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1.  Osteonecrosis of jaws related to intravenous bisphosphonates: the experience of a Jordanian teaching hospital 
We describe our experience with oncology patients on a frequent dosing schedule of intravenous (i.v.) bisphosphonates at the Jordan University Hospital (JUH).
Patients treated by i.v. bisphosphonates in the medical oncology unit at the JUH were examined for bisphosphonate-related osteonecrosis of the jaws (BRONJ). Diagnosis was made according to the guidelines of the American Association of Oral and Maxillofacial Surgeons (AAOMS) original position paper.
Of the 41 patients, four developed BRONJ, two in maxilla, one in mandible and one bimaxillary. Patients with BRONJ were older; mean age was 69.3 ±3.1 years compared to 62.8 ± 12.5 years (P = 0.022). Dental co-morbidities were more commonly present in patients with the disease (P = 0.038). Patients who developed BRONJ were on treatment for a longer duration of time; the mean duration of treatment was 23.5 ± 8.4 months compared to 11.9 ± 13.4 months (P = 0.10).
The results of this case series demonstrated that age and poor oral health status are significant risk factors of BRONJ for oncology patients on long-term frequent dosing schedule of i.v. bisphosphonates.
PMCID: PMC3182791  PMID: 20522306
Bisphosphonates; Osteonecrosis of jaw; Chemotherapy
2.  An effective active surveillance method for controlling nosocomial MRSA transmission in a Japanese hospital 
Hospital-wide active surveillance for methicillin-resistant Staphylococcus aureus (MRSA) targeted to adult patients with a history of MRSA carriage within the past 5 years was performed in Juntendo University Hospital (JUH) over a 2-year period. In the first year, MRSA screening culture was ordered by physicians in charge. In the second year, infection-control practitioners (ICPs) took samples for active surveillance culture. The average monthly transmission rate of MRSA in JUH was 0.35 per 1,000 bed-days in the first year and decreased significantly to 0.26 per 1,000 bed-days in the second year (P < 0.05). In the second year, more active commitment of ICPs to MRSA screening was effective in improving the performance rate of screening, shortening turn-around time of screening results, and decreasing transmission rate. Increasing compliance with active MRSA surveillance by involvement of ICPs, targeting patients with a previous history of MRSA carriage in the previous 5 years, was effective to control nosocomial MRSA transmission.
PMCID: PMC3824935  PMID: 23558667
Methicillin-resistant Staphylococcus aureus; Active surveillance; Horizontal transmission
3.  Coordination in networks for improved mental health service 
Well-organised clinical cooperation between health and social services has been difficult to achieve in Sweden as in other countries. This paper presents an empirical study of a mental health coordination network in one area in Stockholm. The aim was to describe the development and nature of coordination within a mental health and social care consortium and to assess the impact on care processes and client outcomes.
Data was gathered through interviews with ‘joint coordinators’ (n=6) from three rehabilitation units. The interviews focused on coordination activities aimed at supporting the clients’ needs and investigated how the joint coordinators acted according to the consortium's holistic approach. Data on The Camberwell Assessment of Need (CAN-S) showing clients’ satisfaction was used to assess on set of outcomes (n=1262).
The findings revealed different coordination activities and factors both helping and hindering the network coordination activities. One helpful factor was the history of local and personal informal cooperation and shared responsibilities evident. Unclear roles and routines hindered cooperation.
This contribution is an empirical example and a model for organisations establishing structures for network coordination. One lesson for current policy about integrated health care is to adapt and implement joint coordinators where full structural integration is not possible. Another lesson, based on the idea of patient quality by coordinated care, is specifically to adapt the work of the local addiction treatment and preventive team (ATPT)—an independent special team in the psychiatric outpatient care that provides consultation and support to the units and serves psychotic clients with addictive problems.
PMCID: PMC2948678  PMID: 20922065
coordination; integrated care planning; mental health care
4.  The eMERGE Network: A consortium of biorepositories linked to electronic medical records data for conducting genomic studies 
BMC Medical Genomics  2011;4:13.
The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science. eMERGE also includes a special emphasis on the ethical, legal and social issues related to these endeavors.
The five sites are supported by an Administrative Coordinating Center. Setting of network goals is initiated by working groups: (1) Genomics, (2) Informatics, and (3) Consent & Community Consultation, which also includes active participation by investigators outside the eMERGE funded sites, and (4) Return of Results Oversight Committee. The Steering Committee, comprised of site PIs and representatives and NHGRI staff, meet three times per year, once per year with the External Scientific Panel.
