bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of metagenomic samples using sequence signatures
Authors: Jiang Bai , Song Kai , Ren Jie , Deng Minghua , Sun Fengzhu , Zhang Xuegong 
Published: December 2012

AbstractBackgroundSequence signatures, as defined by the frequencies ofk-tuples (ork-mers,k-grams), have been used extensively to compare genomic sequences of individual organisms, to identifycis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied.ResultsWe studied several dissimilarity measures, includingd2,d2*andd2Srecently developed from our group, a measure (hereinafter noted asHao) used in CVTree developed from Hao’s group (Qiet al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willneret al. (2009), as well as standardlpmeasures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measured2Scan achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature.ConclusionsSequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. Thed2Sdissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths.
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
Authors: Haas Brian J , Chin Melissa , Nusbaum Chad , Birren Bruce W , Livny Jonathan 
Published: December 2012

Abstract

Background
High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance.

Results
We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified.

Conclusions
Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species.
Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD)
Authors: Hu Tingsong , Zheng Ying , Zhang Yan , Li Gangshan , Qiu Wei , Yu Jing , Cui Qinghua , Wang Yiyin , Zhang Chaoxiong , Zhou Xiaofang , Feng Ziliang , Zhou Weiguo , Fan Quanshui , Zhang Fuqiang 
Published: December 2012

Abstract

Background
The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA - random amplified polymorphic DNA (cDNA-RAPD) technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR) method.

Results
A novel Getah virus was identified by VIDISCR from suckling mice exposed to mosquitoes (Aedes albopictus) collected in Yunnan Province, China. The non-structural protein gene, nsP3, the structural protein gene, the capsid protein gene, and the 3'-untranslated region (UTR) of the novel Getah virus isolate were cloned and sequenced. Nucleotide sequence identities of each gene were determined to be 97.1–99.3%, 94.9–99.4%, and 93.6–99.9%, respectively, when compared with the genomes of 10 other representative strains of Getah virus.

Conclusions
The VIDISCR method was able to identify known virus isolates and a novel isolate of Getah virus from infected mice. Phylogenetic analysis indicated that the YN08 isolate was more closely related to the Hebei HB0234 strain than the YN0540 strain, and more genetically distinct from the MM2021 Malaysia primitive strain.
PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data
Authors: Weissbrodt David G , Shani Noam , Sinclair Lucas , Lefebvre Grégory , Rossi Pierre , Maillard Julien , Rougemont Jacques , Holliger Christof 
Published: December 2012

Abstract

Background
In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems.

Results
PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes.

Conclusions
PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.
Hepatitis B Infection among high risk population: a seroepidemiological survey in Southwest of Iran
Authors: Khosravani Abdolmajid , Sarkari Bahador , Negahban Halimeh , Sharifi Asghar , Toori Mehdi Akbartabar , Eilami Owrang 
Published: December 2012

Abstract

Background
Hepatitis B virus (HBV) infection remains a major global health problem. This study aimed to assess the prevalence and risk behaviors for HBV infection among high risk groups in Kohgiloyeh and Boyerahmad province, in Southwest of Iran.

Methods
Blood samples were collected from 2009 subjects, between 2009 and 2010 in Kohgiloyeh and Boyerahmad province, in southwest of Iran. Recruited subjects were the high risk groups for HBV infection, including inmates, injecting drug users, health care workers, patients on maintenance haemodialysis, hemophilic patients and patients with a history of blood transfusion. Their serum samples were tested for the presence of antibodies to hepatitis B core antigen (HBc IgM, IgG) by enzyme-linked immunosorbent assay (ELISA). Seropositive specimens were tested for HBsAg. Demographic features of participants were recorded during sample collecting.

Results
HBsAg was detected in 24 of the 2009 subjects, giving an overall prevalence of 1.2%. All HBsAg positive cases were males. The prevalence of HBsAg among injection drug users was 3.2%. Significant correlation was found between HBV infection and drug abuse, level of education and place of residence (p<0.05), while no significant correlation was found between HBV infection and previous history of blood transfusion, unprotected sexual behavior, and thalassemia.

