bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles
Authors: Edwards Jessica A , Chen Chenxi , Kemski Megan M , Hu Jinnan , Mitchell Thomas K , Rappleye Chad A 
Published: October 2013

Abstract

Background
The dimorphic fungus Histoplasma capsulatum causes respiratory and systemic disease in mammalian hosts by expression of factors that enable survival within phagocytic cells of the immune system. Histoplasma’s dimorphism is distinguished by growth either as avirulent mycelia or as pathogenic yeast. Geographically distinct strains of Histoplasma differ in their relative virulence in mammalian hosts and in production of and requirement for specific virulence factors. The close similarity in the genome sequences of these diverse strains suggests that phenotypic variations result from differences in gene expression rather than gene content. To provide insight into how the transcriptional program translates into morphological variation and the pathogenic lifestyle, we compared the transcriptional profile of the pathogenic yeast phase and the non-pathogenic mycelial phase of two clinical isolates of Histoplasma.

Results
To overcome inaccuracies in ab initio genome annotation of the Histoplasma genome, we used RNA-seq methodology to generate gene structure models based on experimental evidence. Quantitative analyses of the sequencing reads revealed 6% to 9% of genes are differentially regulated between the two phases. RNA-seq-based mRNA quantitation was strongly correlated with gene expression levels determined by quantitative RT-PCR. Comparison of the yeast-phase transcriptomes between strains showed 7.6% of all genes have lineage-specific expression differences including genes contributing, or potentially related, to pathogenesis. GFP-transcriptional fusions and their introduction into both strain backgrounds revealed that the difference in transcriptional activity of individual genes reflects both variations in the cis- and trans-acting factors between Histoplasma strains.

Conclusions
Comparison of the yeast and mycelial transcriptomes highlights genes encoding virulence factors as well as those involved in protein glycosylation, alternative metabolism, lipid remodeling, and cell wall glycanases that may contribute to Histoplasma pathogenesis. These studies lay an essential foundation for understanding how gene expression variations contribute to the strain- and phase-specific virulence differences of Histoplasma.
Descending necrotizing Mediastinitis caused by Kocuria rosea: a case report
Authors: Lee Mi Kyung , Choi Soon Ho , Ryu Dae Woong 
Published: October 2013

Abstract

Background

Kocuria species are gram-positive, non-pathogenic commensals. However, in immunocompromised patients such as transplant recipients, cancer patients, or patients with chronic medical conditions, they can cause opportunistic infections.

Case presentation
We report the first case of descending necrotizing mediastinitis in a 58-year-old, relatively healthy woman caused by Kocuria rosea.

Conclusion
Descending necrotizing mediastinitis due to Kocuria rosea can be successfully treated with prompt surgical drainage combined with antimicrobial therapy.
Classification tree analysis to enhance targeting for follow-up exam of colorectal cancer screening
Authors: Ishikawa Yoshiki , Zheng Ying-Fang , Nishiuchi Hiromu , Suda Takeo , Hasumi Tadahiko , Saito Hiroshi 
Published: October 2013

Abstract

Background
Follow-up rate after a fecal occult blood test (FOBT) is low worldwide. In order to increase the follow-up rate, segmentation of the target population has been proposed as a promising strategy, because an intervention can then be tailored toward specific subgroups of the population rather than using one type of intervention for all groups. The aim of this study is to identify subgroups that share the same patterns of characteristics related to follow-up exams after FOBT.

Methods
The study sample consisted of 143 patients aged 50–69 years who were requested to undergo follow-up exams after FOBT. A classification tree analysis was performed, using the follow-up rate as a dependent variable and sociodemographic variables, psychological variables, past FOBT and follow-up exam, family history of colorectal cancer (CRC), and history of bowel disease as predictive variables.

Results
The follow-up rate in 143 participants was 74.1% (n = 106). A classification tree analysis identified four subgroups as follows; (1) subgroup with a high degree of fear of CRC, unemployed and with a history of bowel disease (n = 24, 100.0% follow-up rate), (2) subgroup with a high degree of fear of CRC, unemployed and with no history of bowel disease (n = 17, 82.4% follow-up rate), (3) subgroup with a high degree of fear of CRC and employed (n = 24, 66.7% follow-up rate), and (4) subgroup with a low degree of fear of CRC (n = 78, 66.7% follow-up rate).