Current progress
The primary site-specific phenotypes for which samples have undergone genome-wide association study (GWAS) genotyping are cataract and HDL, dementia, electrocardiographic QRS duration, peripheral arterial disease, and type 2 diabetes. A GWAS is also being undertaken for resistant hypertension in ≈2,000 additional samples identified across the network sites, to be added to data available for samples already genotyped. Funded by ARRA supplements, secondary phenotypes have been added at all sites to leverage the genotyping data, and hypothyroidism is being analyzed as a cross-network phenotype. Results are being posted in dbGaP. Other key eMERGE activities include evaluation of the issues associated with cross-site deployment of common algorithms to identify cases and controls in EMRs, data privacy of genomic and clinically-derived data, developing approaches for large-scale meta-analysis of GWAS data across five sites, and a community consultation and consent initiative at each site.
Future activities
Plans are underway to expand the network in diversity of populations and incorporation of GWAS findings into clinical care.
By combining advanced clinical informatics, genome science, and community consultation, eMERGE represents a first step in the development of data-driven approaches to incorporate genomic information into routine healthcare delivery.
PMCID: PMC3038887  PMID: 21269473
5.  The acceptability of the female condom: Perspectives of family planning providers in New York City, South Africa, and Nigeria 
This article seeks to fill the gap in female condom acceptability research by examining family planning (FP) providers' attitudes and experiences regarding the female condom in three countries (South Africa, the US, and Nigeria) to highlight providers' potential integral role in the introduction of the female condom. The case studies used data drawn from three independent projects, each of which was designed to study or to change FP providers' attitudes and practices in relation to the female condom. The case study for New York City used data from semistructured interviews with providers in one FP consortium in which no special female condom training had been undertaken. The data from South Africa were drawn from transcripts and observations of a female condom training program and from interviews conducted in preparation for the training. The Nigerian study used observations of client visits before and after providers were trained concerning the female condom. In New York City, providers were skeptical about the contraceptive efficacy of the female condom, with only 8 of 22 providers (36%) reporting they would recommend it as a primary contraceptive. In South Africa, providers who had practiced insertion of the female condom as part of their training expressed concern about its physical appearance and effects on sexual pleasure. However, they also saw the female condom as a tool to empower clients to increase their capacity for self-protection. Structured observations of providers' counseling interactions with clients following training indicated that Nigerian providers discussed the female condom with clients in 80% of the visits observed. Despite the lack of a uniform methodology, the three case studies illuminate various dimensions of FP providers' perceptions of the acceptability of the female condom. FP providers must be viewed as a critical factor in female condom acceptability, uptake, and continued use. Designing training programs and other interventions that address sources of provider resistance and enhance providers' skills in teaching female condom negotiation strategies may help to increase clients' use of the female condom.
PMCID: PMC3455873  PMID: 11796812
Acceptability; Dual protection; Family planning; Female condom; Health care providers; HIV/AIDS and STD prevention; Training
The Journal of General Physiology  1941;25(1):147-165.
These papers give an account of an optical and x-ray examination of preparations of plant virus substances isolated by Bawden and Pirie, in particular of those of tobacco mosaic disease. They open with a historical survey of the work, indicating the order in which new phenomena were discovered. The subsequent treatment is divided into three parts: I. Introduction and preparation of specimens. II. Modes of aggregation of virus particles. III. (1) The structure of the particles. (2) Biological implications. Part I, after an historical introduction, describes the method of preparation, from solutions of the virus, of optically oriented specimens of different concentrations. For their examination special x-ray apparatus was developed, in particular cameras working with very low angles and capable of indicating spacings up to 1000 Å. In Part III, Section 1 deals with the x-ray evidence on the internal structure of the particles. Even in solution, they have an inner regularity like that of a crystal. Virus preparations are thus in a sense doubly crystalline. Closer analysis reveals that the x-ray patterns are not directly comparable to those of a crystal as many of the reflections do not obey Bragg's law, but can be understood on the theory of gratings of limited size. The structure seems to consist of sub-units of the dimensions of approximately 11 Å cube, fitted together in a hexagonal or pseudohexagonal lattice of dimensions—a = 87 Å, c = 68 Å. Contrary to what earlier observations seemed to indicate, the particle seems to be virtually unchanged by drying and must therefore contain little water. There are marked resemblances with the structure of both crystalline and fibrous protein, but the virus structure does not belong to any of the classes hitherto studied. There are indications that the inner structure is of a simpler character than that of the molecules of crystalline proteins. Part III, Section 2 contains a comparative study of the optical and x-ray examinations of three strains of tobacco mosaic virus, two of cucumber disease virus, two of potato virus X, and the virus of bushy stunt disease of tomato. In the last case x-ray measurement confirmed the deduction from its cubic crystal habit that it was composed of spherical rather than long particles, and showed that these had a diameter when dry of 276 Å and were arranged in a body-centred cubic close packing. This single example is sufficient to show that the elongated particle form which gives rise to all the anomalous physical properties of the other viruses studied is of no essential biological importance. The similarity and differences observed between the physical properties of these preparations run closely parallel to their clinical and serological classification. Finally, the biological implications of these results are discussed together with possible applications of the new methods of examination to the study of colloid and biological problems.
