bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug Trimethoprim
Authors: Sangurdekar Dipen P , Zhang Zhigang , Khodursky Arkady B 
Published: November 2011

Abstract

Background
Trimethoprim is a widely prescribed antibiotic for a variety of bacterial infections. It belongs to a class of anti-metabolites - antifolates - which includes drugs used against malarial parasites and in cancer therapy. However, spread of bacterial resistance to the drug has severely hampered its clinical use and has necessitated further investigations into its mechanism of action and treatment regimen. Trimethoprim selectively starves bacterial cells for tetrahydrofolate, a vital cofactor necessary for the synthesis of several metabolites. The outcome (bacteriostatic or bactericidal) of such starvation, however, depends on the availability of folate-dependent metabolites in the growth medium. To characterize this dependency, we investigated in detail the regulatory and structural components of Escherichia coli cellular response to trimethoprim in controlled growth and supplementation conditions.

Results
We surveyed transcriptional responses to trimethoprim treatment during bacteriostatic and bactericidal conditions and analyzed associated gene sets/pathways. Concurrent starvation of all folate dependent metabolites caused growth arrest, and this was accompanied by induction of general stress and stringent responses. Three gene sets were significantly associated with the bactericidal effect of TMP in different media including LB: genes of the SOS regulon, genes of the pyrimidine nucleotide biosynthetic pathway and members of the multiple antibiotic resistance (mar) regulon controlled by the MarR repressor. However, the SOS response was identified as the only universal transcriptional signature associated with the loss of viability by direct thymine starvation or by folate stress. We also used genome-wide gene knock-out screen to uncover means of sensitization of bacteria to the drug. We observed that among a number of candidate genes and pathways, the effect of knock-outs in the deoxyribose nucleotide salvage pathway, encoded by the deoCABD operon and under the control of the DeoR repressor, was most informative.

Conclusion
Transcriptional induction of DNA damage response is an essential feature of the bactericidal effect of trimethoprim. Either the observation of the transcriptional response or DNA damage itself, or both, is made possible by thymine starvation when other folate-dependent metabolites are not limited. The effect of DNA damage by the drug takes place prior to its bactericidal effect, at the beginning of the lag stage of the treatment. Mutations in the deoxyribose nucleotide salvage pathway can affect duration of the lag as well as the rate of killing. This information can be used to postulate certain mechanistic differences between direct thymine starvation in thymidylate synthase deficient mutants and thymine starvation by anti-folate inhibitors.
Effectiveness of laxatives in elderly - a cross sectional study in nursing homes
Authors: Fosnes Gunvor S , Lydersen Stian , Farup Per G 
Published: November 2011

AbstractBackgroundLaxatives are efficient drugs, but the effectiveness has been questioned. In nursing homes, the prevalence of constipation is high and laxatives are commonly used drugs. The aims of the study were to assess the effectiveness of laxative therapy in an everyday setting in Norwegian nursing homes, study differences between treatment regimens and factors associated with normal bowel function.MethodsA cross-sectional study. After giving informed consent, residents above 60 years of age using laxatives for functional constipation were included, and their characteristics, medical history, use of drugs and bowel functions were recorded. Normal bowel function was defined as bowel movements from 3 times/week to 3 times/day and stool consistency 3-5 on Bristol Stool Form Scale.ResultsOut of 647 residents in the nursing homes, 197 were included and 116 (59%) had normal bowel function. The treatment effect did not differ significantly between the laxatives, treatment regimens or expected efficacy of the regimens. The treatment was unsatisfactorily adapted to individual needs. In subjects with normal bowel function, 113 (97%) had persistent complaints; 68 (59.5%), 10 (8.0%), 34 (28.6%) and 26 (22.5%) reported straining, manual manoeuvre to facilitate bowel movements, feeling of incomplete bowel movements, and feeling of anorectal obstruction respectively. Good nutritional status, previous or present cancer disease and anxiety/depression were predictors of normal bowel function.ConclusionsTreatment of constipation in nursing homes was unsatisfactory. Nearly all patients with normal stool frequency and consistence had some persistent complaints. Improved nutrition and individualization of the treatment could improve the outcome.
A bacteria colony-based screen for optimal linker combinations in genetically encoded biosensors
Authors: Ibraheem Andreas , Yap Hongkin , Ding Yidan , Campbell Robert E 
Published: November 2011

Abstract

Background
Fluorescent protein (FP)-based biosensors based on the principle of intramolecular Förster resonance energy transfer (FRET) enable the visualization of a variety of biochemical events in living cells. The construction of these biosensors requires the genetic insertion of a judiciously chosen molecular recognition element between two distinct hues of FP. When the molecular recognition element interacts with the analyte of interest and undergoes a conformational change, the ratiometric emission of the construct is altered due to a change in the FRET efficiency. The sensitivity of such biosensors is proportional to the change in ratiometric emission, and so there is a pressing need for methods to maximize the ratiometric change of existing biosensor constructs in order to increase the breadth of their utility.

