bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization of tlyA gene product, Rv1694 of Mycobacterium tuberculosis: A non-conventional hemolysin and a ribosomal RNA methyl transferase
Authors: Rahman Aejazur , Srivastava Saumya S , Sneh Amita , Ahmed Neesar , Krishnasastry Musti V 
Published: September 2010

AbstractBackgroundMycobacterium tuberculosisis a virulent bacillus causing tuberculosis, a disease responsible for million deaths each year worldwide. In order to understand its mechanism of pathogenesis in humans and to help control tuberculosis, functions of numerousMycobacterium tuberculosisgenes are being characterized. In this study we report the dual functionality oftlyAgene product ofMycobacterium tuberculosisannotated as Rv1694, a 268 amino acid long basic protein.ResultsThe recombinant purified Rv1694 protein was found to exhibit hemolytic activityin vitro. It showed concentration and time-dependent hemolysis of rabbit and human erythrocytes. Multiple oligomeric forms (dimers to heptamers) of this protein were seen on the membranes of the lysed erythrocytes. Like the oligomers of conventional, well-known, pore-forming toxins, the oligomers of Rv1694 were found to be resistant to heat and SDS, but were susceptible to reducing agents like β-mercaptoethanol as it had abolished the hemolytic activity of Rv1694 indicating the role of disulfide bond(s). The Rv1694 generatedde novobyin vitrotranscription and translation also exhibited unambiguous hemolysis confirming the self assembly and oligomerization properties of this protein. Limited proteolytic digestion of this protein has revealed that the amino terminus is susceptible while in solution but is protected in presence of membrane. Striking feature of Rv1694 is its presence on the cell wall ofE. colias visualized by confocal microscopy. The surface expression is consistent with the contact dependent haemolytic ability ofE. coliexpressing this protein. Also, immune serum specific to this protein inhibits the contact dependent hemolysis. Moreover, Rv1694 protein binds to and forms stable oligomers on the macrophage phagosomal membranes. In addition to all these properties,E. coliexpressing Rv1694 was found to be susceptible to the antibiotic capreomycin as its growth was significantly slower than mock vector transformedE. coli. The S30 extract ofE. coliexpressing the Rv1694 had poor translational activity in presence of capreomycin, further confirming its methylation activity. Finally, incorporation of methyl group of [3H]-S-adenosylmethionine in isolated ribosomes also confirmed its methylation activity.ConclusionsThe Rv1694 has an unusual dual activity. It appears to contain two diverse functions such as haemolytic activity and ribosomal RNA methylation activity. It is possible that the haemolytic activity might be relevant to intra-cellular compartments such as phagosomes rather than cell lysis of erythrocytes and the self-assembly trait may have a potential role after successful entry into macrophages byMycobacterium tuberculosis.
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations
Authors: Shetty Amol Carl , Athri Prashanth , Mondal Kajari , Horner Vanessa L , Steinberg Karyn Meltz , Patel Viren , Caspary Tamara , Cutler David J , Zwick Michael E 
Published: September 2010

Abstract

Background
The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research.

Results
SeqAnt (Seq uence An notator) is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds.

Conclusion
SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies
Authors: Uebe Steffen , Pasutto Francesca , Krumbiegel Mandy , Schanze Denny , Ekici Arif B , Reis André 
Published: September 2010

Abstract

Background
Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.

Results
Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool.

Conclusions
Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.
Sequential introduction of single room isolation and hand hygiene campaign in the control of methicillin-resistant Staphylococcus aureus in intensive care unit
Authors: Cheng Vincent CC , Tai Josepha WM , Chan WM , Lau Eric HY , Chan Jasper FW , To Kelvin KW , Li Iris WS , Ho PL , Yuen KY 
Published: September 2010

Abstract

Background
After renovation of the adult intensive care unit (ICU) with installation of ten single rooms, an enhanced infection control program was conducted to control the spread of methicillin-resistant Staphylococcus aureus (MRSA) in our hospital.

Methods
Since the ICU renovation, all patients colonized or infected with MRSA were nursed in single rooms with contact precautions. The incidence of MRSA infection in the ICU was monitored during 3 different phases: the baseline period (phase 1); after ICU renovation (phase 2) and after implementation of a hand hygiene campaign with alcohol-based hand rub (phase 3). Patients infected with extended spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella species were chosen as controls because they were managed in open cubicles with standard precautions.

