions in lowland eastern Austria. Moths sampled with light traps were segregated into resident and stray species. Resident moths were further partitioned into arboreal and ground‐layer species based on their larval habitat.2. Regional differences in species diversity and species composition were far stronger than local differences related to flood regime.3. Stray species (17% of all species and 6% of all individuals sampled) as well as uniques had only negligible influence on diversity and species composition patterns. The single most abundant species turned out to be more problematic for diversity comparisons across regions and habitats than the many rare species and strays.4. Overall moth diversity and ground‐layer moth diversity were generally not reduced in flooded habitats relative to non‐flooded habitats, and diversity of arboreal moths did not show significant differences between flood regimes.5. Differences between habitats in their ground‐layer vegetation appear to be more important for floodplain forest moth diversity than variation in woody vegetation with its associated arboreal moth fauna.6. Patterns in species composition were largely governed by ubiquitous forest species and not by floodplain or wetland habitat specialists. Eighteen of the 44 commonest species were more abundant in flooded habitats, and only 10 of them were more frequent in non‐flooded habitats.7. Our results revealed no general negative impact of flooding on the diversity and species composition of one rich group of terrestrial herbivorous insects.
Comparison and assessment of semi‐automatic image segmentation in computed tomography scans for image‐guided kidney surgery
Authors: Glisson Courtenay L. , Altamar Hernan O. , Herrell S. Duke , Clark Peter , Galloway Robert L. 
Published: October 2011

Purpose:Image segmentation is integral to implementing intraoperative guidance for kidney tumor resection. Results seen in computed tomography (CT) data are affected by target organ physiology as well as by the segmentation algorithm used. This work studies variables involved in using level set methods found in the Insight Toolkit to segment kidneys from CT scans and applies the results to an image guidance setting.Methods:A composite algorithm drawing on the strengths of multiple level set approaches was built using the Insight Toolkit. This algorithm requires image contrast state and seed points to be identified as input, and functions independently thereafter, selecting and altering method and variable choice as needed.Results:Semi‐automatic results were compared to expert hand segmentation results directly and by the use of the resultant surfaces for registration of intraoperative data. Direct comparison using the Dice metric showed average agreement of 0.93 between semi‐automatic and hand segmentation results. Use of the segmented surfaces in closest point registration of intraoperative laser range scan data yielded average closest point distances of approximately 1 mm. Application of both inverse registration transforms from the previous step to all hand segmented image space points revealed that the distance variability introduced by registering to the semi‐automatically segmented surface versus the hand segmented surface was typically less than 3 mm both near the tumor target and at distal points, including subsurface points.Conclusions:Use of the algorithm shortened user interaction time and provided results which were comparable to the gold standard of hand segmentation. Further, the use of the algorithm's resultant surfaces in image registration provided comparable transformations to surfaces produced by hand segmentation. These data support the applicability and utility of such an algorithm as part of an image guidance workflow.
Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1
Authors: Bottacini Francesca , Dal Bello Fabio , Turroni Francesca , Milani Christian , Duranti Sabrina , Foroni Elena , Viappiani Alice , Strati Francesco , Mora Diego , van Sinderen Douwe , Ventura Marco 
Published: October 2011

ABSTRACT

Bifidobacterium animalis
subsp.
lactis
BLC1 is a probiotic bacterium that is widely exploited by food industries as the active ingredient of various functional foods. Here we report the complete genome sequence of
B. animalis
subsp.
lactis
BLC1, which is expected to provide insights into the biology of this health-promoting microorganism and improve our understanding of its phylogenetic relatedness with other members of the
B. animalis
subsp.
lactis
taxon.
Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5
T
Authors: Beneduzi Anelise , Campos Samanta , Ambrosini Adriana , de Souza Rocheli , Granada Camille , Costa Pedro , Arruda Letícia , Moreira Fernanda , Vargas Luciano K. , Weiss Vinícius , Tieppo Eduardo , Faoro Helisson , de Souza Emanuel M. , Pedrosa Fábio O. , Passaglia Luciane M. P. 
Published: October 2011