Results
To accelerate the development and optimization of improved FRET-based biosensors, we have developed a method for function-based high-throughput screening of biosensor variants in colonies of Escherichia coli. We have demonstrated this technology by undertaking the optimization of a biosensor for detection of methylation of lysine 27 of histone H3 (H3K27). This effort involved the construction and screening of 3 distinct libraries: a domain library that included several engineered binding domains isolated by phage-display; a lower-resolution linker library; and a higher-resolution linker library.

Conclusion
Application of this library screening methodology led to the identification of an optimized H3K27-trimethylation biosensor that exhibited an emission ratio change (66%) that was 2.3 × improved relative to that of the initially constructed biosensor (29%).
Modified expression of alternative oxidase in transgenic tomato and petunia affects the level of tomato spotted wilt virus resistance
Authors: Ma Hao , Song Congfeng , Borth Wayne , Sether Diane , Melzer Michael , Hu John 
Published: November 2011

Abstract

Background

Tomato spotted wilt virus (TSWV) has a very wide host range, and is transmitted in a persistent manner by several species of thrips. These characteristics make this virus difficult to control. We show here that the over-expression of the mitochondrial alternative oxidase (AOX) in tomato and petunia is related to TSWV resistance.

Results
The open reading frame and full-length sequence of the tomato AOX gene LeAox1au were cloned and introduced into tomato 'Healani' and petunia 'Sheer Madness' using Agrobacterium-mediated transformation. Highly expressed AOX transgenic tomato and petunia plants were selfed and transgenic R1 seedlings from 10 tomato lines and 12 petunia lines were used for bioassay. For each assayed line, 22 to 32 tomato R1 progeny in three replications and 39 to 128 petunia progeny in 13 replications were challenged with TSWV. Enzyme-Linked Immunosorbent Assays showed that the TSWV levels in transgenic tomato line FKT4-1 was significantly lower than that of wild-type controls after challenge with TSWV. In addition, transgenic petunia line FKP10 showed significantly less lesion number and smaller lesion size than non-transgenic controls after inoculation by TSWV.

Conclusion
In all assayed transgenic tomato lines, a higher percentage of transgenic progeny had lower TSWV levels than non-transgenic plants after challenge with TSWV, and the significantly increased resistant levels of tomato and petunia lines identified in this study indicate that altered expression levels of AOX in tomato and petunia can affect the levels of TSWV resistance.
Prevalence of apical periodontitis and endodontic treatment in a Kosovar adult population
Authors: Kamberi Blerim , Hoxha Veton , Stavileci Miranda , Dragusha Edmond , Kuçi Astrit , Kqiku Lumnije 
Published: November 2011

Abstract

Background
Despite numerous studies on the prevalence of apical periodontitis (AP) and endodontic treatment in diverse geographical populations, there are currently no data on the prevalence of these conditions in populations of adults native to Kosovo. Therefore, little is known about how widespread these conditions are, and whether there is any correlation between root canal treatment and AP. The purpose of our research was to address this anomaly by investigating AP and endodontic treatment in an adult Kosovar population based on radiographic examination.

Methods
The sample used for this study consisted of randomly selected individuals referred to the University Dentistry Clinical Center of Kosovo in the years 2006-2007. Orthopantomographs of 193 patients were evaluated. The periapical status of all teeth (with the exception of third molars) was examined according to Ørstavik's Periapical Index. The quality of the root canal filling was rated as 'adequate' or 'inadequate' based on whether all canals were filled, the depth of fill relative to the radiographic apex and the quality of compaction (absence/presence of voids). Data were analyzed statistically using the Chi-square test and calculation of odds ratios.

Results
Out of 4131 examined teeth, the prevalence of apical periodontitis (AP) and endodontic treatment was 12.3% and 2.3%, respectively. Of 95 endodontically-treated teeth, 46.3% were associated with AP. The prevalence of AP increased with age. The prevalence in subjects aged over 60 years old (20.2%) was higher than in other age groups. A statistically significant difference was found for the frequency of endodontically-treated teeth associated with AP in the 40-49 year age group (P < 0.001). Of some concern was the discovery that only 30.5% of the endodontically-treated teeth examined met the criteria of an acceptable root canal filling. Inadequately root-filled teeth were associated with an increased AP risk.