Conclusion
Based on the findings of this study, incarceration and drug abuse are the most important risk factors for acquiring HBV infection in this region. Modifying behavior, improving the individual education and expanding the HBV vaccination coverage may reduce the rate of infection in the region.
Negative effect of smoking on the performance of the QuantiFERON TB gold in tube test
Authors: Aabye Martine G , Hermansen Thomas Stig , Ruhwald Morten , PrayGod George , Faurholt-Jepsen Daniel , Jeremiah Kidola , Faurholt-Jepsen Maria , Range Nyagosya , Friis Henrik , Changalucha John , Andersen Aase B , Ravn Pernille 
Published: December 2012

Abstract

Background
False negative and indeterminate Interferon Gamma Release Assay (IGRA) results are a well documented problem. Cigarette smoking is known to increase the risk of tuberculosis (TB) and to impair Interferon-gamma (IFN-γ) responses to antigenic challenge, but the impact of smoking on IGRA performance is not known. The aim of this study was to evaluate the effect of smoking on IGRA performance in TB patients in a low and high TB prevalence setting respectively.

Methods
Patients with confirmed TB from Denmark (DK, n = 34; 20 smokers) and Tanzania (TZ, n = 172; 23 smokers) were tested with the QuantiFERON-TB Gold In tube (QFT). Median IFN-γ level in smokers and non smokers were compared and smoking was analysed as a risk factor for false negative and indeterminate QFT results.

Results
Smokers from both DK and TZ had lower IFN-γ antigen responses (median 0.9 vs. 4.2 IU/ml, p = 0.04 and 0.4 vs. 1.6, p < 0.01), less positive (50 vs. 86%, p = 0.03 and 48 vs. 75%, p < 0.01) and more false negative (45 vs. 0%, p < 0.01 and 26 vs. 11%, p = 0.04) QFT results. In Tanzanian patients, logistic regression analysis adjusted for sex, age, HIV and alcohol consumption showed an association of smoking with false negative (OR 17.1, CI: 3.0-99.1, p < 0.01) and indeterminate QFT results (OR 5.1, CI: 1.2-21.3, p = 0.02).

Conclusions
Cigarette smoking was associated with false negative and indeterminate IGRA results in both a high and a low TB endemic setting independent of HIV status.
Primitive neuroectodermal tumor of the kidney: case report and review of literature
Authors: Sun Chuanyu , Du Zunguo , Tong Shijun , Xu Ke , Ding Weihong , Sun Jianliang , Ding Qiang 
Published: December 2012

Abstract

Background
Renal primitive neuroectodermal tumor (rPNET) as a member of Ewing’s sarcoma family is extremely rare and usually occurs in children and young adults. Most literature about rPNET was isolated case reports.

Case presentation
We reported a case of 45-year-old man with the complaint of right flank pain. Computerized tomography (CT) scan demonstrated a large substantive tumor involving the lower pole of the right kidney. Then the patient underwent radical nephrectomy. Pathologic characteristics and immunohistochemical analysis confirmed the diagnosis of rPNET. Additionally, the patient received three cycles of chemotherapy, and was still alive without metastasis at 15-months follow-up.

Conclusion
rPNET is rare and presents aggressive clinical behavior and worse prognosis. We expect that further awareness and study of this rare tumor can be had by presenting our case.
Impact of leachate on groundwater pollution due to non-engineered municipal solid waste landfill sites of erode city, Tamil Nadu, India
Authors: Nagarajan Rajkumar , Thirumalaisamy Subramani , Lakshumanan Elango 
Published: December 2012