ABSTRACT

Paenibacillus riograndensis
SBR5
T
, a nitrogen-fixing Gram-positive rhizobacterium isolated from a wheat field in the south of Brazil, has a great potential for agricultural applications due to its plant growth promotion effects. Here we present the draft genome sequence of
P. riograndensis
SBR5
T
. Its 7.37-Mb genome encodes determinants of the diazotrophic lifestyle and plant growth promotion, such as nitrogen fixation, antibiotic resistance, nitrate utilization, and iron uptake.
Complete Genome Sequence of the Denitrifying and N
2
O-Reducing Bacterium Pseudogulbenkiania sp. Strain NH8B
Authors: Ishii Satoshi , Tago Kanako , Nishizawa Tomoyasu , Oshima Kenshiro , Hattori Masahira , Senoo Keishi 
Published: October 2011

ABSTRACT

Pseudogulbenkiania
sp. strain NH8B is a
Neisseriales
bacterium isolated from an agricultural field. This strain has strong denitrification and N
2
O reduction activities. Here, we report the finished and annotated genome sequence of this organism.
Genome Sequence of Lentibacillus jeotgali Grbi
T
, Isolated from Traditional Korean Salt-Fermented Seafood
Authors: Jung Mi-Ja , Roh Seong Woon , Kim Min-Soo , Whon Tae Woong , Bae Jin-Woo 
Published: October 2011

ABSTRACT

Lentibacillus jeotgali
Grbi
T
, isolated from a traditional Korean salt-fermented seafood, is a strictly aerobic, Gram-positive, nonmotile, endospore-forming, moderately halophilic bacterium belonging to the family
Bacillaceae
in the phylum
Firmicutes
. Here, the draft genome sequence of
L. jeotgali
Grbi
T
(3,775,822 bp with a G+C content of 42.5%) is reported. This is the first reported genome sequence from a
Lentibacillus
species.
Genome Sequence of the Thermophilic Strain Bacillus coagulans XZL4, an Efficient Pentose-Utilizing Producer of Chemicals
Authors: Su Fei , Xu Ke , Zhao Bo , Tai Cui , Tao Fei , Tang Hongzhi , Xu Ping 
Published: October 2011

ABSTRACT

Bacillus coagulans
XZL4 is an efficient pentose-utilizing producer of important platform compounds, such as
l
-lactic acid, 2,3-butanediol, and acetoin. Here we present a 2.8-Mb assembly of its genome. Simple and efficient carbohydrate metabolism systems, especially the transketolase/transaldolase pathway, make it possible to convert pentose sugars to products at high levels.
Mortality from Parkinson's disease and other causes among a workforce manufacturing paraquat: a retrospective cohort study
Authors: Tomenson John Andrew , Campbell Clive 
Published: October 2011

ObjectiveTo assess the risk of Parkinson's disease (PD) and update information on mortality from major causes of death among a UK workforce who manufactured paraquat (PQ) between 1961 and 1995. There have been no previous studies of the incidence of PD among PQ production workers, although much epidemiological literature exists concerning the relationship between pesticides and PD, and interest has focused on PQ and its users.MethodsThe cohort included all employees who had ever worked on any of the four plants at Widnes where PQ was manufactured between 1961 and 1995, and 926 male and 42 female workers were followed through 30 June 2009. Mortalities for males were compared with national and local rates, including rates for PD as a mentioned cause of death.ResultsOverall, 307 workers had died by 30 June 2009. One male death was due to PD, and no other death certificate mentioned PD. At least 3.3 death certificates of male employees would have been expected to have mentioned PD (standardised mortality ratio=31; 95% CI 1 to 171). Personal monitoring results were indicative that the exposure of a PQ production worker on a daily basis was at least comparable with that of a PQ sprayer or mixer/loader. Reduced mortalities compared with local rates were found for major causes of death.ConclusionsThe study provided no evidence of an increased risk of PD, or increased mortalities from other causes.
Characteristics of randomised trials on diseases in the digestive system registered in ClinicalTrials.gov: a retrospective analysis
Authors: Wildt Signe , Krag Aleksander , Gluud LiseLotte 
Published: October 2011