Conclusions
The prevalence of AP and the frequency of endodontically-treated teeth with AP in this Kosovar population are higher than those found in other countries. Inadequate root canal fillings were associated with an increased prevalence of AP.
Antimicrobial activity against oral pathogens and immunomodulatory effects and toxicity of geopropolis produced by the stingless bee Melipona fasciculata Smith
Authors: Liberio Silvana A , Pereira Antônio Luís A , Dutra Richard P , Reis Aramys S , Araújo Maria José AM , Mattar Nadia S , Silva Lucilene A , Ribeiro Maria Nilce S , Nascimento Flávia Raquel F , Guerra Rosane NM , Monteiro-Neto Valério 
Published: November 2011

AbstractBackgroundNative bees of the tribe Meliponini produce a distinct kind of propolis called geopropolis. Although many pharmacological activities of propolis have already been demonstrated, little is known about geopropolis, particularly regarding its antimicrobial activity against oral pathogens. The present study aimed at investigating the antimicrobial activity ofM. fasciculatageopropolis against oral pathogens, its effects onS. mutansbiofilms, and the chemical contents of the extracts. A gel prepared with a geopropolis extract was also analyzed for its activity onS. mutansand its immunotoxicological potential.MethodsAntimicrobial activities of three hydroalcoholic extracts (HAEs) of geopropolis, and hexane and chloroform fractions of one extract, were evaluated using the agar diffusion method and the broth dilution technique. Ethanol (70%, v/v) and chlorhexidine (0.12%, w/w) were used as negative and positive controls, respectively. Total phenol and flavonoid concentrations were assayed by spectrophotometry. Immunotoxicity was evaluated in mice by topical application in the oral cavity followed by quantification of biochemical and immunological parameters, and macro-microscopic analysis of animal organs.ResultsTwo extracts, HAE-2 and HAE-3, showed inhibition zones ranging from 9 to 13 mm in diameter forS. mutansandC. albicans, but presented no activity againstL.acidophilus. The MBCs for HAE-2 and HAE-3 againstS. mutanswere 6.25 mg/mL and 12.5 mg/mL, respectively. HAE-2 was fractionated, and its chloroform fraction had an MBC of 14.57 mg/mL. HAE-2 also exhibited bactericidal effects onS. mutansbiofilms after 3 h of treatment. Significant differences (p < 0.05) in total phenol and flavonoid concentrations were observed among the samples. Signs toxic effects were not observed after application of the geopropolis-based gel, but an increase in the production of IL-4 and IL-10, anti-inflammatory cytokines, was detected.ConclusionsIn summary, geopropolis produced byM. fasciculatacan exert antimicrobial action againstS. mutansandC. albicans, with significant inhibitory activity againstS. mutansbiofilms. The extract with the highest flavonoid concentration, HAE-2, presented the highest antimicrobial activity. In addition, a geopropolis-based gel is not toxic in an animal model and displays anti-inflammatory effect.
Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain
Authors: Dominkovics Pau , Granell Carlos , Pérez-Navarro Antoni , Casals Martí , Orcau Àngels , Caylà Joan A 
Published: November 2011

Abstract

Background
Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information.

Methods
Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database.

Results
The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts.

Conclusions
In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios.
Ancient founder mutation is responsible for Imerslund-Gräsbeck Syndrome among diverse ethnicities
Authors: Beech Cameron M , Liyanarachchi Sandya , Shah Nidhi P , Sturm Amy C , Sadiq May F , de la Chapelle Albert , Tanner Stephan M 
Published: November 2011

Abstract

Background
Imerslund-Gräsbeck syndrome (IGS) was described just over 50 years ago by Olga Imerslund and Ralph Gräsbeck and colleagues. IGS is caused by specific malabsorption of cobalamin (Cbl) due to bi-allelic mutations in either the cubilin gene (CUBN) or the human amnionless homolog (AMN). Mutations in the two genes are commonly seen in founder populations or in societies with a high degree of consanguineous marriages. One particular mutation in AMN, c.208-2A>G, causing an out-of-frame loss of exon 4 in the mRNA, is responsible for some 15% of IGS cases globally. We present evidence that this founder mutation causes a substantial percentage of cases among diverse ethnicities and that the mutation is as old as human civilization.

Methods
Partial genotyping indicated a founder event but its presence in diverse peoples of Arabic, Turkish, Jewish, and Hispanic ancestry suggested that the mutation might be recurrent. We therefore studied the flanking sequence spanning 3.5 Mb to elucidate the origin of the haplotype and estimate the age of the mutation using a Bayesian inference method based on observed linkage disequilibrium.

Results
The mutation's distribution, the size of the shared haplotype, and estimates of growth rate and carrier frequency indicated that the mutation was a single prehistoric event. Dating back to the ancient Middle East around 11,600 BC, the mutation predates the advent of writing, farming, and the monotheistic religions of the region.

