bluuebunny/crossref_metadata_2025_split huggingface dataset:
Waterborne norovirus outbreak in a municipal drinking-water supply in Sweden
Authors: RIERA-MONTES M. , BRUS SJÖLANDER K. , ALLESTAM G. , HALLIN E. , HEDLUND K.-O. , LÖFDAHL M. 
Published: January 2011

SUMMARYDuring Easter 2009, almost 200 people resident in a small Swedish village fell ill with gastrointestinal symptoms. We conducted a retrospective cohort study and a molecular investigation in order to identify the source of the outbreak. Residents living in households connected to the public water network were at an increased risk of developing disease (relative risk 4·80, 95% confidence interval 1·68–13·73) compared to those with no connection to the public network. Norovirus genotype GI.3 was identified in stool samples from six patients and in a sample from the public water network. Contamination of one of the wells supplying the public water network was thought to be the source of the outbreak. This is a description of a norovirus outbreak linked to a municipal drinking-water supply in Sweden. Information from epidemiological and molecular investigations is of utmost importance to guide outbreak control measures and to prevent future outbreaks.
Nader Shah and Persian Naval Expansion in the Persian Gulf, 1700–1747
Authors: AXWORTHY MICHAEL 
Published: January 2011

AbstractThe purpose of this article is to relate a remarkable episode involving Nader Shah's navy and to connect it directly to the wider aims and projects of his regime (notably his ambitions in India), and the central events of his reign. In this way his Persian Gulf policy may emerge not as the oddity it might at first appear, but rather as a consistent element in a coherent larger whole.
Advising the State: Bureaucratic Leadership and the Crisis of Governance in Pakistan, 1952–2000
Authors: NIAZ ILHAN 
Published: January 2011

AbstractThis article examines four important turning points (1952, 1961, 1982 and 2000) in Pakistan's history. In each case, the government of the day, faced with serious challenges, solicited/received advice from the bureaucratic leadership. In each case, the latter placed before the former options that, though often different from conventional wisdom or popular prescriptions, offered real hope of a long-term solution to some of Pakistan's problems. And on each occasion, this advice was rejected or ignored by the politicians, arguably at great cost to the country and to its rulers. This article employs a historian's hindsight and argues that at key points in Pakistan's history the bureaucratic leadership did what it was supposed to – provide sound advice based on empirical appreciation of Pakistan's predicament and the enlightened self-interest of the government. Today, it is widely perceived that Pakistan's senior civil servants do not even bother to advise the politicians in power. Indeed, Pakistan's crisis of state cannot be overcome unless the esprit de corps and professional integrity of the civil service are rebuilt. The consequences of failure on this front are so greatly negative for the entire region that focused and sustained efforts are needed to rehabilitate Pakistan's bureaucratic leadership.
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
Authors: Ogata Hiroyuki , Ray Jessica , Toyoda Kensuke , Sandaa Ruth-Anne , Nagasaki Keizo , Bratbak Gunnar , Claverie Jean-Michel 
Published: January 2011

Abstract
MutS proteins are ubiquitous in cellular organisms and have important roles in DNA mismatch repair or recombination. In the virus world, the amoeba-infecting Mimivirus, as well as the recently sequenced Cafeteria roenbergensis virus are known to encode a MutS related to the homologs found in octocorals and ɛ-proteobacteria. To explore the presence of MutS proteins in other viral genomes, we performed a genomic survey of four giant viruses (‘giruses’) (Pyramimonas orientalis virus (PoV), Phaeocystis pouchetii virus (PpV), Chrysochromulina ericina virus (CeV) and Heterocapsa circularisquama DNA virus (HcDNAV)) that infect unicellular marine algae. Our analysis revealed the presence of a close homolog of Mimivirus MutS in all the analyzed giruses. These viral homologs possess a specific domain structure, including a C-terminal HNH-endonuclease domain, defining the new MutS7 subfamily. We confirmed the presence of conserved mismatch recognition residues in all members of the MutS7 subfamily, suggesting their role in DNA mismatch repair rather than DNA recombination. PoV and PpV were found to contain an additional type of MutS, which we propose to call MutS8. The MutS8 proteins in PoV and PpV were found to be closely related to homologs from ‘Candidatus Amoebophilus asiaticus’, an obligate intracellular amoeba-symbiont belonging to the Bacteroidetes. Furthermore, our analysis revealed that MutS7 and MutS8 are abundant in marine microbial metagenomes and that a vast majority of these environmental sequences are likely of girus origin. Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world.
CO2 and vitamin B12 interactions determine bioactive trace metal requirements of a subarctic Pacific diatom
Authors: King Andrew L , Sañudo-Wilhelmy Sergio A , Leblanc Karine , Hutchins David A , Fu Feixue 
Published: January 2011

