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1.  High-throughput screen of essential gene modules in Mycobacterium tuberculosis: a bibliometric approach 
BMC Infectious Diseases  2013;13:227.
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). The annotation of functional genome and signaling network in M. tuberculosis are still not systematic. Essential gene modules are a collection of functionally related essential genes in the same signaling or metabolic pathway. The determination of essential genes and essential gene modules at genomic level may be important for better understanding of the physiology and pathology of M. tuberculosis, and also helpful for the development of drugs against this pathogen. The establishment of genomic operon database (DOOR) and the annotation of gene pathways have felicitated the genomic analysis of the essential gene modules of M. tuberculosis.
Bibliometric approach has been used to perform a High-throughput screen for essential genes of M. tuberculosis strain H37Rv. Ant colony algorithm were used to identify the essential genes in other M. tuberculosis reference strains. Essential gene modules were analyzed by operon database DOOR. The pathways of essential genes were assessed by Biocarta, KEGG, NCI-PID, HumanCyc and Reactome. The function prediction of essential genes was analyzed by Pfam.
A total approximately 700 essential genes were identified in M. tuberculosis genome. 40% of operons are consisted of two or more essential genes. The essential genes were distributed in 92 pathways in M. tuberculosis. In function prediction, 61.79% of essential genes were categorized into virulence, intermediary metabolism/respiration,cell wall related and lipid metabolism, which are fundamental functions that exist in most bacteria species.
We have identified the essential genes of M. tuberculosis using bibliometric approach at genomic level. The essential gene modules were further identified and analyzed.
PMCID: PMC3680244  PMID: 23687949
Mycobacterium tuberculosis; Essential gene modules; Operon; Pathway
2.  A new tool for the paediatric HIV research: general data from the Cohort of the Spanish Paediatric HIV Network (CoRISpe) 
There are approximately from 1,100 to 1,200 HIV-infected children in a follow-up in Spain. In 2008 an open, multicentral, retrospective and prospective Cohort of the Spanish Paediatric HIV Network (CoRISpe) was founded. The CoRISpe is divided into the node 1 and node 2 representing geographically almost the whole territory of Spain. Since 2008 seventy-five hospitals have been participating in the CoRISpe. All the retrospective data of the HIV-infected children have been kept in the CoRISpe since 1995 and prospective data since 2008. In this article we are going to present the notion of CoRISpe, its role, the structure, how the CoRISpe works and the process how a child is transferred from Paediatric to Adults Units.
The main objective of the CoRISpe is to contribute to furthering scientific knowledge on paediatric HIV infection by providing demographic, sociopsychological, clinical and laboratory data from HIV-infected paediatric patients. Its aim is to enable high-quality research studies on HIV-infected children.
PMCID: PMC3544738  PMID: 23282073
HIV paediatric cohort; Paediatric HIV infection; Spanish HIV HGM biobank
3.  The prevalence of anal human papillomavirus among young HIV negative men who have sex with men 
BMC Infectious Diseases  2012;12:341.
Men who have sex with men (MSM) especially those who are HIV positive are at risk for HPV-associated anal cancer. We systematically reviewed studies with data on the prevalence of vaccine preventable anal HPV among men who have sex with men aged 25 or younger and identified 6 studies. None of these studies were specifically designed to determine the prevalence of HPV in this population. Available data, albeit limited, suggest many young MSM may not already be HPV infected. Further studies using representative sampling focused on teenage MSM are required to confirm this.
PMCID: PMC3538051  PMID: 23217024
Human papillomavirus (HPV); Men who have sex with men; Prevalence
4.  Does the adoption of EUCAST susceptibility breakpoints affect the selection of antimicrobials to treat acute community-acquired respiratory tract infections? 
BMC Infectious Diseases  2012;12:181.
In several European Countries, by the end of 2012, CLSI guidelines will be replaced by EUCAST. We compared antimicrobial susceptibility results of a large number of respiratory pathogens using both EUCAST and previously adopted CLSI criteria to evaluate the impact on susceptibility patterns and the possible consequences that could occur in clinical practice due to this replacement.
For S. pyogenes and S. aureus, the interpretation of susceptibility data using the EUCAST criteria did not produce relevant changes in comparison to CLSI.
