bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays
Authors: Patenge Nadja , Billion André , Raasch Peter , Normann Jana , Wisniewska-Kucper Aleksandra , Retey Julia , Boisguérin Valesca , Hartsch Thomas , Hain Torsten , Kreikemeyer Bernd 
Published: October 2012

AbstractBackgroundSmall non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogenStreptococcus pyogenesM49 (Group AStreptococcus, GAS M49), employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases.ResultsWe identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5′rapid amplification of cDNA ends-PCR (RACE-PCR) analysis.ConclusionsIn accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of sRNAs expressed by a given organism requires the complementary use of different methods and the investigation of several environmental conditions. Despite a high conservation of sRNA genes within streptococci, the expression of sRNAs appears to be strain specific.
Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response
Authors: Geijer Cecilia , Pirkov Ivan , Vongsangnak Wanwipa , Ericsson Abraham , Nielsen Jens , Krantz Marcus , Hohmann Stefan 
Published: October 2012

AbstractBackgroundSpore germination of the yeastSaccharomyces cerevisiaeis a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carbon source and nutrients, the outer layers of the protective spore wall are locally degraded, the tightly packed spore gains volume and an elongated shape, and eventually the germinating spore re-enters the cell cycle. The regulatory pathways driving this process are still largely unknown. Here we characterize the global gene expression profiles of germinating spores and identify potential transcriptional regulators of this process with the aim to increase our understanding of the mechanisms that control the transition from cellular dormancy to proliferation.ResultsEmploying detailed gene expression time course data we have analysed the reprogramming of dormant spores during the transition to proliferation stimulated by a rich growth medium or pure glucose. Exit from dormancy results in rapid and global changes consisting of different sequential gene expression subprograms. The regulated genes reflect the transition towards glucose metabolism, the resumption of growth and the release of stress, similar to cells exiting a stationary growth phase. High resolution time course analysis during the onset of germination allowed us to identify a transient up-regulation of genes involved in protein folding and transport. We also identified a network of transcription factors that may be regulating the global response. While the expression outputs following stimulation by rich glucose medium or by glucose alone are qualitatively similar, the response to rich medium is stronger. Moreover, spores sense and react to amino acid starvation within the first 30 min after germination initiation, and this response can be linked to specific transcription factors.ConclusionsResumption of growth in germinating spores is characterized by a highly synchronized temporal organisation of up- and down-regulated genes which reflects the metabolic reshaping of the quickening spores.
Automated bolus advisor control and usability study (ABACUS): does use of an insulin bolus advisor improve glycaemic control in patients failing multiple daily insulin injection (MDI) therapy? [NCT01460446]
Authors: Cavan David A , Ziegler Ralph , Cranston Iain , Barnard Katharine , Ryder Jacqueline , Vogel Claudia , Parkin Christopher G , Koehler Walter , Vesper Iris , Petersen Bettina , Wagner Robin S 
Published: October 2012

Abstract

Background
People with T1DM and insulin-treated T2DM often do not follow and/or adjust their insulin regimens as needed. Key contributors to treatment non-adherence are fear of hypoglycaemia, difficulty and lack of self-efficacy associated with insulin dose determination. Because manual calculation of insulin boluses is both complex and time consuming, people may rely on empirical estimates, which can result in persistent hypoglycaemia and/or hyperglycaemia. Use of automated bolus advisors (BA) has been shown to help insulin pump users to more accurately meet prandial insulin dosage requirements, improve postprandial glycaemic excursions, and achieve optimal glycaemic control with an increased time within optimal range. Use of a BA containing an early algorithm based on sliding scales for insulin dosing has also been shown to improve HbA1c levels in people treated with multiple daily insulin injections (MDI). We designed a study to determine if use of an automated BA can improve clinical and psychosocial outcomes in people treated with MDI.

Methods/design
The Automated Bolus Advisor Control and Usability Study (ABACUS) is a 6-month, prospective, randomised, multi-centre, multi-national trial to determine if automated BA use improves glycaemic control as measured by a change in HbA1c in people using MDI with elevated HbA1c levels (#62;7.5%). A total of 226 T1DM and T2DM participants will be recruited. Anticipated attrition of 20% will yield a sample size of 90 participants, which will provide #62;80% power to detect a mean difference of 0.5%, with SD of 0.9%, using a one-sided 5% t-test, with 5% significance level. Other measures of glycaemic control, self-care behaviours and psychosocial issues will also be assessed.

Discussion
It is critical that healthcare providers utilise available technologies that both facilitate effective glucose management and address concerns about safety and lifestyle. Automated BAs may help people using MDI to manage their diabetes more effectively and minimise the risk of long-term diabetes related complications. Findings from a recent study suggest that BA use positively addresses both safety and lifestyle concerns; however, randomised trials are needed to confirm these perceptions and determine whether bolus advisor use improves clinical outcomes. Our study is designed to make these assessments.