Conclusion
The identification of four subgroups with a diverse range of follow-up rates for CRC screening indicates the direction to take in future development of an effective tailored intervention strategy.
Changes in use of time, activity patterns, and health and wellbeing across retirement: design and methods of the life after work study
Authors: Maher Carol A , Burton Nicola W , van Uffelen Jannique GZ , Brown Wendy J , Sprod Judy A , Olds Tim S 
Published: October 2013

Abstract

Background
Retirement is a major life transition during which people restructure everyday activities; however little is known about this. The primary aim of the Life After Work study is to comprehensively measure changes in time use and patterns of physical activity and sedentary behaviour, and its associations with health and wellbeing, across the retirement transition.

Methods/Design
A target sample of 120 participants aged 50 years and over will be recruited in two Australian state capital cities, Adelaide and Brisbane. Participants will undertake a battery of assessments approximately 3 months prior to retirement, and 3, 6 and 12 months post-retirement. Measures will include self-reported use of time (using the Multimedia Activity Recall for Children and Adults), objectively assessed physical activity and sedentary behaviour (using Actigraph GT3X+ accelerometers), self-reported health and well-being (using a battery of questionnaires including the Short-Form Health Survey (SF-36), Australian Unity Personal Well-being Index (AUPWI), Depression Anxiety Stress Scales 21 (DASS21), Short Warwick-Edinburgh Mental Well-being Scale, UCLA Loneliness Scale, Rosenberg Self-Esteem Scale), retirement circumstances and socio-demographic characteristics, objectively assessed anthropometric measures (height, weight and waist circumference), and resting blood pressure. Multivariate mixed models will be used to examine changes in use of time, health and well-being across retirement.

Discussion
The results will provide important new information that will inform the development of lifestyle and policy interventions to address and improve health and well-being in retirement.
Clinical profile of recurrent community-acquired pneumonia in children
Authors: Patria Francesca , Longhi Benedetta , Tagliabue Claudia , Tenconi Rossana , Ballista Patrizia , Ricciardi Giuseppe , Galeone Carlotta , Principi Nicola , Esposito Susanna 
Published: October 2013

AbstractBackgroundThe aim of this case–control study was to analyse the clinical characteristics of children with recurrent community-acquired pneumonia (rCAP) affecting different lung areas (DLAs) and compare them with those of children who have never experienced CAP in order to contribute to identifying the best approach to such patients.MethodsThe study involved 146 children with ≥2 episodes of radiographically confirmed CAP in DLA in a single year (or ≥3 episodes in any time frame) with radiographic clearing of densities between occurrences, and 145 age- and gender-matched controls enrolled in Milan, Italy, between January 2009 and December 2012. The demographic and clinical characteristics of the cases and controls were compared, and a comparison was also made between the cases with rCAP (i.e. ≤3 episodes) and those with highly recurrent CAP (hrCAP: i.e. >3 episodes).ResultsGestational age at birth (p = 0.003), birth weight (p = 0.006), respiratory distress at birth (p < 0.001), and age when starting day care attendance (p < 0.001) were significantly different between the cases and controls, and recurrent infectious wheezing (p < 0.001), chronic rhinosinusitis with post-nasal drip (p < 0.001), recurrent upper respiratory tract infections (p < 0.001), atopy/allergy (p < 0.001) and asthma (p < 0.001) were significantly more frequent. Significant risk factors for hrCAP were gastroesophageal reflux disease (GERD; p = 0.04), a history of atopy and/or allergy (p = 0.005), and a diagnosis of asthma (p = 0.0001) or middle lobe syndrome (p = 0.001). Multivariate logistic regression analysis, adjusted for age and gender, showed that all of the risk factors other than GERD and wheezing were associated with hrCAP.ConclusionsThe diagnostic approach to children with rCAP in DLAs is relatively easy in the developed world, where the severe chronic underlying diseases favouring rCAP are usually identified early, and patients with chronic underlying disease are diagnosed before the occurrence of rCAP in DLAs. When rCAP in DLAs does occur, an evaluation of the patients’ history and clinical findings make it possible to limit diagnostic investigations.
Water vapour is a pre-oviposition attractant for the malaria vector Anopheles gambiae sensu stricto
Authors: Okal Michael N , Francis Benjamin , Herrera-Varela Manuela , Fillinger Ulrike , Lindsay Steven W 
Published: October 2013

