bluuebunny/crossref_metadata_2025_split huggingface dataset:
High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study
Authors: Hoban Sean M , Mezzavilla Massimo , Gaggiotti Oscar E , Benazzo Andrea , van Oosterhout Cock , Bertorelle Giorgio 
Published: October 2013

AbstractBackgroundDemographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity.ResultsWith large variance in reproductive success (Vk≥ 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima’sDtest) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR.ConclusionsOur results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck.
Facial skin and soft tissue infection caused by Mycobacterium wolinskyi associated with cosmetic procedures
Authors: Yoo Seung Jin , Lee Keun Hwa , Jung Sung-No , Heo Sang Taek 
Published: October 2013

Abstract

Background

Mycobacteirum wolinskyi is a member of the Mycobacterium smegmatis group, which is less frequently found in clinical settings than other nontuberculous mycobacterium (NTM) species. However, its clinical significance has recently increased in opportunistic infections. This case is the first report of facial skin and soft tissue infection by M. wolinskyi complicating cosmetic procedures.

Case presentation
A 56-year-old Asian female patient with a history of receiving multiple facial cosmetic procedures over the preceding 2 years was admitted to our institution with swelling, local pain, and erythema on the right cheek. Mycobacteirum fortuitum complex isolated from a pus culture was identified as M. wolinskyi by rpoB sequencing. Metallic foreign bodies and abscess were detected by radiologic imaging. The pus was incised and drained. Treatment comprised clarithromycin (500 mg every 12 h), amikacin (200 mg every 8 h), and ciprofloxacin (400 mg every 6 h).

Conclusion
We report the first case of facial skin and soft tissue infection with M. wolinskyi after multiple cosmetic procedures of filler injection and laser lipolysis. Increased occurrence of NTM infection in nosocomial settings suggests the importance of appropriate treatment including culturing and rpoB gene sequencing when patients who have undergone cosmetic procedures display symptoms and signs of soft tissue infection indicative of NTM infection.
Vaginal microbiome in women from Greenland assessed by microscopy and quantitative PCR
Authors: Datcu Raluca , Gesink Dionne , Mulvad Gert , Montgomery-Andersen Ruth , Rink Elisabeth , Koch Anders , Ahrens Peter , Jensen Jørgen Skov 
Published: October 2013

Abstract

Background
Bacterial vaginosis (BV) is a common condition, although its aetiology remains unexplained. The aim of this study was to analyse the composition of vaginal microbiota in women from Greenland to provide a quantitative description and improve the understanding of BV.

Methods
Self-collected vaginal smears and swabs were obtained from 177 women. The vaginal smears were graded for BV according to Nugent’s criteria. The vaginal swab samples were analysed by 19 quantitative PCRs (qPCRs) for selected vaginal bacteria and by PCR for four sexually transmitted infections (STIs).

Results
STIs were common: Mycoplasma genitalium 12%, Chlamydia trachomatis 7%, Neisseria gonorrhoeae 1%, and Trichomonas vaginalis 0.5%. BV was found in 45% of women, but was not associated with individual STIs. Seven of the 19 vaginal bacteria (Atopobium vaginae, Prevotella spp., Gardnerella vaginalis, BVAB2, Eggerthella-like bacterium, Leptotrichia amnionii, and Megasphaera type 1) had areas under the receiver operating characteristic (ROC) curve > 85%, suggesting they are good predictors of BV according to Nugent. Prevotella spp. had the highest odds ratio for BV (OR 437; 95% CI 82–2779) in univariate analysis considering only specimens with a bacterial load above the threshold determined by ROC curve analysis as positive, as well as the highest adjusted odds ratio in multivariate logistic regression analysis (OR 4.4; 95% CI 1.4-13.5). BV could be subdivided into clusters dominated by a single or a few species together.