Trial registration
NCT01460446
Characteristics of progressive multifocal leukoencephalopathy clarified through internet-assisted laboratory surveillance in Japan
Authors: Nakamichi Kazuo , Mizusawa Hidehiro , Yamada Masahito , Kishida Shuji , Miura Yoshiharu , Shimokawa Toshio , Takasaki Tomohiko , Lim Chang-Kweng , Kurane Ichiro , Saijo Masayuki 
Published: October 2012

AbstractBackgroundProgressive multifocal leukoencephalopathy (PML), a rare but fatal demyelinating disease caused by JC virus (JCV), occurs mainly in immunocompromised patients. As PML develops in individuals with various underlying disorders sporadically and infrequently, a nationwide survey of PML is difficult. This study was conducted to elucidate the characteristics of PML in Japan through an internet-assisted laboratory surveillance program.MethodsA diagnostic support system for PML was established using a real-time PCR assay of JCV DNA in cerebrospinal fluid (CSF), and requests for testing were received from clinicians via specialized websites. Medical histories of patients were collected through standardized questionnaires, and a database of CSF JCV loads and clinical information was created and analyzed.ResultsFor 4 years from April 2007 to March 2011, CSF specimens from 419 patients were tested. Forty-eight individuals were found positive for JCV DNA in their CSF and were diagnosed with PML. PML primarily occurred not only in HIV-positive patients (33.3%) but also in patients with hematologic disorders after receiving stem cell transplantation, chemotherapy, and/or immunosuppressive treatment (39.6%). The frequencies of PML cases among the subjects in these two categories were 20.3% and 23.5%, respectively. Although no significant features were observed with respect to CSF JCV loads in PML patients with an HIV infection or hematologic disorder, males were predominant in both groups (100% and 89.5%, respectively). The proportion of PML cases with autoimmune disorders (6.3%) or solid-organ transplants (2.1%) was smaller than those with HIV infection or hematologic disorders, probably due to the limited availability of therapeutic monoclonal antibodies and transplantation from brain dead donors.ConclusionsThe results suggest that the internet-assisted laboratory surveillance program might be a useful strategy for collecting precise real-time information on PML on a national level. The current database provides important background information for the diagnosis and treatment of patients with risk factors for PML.
Application of the Western-based adjuvant online model to Korean colon cancer patients; a single institution experience
Authors: Jung Minkyu , Kim Geon Woo , Jung Inkyung , Ahn Joong Bae , Roh Jae Kyung , Rha Sun Young , Chung Hyun Cheol , Kim Nam Kyu , Kim Tae Il , Shin Sang Joon 
Published: October 2012

Abstract

Background
Adjuvant Online (AOL) is web-accessible risk-assessment model that predicts the mortality and the benefits of adjuvant therapy (http://www.newadjuvantonline.com). AOL has never been validated for Asian colon cancer patients.

Methods
Using the Yonsei Tumor Registry database, patients who were treated within the Yonsei University Health System between 1990 and 2005 for T1-4, N0-2, and M0 colon cancer were included in the calculations for survival. Observed and predicted 5-year overall survival was compared for each patient.

Results
The median age of the study population of 1431 patients was 60 years (range, 15–87 years), and the median follow-up duration was 7.9 years (range, 0.06–19.8 years). The predicted 5-year overall survival rate (77.7%) and observed survival (79.5%) was not statistically different (95% Confidential interval, 76.3–81.5) in all patients. Predicted outcomes were within 95% confidential interval of observed survival in both stage II and III disease, including most demographic and pathologic subgroups. Moreover, AOL more accurately predicted OS for patients with stage II than stage III.

Conclusions
AOL tended to offer reliable prediction for 5-year overall survival and could be used as a decision making tool for adjuvant treatment in Korean colon cancer patients whose prognosis is similar to other Asian patients.
Population-based study of breast cancer in older women: prognostic factors of relative survival and predictors of treatment
Authors: Dialla Pegdwende Olivia , Dabakuyo Tienhan Sandrine , Marilier Sophie , Gentil Julie , Roignot Patrick , Darut-Jouve Ariane , Poillot Marie-Laure , Quipourt Valérie , Arveux Patrick 
Published: October 2012

Abstract

Background
A large proportion of women with breast cancer (BC) are elderly. However, there is a lack of information regarding BC prognostic factors and care in this population. The aims of this study were to assess the prognostic factors of relative survival (RS) among women with BC aged ≥ 75 years old and to identify the predictive factors of treatments administered to this population.