Against S. pneumoniae, more restrictive EUCAST breakpoints could lead to increased benzylpenicillin and/or amoxicillin-clavulanate resistance rates, which in turn could translate in increased dosages of these antibiotics or usage of alternative agents for respiratory tract infections.
Against S. pneumoniae, M. catarrhalis and H. influenzae, cefuroxime-axetil and cefaclor produced the most divergent results depending on the breakpoints adopted and these striking differences could lead to the revision of those guidelines suggesting these two cephalosporins as alternatives in the management of upper respiratory tract infections.
Many differences exist between CLSI and EUCAST breakpoints. However, only in a few cases do these differences translate in major interpretive category discrepancies. In countries adopting more restrictive EUCAST breakpoints, clinicians should be aware of these discrepancies and that they could be faced with antibiotic-resistant respiratory pathogens more frequently than before.
The interpretive discrepancies between EUCAST and CLSI suggest that the discussion on the management of community-acquired respiratory tract infections is still open and further studies are desirable to better define the role of some antibiotics.
PMCID: PMC3449191  PMID: 22866984
CLSI; Interpretive criteria; Resistance; Antibiotics; S. pneumoniae; H. influenzae; S. aureus; M. catarrhalis
5.  “Blind periods” in screening for toxoplasmosis in pregnancy in Austria – a debate 
BMC Infectious Diseases  2012;12:118.
Recent studies from Austria, France and Italy have shown that there is a poor adherence to the screening scheme for maternal Toxoplasma infections in pregnancy demonstrated by the fact that many recommended examinations are missed. This leads to undetected infections and limits our knowledge of incidence of the disease. We discuss the negative consequences of this situation on research on treatment effectiveness and the outcomes of congenital toxoplasmosis. The responsible public health institutions should assume responsibility for appropriate surveillance of the screening programme and take measures to improve screening adherence during pregnancy. Screening should start as early as possible in pregnancy and the latest test should be done at delivery. Screening schedule should allow distinguishing infections from the first, second and third trimester of pregnancy, as the risk of materno-foetal transmission and outcomes in case of foetal infections varies by time.
PMCID: PMC3476441  PMID: 22591211
6.  Ebola haemorrhagic fever outbreak in Masindi District, Uganda: outbreak description and lessons learned 
BMC Infectious Diseases  2011;11:357.
Ebola haemorrhagic fever (EHF) is infamous for its high case-fatality proportion (CFP) and the ease with which it spreads among contacts of the diseased. We describe the course of the EHF outbreak in Masindi, Uganda, in the year 2000, and report on response activities.
We analysed surveillance records, hospital statistics, and our own observations during response activities. We used Fisher's exact tests for differences in proportions, t-tests for differences in means, and logistic regression for multivariable analysis.
The response to the outbreak consisted of surveillance, case management, logistics and public mobilisation. Twenty-six EHF cases (24 laboratory confirmed, two probable) occurred between October 21st and December 22nd, 2000. CFP was 69% (18/26). Nosocomial transmission to the index case occurred in Lacor hospital in Gulu, outside the Ebola ward. After returning home to Masindi district the index case became the origin of a transmission chain within her own extended family (18 further cases), from index family members to health care workers (HCWs, 6 cases), and from HCWs to their household contacts (1 case). Five out of six occupational cases of EHF in HCWs occurred after the introduction of barrier nursing, probably due to breaches of barrier nursing principles. CFP was initially very high (76%) but decreased (20%) due to better case management after reinforcing the response team. The mobilisation of the community for the response efforts was challenging at the beginning, when fear, panic and mistrust had to be countered by the response team.
Large scale transmission in the community beyond the index family was prevented by early case identification and isolation as well as quarantine imposed by the community. The high number of occupational EHF after implementing barrier nursing points at the need to strengthen training and supervision of local HCWs. The difference in CFP before and after reinforcing the response team together with observations on the ward suggest a critical role for intensive supportive treatment. Collecting high quality clinical data is a priority for future outbreaks in order to identify the best possible FHF treatment regime under field conditions.