Results
Without a major change in bed occupancy rate, nursing workforce, or the protocol of environmental cleansing throughout the study period, a stepwise reduction in ICU onset nonbacteraemic MRSA infection was observed: from 3.54 (phase 1) to 2.26 (phase 2, p = 0.042) and 1.02 (phase 3, p = 0.006) per 1000-patient-days. ICU onset bacteraemic MRSA infection was significantly reduced from 1.94 (phase 1) to 0.9 (phase 2, p = 0.005) and 0.28 (phase 3, p = 0.021) per 1000-patient-days. Infection due to ESBL-producing organisms did not show a corresponding reduction. The usage density of broad-spectrum antibiotics and fluoroquinolones increased from phase 1 to 3. However a significant trend improvement of ICU onset MRSA infection by segmented regression analysis can only be demonstrated when comparison was made before and after the severe acute respiratory syndrome (SARS) epidemic. This suggests that the deaths of fellow healthcare workers from an occupational acquired infection had an overwhelming effect on their compliance with infection control measures.

Conclusion
Provision of single room isolation facilities and promotion of hand hygiene practice are important. However compliance with infection control measures relies largely on a personal commitment, which may increase when personal safety is threatened.
A SRY-HMG box frame shift mutation inherited from a mosaic father with a mild form of testicular dysgenesis syndrome in Turner syndrome patient
Authors: Shahid Mohammad , Dhillon Varinderpal S , Khalil Hesham Saleh , Haque Shameemul , Batra Swaraj , Husain Syed Akhtar , Looijenga LHJ 
Published: September 2010

Abstract

Background
Sex determining factor (SRY) located on the short arm of the Y chromosome, plays an important role in initiating male sex determination, resulting in development of testicular tissue. Presence of the SRY gene in females results in XY sex reversal and increased risk of gonadal germ cell tumours if the karyotype also includes the so-called GonadoBlastoma on the Y chromosome (GBY) region. The majority of mutations within the SRY gene are de novo affecting only a single individual in the family. The mutations within the high-mobility group (HMG) region have the potential to affect its DNA binding activity.

Case Presentation
We performed G- and R-banding cytogenetic analysis of the patient and her family members including her father. We also performed molecular genetic analysis of SRY gene. Cytogenetic analysis in the patient (Turner Syndrome) revealed the mosaic karyotype as 45, X/46, XY (79%/21% respectively) while her father (milder features with testicular dysgenesis syndrome) has a normal male karyotype (46, XY). Using molecular approach, we screened the patient and her father for mutations in the SRY gene. Both patient and her father showed the same deletion of cytosine within HMG box resulting in frame shift mutation (L94fsX180), the father in a mosaic pattern. Histological examination of the gonads from the patient revealed the presence of gonadoblastoma formation, while the father presented with oligoasthenozoospermia and a testicular seminoma. The frameshift mutation at this codon is novel, and may result in a mutated SRY protein.

Conclusion
Our results suggest that lack of a second sex chromosome in majority cells of the patient may have triggered the short stature and primary infertility, and the mutated SRY protein may be associated with the development of gonadoblastoma. It is of importance to note that mosaic patients without a SRY mutation also have a risk for malignant germ cell tumors.
Dysregulated miR-183 inhibits migration in breast cancer cells
Authors: Lowery Aoife J , Miller Nicola , Dwyer Roisin M , Kerin Michael J 
Published: September 2010

Abstract

Background
The involvement of miRNAs in the regulation of fundamental cellular functions has placed them at the fore of ongoing investigations into the processes underlying carcinogenesis. MiRNA expression patterns have been shown to be dysregulated in numerous human malignancies, including breast cancer, suggesting their probable involvement as novel classes of oncogenes or tumour suppressor genes. The identification of differentially expressed miRNAs and elucidation of their functional roles may provide insight into the complex and diverse molecular mechanisms of tumorigenesis. MiR-183 is located on chromosome 7q32 and is part of a miRNA family which are dysregulated in numerous cancers. The aims of this study were to further examine the expression and functional role of miR-183 in breast cancer.

Methods

MiR-183 expression was quantitated in primary breast tumours, tumour associated normal tissue and breast cancer cell lines using RQ-PCR. Gain of function analysis was performed in breast cancer cells using pre-miR-183 and the effect of miR-183 overexpression on cell viability, proliferation, apoptosis and migration was examined. Customized Taqman Low Density Arrays (TLDA) were used to identify dysregulated genes in breast cancer cells transfected with pre-miR-183.

Results
We demonstrate that miR-183 is dysregulated in breast cancer and expression correlates with estrogen receptor and HER2/neu receptor expression. Induced overexpression of miR-183 inhibited migration of breast cancer cells. This finding was substantiated by RQ-PCR of mRNA from cells overexpressing miR-183 which showed dysregulation of several migration and invasion related genes. Specifically, the VIL2-coding protein Ezrin was confirmed as a target of miR-183 and downregulation of this protein was confirmed with immunocytochemistry.