PMCID: PMC2142028  PMID: 19873256
7.  Use of physical restraints and antipsychotic medications in nursing homes: a cross-national study 
This study compares inter- and intra-country differences in the prevalence of physical restraints and antipsychotic medications in nursing homes, and examines aggregated resident conditions and organizational characteristics correlated with these treatments.
Population-based, cross-sectional data were collected using a standardized Resident Assessment Instrument (RAI) from 14,504 long-term care facilities providing nursing home level services in five countries participating in the interRAI consortium, including Canada, Finland, Hong Kong (Special Administrative Region, China), Switzerland, and the United States. Facility-level prevalence rates of physical restraints and antipsychotic use were examined both between and within the study countries.
The prevalence of physical restraint use varied more than five-fold across the study countries, from an average 6% in Switzerland, 9% in the US, 20% in Hong Kong, 28% in Finland, and over 31% in Canada. The prevalence of antipsychotic use ranged from 11% in Hong Kong, between 26–27% in Canada and the US, 34% in Switzerland, and nearly 38% in Finland. Within each country, substantial variations existed across facilities in both physical restraint and antipsychotic use rates. In all countries, neither facility case mix nor organizational characteristics were particularly predictive of the prevalence of either treatment.
There exists large, unexplained variability in the prevalence of physical restraint and antipsychotic use in nursing home facilities both between and within countries. Since restraints and antipsychotics are associated with adverse outcomes, it is important to understand the idiosyncratic factors specific to each country that contribute to variation in use rates.
PMCID: PMC3764453  PMID: 19280680
physical restraints; antipsychotics; nursing homes; Resident Assessment Instrument (RAI); Minimum Data Set (MDS); cross-national study
8.  Widespread Cortical Dysfunction in Schizophrenia: The FBIRN Imaging Consortium 
Schizophrenia Bulletin  2008;35(1):15-18.
This Special Theme issue presents a series of related papers describing fMRI data collected as part of a multi-site brain imaging consortium, the Functional Imaging Biomedical Informatics Research Network (FBIRN) on the same subject population (∼125 patients and ∼125 controls), a larger sample than would have been possible from a single-site, and from a broader clinical and demographic range of patients. Potkin et al observe cortical inefficiency during retrieval of items from memory but not during encoding of those items; Brown et al showed that the lawful relationship between memory retrieval time and neural activation is decoupled in patients with schizophrenia. Wible et al analyzed the same memory data and report activations of left auditory and parietal cortices are especially abnormal in patients who tend to hallucinate. Using an auditory target detection task, Ford et al report abnormal activation of left primary auditory cortex in the hallucinators. A multivariate analysis of those auditory data by Kim et al found differences in connectivity in patients and controls. These studies on the same patient sample suggest that abnormal circuitry characterizes schizophrenic performance in both auditory target detection and memory retrieval, and that patients who hallucinate have reduced left auditory cortical activation on both tasks. Segall et al report anatomical differences between patients and controls in the largest sample yet published. Finally, Potkin et al. identified six genes that influence DLPFC activation and have functions related to forebrain development and stress responses in schizophrenia. These related publications indicate the power of multisite neuroimaging.
PMCID: PMC2643955  PMID: 19023124
multi-site neuroimaging studies; cortical dysfunction; sternberg item recognition paradigm; detection paradigm; auditory oddball paradigm; working memory; genome wide association study
9.  Foreword: Lesson learning about getting research into policy and practice 
The UK Department for International Development (DFID) is committed to investing in research to combat poverty, reduce high mortality and morbidity in resource poor contexts and support progress towards meeting the Millennium Development Goals. Research helps us to identify what works, what does not work and how to understand the local context when introducing new ways of working. There is no point doing research if the findings do not get into policy and practice. DFID strongly encourages all research programmes to consider research uptake activities as an integral part of the research.