Abstract
Phytoplankton growth can be limited by numerous inorganic nutrients and organic growth factors. Using the subarctic diatom Attheya sp. in culture studies, we examined how the availability of vitamin B12 and carbon dioxide partial pressure (pCO2) influences growth rate, primary productivity, cellular iron (Fe), cobalt (Co), zinc (Zn) and cadmium (Cd) quotas, and the net use efficiencies (NUEs) of these bioactive trace metals (mol C fixed per mol cellular trace metal per day). Under B12-replete conditions, cells grown at high pCO2 had lower Fe, Zn and Cd quotas, and used those trace metals more efficiently in comparison with cells grown at low pCO2. At high pCO2, B12-limited cells had ∼50% lower specific growth and carbon fixation rates, and used Fe ∼15-fold less efficiently, and Zn and Cd ∼3-fold less efficiently, in comparison with B12-replete cells. The observed higher Fe, Zn and Cd NUE under high pCO2/B12-replete conditions are consistent with predicted downregulation of carbon-concentrating mechanisms. Co quotas of B12-replete cells were ∼5- to 14-fold higher in comparison with B12-limited cells, suggesting that &gt;80% of cellular Co of B12-limited cells was likely from B12. Our results demonstrate that CO2 and vitamin B12 interactively influence growth, carbon fixation, trace metal requirements and trace metal NUE of this diatom. This suggests the need to consider complex feedback interactions between multiple environmental factors for this biogeochemically critical group of phytoplankton in the last glacial maximum as well as the current and future changing ocean.
Analysis of N-Glycosylation Sites in HIV glycoprotein 160
Authors: Mandage Rajendra 
Published: January 2011

AbstractHIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system, which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that there are increased numbers of isoleucine and threonine residues around the N-glycosylation sites in comparison with the nonglycosylated asparagine residues. Preferential occurrence of amino acid residues around the glycosylation site shows that T has the maximum preference around the N-glycosylation site. T at 3 and/or -3 positions strongly favors glycosylation irrespective of other glycosylation sites. The data presented in the present work clearly indicate that there is a pronounced positional preference for the hydrophobic and neutral amino acids at various positions around the N-glycosylation site. In the future it will be of much interest to investigate further the possible structural and conformational implications of some of these suggested positional preferences of the various amino acids around the site of glycosylation. This is a potentially important study, and such analyses will surely contribute an important part of our knowledge base in the future on HIV research. These results will be of interest to molecular biologists and protein engineers to identify N-glycosylation sites important in molecular recognition processes in HIV virus.
Efficient simulation under a population genetics model of carcinogenesis
Authors: Zhu Tianqi , Hu Yucheng , Ma Zhi-Ming , Zhang De-Xing , Li Tiejun , Yang Ziheng 
Published: January 2011