Abstract
Leachate and groundwater samples were collected from Vendipalayam, Semur and Vairapalayam landfill sites in Erode city, Tamil Nadu, India, to study the possible impact of leachate percolation on groundwater quality. Concentrations of various physicochemical parameters including heavy metals (Cd, Cr, Cu, Fe, Ni, Pb, Fe and Zn) were determined in leachate samples and are reported. The concentrations of Cl-, NO3
-, SO4
2-, NH4
+ were found to be in considerable levels in the groundwater samples particularly near to the landfill sites, likely indicating that groundwater quality is being significantly affected by leachate percolation. Further they were proved to be the tracers for groundwater contamination near Semur and Vendipalayam dumpyards. The presence of contaminants in groundwater particularly near the landfill sites warns its quality and thus renders the associated aquifer unreliable for domestic water supply and other uses. Although some remedial measures are suggested to reduce further groundwater contamination via leachate percolation, the present study demands for the proper management of waste in Erode city.
Genetic association between APOE*4 and neuropsychiatric symptoms in patients with probable Alzheimer's disease is dependent on the psychosis phenotype
Authors: Christie Drew , Shofer Jane , Millard Steven P , Li Ellen , DeMichele-Sweet Mary Ann , Weamer Elise A , Kamboh M Ilyas , Lopez Oscar L , Sweet Robert A , Tsuang Debby 
Published: December 2012

Abstract

Background
Neuropsychiatric symptoms such as psychosis are prevalent in patients with probable Alzheimer’s disease (AD) and are associated with increased morbidity and mortality. Because these disabling symptoms are generally not well tolerated by caregivers, patients with these symptoms tend to be institutionalized earlier than patients without them. The identification of protective and risk factors for neuropsychiatric symptoms in AD would facilitate the development of more specific treatments for these symptoms and thereby decrease morbidity and mortality in AD. The E4 allele of the apolipoprotein E (APOE) gene is a well-documented risk factor for the development of AD. However, genetic association studies of the APOE 4 allele and BPS in AD have produced conflicting findings.

Methods
This study investigates the association between APOE and neuropsychiatric symptoms in a large sample of clinically well-characterized subjects with probable AD (n=790) who were systematically evaluated using the Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) Behavioral Rating Scale for Dementia (BRSD).

Results
Our study found that hallucinations were significantly more likely to occur in subjects with no APOΕ 4 alleles than in subjects with two Ε4 alleles (15% of subjects and 5% of subjects, respectively; p=.0066), whereas there was no association between the occurrence of delusions, aberrant motor behavior, or agitation and the number of Ε4 alleles. However, 94% of the subjects with hallucinations also had delusions (D+H).

Conclusion
These findings suggest that in AD the Ε4 allele is differentially associated with D+H but not delusions alone. This is consistent with the hypothesis that distinct psychotic subphenotypes may be associated with the APOE allele.
Impact of pharmaceutical care on the quality of life of patients with Chagas disease and heart failure: randomized clinical trial
Authors: da Silva Gilberto M Sperandio , Chambela Mayara C , Sousa Andrea S , Sangenis Luiz Henrique C , Xavier Sergio S , Costa Andréa R , Brasil Pedro Emmanuel AA , Hasslocher-Moreno Alejandro M , Saraiva Roberto M 
Published: December 2012

Abstract

Background
Pharmaceutical care is the direct interaction between pharmacist and patient, in order to improve therapeutic compliance, promote adequate pharmacotherapeutic follow-up, and improve quality of life. Pharmaceutical care may be effective in reducing complications and in improving the quality of life of patients with chronic diseases, like Chagas heart disease, while bringing a positive impact on health system costs. The morbidity and mortality indexes for patients with Chagas heart disease are high, especially if this heart disease is complicated by heart failure. In this setting, we hypothesize that pharmaceutical care might be an important tool for the clinical management of these patients by improving their quality of life, as a better compliance to their treatment and the avoidance and prompt correction of drug-related problems will minimize their symptoms, improve their functional class, and decrease the number of hospital admissions. Therefore, the aim of this trial is to evaluate the contribution of pharmaceutical care to clinical treatment of patients with Chagas heart disease complicated by heart failure.