Conclusions
BV by Nugent score was highly prevalent. Two of seven key species (Prevotella spp. and A. vaginae) remained significantly associated with BV in a multivariate model after adjusting for other bacterial species. G. vaginalis and Prevotella spp. defined the majority of BV clusters.
A dynamic method for the investigation of induced state metabolic capacities as a function of temperature
Authors: Sagmeister Patrick , Langemann Timo , Wechselberger Patrick , Meitz Andrea , Herwig Christoph 
Published: October 2013

Abstract

Background
Science-based recombinant bioprocess designs as well as the design of statistical experimental plans for process optimization (Design of Experiments, DoE) demand information on physiological bioprocess boundaries, such as the onset of acetate production, adaptation times, mixed feed metabolic capabilities or induced state maximum metabolic rates as at the desired cultivation temperature. Dynamic methods provide experimental alternatives to determine this information in a fast and efficient way. Information on maximum metabolic capabilities as a function of temperature is needed in case a reduced cultivation temperature is desirable (e.g. to avoid inclusion body formation) and an appropriate feeding profile is to be designed.

Results
Here, we present a novel dynamic method for the determination of the specific growth rate as a function of temperature for induced recombinant bacterial bioprocesses. The method is based on the control of the residual substrate concentration at non-limiting conditions with dynamic changes in cultivation temperature. The presented method was automated in respect to information extraction and closed loop control by means of in-line Fourier Transformation Infrared Spectroscopy (FTIR) residual substrate measurements and on-line first principle rate-based soft-sensors. Maximum induced state metabolic capabilities as a function of temperature were successfully extracted for a recombinant E. coli C41 fed-batch bioprocess without the need for sampling in a time frame of 20 hours.

Conclusions
The presented method was concluded to allow the fast and automated extraction of maximum metabolic capabilities (specific growth rate) as a function of temperature. This complements the dynamic toolset necessary for science-based recombinant bacterial bioprocess design and DoE design.
The national employment guarantee scheme and inequities in household spending on food and non-food determinants of health in rural India
Authors: Dilip TR , Dandona Rakhi , Dandona Lalit 
Published: October 2013

Abstract

Introduction
Inequities in a population in spending on food and non-food items can contribute to disparities in health status. The Mahatma Gandhi National Rural Employment Guarantee Scheme (MGNREGS) was launched in rural India in 2006, aimed at providing at least 100 days of manual work to a member in needy households.

Methods
We used nationally representative data from the consumer expenditure surveys of 2004–05 and 2009–10 and the employment survey of 2009–10 conducted by National Sample Survey Organisation to assess the effect of MGNREGS in reducing inequities in consumption of food and non-food items between poor and non-poor households in the states of India. Variations among the states in implementation of MGNREGS were examined using the employment and unemployment survey data, and compared with official programme data up to 2012–13. Inequity in spending on food and non-food items was assessed using the ratio of monthly per capita consumer expenditure (MPCE) between the most vulnerable (labourer) and least vulnerable categories of households.

Results
The survey data suggested 1.42 billion person-days of MGNRGES employment in the 2009–10 financial year, whereas the official programme data reported 2.84 billion person-days. According to the official data, the person-days of MGNRGES employment decreased by 43.3% from 2009–10 to 2012–13 for the 9 large less developed states of India. Survey data revealed that the average number of MGNREGS work days in a year per household varied from 42 days in Rajasthan to less than 10 days in 14 of the 20 major states in India in 2009–10. Rajasthan with the highest implementation of MGNRGES among the 9 less developed states of India had the highest relative decline of 10.4% in the food spending inequity from 2004–05 to 2009–10 between the most vulnerable and less vulnerable households. The changes in inequity for non-food spending did not have any particular pattern across the less developed states. In the most vulnerable category, the households in Rajasthan that got 100 or more days of work in a year under MGNREGS had a 25.9% increase in MPCE.