Methods
A population-based study was performed using data from the Cote d’Or breast and gynaecological cancer registry. Women aged 75 years and older with primary invasive BC and resident in Cote d’Or at the time of diagnosis made between January 1998 and December 2008 were retrospectively selected. Prognostic factors of RS were estimated in a generalized linear model with a Poisson error structure. RS rate for the whole population was given at 5 years. Logistic regression models were used to identify the predictors of the treatments administered.

Results
Six hundred and eighty-one women were included. Median age at diagnosis was 80. Comorbidities (p=0.02), pT stage (p=0.04), metastases (p=<0.001), having a family doctor (p=0.03) and hormone-receptor status (p=0.006) were independent prognostic factors of RS. The RS rate at 5 years for the whole population was 78.2%, 95%CI = [72.2-83.0]. Age, pT stage, metastases, histoprognostic SBR grade, hormone receptor status and comorbidities were frequently found to be predictors of treatment with surgery alone, hormone therapy alone, breast conserving surgery plus adjuvant therapy and mastectomy plus adjuvant therapy.

Conclusions
Comorbid conditions adversely affect survival in older women with breast cancer. Moreover the results of this study showed that there are numerous predictors of the type of treatment administered, and that the most important were age and comorbidities.
Adherence evaluation of endocrine treatment in breast cancer: methodological aspects
Authors: Oberguggenberger Anne S , Sztankay Monika , Beer Beate , Schubert Birthe , Meraner Verena , Oberacher Herbert , Kemmler Georg , Giesinger Johannes , Gamper Eva , Sperner-Unterweger Barbara , Marth Christian , Holzner Bernhard , Hubalek Michael 
Published: October 2012

Abstract

Background
Current studies on adherence to endocrine therapy in breast cancer patients suffer from methodological limitations due to a lack of well-validated methods for assessing adherence. There is no gold standard for measuring adherence. The aim of our study was to compare four different approaches for evaluating adherence to anastrozole therapy for breast cancer with regard to concordance between methods.

Methods
Outpatients with early breast cancer treated with anastrozole completed the multi-method assessment of adherence. We implemented a self-report scale (the Simplified Medication Adherence Questionnaire), physician- ratings, refill records and determination of anastrozole serum concentration.

Results
Comparison of the four approaches using Spearman rank correlation revealed poor concordance across all methods reflecting weak correlations of 0.2-0.4. Considering this data incomparability across methods, we still observed high adherence rates of 78%-98% across measures.

Conclusion
Our findings contribute to the growing body of knowledge on the impact that methodological aspects exert on the results of adherence measurement in breast cancer patients receiving endocrine treatment. Our findings suggest that the development and validation of instruments specific to patients receiving endocrine agents is imperative in order to arrive at a more accurate assessment and to subsequently obtain more precise estimates of adherence rates in this patient population.
Histopathological changes in anatomical distribution of inflammatory bowel disease in children: a retrospective cohort study
Authors: Tsang Jessica , Sikora Sheena , Spady Donald , El-Matary Wael 
Published: October 2012

Abstract

Background
Anatomical progression of pediatric inflammatory bowel disease is under-reported. The aim of this work was to examine possible changes in the anatomical distribution of IBD in pediatric patients at diagnosis and at follow up.

Methods
In a retrospective cohort study, the medical records of children with inflammatory bowel disease were examined. Patients who had at least 2 endoscopic/colonoscopic examinations were included. Primary outcome was histopathological progression based on histopathological examination of biopsies taken during endoscopic and colonoscopic bowel examination. Factors predictive of disease progression were also examined.

Results
A total of 98 patients fulfilled inclusion criteria (49 female, 54 with ulcerative colitis, range 2 – 17 years, mean age at diagnosis was 10.6 years, SD ± 3.67), the mean duration of follow up was 32.9 months (range 0.1 – 60 months, SD ± 8.54). In the ulcerative colitis group, 41% had disease progression and none of the examined variables (age, gender, laboratory markers, growth and disease activity at diagnosis) appeared to effect disease progression. In the Crohn’s disease group, 75% had disease progression. Girls (OR = 0.13, 95% CI 0.02 – 0.79) and patients with high erythrocytic sedimentation rate (OR=0.942, 95% CI 0.894 – 0.99) were predictive for disease progression.