This special supplement draws on the work of the Sexual Health HIV Evidence into Practice (SHHEP) initiative. SHHEP is a collaboration across four DFID Research Programme Consortia (RPC) that undertake research and action on HIV and Sexual and Reproductive Health in resource poor contexts. Each consortium consists of 5 or more research, advocacy or service provider institutions from the south and the north working together over a five year period on critical areas of sexual and reproductive health. The essence of SHHEP is to share learning on research uptake and research engagement in Sexual and Reproductive Health, including HIV. The group has formulated a range of targeted mechanisms to communicate health research to different audiences and spearhead change, and were finalists for the British Medical Journal 2010 Getting Research into Practice (GRiP) prize.
The papers in this special supplement focus on lesson learning on getting research into policy and practice. They highlight the range of methodologies and approaches researchers and communication specialists have used in different contexts to try to ensure research does not simply gather dust on library shelves but feeds into and is relevant to policy and practice in different contexts (for example South Africa, Swaziland, Tanzania, Uganda, Malawi, Ghana, Bangladesh) and on a diversity of topic areas (Gender based violence, sexualities, orphans and vulnerable children, HIV care and treatment including male circumcision, cotrimoxazole and links with nutrition).
The work reported in this supplement provides examples of approaches that have been tried and from which other researchers can learn. They demonstrate that getting research into policy and practice is complex, dynamic and multi-faceted; and a wide range of context and issue specific conceptual and practical approaches have to be used. I hope that the innovative approaches and promising ways forward, presented in these papers, will inspire and motivate others.
Professor Christopher Whitty
Director Research and Evidence Division
Department for International Development
Dr Sue Kinn
Head of Health Research
Department for International Development
PMCID: PMC3121126  PMID: 21679376
10.  Are People Aware of Oral and Maxillofacial Surgery in India? 
Maxillofacial surgery is one of the most rapidly expanding specialities in India. There is however a very poor understanding of the scope of the speciality. This paper attempts to find out the awareness of the speciality in India.
Materials and methods
A questionnaire was given to 50 medical, dental undergraduate students, 50 medical and dental practitioners, and 50 lay persons giving us a total of 250 responses. 10 common anomalies were chosen and they were asked to choose the most appropriate speciality which they would ask to treat the problem.
While trauma and facial deformity correction were recognised to be mainly treated by maxillofacial surgeons, the other maxillofacial problems were poorly recognised to be treated by our speciality.
This study highlights the need to promote our speciality among the dentists, doctors and general public. and if need be even change the name of our speciality from oral and maxillofacial surgery to a more simple but more easily understood facial surgery.
PMCID: PMC3238559  PMID: 22942584
Oral and maxillofacial surgery; Awareness; Dental and medical doctors; General public; Facial surgery in India
11.  A western gray whale mitigation and monitoring program for a 3-D seismic survey, Sakhalin Island, Russia 
The introduction of anthropogenic sounds into the marine environment can impact some marine mammals. Impacts can be greatly reduced if appropriate mitigation measures and monitoring are implemented. This paper concerns such measures undertaken by Exxon Neftegas Limited, as operator of the Sakhalin-1 Consortium, during the Odoptu 3-D seismic survey conducted during 17 August’ September 2001. The key environmental issue was protection of the critically endangered western gray whale (Eschrichtius robustus), which feeds in summer and fall primarily in the Piltun feeding area off northeast Sakhalin Island. Existing mitigation and monitoring practices for seismic surveys in other jurisdictions were evaluated to identify best practices for reducing impacts on feeding activity by western gray whales. Two buffer zones were established to protect whales from physical injury or undue disturbance during feeding. A 1 km buffer protected all whales from exposure to levels of sound energy potentially capable of producing physical injury. A 4’ km buffer was established to avoid displacing western gray whales from feeding areas. Trained Marine Mammal Observers (MMOs) on the seismic ship Nordic Explorer had the authority to shut down the air guns if whales were sighted within these buffers.
Additional mitigation measures were also incorporated: Temporal mitigation was provided by rescheduling the program from June–August to August–September to avoid interference with spring arrival of migrating gray whales. The survey area was reduced by 19% to avoid certain waters <20 m deep where feeding whales concentrated and where seismic acquisition was a lower priority. The number of air guns and total volume of the air guns were reduced by about half (from 28 to 14 air guns and from 3,390 in3 to 1,640 in3) relative to initial plans. ‘Ramp-up’(=‘soft-start’ procedures were implemented.