ObjectivesTo evaluate the adequacy of reporting of protocols for randomised trials on diseases of the digestive system registered inhttp://ClinicalTrials.govand the consistency between primary outcomes, secondary outcomes and sample size specified inhttp://ClinicalTrials.govand published trials.MethodsRandomised phase III trials on adult patients with gastrointestinal diseases registered before January 2009 inhttp://ClinicalTrials.govwere eligible for inclusion. Fromhttp://ClinicalTrials.govall data elements in the database required by the International Committee of Medical Journal Editors (ICMJE) member journals were extracted. The subsequent publications for registered trials were identified. For published trials, data concerning publication date, primary and secondary endpoint, sample size, and whether the journal adhered to ICMJE principles were extracted. Differences between primary and secondary outcomes, sample size and sample size calculations data inhttp://ClinicalTrials.govand in the published paper were registered.Results105 trials were evaluated. 66 trials (63%) were published. 30% of trials were registered incorrectly after their completion date. Several data elements of the required ICMJE data list were not filled in, with missing data in 22% and 11%, respectively, of cases concerning the primary outcome measure and sample size. In 26% of the published papers, data on sample size calculations were missing and discrepancies between sample size reporting inhttp://ClinicalTrials.govand published trials existed.ConclusionThe quality of registration of randomised controlled trials still needs improvement.
What determines adherence to treatment in cardiovascular disease prevention? Protocol for a mixed methods preference study: Table 1
Authors: Jan Stephen , Usherwood Tim , Brien Jo Anne , Peiris David , Rose John , Hayman Noel , Howard Kirsten , Redfern Julie , Laba Tracey , Cass Alan , Patel Anushka 
Published: October 2011

BackgroundSignificant gaps exist between guidelines-recommended therapies for cardiovascular disease prevention and current practice. Fixed-dose combination pills (‘polypills’) potentially improve adherence to therapy. This study is a preference study undertaken in conjunction with a clinical trial of a polypill and seeks to examine the underlying reasons for variations in treatment adherence to recommended therapy.Methods/designA preference study comprising: (1) Discrete Choice Experiment for patients; and (2) qualitative study of patients and providers. Both components will be conducted on participants in the trial. A joint model combining the observed adherence in the clinical trial (revealed preference) and the Discrete Choice Experiment data (stated preference) will be estimated. Estimates will be made of the marginal effect (importance) of each attribute on overall choice, the extent to which respondents are prepared to trade-off one attribute for another and predicted values of the level of adherence given a fixed set of attributes, and contextual and socio-demographic characteristics. For the qualitative study, a thematic analysis will be used as a means of exploring in depth the preferences and ultimately provide important narratives on the experiences and perspectives of individuals with regard to adherence behaviour.Ethics and disseminationPrimary ethics approval was received from Sydney South West Area Health Service Human Research Ethics Committee (Royal Prince Alfred Hospital zone). In addition to usual scientific forums, the findings will be reported back to the communities involved in the studies through site-specific reports and oral presentations.
Impact of influenza across 27 public emergency departments in Australia: a 5-year descriptive study
Authors: Boyle Justin , Crilly Julia , Keijzers Gerben , Wallis Marianne , Lind James , Sparks Ross , Ryan Louise 
Published: October 2011