Abstract
Motivation: Cancer is well known to be the end result of somatic mutations that disrupt normal cell division. The number of such mutations that have to be accumulated in a cell before cancer develops depends on the type of cancer. The waiting time Tm until the appearance of m mutations in a cell is thus an important quantity in population genetics models of carcinogenesis. Such models are often difficult to analyze theoretically because of the complex interactions of mutation, drift and selection. They are also computationally expensive to simulate because of the large number of cells and the low mutation rate.
Results: We develop an efficient algorithm for simulating the waiting time Tm until m mutations under a population genetics model of cancer development. We use an exact algorithm to simulate evolution of small cell populations and coarse-grained τ-leaping approximation to handle large populations. We compared our hybrid simulation algorithm with the exact algorithm in small populations and with available asymptotic results for large populations. The comparison suggested that our algorithm is accurate and computationally efficient. We used the algorithm to study the waiting time for up to 20 mutations under a Moran model with variable population sizes. Our new algorithm may be useful for studying realistic models of carcinogenesis, which incorporates variable mutation rates and fitness effects.
Contact: z.yang@ucl.ac.uk
Convalescent Plasma Treatment Reduced Mortality in Patients With Severe Pandemic Influenza A (H1N1) 2009 Virus Infection
Authors: Hung Ivan FN , To Kelvin KW , Lee Cheuk-Kwong , Lee Kar-Lung , Chan Kenny , Yan Wing-Wah , Liu Raymond , Watt Chi-Leung , Chan Wai-Ming , Lai Kang-Yiu , Koo Chi-Kwan , Buckley Tom , Chow Fu-Loi , Wong Kwan-Keung , Chan Hok-Sum , Ching Chi-Keung , Tang Bone SF , Lau Candy CY , Li Iris WS , Liu Shao-Haei , Chan Kwok-Hung , Lin Che-Kit , Yuen Kwok-Yung 
Published: January 2011

Background. Experience from treating patients with Spanish influenza and influenza A(H5N1) suggested that convalescent plasma therapy might be beneficial. However, its efficacy in patients with severe pandemic influenza A(H1N1) 2009 virus (H1N1 2009) infection remained unknown.Methods. During the period from 1 September 2009 through 30 June 2010, we conducted a prospective cohort study by recruiting patients aged ≥18 years with severe H1N1 2009 infection requiring intensive care. Patients were offered treatment with convalescent plasma with a neutralizing antibody titer of ≥1:160, harvested by apheresis from patients recovering from H1N1 2009 infection. Clinical outcome was compared with that of patients who declined plasma treatment as the untreated controls.Results. Ninety-three patients with severe H1N1 2009 infection requiring intensive care were recruited. Twenty patients (21.5%) received plasma treatment. The treatment and control groups were matched by age, sex, and disease severity scores. Mortality in the treatment group was significantly lower than in the nontreatment group (20.0% vs 54.8%; P =  .01). Multivariate analysis showed that plasma treatment reduced mortality (odds ratio [OR], .20; 95% confidence interval [CI], .06-.69; P =  .011), whereas complication of acute renal failure was independently associated with death (OR, 3.79; 95% CI, 1.15-12.4; P =  .028). Subgroup analysis of 44 patients with serial respiratory tract viral load and cytokine level demonstrated that plasma treatment was associated with significantly lower day 3, 5, and 7 viral load, compared with the control group (P &lt;  .05). The corresponding temporal levels of interleukin 6, interleukin 10, and tumor necrosis factor α (P &lt;  .05) were also lower in the treatment group.Conclusions. Treatment of severe H1N1 2009 infection with convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality.
Coexpression-Based Clustering of Arabidopsis Root Genes Predicts Functional Modules in Early Phosphate Deficiency Signaling
Authors: Lin Wen-Dar , Liao Ya-Yun , Yang Thomas J.W. , Pan Chao-Yu , Buckhout Thomas J. , Schmidt Wolfgang 
Published: January 2011

AbstractPhosphate (Pi) deficiency triggers the differential expression of a large set of genes, which communally adapt the plant to low Pi bioavailability. To infer functional modules in early transcriptional responses to Pi deficiency, we conducted time-course microarray experiments and subsequent coexpression-based clustering of Pi-responsive genes by pairwise comparison of genes against a customized database. Three major clusters, enriched in genes putatively functioning in transcriptional regulation, root hair formation, and developmental adaptations, were predicted from this analysis. Validation of gene expression by quantitative reverse transcription-PCR revealed that transcripts from randomly selected genes were robustly induced within the first hour after transfer to Pi-deplete medium. Pectin-related processes were among the earliest and most robust responses to Pi deficiency, indicating that cell wall alterations are critical in the early transcriptional response to Pi deficiency. Phenotypical analysis of homozygous mutants defective in the expression of genes from the root hair cluster revealed eight novel genes involved in Pi deficiency-induced root hair elongation. The plants responded rapidly to Pi deficiency by the induction of a subset of transcription factors, followed by a repression of genes involved in cell wall alterations. The combined results provide a novel, integrated view at a systems level of the root responses that acclimate Arabidopsis (Arabidopsis thaliana) to suboptimal Pi levels.
Development of an automated MODS plate reader to detect early growth of Mycobacterium tuberculosis
Authors: COMINA G. , MENDOZA D. , VELAZCO A. , CORONEL J. , SHEEN P. , GILMAN R.H. , MOORE D.A.J. , ZIMIC M. 
Published: January 2011