AbstractBackgroundTo date no semiochemicals affecting the pre-oviposition behaviour of the malaria vectorAnopheles gambiae sensu latohave been described. Water vapour must be the major chemical signal emanating from a potential larval habitat, and although one might expect that gravidAn. gambiae s.l.detect and respond to water vapour in their search for an aquatic habitat, this has never been experimentally confirmed for this species. This study aimed to investigate the role of relative humidity or water vapour as a general cue for inducing gravidAn. gambiae sensu strictoto make orientated movements towards the source.MethodsThree experiments were carried out with insectary-rearedAn. gambiae s.s.One with unfed females and two with gravid females during their peak oviposition time in the early evening. First, unfed females and gravid females were tested separately in still air where a humidity difference was established between opposite ends of a WHO bioassay tube and mosquitoes released individually in the centre of the tube. Movement of mosquitoes to either low or high humidity was recorded. Additionally, gravid mosquitoes were released into a larger air-flow olfactometer and responses measured towards collection chambers that contained cups filled with water or empty cups.ResultsUnfed females equally dispersed in the small bioassay tubes to areas of high and low humidity (mean 50% (95% confidence interval (CI) 38-62%). In contrast, gravid females were 2.4 times (95% CI 1.3-4.7) more likely to move towards high humidity than unfed females. The results were even more pronounced in the airflow olfactometer. Gravid females were 10.6 times (95% CI 5.4-20.8) more likely to enter the chamber with water than a dry chamber.ConclusionsWater vapour is a strong pre-oviposition attractant to gravidAn. gambiae s.s.in still and moving air and is likely to be a general cue used by mosquitoes for locating aquatic habitats.
First report of granulomatous mastitis associated with Sjögren’s syndrome
Authors: Letourneux Christel , Diemunsch Pierre , Korganow Anne-Sophie , Akladios Cherif Youssef , Bellocq Jean-Pierre , Mathelin Carole 
Published: October 2013

Abstract
Granulomatous mastitis is a rare and often considered as idiopathic disease. However, clinical examination and thorough diagnostic investigations have to be carried out in order to identify cases that are secondary to infections or systemic diseases since these forms may be cured with appropriate etiologic treatment. To the best of our knowledge, this report is the first to describe the association of granulomatous mastitis with Sjögren’s syndrome. We discuss the clinical, pathological and therapeutic implications of this association.
Caveolin-1 in renal cell carcinoma promotes tumour cell invasion, and in co-operation with pERK predicts metastases in patients with clinically confined disease
Authors: Campbell Lee , Al-Jayyoussi Ghaith , Gutteridge Robert , Gumbleton Nigel , Griffiths Rosie , Gumbleton Simon , Smith Mathew W , Griffiths David FR , Gumbleton Mark 
Published: October 2013

Abstract

Background
Up to 40% of patients initially diagnosed with clinically-confined renal cell carcinoma (RCC) and who undergo curative surgery will nevertheless relapse with metastatic disease (mRCC) associated with poor long term survival. The discovery of novel prognostic/predictive biomarkers and drug targets is needed and in this context the aim of the current study was to investigate a putative caveolin-1/ERK signalling axis in clinically confined RCC, and to examine in a panel of RCC cell lines the effects of caveolin-1 (Cav-1) on pathological processes (invasion and growth) and select signalling pathways.

Methods
Using immunohistochemistry we assessed the expression of both Cav-1 and phosphorylated-ERK (pERK) in 176 patients with clinically confined RCC, their correlation with histological parameters and their impact upon disease-free survival. Using a panel of RCC cell lines we explored the functional effects of Cav-1 knockdown upon cell growth, cell invasion and VEGF-A secretion, as well Cav-1 regulation by cognate cell signalling pathways.