Monitoring activities were conducted as needed to implement some mitigation measures, and to assess residual impacts. Aerial and vessel-based surveys determined the distribution of whales before, during and after the seismic survey. Daily aerial reconnaissance helped verify whale-free areas and select the sequence of seismic lines to be surveyed. A scout vessel with MMOs aboard was positioned 4 km shoreward of the active seismic vessel to provide better visual coverage of the 4’ km buffer and to help define the inshore edge of the 4’ km buffer. A second scout vessel remained near the seismic vessel. Shore-based observers determined whale numbers, distribution, and behavior during and after the seismic survey. Acoustic monitoring documented received sound levels near and in the main whale feeding area.
Statistical analyses of aerial survey data indicated that about 5’0 gray whales moved away from waters near (inshore of) the seismic survey during seismic operations. They shifted into the core gray whale feeding area farther south, and the proportion of gray whales observed feeding did not change over the study period.
Five shutdowns of the air guns were invoked for gray whales seen within or near the buffer. A previously unknown gray whale feeding area (the Offshore feeding area) was discovered south and offshore from the nearshore Piltun feeding area. The Offshore area has subsequently been shown to be used by feeding gray whales during several years when no anthropogenic activity occurred near the Piltun feeding area.
Shore-based counts indicated that whales continued to feed inshore of the Odoptu block throughout the seismic survey, with no significant correlation between gray whale abundance and seismic activity. Average values of most behavioral parameters were similar to those without seismic surveys. Univariate analysis showed no correlation between seismic sound levels and any behavioral parameter. Multiple regression analyses indicated that, after allowance for environmental covariates, 5 of 11 behavioral parameters were statistically correlated with estimated seismic survey-related variables; 6 of 11 behavioral parameters were not statistically correlated with seismic survey-related variables. Behavioral parameters that were correlated with seismic variables were transient and within the range of variation attributable to environmental effects.
Acoustic monitoring determined that the 4’ km buffer zone, in conjunction with reduction of the air gun array to 14 guns and 1,640 in3, was effective in limiting sound exposure. Within the Piltun feeding area, these mitigation measures were designed to insure that western gray whales were not exposed to received levels exceeding the 163 dB re 1 μPa (rms) threshold.
This was among the most complex and intensive mitigation programs ever conducted for any marine mammal. It provided valuable new information about underwater sounds and gray whale responses during a nearshore seismic program that will be useful in planning future work. Overall, the efforts in 2001 were successful in reducing impacts to levels tolerable by western gray whales. Research in 2002’005 suggested no biologically significant or population-level impacts of the 2001 seismic survey.
PMCID: PMC2798040  PMID: 17657576
Seismic survey; Mitigation; Monitoring; Western gray whale; Eschrichtius robustus; Sakhalin Island; Okhotsk Sea; Russia
12.  The Introduction of Bioptic Driving in The Netherlands 
Visual impairment research  2008;10(1):1-16.
In many states of the U.S.A., people with moderately reduced visual acuity e.g., 20/50 – 20/200) can legally drive with the aid of a small, spectacle-mounted (“bioptic”) telescope. We conducted a demonstration project to assess the viability of implementing bioptic driving in The Netherlands. In this paper we describe the framework of the project from conception through to realization of our primary objective – the introduction of bioptic driving as a legal option for visually impaired people in The Netherlands.
The project was based on bioptic driving programs in the U.S.A., which were adapted to fit within current driving training and assessment practices in The Netherlands. The project convened a consortium of organizations including the Netherlands Bureau of Driving Skills Certificates (CBR), service organizations for the visually impaired, and research departments at universities investigating driving and vision. All organizations were educated about bioptic driving and participating professionals were trained in their specific aspects of the project. Media publicity led to significant interest and helped recruitment that enabled the screening and selection of potential participants.
The project demonstrated that people with moderately reduced visual acuity can be trained to achieve an adequate level of proficient and safe driving (as assessed by the local official driving licensing professionals) when using a bioptic telescope for the road conditions in the Netherlands. Based on the successful project outcomes, a request was made to the Minister to allow bioptic driving in the Netherlands. This request has been accepted; the legal procedures for implementation are in process.
PMCID: PMC2453517  PMID: 19122754
13.  NLM's Medical Library Resource Improvement Grant for Consortia Development: a proposed outline to simplify the application process. 
The National Library of Medicine's Resource Improvement Grant for Consortia is available to assist with developing hospital library consortia, and to support the development of basic healthy information collections. In an effort to simplify the grant application process, this paper presents suggestions for writing the narrative section of the first budget-period application, using the outline in NLM's Application Instructions for Consortium Applicants. Suggestions for writing the narratives of the second budget-period application and the collection development application are also included.