Conclusions
Despite maximum therapy, the majority of children with Crohn’s disease appeared to have histopathological disease progression. Female sex and high erythrocytic sedimentation rate seemed to be predictive for disease progression. None of the factors analyzed seemed predictive of disease progression in ulcerative colitis.
Immunogenicity when utilizing adenovirus serotype 4 and 5 vaccines expressing circumsporozoite protein in naïve and Adenovirus (Ad5) immune mice
Authors: Schuldt Nathaniel J , Aldhamen Yasser A , Godbehere-Roosa Sarah , Seregin Sergey S , Kousa Youssef A , Amalfitano Andrea 
Published: October 2012

AbstractBackgroundInduction of potent long lasting effector T cell responses against liver stage malaria antigens strongly correlates with protection from malaria. While Adenovirus serotype 5 (Ad5) based malaria vaccine platforms have the ability to induce potent effector T cell responses against transgenes, high rates of pre-existing Ad5 immunity in malaria endemic regions has prompted study of alternative Ad serotype based malaria vaccines as replacements for Ad5 based malaria vaccines. The research described in this article examines the utility of alternative serotype adenovirus serotype 4 (Ad4) expressing a sporozoite surface protein (circumsporozoite protein (CSP)) (Ad4-CSP) to induce immune responses against CSP. The immunogenicity of Ad4-CSP was also tested in homologous and heterologous prime boost vaccinations in both Ad5 naïve and Ad5 immune backgrounds as compared to use of Ad5-CSP.ResultsIn Ad5 naïve animals, use of Ad4-CSP priming vaccinations followed by boosting with Ad5-CSP (Ad4-CSP/Ad5-CSP) maximally increased the numbers of CSP specific cytokine secreting cytotoxic T cells relative to repeated use of Ad5-CSP. The Ad4-CSP/Ad5-CSP regimen also induced equivalent levels of CSP specific cell killing as did homologous prime-boost vaccinations with Ad5-CSP, despite stimulating lower numbers of CSP specific cytotoxic T cells. Priming with Ad4-CSP followed by a homologous boost resulted in significantly less CSP specific humoral responses than any other vaccination regimen tested in Ad naïve animals. In Ad5 immune animals, addition of Ad4-CSP in homologous or heterologous prime boost resulted in inductions of higher CSP specific responses than animals repeatedly vaccinated with Ad5-CSP alone. However, the observed responses were well below those observed in similarly treated Ad naïve mice.ConclusionsWhile the Ad4-CSP/Ad5-CSP and Ad5-CSP/Ad5-CSP vaccination regimens resulted in equivalent CSP specific killing in Ad naïve animals, Ad4-CSP/Ad5-CSP achieved this result with a lower percentage of CSP specific CD8+T cells and a higher number of IFNγ secreting cells, suggesting that the Ad4-CSP/Ad5-CSP vaccination regimen elicits more efficient cytotoxic T cells. In Ad5 immune animals use of Ad4-CSP improved CSP specific immune responses as compared to repeated use of Ad5-CSP, but could not achieve the levels of immunogenicity observed when the same vaccine regimens were used in Ad naïve animals. These data indicate the existence of some level of immunological cross-reactivity between these two adenovirus subgroups. Based on these results, it is suggested that future studies should undertake similarly stringent analyses of alternative Ad serotypes to establish their effectiveness as replacements for Ad5.
Weight status and perception of body image in children: the effect of maternal immigrant status
Authors: Gualdi-Russo Emanuela , Manzon Vanessa Samantha , Masotti Sabrina , Toselli Stefania , Albertini Augusta , Celenza Francesca , Zaccagni Luciana 
Published: October 2012

Abstract

Background
Recent studies have shown that body image perception is an important factor in weight control and may be influenced by culture and ethnicity. The aim of the present study was to assess the relationship between immigrant status of the mother and weight status and body image perception of the child.

Methods
In total, 2706 schoolchildren (1405 boys and 1301 girls) aged 8–9 years and their mothers participated in a cross-sectional survey in Emilia-Romagna region (northern Italy). Weight and height of the children were measured and Body Mass Index (BMI) was calculated. Actual and ideal body image perception by the children and by the mothers with respect to their children was evaluated according to Collins’ body image silhouettes.

Results
The BMI values were significantly lower in children of immigrants than in children of Italian mothers (F:17.27 vs 17.99 kg/m2; M:17.77 vs 18.13 kg/m2). The prevalence of overweight/obesity was lower, and the prevalence of underweight higher, in children of immigrant mothers than in those of Italian mothers (overweight- F:21.3 vs 29.1%; M. 28.3 vs 31.4%; underweight- F:5.16 vs 3.84%; M:6.63 vs 2.82%). The children's body image perception was consistent with the differing pattern of nutritional status. In the comparison between actual and ideal figures, the Feel-Ideal Difference Index (FID) scores resulted different between the subsample with foreign-born mother in comparison to the native one (significantly lower in daughters of immigrants) (FID- F: 0.31 vs 0.57; M: 0.35 vs 0.32). There were significant differences in the choice of the ideal figure of the child between immigrant mothers and Italian mothers (FID- F: -0.05 vs 0.19; M: -0.35 vs −0.03): the ideal figure values were higher in the immigrant mothers of male children and lower in the Italian mothers of female children.

Conclusion
Our results suggest that cultural and behavioral factors linked to ethnicity play an important role in the nutritional status of children and in the perceived and ideal body image.