ObjectiveTo describe the incidence, characteristics and outcomes of patients with influenza-like symptoms presenting to 27 public hospital emergency departments (EDs) in Queensland, Australia.MethodsA descriptive retrospective study covering 5 years (2005–9) of historical data from 27 hospital EDs was undertaken. State-wide hospital ED Information System data were analysed. Annual comparisons between influenza and non-influenza cases were made across the southern hemisphere influenza season (June–September) each year.ResultsInfluenza-related presentations increased significantly over the 5 years from 3.4% in 2005 to 9.4% in 2009, reflecting a 276% relative increase. Differences over time regarding characteristics of patients with influenza-like symptoms, based on the influenza season, occurred for admission rate (decreased over time from 28% in 2005 to 18% in 2009), length of stay (decreased over time from a median of 210 min in 2005 to 164 min in 2009) and access block (increased over time from 33% to 41%). Also, every year there was a significantly (p<0.001) higher percentage of access block in the influenza cohort than in the non-influenza cohort.ConclusionsAlthough there was a large increase over time in influenza-related ED presentations, most patients were discharged home from the ED. Special consideration of health service delivery management (eg, establishing an ‘influenza clinic border protection and public rollout of vaccination, beginning with those most at risk’) for this group of patients is warranted but requires evaluation. These results may inform planning for service delivery models during the influenza season.
Comparative performance of culture using swabs transported in Amies medium and the Aptima Combo 2 nucleic acid amplification test in detection ofNeisseria gonorrhoeaefrom genital and extra-genital sites: a retrospective study: Table 1
Authors: Harryman Lindsey , Scofield Sara , Macleod John , Carrington David , Williams O Martin , Fernandes Arnold , Horner Paddy 
Published: October 2011

BackgroundNucleic acid amplification tests are being increasingly used for the routine diagnosis ofNeisseria gonorrhoeae(GC), although culture remains essential for monitoring antimicrobial resistance. The authors investigated how symptoms and infection site influenced test sensitivity.MethodsThis was a retrospective study at two centres of patients diagnosed as having GC by Aptima Combo 2 (AC2) confirmed with Aptima GC and/or culture.ResultsThe study included 251 men (71%) and 105 women (29%). The sensitivity for AC2 and culture in the lower genital tract of men with symptoms was 99% (95% CI 95% to 100%) and 79% (95% CI 71% to 85%) and for asymptomatic men was 94% (95% CI 69% to 100%) and 29% (95% CI 11% to 56%), respectively. At the rectum, the sensitivity in symptomatic men was 91% (95% CI 57% to 100%) and 55% (95% CI 25% to 82%) and in asymptomatic men 75% (95% CI 47% to 92%) and 44% (95% CI 21% to 69%) for AC2 and culture, respectively. In symptomatic women, the sensitivity from the genital site was 100% (95% CI 95% to 100%) and 53% (95% CI 38% to 68%) and for asymptomatic women 100% (95% CI 87% to 100%) and 47% (95% CI 30% to 65%) for AC2 and culture, respectively.ConclusionsThe AC2 with AGC confirmation performs well at genital and extra-genital sites for detecting GC. Culture for GC using transport swabs performs poorly in asymptomatic men, symptomatic and asymptomatic women and at extra-genital sites. With the improved performance of nucleic acid amplification tests and the increase in GC antimicrobial resistance, research is needed into how best to optimise GC culture in settings where direct plating is not feasible.
Aryl Hydrocarbon Receptor Agonists Induce MicroRNA-335 Expression and Inhibit Lung Metastasis of Estrogen Receptor Negative Breast Cancer Cells
Authors: Zhang Shu , Kim KyoungHyun , Jin Un Ho , Pfent Catherine , Cao Huojun , Amendt Brad , Liu Xinyi , Wilson-Robles Heather , Safe Stephen 
Published: October 2011