Results
We found a significant correlation (P = 0.03) between Cav-1 and pERK in a cohort of patients with clinically confined disease which represented a prognostic biomarker combination (HR = 4.2) that effectively stratified patients into low, intermediate and high risk groups with respect to relapse, even if the patients’ tumours displayed low grade and/or low stage disease. In RCC cell lines Cav-1 knockdown unequivocally reduced cell invasive capacity while also displaying both pro-and anti-proliferative effects; targeted knockdown of Cav-1 also partially suppressed VEGF-A secretion in VHL-negative RCC cells. The actions of Cav-1 in the RCC cell lines appeared independent of both ERK and AKT/mTOR signalling pathways.

Conclusion
The combined expression of Cav-1 and pERK serves as an independent biomarker signature with potential merit in RCC surveillance strategies able to predict those patients with clinically confined disease who will eventually relapse. In a panel of in-vitro RCC cells Cav-1 promotes cell invasion with variable effects on cell growth and VEGF-A secretion. Cav-1 has potential as a therapeutic target for the prevention and treatment of mRCC.
Metal-sensitive and thermostable trypsin from the crevalle jack (Caranx hippos) pyloric caeca: purification and characterization
Authors: Costa Helane MS , Freitas Júnior Augusto CV , Amaral Ian PG , Hirata Izaura Y , Paiva Patrícia MG , Carvalho Luiz B , Oliveira Vitor , Bezerra Ranilson S 
Published: October 2013

Abstract
Background
Over the past decades, the economic development and world population growth has led to increased for food demand. Increasing the fish production is considered one of the alternatives to meet the increased food demand, but the processing of fish leads to by-products such as skin, bones and viscera, a source of environmental contamination. Fish viscera have been reported as an important source of digestive proteases with interesting characteristics for biotechnological processes. Thus, the aim of this study was to purify and to characterize a trypsin from the processing by-products of crevalle jack (Caranx hippos) fish.

Results
A 27.5 kDa trypsin with N-terminal amino acid sequence IVGGFECTPHVFAYQ was easily purified from the pyloric caeca of the crevalle jack. Its physicochemical and kinetic properties were evaluated using N-α-benzoyl-DL-arginine-p-nitroanilide (BApNA) as substrate. In addition, the effects of various metal ions and specific protease inhibitors on trypsin activity were determined. Optimum pH and temperature were 8.0 and 50°C, respectively. After incubation at 50°C for 30 min the enzyme lost only 20% of its activity. Km, kcat, and kcat/Km values using BApNA as substrate were 0.689 mM, 6.9 s-1, and 10 s-1 mM-1, respectively. High inhibition of trypsin activity was observed after incubation with Cd2+, Al3+, Zn2+, Cu2+, Pb2+, and Hg2+ at 1 mM, revealing high sensitivity of the enzyme to metal ions.

Conclusions
Extraction of a thermostable trypsin from by-products of the fishery industry confirms the potential of these materials as an alternative source of these biomolecules. Furthermore, the results suggest that this trypsin-like enzyme presents interesting biotechnological properties for industrial applications.
Nebulised amphotericin B to eradicate Candida colonisation from the respiratory tract in critically ill patients receiving selective digestive decontamination: a cohort study
Authors: Ong David SY , MC Klein Klouwenberg Peter , Spitoni Cristian , Bonten Marc JM , Cremer Olaf L 
Published: October 2013

Abstract
Introduction
Colonisation of the lower respiratory tract with Candida species occurs in 25% of mechanically ventilated critically ill patients, and is associated with increased morbidity. Nebulised amphotericin B has been used to eradicate Candida as part of selective decontamination of the digestive tract (SDD) protocols, but its effectiveness is unknown. We aimed to determine the effectiveness of nebulised amphotericin B in eradicating Candida respiratory tract colonisation in patients receiving SDD.