PMCID: PMC3276451  PMID: 22204600
7.  Pattern and determinants of HIV research productivity in sub-Saharan Africa: bibliometric analysis of 1981 to 2009 PubMed papers 
Several bibliometric studies have been published on AIDS. The findings obtained from these studies have provided a general picture of the history and growth of AIDS literature. However, factors related to variation in HIV research productivity in sub-Saharan Africa have not been examined. Therefore, this study aims to fill some of the gap in existing research to provide insights into factors associated with HIV research productivity in sub-Saharan Africa.
A bibliometric analysis regarding sub-Saharan Africa HIV/AIDS research was conducted in the PubMed database for the period of 1981 to 2009. The numbers of HIV research articles indexed in PubMed was used as surrogate for total HIV research productivity. Series of univariable and multivariable negative binomial regression models were used to explore factors associated with variation in HIV research productivity in sub-Saharan Africa.
First authors from South Africa, Uganda and Kenya contributed almost half of the total number of HIV articles indexed in PubMed between 1981 and 2009. Uganda, Zimbabwe and Malawi had better records when the total production was adjusted for gross domestic product (GDP). Comoros, the Gambia and Guinea-Bissau were the most productive countries when the total products were normalized by number of people with HIV. There were strong positive and statistically significant correlation between countries number of indexed journal (Pearson correlation r = 0.77, p = .001), number of higher institutions (r = 0.60, p = .001), number of physicians (r = 0.83, p = .001) and absolute numbers of HIV articles.
HIV research productivity in Africa is highly skewed. To increase HIV research output, total expenditure on health (% of GDP), private expenditure on health, and adult literacy rate may be important factors to address.
PMCID: PMC2841182  PMID: 20205717
8.  Evidence and rationale for the World Health Organization recommended standards for Japanese encephalitis surveillance 
Japanese encephalitis (JE) is the most important form of viral encephalitis in Asia. Surveillance for the disease in many countries has been limited. To improve collection of accurate surveillance data in order to increase understanding of the full impact of JE and monitor control programs, World Health Organization (WHO) Recommended Standards for JE Surveillance have been developed. To aid acceptance of the Standards, we describe the process of development, provide the supporting evidence, and explain the rationale for the recommendations made in the document.
A JE Core Working Group was formed in 2002 and worked on development of JE surveillance standards. A series of questions on specific topics was initially developed. A literature review was undertaken and the findings were discussed and documented. The group then prepared a draft document, with emphasis placed on the feasibility of implementation in Asian countries. A field test version of the Standards was published by WHO in January 2006. Feedback was then sought from countries that piloted the Standards and from public health professionals in forums and individual meetings to modify the Standards accordingly.
After revisions, a final version of the JE surveillance standards was published in August 2008. The supporting information is presented here together with explanations of the rationale and levels of evidence for specific recommendations.
Provision of the supporting evidence and rationale should help to facilitate successful implementation of the JE surveillance standards in JE-endemic countries which will in turn enable better understanding of disease burden and the impact of control programs.
PMCID: PMC2809064  PMID: 20038298
9.  Mapping the history and current situation of research on John Cunningham virus – a bibliometric analysis 
John Cunningham virus (JCV) constitutes a family of polyoma viruses, which plays important roles in the progressive multifocal leukoencephalopathy (PML) and tumorigenesis. However, no bibliometric investigation has been reported to guide the researchers and potential readers.
Papers were collected from database Sci-expanded and Pubmed until May 22, 2008. The highly-productive authors, institutes and countries, highly-cited authors and journals were ranked. The highly-cited articles were subjected to co-citation and chronological analysis with highly-frequent MeSH words for co-occurrence analysis.
Until now, 1785 articles about JCV were indexed in Sci-expanded and 1506 in Pubmed. The main document type was original article. USA, Japan and Italy were the largest three producers about JCV. Temple University published 128 papers and ranked the top, followed by University of Tokyo. Khalili K and Yogo Y became the core authors due to more than 20 documents produced. Journal of Neurovirology published more than 15 papers and ranked the top. Padgett BL and Berger JR were the first two highly-cited authors. Journal of Virology and Journal of Neurovirology respectively ranked to the first two highly-cited journals. These top highly-cited articles were divided into 5 aspects: (1) The correlation between JC virus and tumors; (2) Causal correlation of JCV with PML; (3) Polyoma virus infection and its related diseases in renal-allograft recipients; (4) Detection of JCV antibody, oncogene and its encoding protein; (5) Genetics and molecular biology of JCV. The MeSH/subheadings were classified into five groups: (1) JCV and virus infectious diseases; (2) JCV pathogenicity and pathological appearance of PML; (3) JCV isolation and detection; (4) Immunology of JCV and PML; (5) JCV genetics and tumors.