Conclusions
These findings indicate that miR-183 targets VIL2 and may play a central role in the regulation of migration and metastasis in breast cancer. Consequently, this miRNA may present an attractive target for therapeutic intervention.
Development of a serum-free medium for in vitro expansion of human cytotoxic T lymphocytes using a statistical design
Authors: Jeon Min Kyoung , Lim Jong-Baeck , Lee Gyun Min 
Published: September 2010

AbstractBackgroundSerum-containing medium (SCM), which has a number of poorly defined components with varying concentrations, hampers standardization of lymphocyte cultures. In order to develop a serum-free medium (SFM) for the expansion of human lymphocytes from peripheral blood mononuclear cells (PBMCs), a statistical optimization approach based on a fractional factorial method and a response surface method was adopted. A basal medium was prepared by supplementing RPMI1640 medium with insulin, albumin, ferric citrate, ethanolamine, fatty acids, glutamine, sodium pyruvate, 2-mercaptoethanol, 1-thioglycerol, nonessential amino acids, and vitamins. We identified additional positive determinants and their optimal concentrations for cell growth through a statistical analysis.ResultsFrom a statistical analysis using the fractional factorial method, cholesterol and polyamine supplement were identified as positive determinants for cell growth. Their optimal concentrations were determined by the response surface method. The maximum viable cell concentration in the developed SFM was enhanced by more than 1.5-fold when compared to that in RPMI1640 supplemented with 10% fetal bovine serum (FBS). Furthermore, a cytotoxicity assay and an enzyme-linked immunospot assay revealed that the effector function of cytotoxic T lymphocytes generated from PBMCs grown in SFM, by stimulation of peptide-presenting dendritic cells, was retained or even better than that in SCM.ConclusionsThe use of a developed SFM with cholesterol and polyamine supplement for human lymphocyte culture resulted in better growth without loss of cellular function when compared to SCM.
Home healthcare services in Taiwan: a nationwide study among the older population
Authors: Chang Hsiao-Ting , Lai Hsiu-Yun , Hwang I-Hsuan , Ho Mei-Man , Hwang Shinn-Jang 
Published: September 2010

Abstract

Background
Home healthcare services are important in aging societies worldwide. The present nationwide study of health insurance data examined the utilization and delivery patterns, including diagnostic indications, for home healthcare services used by seniors in Taiwan.

Methods
Patients ≥65 years of age who received home healthcare services during 2004 under the Taiwanese National Health Insurance Program were identified and reimbursement claims were analyzed. Age, gender, disease diagnoses, distribution of facilities providing home healthcare services, and patterns of professional visits, including physician and skilled nursing visits, were also explored.

Results
Among 2,104,978 beneficiaries ≥65 years of age, 19,483 (0.9%) patients received 127,753 home healthcare visits during 2004 with a mean number of 6.0 ± 4.8 visits per person. The highest prevalence of home healthcare services was in the 75-84 year age group in both sexes. Females received more home healthcare services than males in all age groups. Cerebrovascular disease was the most frequent diagnosis in these patients (50.7%). More than half of home healthcare visits and around half of the professional home visits were provided by community home nursing care institutions. The majority of the home skilled nursing services were tube replacements, including nasogastric tubes, Foley catheter, tracheostomy, nephrostomy or cystostomy tubes (95%).

Conclusions
Nine out of 1,000 older patients in Taiwan received home healthcare services during 2004, which was much lower than the rate of disabled older people in Taiwan. Females used home healthcare services more frequently than males and the majority of skilled nursing services were tube replacements. The rate of tube replacement of home healthcare patients in Taiwan deserves to be paid more attention.
Image resizing using saliency strength map and seam carving for white blood cell analysis
Authors: Ko ByoungChul , Kim SeongHoon , Nam JaeYeal 
Published: September 2010

Abstract

Background
A new image-resizing method using seam carving and a Saliency Strength Map (SSM) is proposed to preserve important contents, such as white blood cells included in blood cell images.

Methods
To apply seam carving to cell images, a SSM is initially generated using a visual attention model and the structural properties of white blood cells are then used to create an energy map for seam carving. As a result, the energy map maximizes the energies of the white blood cells, while minimizing the energies of the red blood cells and background. Thus, the use of a SSM allows the proposed method to reduce the image size efficiently, while preserving the important white blood cells.

Results
Experimental results using the PSNR (Peak Signal-to-Noise Ratio) and ROD (Ratio of Distortion) of blood cell images confirm that the proposed method is able to produce better resizing results than conventional methods, as the seam carving is performed based on an SSM and energy map.