PMCID: PMC226410  PMID: 7356494
14.  The GUDMAP database – an online resource for genitourinary research 
Development (Cambridge, England)  2011;138(13):2845-2853.
The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system. GUDMAP data are freely accessible at via easy-to-use interfaces. This curated, high-resolution dataset serves as a powerful resource for biologists, clinicians and bioinformaticians interested in the developing urogenital system. This paper gives examples of how the data have been used to address problems in developmental biology and provides a primer for those wishing to use the database in their own research.
PMCID: PMC3188593  PMID: 21652655
Database; Gene expression; Genitourinary; In situ hybridisation; Microarray
15.  NMR in a crystallography-based high-throughput protein structure-determination environment 
As an introduction to three papers on comparisons of corresponding crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG), an outline is provided of the JCSG strategy for combined use of the two techniques. A special commentary addresses the potentialities of the concept of ‘reference crystal structures’, which is introduced in the following three papers.
An introduction is provided to three papers which compare corresponding protein crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG). Special mention is made of the JCSG strategy for combined use of the two techniques, and of potential applications of the concept of ‘reference crystal structures’, which is introduced in the following three papers.
PMCID: PMC2954227  PMID: 20944233
NMR in structural genomics; NMR structures of proteins; NMR and crystal structure comparison
16.  A new scoring system derived from base excess and platelet count at presentation predicts mortality in paediatric meningococcal sepsis 
Critical Care  2013;17(2):R68.
The aim of this study was to derive a novel prognostic score for mortality in paediatric meningococcal sepsis (MS) based on readily available laboratory markers.
A multicentre retrospective cohort study for the consortium set and a single centre retrospective study for replication set. The consortium set were 1,073 children (age 1 week to 17.9 years) referred over a 15-year period (1996 to 2011), who had an admission diagnosis of MS, referred to paediatric intensive care units (PICUs) in six different European centres. The consortium set was split into a development set and validation set to derive the score. The replication set were 134 children with MS (age 2 weeks to 16 years) referred over a 4-year period (2007 to 2011) to PICUs via the Children's Acute Transport Service (CATS), London.
A total of 85/1,073 (7.9%) children in the consortium set died. A total of 16/134 (11.9%) children in the replication set died. Children dying in the consortium set had significantly lower base excess, C-reactive protein (CRP), platelet and white cell count, more deranged coagulation and higher lactate than survivors. Paediatric risk of mortality (PRISM) score, Glasgow meningococcal septicaemia prognosis score (GMSPS) and Rotterdam score were also higher. Using the consortium set, a new scoring system using base excess and platelet count at presentation, termed the BEP score, was mathematically developed and validated. BEP predicted mortality with high sensitivity and specificity scores (area under the curve (AUC) in the validation set = 0.86 and in the replication set = 0.96). In the validation set, BEP score performance (AUC = 0.86, confidence interval (CI): 0.80 to 0.91) was better than GMSPS (AUC = 0.77, CI: 0.68, 0.85), similar to Rotterdam (AUC = 0.87, CI: 0.81 to 0.93) and not as good as PRISM (AUC = 0.93, CI: 0.85 to 0.97).
The BEP score, relying on only two variables that are quickly and objectively measurable and readily available at presentation, is highly sensitive and specific in predicting death from MS in childhood.
PMCID: PMC3672696  PMID: 23577792
17.  Comparative analysis of various gene finders specific to Caenorhabditis elegans genome 
Bioinformation  2006;1(6):203-207.
Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.
PMCID: PMC1891687  PMID: 17597889
gene prediction; multiple transcripts; exons; isoforms; C. elegans
18.  The Establishment of the GENEQOL Consortium to Investigate the Genetic Disposition of Patient-Reported Quality-of-Life Outcomes 
To our knowledge, no comprehensive, interdisciplinary initiatives have been taken to examine the role of genetic variants on patient-reported quality-of-life outcomes. The overall objective of this paper is to describe the establishment of an international and interdisciplinary consortium, the GENEQOL Consortium, which intends to investigate the genetic disposition of patient-reported quality-of-life outcomes. We have identified five primary patient-reported quality-of-life outcomes as initial targets: negative psychological affect, positive psychological affect, self-rated physical health, pain, and fatigue. The first tangible objective of the GENEQOL Consortium is to develop a list of potential biological pathways, genes and genetic variants involved in these quality-of-life outcomes, by reviewing current genetic knowledge. The second objective is to design a research agenda to investigate and validate those genes and genetic variants of patient-reported quality-of-life outcomes, by creating large datasets. During its first meeting, the Consortium has discussed draft summary documents addressing these questions for each patient-reported quality-of-life outcome. A summary of the primary pathways and robust findings of the genetic variants involved is presented here. The research agenda outlines possible research objectives and approaches to examine these and new quality-of-life domains. Intriguing questions arising from this endeavor are discussed. Insight into the genetic versus environmental components of patient-reported quality-of-life outcomes will ultimately allow us to explore new pathways for improving patient care. If we can identify patients who are susceptible to poor quality of life, we will be able to better target specific clinical interventions to enhance their quality of life and treatment outcomes.