Conclusion
MGNREGS seems to have contributed to the reduction in food consumption inequity in rural Rajasthan in 2009–10, and has the potential of making a similar contribution with higher level of implementation of this programme in other states. Non-food consumption inequities benefited less from MGNRGES until 2009–10. The reported decrease in the MGNRGES employment person-days in the less developed states of India from 2009–10 to 2012–13 is of concern.
Tension pneumothorax, is it a really life-threatening condition?
Authors: Yoon Jeong Seob , Choi Si Young , Suh Jong Hui , Jeong Jin Yong , Lee Bae Young , Park Yong Gue , Kim Chi Kyung , Park Chan Beom 
Published: October 2013

Abstract

Background
Tension pneumothorax is a life-threatening occurrence that is infrequently the consequence of spontaneous pneumothorax. The aim of this study was to identify the risk factors for the development of tension pneumothorax and its effect on clinical outcomes.

Methods
We reviewed patients who were admitted with spontaneous pneumothorax between August 1, 2003 and December 31, 2011. Electronic medical records and the radiological findings were reviewed with chest x-ray and high-resolution computed tomography scans that were retrieved from the Picture Archiving Communication System.

Results
Out of the 370 patients included in this study, tension pneumothorax developed in 60 (16.2%). The bullae were larger in patients with tension pneumothorax than in those without (23.8 ± 16.2 mm vs 16.1 ± 19.1 mm; P = 0.007). In addition, the incidence of tension pneumothorax increased with the lung bulla size. Fibrotic adhesion was more prevalent in the tension pneumothorax group than in that without (P = 0.000). The bullae were large in patients with fibrotic adhesion than in those without adhesion (35.0 ± 22.3 mm vs 10.4 ± 11.5 mm; P = 0.000). On multivariate analysis, the size of bullae (odds ratio (OR) = 1.03, P = 0.001) and fibrotic adhesion (OR = 10.76, P = 0.000) were risk factors of tension pneumothorax. Hospital mortality was 3.3% in the tension pneumothorax group and it was not significantly different from those patients without tension pneunothorax (P = 0.252).

Conclusions
Tension pneumothorax is not uncommon, but clinically fatal tension pneumothorax is extremely rare. The size of the lung bullae and fibrotic adhesion contributes to the development of tension pneumothorax.
Visualizing genomic information across chromosomes with PhenoGram
Authors: Wolfe Daniel , Dudek Scott , Ritchie Marylyn D , Pendergrass Sarah A 
Published: October 2013

Abstract

Background
With the abundance of information and analysis results being collected for genetic loci, user-friendly and flexible data visualization approaches can inform and improve the analysis and dissemination of these data. A chromosomal ideogram is an idealized graphic representation of chromosomes. Ideograms can be combined with overlaid points, lines, and/or shapes, to provide summary information from studies of various kinds, such as genome-wide association studies or phenome-wide association studies, coupled with genomic location information. To facilitate visualizing varied data in multiple ways using ideograms, we have developed a flexible software tool called PhenoGram which exists as a web-based tool and also a command-line program.

Results
With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail. We have now used PhenoGram to produce a variety of different plots, and provide these as examples herein. These plots include visualization of the genomic coverage of SNPs from a genotyping array, highlighting the chromosomal coverage of imputed SNPs, copy-number variation region coverage, as well as plots similar to the NHGRI GWA Catalog of genome-wide association results.

Conclusions
PhenoGram is a versatile, user-friendly software tool fostering the exploration and sharing of genomic information. Through visualization of data, researchers can both explore and share complex results, facilitating a greater understanding of these data.
FSH in vitro versus LH in vivo: similar genomic effects on the cumulus
Authors: Assidi Mourad , Richard François J , Sirard Marc-André 
Published: October 2013