Conclusions
For further improvement, a faster medical image resizing method is currently being investigated to reduce the computation time, while maintaining the same image quality.
Anti-hepatitis B core antigen testing with detection and characterization of occult hepatitis B virus by an in-house nucleic acid testing among blood donors in Behrampur, Ganjam, Orissa in southeastern India: implications for transfusion
Authors: Panigrahi Rajesh , Biswas Avik , Datta Sibnarayan , Banerjee Arup , Chandra Partha K , Mahapatra Pradip K , Patnaik Bharat , Chakrabarti Sekhar , Chakravarty Runu 
Published: September 2010

Abstract

Background
Occult hepatitis B virus (HBV) infection might transmit viremic units into the public blood supply if only hepatitis B surface antigen (HBsAg) testing is used for donor screening. Our aim was to evaluate the prevalence of occult HBV infection among the HBsAg negative/antiHBc positive donations from a highly HIV prevalent region of India.

Methods
A total of 729 HBsAg negative donor units were included in this study. Surface gene and precore region were amplified by in house nucleic acid test (NAT) for detection of occult HBV infection and surface gene was analyzed after direct sequencing.

Results
A total of 220 (30.1%) HBsAg negative donors were antiHBc positive, of them 66 (30%) were HBV DNA positive by NAT. HBV DNA positivity among 164 antiHBc only group, was 27.1% and among 40 antiHBs positive group was 30.0%. HBV/D (93.3%) was predominant and prevalence of both HBV/C and HBV/A was 3.3%. Single or multiple amino acids substitutions were found in 95% samples.

Conclusion
Thus, a considerable number of HBV infected donors remain undiagnosed, if only HBsAg is used for screening. Addition of antiHBc testing for donor screening, although will lead to rejection of a large number of donor units, will definitely eliminate HBV infected donations and help in reducing HBV transmission with its potential consequences, especially among the immunocompromised population. The HBV genetic diversity found in this donor population are in accordance with other parts of India.
Evaluation of a rapid diagnostic test, NanoSign® Influenza A/B Antigen, for detection of the 2009 pandemic influenza A/H1N1 viruses
Authors: Lee Gyu-Cheol , Jeon Eun-Sung , Kim Won-Shik , Le Dung Tien , Yoo Jong-Ha , Chong Chom-Kyu 
Published: September 2010

Abstract

Background
This study evaluated the clinical accuracy and analytical sensitivity of the NanoSign® Influenza A/B antigen kit in detecting 2009 pandemic influenza A/H1N1 viruses. The kit is one of the most popular rapid diagnostic tests for detecting influenza in Republic of Korea.

Results
The NanoSign® Influenza A/B kit resulted in 79.4% sensitivity and 97.2% specificity compared to RT-PCR in the detection of the viruses from 1,023 specimens. In addition, the kit was able to detect two strains of novel influenza viruses, Influenza A/California/12/2009(H1N1) and clinically isolated wild-type novel influenza A/H1N1, both of which are spreading epidemically throughout the world. In addition, the correlation between NanoSign® Influenza A/B test and conventional RT-PCR was approximately 94%, indicating a high concordance rate. Analytical sensitivity of the kit was approximately 73 ± 3.65 ng/mL of the purified viral proteins and 1.13 ± 0.11 hemagglutination units for the cultured virus.

Conclusions
As the NanoSign® Influenza A/B kit showed relatively high sensitivity and specificity and the good correlation with RT-PCR, it will be very useful in the early control of influenza infection and in helping physicians in making early treatment decisions.
Serodiagnosis of sheeppox and goatpox using an indirect ELISA based on synthetic peptide targeting for the major antigen P32
Authors: Tian Hong , Chen Yan , Wu Jinyan , Shang Youjun , Liu Xiangtao 
Published: September 2010

Abstract

Background
Sheeppoxvirus (SPPV), goatpoxvirus (GTPV) and lumpy skin disease virus (LSDV) of cattle belong to the Capripoxvirus genus of the Poxviridae family and can cause significant economic losses in countries where they are endemic. Despite the considerable threat that these viruses pose to livestock production and global trade in sheep, goats, cattle and their products, convenient and effective serodiagnostic tools are not readily available. Toward this goal, two synthetic peptides corresponding to the major antigen P32 were synthesized. These synthetic peptides were then used as antigen to develop an ELISA method to detect anti-SPPV and GTPV antibodies.

Results
The results indicated that the optimal concentration of coated recombinant antigen was 0.2 μg per well for a serum dilution of 1:10. The ELISA performed favorably when sera from sheep immunized experimentally were tested.

Conclusion
This assay offers the prospect of synthetic peptide as antigens for indirect ELISA to detect SPPV and GTPV antibody in sheep and goat sera.