PMCID: PMC2824176  PMID: 19456223
19.  Cephalopod genomics: A plan of strategies and organization 
Standards in Genomic Sciences  2012;7(1):175-188.
The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.
PMCID: PMC3570802  PMID: 23451296
King's law journal : KLJ  2007;18(2):201-208.
This paper provides an introduction to a collection of five papers, published as a special symposium journal issue, under the title: “Governing Genetic Databases: Collection, Storage and Use”. It begins by setting the scene, to provide a backdrop and context for the papers. It describes the evolving scientific landscape around genetic databases and genomic research, particularly within the biomedical and criminal forensic investigation fields. It notes the lack of any clear, coherent or coordinated legal governance regime, either at the national or international level. It then identifies and reflects on key cross-cutting issues and themes that emerge from the five papers, in particular: terminology and definitions; consent; special concerns around population genetic databases (biobanks) and forensic databases; international harmonisation; data protection; data access; boundary-setting; governance; and issues around balancing individual interests against public good values.
PMCID: PMC2493389  PMID: 18841252
21.  Quality Assesment of Mie 2009 Sarajevo Conference Presentations 
Acta Informatica Medica  2010;18(1):25-28.
Introduction: XXII European Congress of Medical Informatics (MIe 2009) took place in Sarajevo from August 30th to September 2nd 2009. Assessment of quality of papers presented at MIe 2009 was a process of observation, measurement, comparison and evaluation of the quality of orally presented papers. Methodology: For this study, and for the first time since EFMI founding (1976) and MIE congresses, the authors introduced a specially created quality assessment form with five relevant paper quality variables (methodological approach, international influence, scientific content, language quality, technical features) which the first author of this article used in peer-review process of papers submitted for publication in the journal Acta Informatica Medica (as Editor-in-Chief for last 18 years). The survey was conducted on the principle of random sampling of participants of MIE 2009 Conference in Sarajevo, where specially trained interviewers (final year students of medicine and engineering at the University of Sarajevo) interviewed 33 session’s chairs and 110 participants/listeners of MIE 2009 paper presentations in 33 sessions (of total 40). Data was collected, entered into a specially created database, analyzed and presented. Results: From the total of 150 oral presentations at the MIE 2009, 110 oral presentations were graded by both chairs and participants/ listeners. Grading results were compared and we found that in 60% of cases (66 papers) session chairs gave higher ratings than other participants of the congress. The highest rating was 10, and the lowest 3. Only 3 of the papers received all four grades 10 from the session chairs. The most common grade given by chairs of the session was 8 (26.36%), followed by 7 (20%), 9 (19.32%), 6 (13.18%), 10 and 5 (7.50%), 4 (5%) and 3 (1.14%). Significant differences in quality assessment of papers done by chairs and those done by other participants/listeners are observed. Conclusion: This work should demonstrate the importance of introducing universal (uniform) scale for assessment of articles at conferences that would provide objective and relevant assessment, which has not been the practice. Results obtained using a single standardized scale can be compared to each other and thus improve the quality of the articles and the congress. Future congresses can be organized in this manner and become leading events in certain fields of medical science.
PMCID: PMC3818745  PMID: 24222932
medical informatics; quality assessment; paper presentation; evaluation
22.  Depression Treatment Non-adherence and its Psychosocial Predictors: Differences between Young and Older Adults? 
Aging and Disease  2013;4(6):329-336.