SummaryIn this work, an automated microscopic observation drug susceptibility (MODS) plate reader has been developed. The reader automatically handles MODS plates and after autofocussing digital images are acquired of the characteristic microscopic cording structures of Mycobacterium tuberculosis, which are the identification method utilized in the MODS technique to detect tuberculosis and multidrug resistant tuberculosis. In conventional MODS, trained technicians manually move the MODS plate on the stage of an inverted microscope while trying to locate and focus upon the characteristic microscopic cording colonies. In centres with high tuberculosis diagnostic demand, sufficient time may not be available to adequately examine all cultures. An automated reader would reduce labour time and the handling of M. tuberculosis cultures by laboratory personnel. Two hundred MODS culture images (100 from tuberculosis positive and 100 from tuberculosis negative sputum samples confirmed by a standard MODS reading using a commercial microscope) were acquired randomly using the automated MODS plate reader. A specialist analysed these digital images with the help of a personal computer and designated them as M. tuberculosis present or absent. The specialist considered four images insufficiently clear to permit a definitive reading. The readings from the 196 valid images resulted in a 100% agreement with the conventional nonautomated standard reading. The automated MODS plate reader combined with open‐source MODS pattern recognition software provides a novel platform for high throughput automated tuberculosis diagnosis.
Making red squirrels more visible: the use of baited visual counts to monitor populations
Authors: GURNELL John , MCDONALD Robbie , LURZ Peter W. W. 
Published: January 2011

ABSTRACTUnderstanding changes in the distribution and abundance of the red squirrel Sciurus vulgaris in Europe, as a result of the spread of the introduced North American grey squirrel Sciurus carolinensis, is vital to planning and implementing red squirrel conservation measures. We studied the effectiveness of a variation on a common method of monitoring squirrels, standardised visual counts that made use of a diffuse baiting approach to increase their detectability. Significantly more sightings of squirrels occurred on baited than on unbaited visual transect lines in trials with the assistance of volunteers, and we recommend the use of baits in future studies.
Developing a holistic approach to obesity management
Authors: Brown Jenny , Wimpenny Peter 
Published: January 2011

Brown J, Wimpenny P. International Journal of Nursing Practice 2011; 17: 9–18 Developing a holistic approach to obesity management The aim of this paper is to discuss the theoretical background and relevance of a holistic approach to obesity management by nurses. There is a global rise in the number of people with obesity, such that it now represents one of the major health challenges. However, nurses are often influenced by physical and dietetic focused approaches and could fail to acknowledge a range of other factors that can impact on weight management. As part of the development of a holistic approach to obesity a literature search was undertaken to establish relevant theoretical perspectives that underpin practice in physical, psychological and social aspects of care (focused on the period 1995–2005). In addition, experiences of working in a secondary care weight management clinic were also drawn upon. Psychobiological, attribution and social support theories were identified that could contribute to a better understanding of obesity. If these theoretical perspectives and supporting evidence can be integrated in a holistic approach to care and management it might be possible to promote better health and well‐being in those with obesity. Creating a greater understanding of the range of theoretical perspectives and supporting evidence related to obesity could, it is argued, provide enhanced care and management.
The changes in health‐related quality of life and related factors during the process of total hip arthroplasty
Authors: Montin Liisa , Suominen Tarja , Haaranen Ella , Katajisto Jouko , Lepistö Jyri , Leino‐Kilpi Helena 
Published: January 2011