Methods
We included consecutive mechanically ventilated patients during a four-year period. Microbiological screening was performed upon admission and twice weekly thereafter according to a standardised protocol. A colonisation episode was defined as the presence of Candida species in two consecutive sputum samples taken at least one day apart. To correct for time-varying bias and possible confounding, we used a multistate approach and performed time-varying Cox regression with adjustment for age, disease severity, Candida load at baseline and concurrent corticosteroid use.

Results
Among 1,819 patients, colonisation with Candida occurred 401 times in 363 patients; 333 of these events were included for analysis. Decolonisation occurred in 51 of 59 episodes (86%) and in 170 of 274 episodes (62%) in patients receiving and not receiving nebulised amphotericin B, respectively. Nebulised amphotericin B was associated with an increased rate of Candida eradication (crude HR 2.0; 95% CI 1.4 to 2.7, adjusted HR 2.2; 95% CI 1.6 to 3.0). Median times to decolonisation were six and nine days, respectively. The incidence rate of ventilator-associated pneumonia, length of stay and mortality did not differ between both groups.

Conclusions
Nebulised amphotericin B reduces the duration of Candida colonisation in the lower respiratory tracts of mechanically ventilated critically ill patients receiving SDD, but data remain lacking that this is associated with a meaningful improvement in clinical outcomes. Until more evidence becomes available, nebulised amphotericin B should not be used routinely as part of the SDD protocol.
Feasibility, acceptability and efficacy of a school-based prevention programme for eating disorders: Cluster randomised controlled trial
Authors: Sharpe Helen , Schober Ilka , Treasure Janet , Schmidt Ulrike 
Published: October 2013

BackgroundBody image dissatisfaction during adolescence is common but not benign. School-based interventions have the potential for wide reach, but scalability of previous programmes is limited by a reliance on external facilitators.AimsTo assess the acceptability, feasibility and efficacy of a teacher-delivered body image intervention.MethodA pilot clustered randomised controlled trial in which 16 classes of adolescent girls were allocated to a 6-session body image programme (n= 261), or usual curriculum control (n= 187) (registration: ISRCTN42594993).ResultsStudents in the intervention group had significantly improved body esteem and self-esteem and reduced thin-ideal internalisation. Effects for body esteem and thin-ideal internalisation were maintained for 3 months. There were no group differences for eating pathology, peer factors or depression. Acceptability, feasibility and efficacy varied between schools.ConclusionsTeacher-delivered body image lessons have promise but further work is needed to increase efficacy and make interventions suitable across a range of schools.
Aerobic scope does not predict the performance of a tropical eurythermal fish at elevated temperatures
Authors: Norin Tommy , Malte Hans , Clark Timothy D. 
Published: October 2013

Summary
Climate warming is predicted to negatively impact fish populations through impairment of oxygen transport systems when temperatures exceed those which are optimal for aerobic scope (AS). This concept of oxygen- and capacity-limited thermal tolerance (OCLTT) is rapidly gaining popularity within climate change research and has been applied to several fish species. Here, we evaluated the relevance of aerobic performance of juvenile barramundi (Lates calcarifer) in the context of thermal preference and tolerance by (1) measuring standard and maximum metabolic rates (SMR and MMR, respectively) and AS of fish acclimated to 29°C and acutely exposed to temperatures from 23 to 38°C, (2) allowing the fish to behaviourally select a preferred temperature between 29 and 38°C, and (3) quantifying alterations to AS after five weeks of acclimation to 29 and 38°C. SMR and MMR both increased continuously with temperature in acutely exposed fish, but the increase was greater for MMR such that AS was highest at 38°C, a temperature approaching the upper lethal limit (40-41°C). Despite 38°C eliciting maximum AS, when given the opportunity the fish selected a median temperature of 31.7±0.5°C and spent only 10±3% of their time at temperatures &gt;36°C. Following acclimation to 38°C, AS measured at 38°C was decreased to the same level as 29°C-acclimated fish measured at 29°C, suggesting that AS may be dynamically modulated independent of temperature to accommodate the requirements of daily life. Together, these results reveal limited power of the OCLTT hypothesis in predicting optimal temperatures and effects of climate warming on juvenile barramundi.