Methods/design
A prospective, single-center randomized clinical trial will be conducted in patients with Chagas heart disease complicated by heart failure. A total of 88 patients will be randomly assigned into two parallel groups: an intervention group will receive standard care and pharmaceutical care, and a control group will receive only standard care. Both groups will be subjected to a follow-up period of 12 months. The primary outcome of this trial is the evaluation of quality of life, measured by the 36-item short-form and the Minnesota Living with Heart Failure Questionnaire. Secondary outcomes include drug-related problems, exercise tolerance as measured by the standard six-minute-walk test, and compliance.

Discussion
Patients with Chagas heart disease complicated by heart failure under pharmaceutical care are expected to improve their quality of life, present with a lower incidence of drug-related problems, improve their functional capacity, and improve in their compliance to treatment.

Trial registration
ClinicalTrials.gov Identifier: NCT01566617
Uneven chances of breastfeeding in Spain
Authors: Río Isabel , Luque Álvaro , Castelló-Pastor Adela , Sandín-Vázquez María del Val , Larraz Rosana , Barona Carmen , Jané Mireia , Bolúmar Francisco 
Published: December 2012

Abstract

Background
No large scale studies on breastfeeding onset patterns have been carried out in Spain. This work aims to explore the prevalence and the risk factors for not initiating breastfeeding in hospitals from Catalonia (CAT) and Valencia (V), two regions accounting approximately for 30% of the annual births in Spain.

Methods
The prevalence of not initiating breastfeeding was calculated by maternal/neonatal characteristics and type of hospital, and logistic regression models were used to estimate crude and adjusted risks of not breastfeeding in each region.

Results
Prevalence of breastfeeding initiation was 81.7% and 82.5% in Catalonia and Valencia, respectively. We identified conspicuous regional differences in the adjusted-risk of not breastfeeding, especially for multiple [CAT = 3.12 (95% CI: 2.93, 3.31), V = 2.44 (95% CI: 2.23, 2.67)] and preterm and low birth weight deliveries [very preterm and very low birth weight: CAT = 7.61 (95% CI: 6.50, 8.92), V = 4.03 (95% CI: 3.13, 5.19); moderate preterm and moderate low birth weight: CAT = 4.28 (95% CI: 4.01, 4.57), V = 2.55 (95% CI:2.34, 2.79)].

Conclusions
Our results suggest the existence of regional variations in breastfeeding initiation in Spain. Taking into account the known short and long-term benefits of breastfeeding it is recommended that further research should explore these differences in order to prevent potential inequities in neonatal, child and adult health.
Role of stem/progenitor cells in reparative disorders
Authors: Pretheeban Thavaneetharajah , Lemos Dario R , Paylor Benjamin , Zhang Regan-Heng , Rossi Fabio M 
Published: December 2012

AbstractAdult stem cells are activated to proliferate and differentiate during normal tissue homeostasis as well as in disease states and injury. This activation is a vital component in the restoration of function to damaged tissue via either complete or partial regeneration. When regeneration does not fully occur, reparative processes involving an overproduction of stromal components ensure the continuity of tissue at the expense of its normal structure and function, resulting in a “reparative disorder”. Adult stem cells from multiple organs have been identified as being involved in this process and their role in tissue repair is being investigated. Evidence for the participation of mesenchymal stromal cells (MSCs) in the tissue repair process across multiple tissues is overwhelming and their role in reparative disorders is clearly demonstrated, as is the involvement of a number of specific signaling pathways. Transforming growth factor beta, bone morphogenic protein and Wnt pathways interact to form a complex signaling network that is critical in regulating the fate choices of both stromal and tissue-specific resident stem cells (TSCs), determining whether functional regeneration or the formation of scar tissue follows an injury. A growing understanding of both TSCs, MSCs and the complex cascade of signals regulating both cell populations have, therefore, emerged as potential therapeutic targets to treat reparative disorders. This review focuses on recent advances on the role of these cells in skeletal muscle, heart and lung tissues.