JCV investigation mainly focused on its isolation and detection, as well as its correlation with PML and tumors. Establishment of transgenic animal model using JCV T antigen would be a hopeful and useful project in the further study.
PMCID: PMC2667186  PMID: 19284593
10.  HIV/AIDS in Nigeria: a bibliometric analysis 
Nigeria is home to more people living with HIV than any other country in the world, except South Africa and India-where an estimated 2.9 million [1.7 million – 4.2 million] people were living with the virus in 2005. A systematic assessment of recent HIV/AIDS research output from Nigeria is not available. Without objective information about the current deficiencies and strengths in the HIV research output from Nigeria, it is difficult to plan substantial improvements in HIV/AIDS research that could enhance population health. The aim of this study was to analyse the trends in Nigeria's SCI publications in HIV/AIDS from 1980 to 2006. Special attention was paid to internationally collaborated works that were identified based on the countries of the authors' affiliation.
A bibliometric analysis regarding Nigerian HIV/AIDS research was conducted in the ISI databases for the period of 1980 to 2006. An attempt was made to identify the patterns of the growth in HIV/AIDS literature, as well as type of document published, authorship, institutional affiliations of authors, and subject content. International collaboration was deemed to exist in an article if any co-author's affiliation was located outside Nigeria. The impact factors in the 2006 Journal Citations Reports Science Edition was arbitrarily adopted to estimate the quality of articles.
Nigeria's ISI publications in HIV/AIDS increased from one articles in 1987 to 33 in 2006, and the articles with international collaboration increased from one articles in 1980 to 16 in 2006. Articles with international collaboration appeared in journals with higher impact factors and received more citations. A high pattern of co-authorship was found. Over 85% of the articles were published in collaboration among two or more authors. The USA, as the most important collaborating partner of Nigeria's HIV/AIDS researchers, contributed 30.8% of articles with international collaboration.
Nigeria has achieved a significant increase in the number of SCI publications and collaborations in HIV literature from 1987 to 2005. There is need to challenge the status, scientists from Nigeria should forge multiple collaborations beyond historical, political, and cultural lines to share knowledge and expertise on HIV/AIDS.
PMCID: PMC2268690  PMID: 18302752
11.  Whole blood gene expression in infants with respiratory syncytial virus bronchiolitis 
Respiratory syncytial virus (RSV) is a major cause of viral bronchiolitis in infants worldwide, and environmental, viral and host factors are all of importance for disease susceptibility and severity. To study the systemic host response to this disease we used the microarray technology to measure mRNA gene expression levels in whole blood of five male infants hospitalised with acute RSV, subtype B, bronchiolitis versus five one year old male controls exposed to RSV during infancy without bronchiolitis. The gene expression levels were further evaluated in a new experiment using quantitative real-time polymerase chain reaction (QRT-PCR) both in the five infants selected for microarray and in 13 other infants hospitalised with the same disease.
Among the 30 genes most differentially expressed by microarray nearly 50% were involved in immunological processes. We found the highly upregulated interferon, alpha-inducible protein 27 (IFI27) and the highly downregulated gene Charcot-Leyden crystal protein (CLC) to be the two most differentially expressed genes in the microarray study. When performing QRT-PCR on these genes IFI27 was upregulated in all but one infant, and CLC was downregulated in all 18 infants, and similar to that given by microarray.
The gene IFI27 is upregulated and the gene CLC is downregulated in whole blood of infants hospitalised with RSV, subtype B, bronchiolitis and is not reported before. More studies are needed to elucidate the specificity of these gene expressions in association with host response to this virus in bronchiolitis of moderate severity.
PMCID: PMC1713240  PMID: 17166282

Results 1-11 (11)