Montin L, Suominen T, Haaranen E, Katajisto J, Lepistö J, Leino‐Kilpi H. International Journal of Nursing Practice 2011; 17: 19–26 The changes in health‐related quality of life and related factors during the process of total hip arthroplasty This study was carried out to measure changes in health‐related quality of life (HRQOL) in patients (n = 100) undergoing total hip arthoplasty. The Sickness Impact Profile was used to measure patients' dysfunctions in 12 different categories post surgery. Improvement was observed in each category and dimension already at 3 months and at 6 months. Preoperative pain showed a statistically significant although declining correlation both with total, and with Physical and the Psychosocial dimensions of HRQOL. The greatest improvements were found in the categories Body Care and Movement, Ambulation, Alertness Behaviour, Social Interaction, Recreation and Pastimes and in Sleep and Rest. Patients' pain decreased, and 72% reported no pain at 6 months post the surgery. Patients' perceptions of their pain should be gathered carefully when deciding the need and timing for the surgery in order to minimize impairments into HRQOL.
Living a meaningful life with chronic pain from a nursing perspective. Narrative approach to a case story
Authors: Dysvik Elin , Sommerseth Rita , Jacobsen Frode F 
Published: January 2011

Dysvik E, Sommerseth R, Jacobsen FF. International Journal of Nursing Practice 2011; 17: 36–42 Living a meaningful life with chronic pain from a nursing perspective. Narrative approach to a case story This paper is a case story discussing the experience of chronic pain from the perspective of the sufferer and suggests ways of improving the use of this perspective in nursing care. A narrative approach is adopted and the analysis was based on content analysis. A condensation of meaning‐units revealed a variation in subthemes: the body in pain, striving to preserve self and self‐fulfilment. The extent to which living a meaningful life is possible seems to depend on several complex factors, including a person's belief system, life experiences, personal resources, the meaning of pain and the extent to which nurses understand the overall situation. This story might indicate that nociceptive pain can be less important than pain that reduces long‐term life quality. A better understanding of living with chronic pain based on cognitive–behavioural techniques could be linked to the information drawn from the narrative and used to improve nursing practice.
Sequential therapy in clarithromycin‐sensitive and ‐resistant Helicobacter pylori based on polymerase chain reaction molecular test
Authors: Mahachai Varocha , Sirimontaporn Nathavut , Tumwasorn Somying , Thong‐Ngam Duangporn , Vilaichone Ratha‐Korn 
Published: January 2011

AbstractBackground and Aim:  The present study was designed to determine the eradication rate of 10 day sequential therapy in genotypic clarithromycin‐resistant Helicobacter pylori group identified by molecular polymerase chain reaction (PCR) detection in Thai patients.Methods:  Between May 2007 and June 2010, patients who had undergone gastroscopic examination at the King Chulalongkorn Memorial Hospital, for dyspeptic symptoms were recruited. Two biopsy samples from gastric antrum were obtained, one for rapid urease test and another for PCR. PCR‐sequencing was performed to determine point mutations in 23S rRNA gene. Patients received 10 day sequential therapy consisting of lanzoprazole 30 mg and amoxicillin 1 g twice daily for 5 days followed by lanzoprazole 30 mg, clarithromycin 500 mg and nitroimidazole 500 mg twice daily for the remaining 5 days. Urea breath test (UBT) was performed to assess eradication therapy.Results:  A total of 151 patients (mean age 52.7 years, 75 males and 76 females) were recruited in this study. All patients completed sequential therapy without significant side effects. Point mutations at A2143G and A2142G were detected in 17 patients (11.3%). Overall eradication rate was 94%. The eradication rate in the group with point mutation was significantly lower than the eradication rate in the group without point mutation (64.7% vs 97.8%; odds ratio = 19.6 and 95% confidence interval = 4.3–88.8; P < 0.0001).Conclusion:  Genotypic clarithromycin resistance was detected in only 11.3% of H. pylori infections in Thailand. Sequential therapy is highly effective in clarithromycin‐sensitive but is less effective in clarithromycin‐resistant H. pylori. PCR‐molecular test could be a useful tool to identify antimicrobial resistance for optimizing an eradication regimen.