AbstractThe use of gonadotropins to trigger oocyte maturation bothin vivoandin vitrohas provided precious and powerful knowledge that has significantly increased our understanding of the ovarian function. Moreover, the efficacy of most assisted reproductive technologies (ART) used in both humans and livestock species relies on gonadotropin input, mainly FSH and LH. Despite the significant progress achieved and the huge impact of gonadotropins, the exact molecular pathways of the two pituitary hormones, FSH and LH, still remain poorly understood. Moreover, these pathways may not be the same when moving from thein vivoto thein vitrocontext. This misunderstanding of the intricate synergy between these two hormones leads to a lack of consensus about their use mainlyin vitroor in ovulation induction schedulesin vivo. In order to optimize their use, additional work is thus required with a special focus on comparing thein vitroversus thein vivoeffects. In this context, this overview will briefly summarize the downstream gene expression pathways induced by both FSHin vitroand LHin vivoin the cumulus compartment. Based on recent microarray comparative analysis, we are reporting thatin vitroFSH stimulation on cumulus cells appears to achieve at least part of the gene expression activity afterin vivoLH stimulation. We are then proposing that the in vitro FSH-response of cumulus cells have similitudes with the in vivo LH-response.
Association Between the Prevalence of Symptoms and Health-Related Quality of Life in Adult Survivors of Childhood Cancer: A Report From the St Jude Lifetime Cohort Study
Authors: Huang I-Chan , Brinkman Tara M. , Kenzik Kelly , Gurney James G. , Ness Kirsten K. , Lanctot Jennifer , Shenkman Elizabeth , Robison Leslie L. , Hudson Melissa M. , Krull Kevin R. 
Published: October 2013

Purpose We investigated the association between prevalence of symptoms and health-related quality of life (HRQOL) in adult survivors of childhood cancer enrolled in the St Jude Lifetime Cohort study. Methods Eligibility criteria include childhood malignancy treated at St Jude, survival ≥ 10 years from diagnosis, and current age ≥ 18 years. Study participants were 1,667 survivors (response rate = 65%). Symptoms were self-reported by using a comprehensive health questionnaire and categorized into 12 classes: cardiac; pulmonary; motor/movement; pain in head; pain in back/neck; pain involving sites other than head, neck, and back; sensation abnormalities; disfigurement; learning/memory; anxiety; depression; and somatization. HRQOL was measured by using physical/mental component summary (PCS/MCS) and six domain scores of the Medical Outcomes Study 36-Item Short-Form Health Survey. Multivariable regression analysis was performed to investigate associations between symptom classes and HRQOL. Cumulative prevalence of symptom classes in relation to time from diagnosis was estimated. Results Pain involving sites other than head, neck and back, and disfigurement represented the most frequent symptom classes, endorsed by 58.7% and 56.3% of survivors, respectively. Approximately 87% of survivors reported multiple symptom classes. Greater symptom prevalence was associated with poorer HRQOL. In multivariable analysis, symptom classes explained up to 60% of the variance in PCS and 56% of the variance in MCS; demographic and clinical variables explained up to 15% of the variance in PCS and 10% of the variance in MCS. Longer time since diagnosis was associated with higher cumulative prevalence in all symptom classes. Conclusion A large proportion of survivors suffered from many symptom classes, which was associated with HRQOL impairment.
Level of HER2 Gene Amplification Predicts Response and Overall Survival in HER2-Positive Advanced Gastric Cancer Treated With Trastuzumab
Authors: Gomez-Martin Carlos , Plaza Jose Carlos , Pazo-Cid Roberto , Salud Antonieta , Pons Francesc , Fonseca Paula , Leon Ana , Alsina Maria , Visa Laura , Rivera Fernando , Galan M. Carmen , del Valle Elena , Vilardell Felipe , Iglesias Mar , Fernandez Soledad , Landolfi Stefania , Cuatrecasas Miriam , Mayorga Marta , Jose Paulés M. , Sanz-Moncasi Pilar , Montagut Clara , Garralda Elena , Rojo Federico , Hidalgo Manuel , Lopez-Rios Fernando 
Published: October 2013