Depression is a common disease among young and older adults. Although it can be treated, non-adherence is very common among individuals of different ages. The aim of the present paper is to review and summarize research findings regarding depression among young and older adults, with a special focus on the phenomenon of treatment non-adherence among young and older adults with depression. The first section of the review focuses on describing the characteristics of depression in young and older adults. The second section focuses on treatment non-adherence of young and older adults, the prevalence of this phenomenon, and its consequences. The third section focuses on several factors (illness beliefs, treatment beliefs, self-stigma, and self-esteem) that were identified as having a significant association with treatment non-adherence of individuals with depression, with special attention focused on age differences. Results of the review of the literature reveal that research in the area of depression treatment non-adherence and its predictors among young and older adults has received, to date, very minor and limited attention. Thus, there is a need to expand the current body of knowledge and promote future interventions geared towards the unique characteristics of depression among young and older adults, in order to increase their treatment adherence.
PMCID: PMC3843650  PMID: 24307966
depression; treatment adherence; age differences
23.  Simultaneous Cellulose Degradation and Electricity Production by Enterobacter cloacae in a Microbial Fuel Cell▿  
Applied and Environmental Microbiology  2009;75(11):3673-3678.
Electricity can be directly generated by bacteria in microbial fuel cells (MFCs) from many different biodegradable substrates. When cellulose is used as the substrate, electricity generation requires a microbial community with both cellulolytic and exoelectrogenic activities. Cellulose degradation with electricity production by a pure culture has not been previously demonstrated without addition of an exogenous mediator. Using a specially designed U-tube MFC, we enriched a consortium of exoelectrogenic bacteria capable of using cellulose as the sole electron donor. After 19 dilution-to-extinction serial transfers of the consortium, 16S rRNA gene-based community analysis using denaturing gradient gel electrophoresis and band sequencing revealed that the dominant bacterium was Enterobacter cloacae. An isolate designated E. cloacae FR from the enrichment was found to be 100% identical to E. cloacae ATCC 13047T based on a partial 16S rRNA sequence. In polarization tests using the U-tube MFC and cellulose as a substrate, strain FR produced 4.9 ± 0.01 mW/m2, compared to 5.4 ± 0.3 mW/m2 for strain ATCC 13047T. These results demonstrate for the first time that it is possible to generate electricity from cellulose using a single bacterial strain without exogenous mediators.
PMCID: PMC2687291  PMID: 19346362
24.  The Challenge of Multisite Epidemiologic Studies in Diverse Populations: Design and Implementation of a 22-Site Study of Tuberculosis in Foreign-Born People 
Public Health Reports  2009;124(3):391-399.
We designed a population-based study of the epidemiology of tuberculosis among foreign-born people in the U.S. and Canada. Challenges included standardizing recruitment and data entry at 22 sites, enrolling individuals who did not speak English and may be undocumented, and obtaining clearance from 36 institutional review boards (IRBs).
We used stratified sampling to recruit patients through the Tuberculosis Epidemiologic Studies Consortium, a research consortium funded by the Centers for Disease Control and Prevention. Because recruitment sites were overseen by more than 30 local IRBs, we developed a simple process to designate a central IRB. We translated instruments into 10 main languages, arranged for fast translation of consent “short forms” into other languages, used one telephone interpretation service at all sites, and provided extensive interviewer training including mock interviews with simulated patients.
We interviewed 1,696 participants in 19 states and provinces. Participants from 99 countries were interviewed in 40 languages. Twenty-three percent did not speak English at all; 64% needed an interpreter. More than 20% of participants reported they were undocumented. Participants' age, gender, and birthplaces were broadly similar to the target populations. One-third of local IRBs used the central IRB.
Special confidentiality protections, substantial resources for translation and interpretation, and a centralized IRB made possible the recruitment of a representative sample of foreign-born people. The approaches may be applicable to studies of other diseases in multinational populations in the U.S. and Canada.
PMCID: PMC2663875  PMID: 19445415
25.  Principles of study design in environmental epidemiology. 
Environmental Health Perspectives  1993;101(Suppl 4):23-38.
This paper discusses the principles of study design and related methodologic issues in environmental epidemiology. Emphasis is given to studies aimed at evaluating causal hypotheses regarding exposures to suspected health hazards. Following background sections on the quantitative objectives and methods of population-based research, we present the major types of observational designs used in environmental epidemiology: first, the three basic designs involving the individual as the unit of analysis (i.e., cohort, cross-sectional, and case-control studies) and a brief discussion of genetic studies for assessing gene-environment interactions; second, various ecologic designs involving the group or region as the unit of analysis. Ecologic designs are given special emphasis in this paper because of our lack of resources or inability to accurately measure environmental exposures in large numbers of individuals. The paper concludes with a section highlighting current design issues in environmental epidemiology and several recommendations for future work.
PMCID: PMC1519688  PMID: 8206038

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