Conclusions
This mutation causes over 50% of the IGS cases among Arabic, Turkish, and Sephardic Jewish families, making it a primary target for genetic screening among diverse IGS cases originating from the Middle East. Thus, rare founder mutations may cause a substantial number of cases, even among diverse ethnicities not usually thought to be related.
Low frequency of human papillomavirus infection in conjunctival squamous cell carcinoma of Mexican patients
Authors: Peralta Raúl , Valdivia Alejandra , Estañol Perla , Villegas Vanessa , Pimienta Carolina , Treviño Eugenio , Marrero Daniel , Mendoza Monica , Jimenez Florinda , Villalvazo Leonardo , Tejeda Miriam , Salcedo Mauricio 
Published: November 2011

Abstract

Background
The relationship between Human Papillomavirus (HPV) infection and conjunctiva cancer is controversial. HPV detection will provide more information about the role of this infectious agent in the biology of conjunctiva cancer. In the present study, DNA extracted and purified from 36 Conjunctival Squamous Cell Carcinomas (CSCC) was evaluated by PCR for HPV DNA sequences. The results were correlated with the clinical and histopathological variables.

Results
The results showed that HPV DNA was present in 8 CSCC samples (22%); HPV16 was the sole type detected. Significant association was found between HPV detection and the limbus tumor subtype (p = 0.03). All the samples were non-metastatic squamous cell carcinoma.

Conclusions
The HPV presence in CSCC from Mexican patients is not a common event.
Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies
Authors: Earp Madalene A , Rahmani Maziar , Chew Kevin , Brooks-Wilson Angela 
Published: November 2011

Abstract

Background
Until recently, genome-wide association studies (GWAS) have been restricted to research groups with the budget necessary to genotype hundreds, if not thousands, of samples. Replacing individual genotyping with genotyping of DNA pools in Phase I of a GWAS has proven successful, and dramatically altered the financial feasibility of this approach. When conducting a pool-based GWAS, how well SNP allele frequency is estimated from a DNA pool will influence a study's power to detect associations. Here we address how to control the variance in allele frequency estimation when DNAs are pooled, and how to plan and conduct the most efficient well-powered pool-based GWAS.

Methods
By examining the variation in allele frequency estimation on SNP arrays between and within DNA pools we determine how array variance [var(earray)] and pool-construction variance [var(econstruction)] contribute to the total variance of allele frequency estimation. This information is useful in deciding whether replicate arrays or replicate pools are most useful in reducing variance. Our analysis is based on 27 DNA pools ranging in size from 74 to 446 individual samples, genotyped on a collective total of 128 Illumina beadarrays: 24 1M-Single, 32 1M-Duo, and 72 660-Quad.

Results
For all three Illumina SNP array types our estimates of var(earray) were similar, between 3-4 × 10-4 for normalized data. Var(econstruction) accounted for between 20-40% of pooling variance across 27 pools in normalized data.

Conclusions
We conclude that relative to var(earray), var(econstruction) is of less importance in reducing the variance in allele frequency estimation from DNA pools; however, our data suggests that on average it may be more important than previously thought. We have prepared a simple online tool, PoolingPlanner (available at http://www.kchew.ca/PoolingPlanner/), which calculates the effective sample size (ESS) of a DNA pool given a range of replicate array values. ESS can be used in a power calculator to perform pool-adjusted calculations. This allows one to quickly calculate the loss of power associated with a pooling experiment to make an informed decision on whether a pool-based GWAS is worth pursuing.
Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression
Authors: Ben-Hamo Rotem , Efroni Sol 
Published: November 2011

Abstract
Background
Glioblastoma multiforme (GBM) is the most common, aggressive and malignant primary tumor of the brain and is associated with one of the worst 5-year survival rates among all human cancers. Identification of molecular interactions that associate with disease progression may be key in finding novel treatments.

Methods
Using five independent molecular and clinical datasets with a set of computational algorithms we were able to identify a gene-gene and gene-microRNA network that significantly stratifies patient prognosis. By combining gene expression microarray data with microRNA expression levels, copy number alterations, drug response and clinical data, combined with network knowledge, we were able to identify a single pathway at the core of glioblastoma.

Results
This network, the p38 network, and an associated microRNA, hsa-miR-9, facilitate prognostic stratification. The microRNA hsa-miR-9 correlated with network behavior and presents binding affinities with network members in a manner that suggests control over network behavior. A similar control over network behavior is possible through a set of drugs. These drugs are part of the treatment regimen for a subpopulation of the patients that participated in the TCGA study and for which the study provides clinical information. Interestingly, the patients that were treated with these specific sets of drugs, all of which targeted against p38 network members, demonstrate highly significant stratification of prognosis.

Conclusions
Combined, these results call for attention to p38 network targeted treatment and present the p38 network-hsa-miR-9 control mechanism as critical in GBM progression.