Purpose Previous studies have highlighted the importance of an appropriate human epidermal growth factor receptor 2 (HER2) evaluation for the proper identification of patients eligible for treatment with anti-HER2 targeted therapies. Today, the relationship remains unclear between the level of HER2 amplification and the outcome of HER2-positive gastric cancer treated with first-line chemotherapy with trastuzumab. The aim of this study was to determine whether the level of HER2 gene amplification determined by the HER2/CEP17 ratio and HER2 gene copy number could significantly predict some benefit in overall survival and response to therapy in advanced gastric cancer treated with trastuzumab-based chemotherapy. Patients and Methods Ninety patients with metastatic gastric cancer treated with first-line trastuzumab-based chemotherapy were studied. The optimal cutoff values for HER2/CEP17 ratio and HER2 gene copy number (GCN) for discriminating positive results in terms of response and prolonged survival were determined using receiver operating characteristic curves analyses. Results In this study, a median HER2/CEP17 ratio of 6.11 (95% CI, 2.27 to 21.90) and a median HER2 gene copy number of 11.90 (95% CI, 3.30 to 43.80) were found. A mean HER2/CEP17 ratio of 4.7 was identified as the optimal cutoff value discriminating sensitive and refractory patients (P = .005). Similarly, the optimal cutoff for predicting survival longer than 12 months was 4.45 (P = .005), and for survival longer than 16 months was 5.15 (P = .004). For HER2 GCN, the optimal cutoff values were 9.4, 10.0, and 9.5, respectively (P = .02). Conclusion The level of HER2 gene amplification significantly predicts sensitivity to therapy and overall survival in advanced gastric cancer treated with trastuzumab-based chemotherapy.
Sequential Combination of Gemtuzumab Ozogamicin and Standard Chemotherapy in Older Patients With Newly Diagnosed Acute Myeloid Leukemia: Results of a Randomized Phase III Trial by the EORTC and GIMEMA Consortium (AML-17)
Authors: Amadori Sergio , Suciu Stefan , Stasi Roberto , Salih Helmut R. , Selleslag Dominik , Muus Petra , De Fabritiis Paolo , Venditti Adriano , Ho Anthony D. , Lübbert Michael , Thomas Xavier , Latagliata Roberto , Halkes Constantijn J.M. , Falzetti Franca , Magro Domenico , Guimaraes José E. , Berneman Zwi , Specchia Giorgina , Karrasch Matthias , Fazi Paola , Vignetti Marco , Willemze Roel , de Witte Theo , Marie Jean-Pierre 
Published: October 2013

Purpose This randomized trial evaluated the efficacy and toxicity of sequential gemtuzumab ozogamicin (GO) and standard chemotherapy in older patients with newly diagnosed acute myeloid leukemia (AML). Patients and Methods Patients (n = 472) age 61 to 75 years were randomly assigned to induction chemotherapy with mitoxantrone, cytarabine, and etoposide preceded, or not, by a course of GO (6 mg/m2 on days 1 and 15). In remission, patients received two consolidation courses with or without GO (3 mg/m2 on day 0). The primary end point was overall survival (OS). Results The overall response rate was comparable between the two arms (GO, 45%; no GO, 49%), but induction and 60-day mortality rates were higher in the GO arm (17% v 12% and 22% v 18%, respectively). With median follow-up of 5.2 years, median OS was 7.1 months in the GO arm and 10 months in the no-GO arm (hazard ratio, 1.20; 95% CI, 0.99 to 1.45; P = .07). Other survival end points were similar in both arms. Grade 3 to 4 hematologic and liver toxicities were greater in the GO arm. Treatment with GO provided no benefit in any prognostic subgroup, with the possible exception of patients age < 70 years with secondary AML, but outcomes were significantly worse in the oldest age subgroup because of a higher risk of early mortality. Conclusion As used in this trial, the sequential combination of GO and standard chemotherapy provides no benefit for older patients with AML and is too toxic for those age ≥ 70 years.