Abstract
The aryl hydrocarbon receptor (AHR) was initially identified as a receptor that bound 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related environmental toxicants; however, there is increasing evidence that the AHR is an important new drug target for treating multiple diseases including breast cancer. Treatment of estrogen receptor (ER)-negative MDA-MB-231 and BT474 breast cancer cells with TCDD or the selective AHR modulator 6-methyl-1,3,-trichlorodibenzofuran (MCDF) inhibited breast cancer cell invasion in a Boyden chamber assay. These results were similar to those previously reported for the antimetastic microRNA-335 (miR-335). Both TCDD and MCDF induced miR-335 in MDA-MB-231 and BT474 cells and this was accompanied by downregulation of SOX4, a miR-335-regulated (inhibited) gene. The effects of TCDD and MCDF on miR-335 and SOX4 expression and interactions of miR-335 with the 3′-UTR target sequence in the SOX4 gene were all inhibited in cells transfected with an oligonucleotide (iAHR) that knocks down the AHR, thus confirming AHR-miR-335 interactions. MCDF (40 mg/kg/d) also inhibited lung metastasis of MDA-MB-231 cells in a tail vein injection model, showing that the AHR is a potential new target for treating patients with ER-negative breast cancer, a disease where treatment options and their effectiveness are limited. Mol Cancer Ther; 11(1); 108–18. ©2011 AACR.
The Scaffolding Protein EBP50 Promotes Vascular Smooth Muscle Cell Proliferation and Neointima Formation by Regulating Skp2 and p21
cip1
Authors: Song Gyun Jee , Barrick Stacey , Leslie Kristen L. , Bauer Philip M. , Alonso Veronica , Friedman Peter A. , Fiaschi-Taesch Nathalie M. , Bisello Alessandro 
Published: October 2011

Objective—
The Ezrin-radixin–moesin–binding phosphoprotein 50 (EBP50) is a scaffolding protein known to regulate ion homeostasis in the kidney and intestine. Previous work showed that EBP50 expression increases after balloon injury in rat carotids. This study was designed to determine the role of EBP50 on vascular smooth muscle cells (VSMC) proliferation and the development of neointimal hyperplasia.

Methods and Results—

Wire injury was performed in wild type (WT) and EBP50 knockout (KO) mice. Two weeks after injury, neointima formation was 80% lower in KO than in WT mice. Proliferation of KO VSMC was significantly lower than WT cells and overexpression of EBP50 increased VSMC proliferation. Akt activity and expression of S-phase kinase protein2 decreased in KO cells resulting in the stabilization of the cyclin-dependent kinase inhibitor, p21
cip1
. Consequently, KO cells were arrested in G
0
/G
1
phase. Consistent with these observations, p21
cip1
was detected in injured femoral arteries of KO but not WT mice. No differences in apoptosis between WT and KO were observed.

Conclusion—

EBP50 is critical for neointima formation and induces VSMC proliferation by decreasing S-phase kinase protein2 stability, thereby accelerating the degradation of the cell cycle inhibitor p21
cip1
.
Aging Enhances the Basal Production of IL-6 and CCL2 in Vascular Smooth Muscle Cells
Authors: Song Yang , Shen Hua , Schenten Dominik , Shan Peiying , Lee Patty J. , Goldstein Daniel R. 
Published: October 2011

Objective—
Increased circulating cytokine levels are a prominent feature of aging that may contribute to atherosclerosis. However, the role vascular cells play in chronic inflammation induced by aging is not clear. Here, we examined the role of aging on inflammatory responses of vascular cells.

Methods and Results—

In an ex vivo culture system, we examined the inflammatory response of aortas from young (2–4 months) and aged (16–18 months) mice under nonstimulatory conditions. We found that basal levels of interleukin-6 were increased in aged aortas. Aged aortic vascular smooth muscle cells (VSMC) exhibited a higher basal secretion of interleukin-6 than young VSMC. Gene and protein expression analysis revealed that aged VSMC exhibited upregulation of chemokines (eg, CCL2), adhesion molecules (eg, intracellular adhesion molecule 1), and innate immune receptors (eg, Toll-like receptor [TLR] 4), which all contribute to atherosclerosis. Using VSMC from aged TL4
−/−
and Myd88
−/−
mice, we demonstrate that signaling via TLR4 and its signal adaptor, MyD88, are in part responsible for the age-elevated basal interleukin-6 response.

Conclusion—
Aging induces a proinflammatory phenotype in VSMC due in part to increased signaling of TLR4 and MyD88. Our results provide a potential explanation as to why aging leads to chronic inflammation and enhanced atherosclerosis.