bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do aggregates of multiple questions better capture overall fish consumption than summary questions?
Authors: Mina Kym , Fritschi Lin , Knuiman Matthew 
Published: July 2007

AbstractObjectiveTo compare intake estimates, validity and reliability of two summary questions to measure fish consumption with information from a detailed semi-quantitative food-frequency questionnaire (FFQ) on fish consumption.DesignPopulation-based, cross-sectional study. Participants completed an FFQ and provided blood samples for erythrocyte membrane eicosapentaenoic acid (EPA) analysis. Aggregate measures of consumption of fresh/frozen/canned fish (fresh fish) and smoked/salted/dried fish (preserved fish) were generated from the FFQ and were compared with responses to the summary questions regarding intakes of similar items. Both methods were tested for validity, using correlation and linear regression techniques with EPA, and retest reliability.SettingPerth metropolitan area, Western Australia.SubjectsOne hundred and nine healthy volunteers of both sexes, aged 21–75 years.ResultsThe summary fresh fish measure underestimated frequency and grams per week given by the aggregate question by about 50%, while estimates from the summary preserved fish measure were approximately three times that of the aggregate measure. Multiple linear regression analysis suggested that the aggregates accounted for more of the variation in EPA levels, but the difference was minimal. Intra-class correlations confirmed that both methods were reliable.ConclusionsOur study indicates that extensive questioning results in different absolute intakes of fish compared with brief questioning, but does not add any information if ranking individuals according to overall consumption of fish.
Reply to Comment on “How nature foiled the 2006 hurricane forecasts”
Authors: Lau William K. M. , Kim Kyu‐Myong 
Published: July 2007

The two main objections of Evan [this issue] to our paper are that (1) the 2006 sea surface temperature (SST) in the Atlantic Ocean was actually above normal compared with the long‐term climatology, and (2) the dust radiative forcing in 2006 was not substantially greater than in 2005 and could not have caused the large change in SST.First, we recognize that 2006 was a climatologically warm year. However, the main focus of our study was on the abrupt cooling of the Atlantic SST from 2005 to 2006, not on the long‐term variation. Hence this point is not germane to our study Second, we suggested that Saharan dust may have been important in triggering a series of rapid feedback processes in the ocean‐atmosphere system in the Atlantic in 2006 resulting in conditions that are unfavorable for hurricane formation.Therefore, the real question is, how much initial dust radiative forcing is sufficient to trigger the feedback processes? This is not a simple question to answer, because it depends on the timing of the aerosol forcing and the preexisting state of the large‐scale coupled atmosphere‐landocean system.
Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet
Authors: Tett Adrian , Spiers Andrew J , Crossman Lisa C , Ager Duane , Ciric Lena , Dow J Maxwell , Fry John C , Harris David , Lilley Andrew , Oliver Anna , Parkhill Julian , Quail Michael A , Rainey Paul B , Saunders Nigel J , Seeger Kathy , Snyder Lori A S , Squares Rob , Thomas Christopher M , Turner Sarah L , Zhang Xue-Xian , Field Dawn , Bailey Mark J 
Published: July 2007

Abstract
The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80% of predicted coding sequences cannot be ascribed a function and 60% are orphans. Of those to which function could be assigned, 40% bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other γ-proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra+ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14% of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood.
Pyrosequencing enumerates and contrasts soil microbial diversity
Authors: Roesch Luiz F W , Fulthorpe Roberta R , Riva Alberto , Casella George , Hadwin Alison K M , Kent Angela D , Daroub Samira H , Camargo Flavio A O , Farmerie William G , Triplett Eric W 
Published: July 2007

Abstract
Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26 140 to 53 533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52 000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%–12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.
Molecular and Epidemiologic Study of Polyclonal Outbreaks of Multidrug-ResistantAcinetobacter baumanniiInfection in an Israeli Hospital
Authors: Marchaim Dror , Navon-Venezia Shiri , Leavitt Azita , Chmelnitsky Irina , Schwaber Mitchell J. , Carmeli Yehuda 
Published: July 2007

Objectives.To perform a molecular and epidemiologic investigation of multidrug-resistant (MDR)Acinetobacter baumanniiin an institution were polyclonal outbreaks have been observed and determine whether these polyclonal outbreaks had an endogenous origin or were caused by in-hospital patient-to-patient transmission.Design.Retrospective analysis of prospectively collected data.Setting.An epidemiologic and genotypic investigation of incident cases of MDRA. baumanniiinfection in an Israeli university tertiary care center.Patients.Hospitalized patients with MDRA. baumanniiisolated from clinical samples during a 13-week period, from April 15, 2003, through July 15, 2003.Intervention.All patients with new MDRA. baumanniiinfections were recruited, and isolates were typed using pulsed-field gel electrophoresis. Data on in-hospital movements and consultations were extracted from computerized databases. Quantification of transmission opportunities (TOPs), defined as encounters between an established carrier and a future carrier of MDRA. baumannii, and analysis of ward clusters were performed.Results.We studied 96 MDRA. baumanniiisolates, which belonged to 18 different pulsed-field gel electrophoresis clones. In 65% of cases, TOPs involving patients with the same clone were demonstrated, which is significantly greater than the number of TOPs involving patients with different clones (P= .01).Conclusion.Although outbreaks of MDRA. baumanniiinfection may be polyclonal, we believe that patient-to-patient transmission explains most cases of transmission. Polyclonal local outbreaks reflect several clonal outbreaks occurring simultaneously. The cause of polyclonal outbreaks ofA. baumanniiinfections clustered by ward and time remains to be explained.
Identification of Patients WithPseudomonas aeruginosaRespiratory Tract Infections at Greatest Risk of Infection With Carbapenem-Resistant Isolates
Authors: Lodise Thomas P. , Miller Chris , Patel Nimish , Graves Jeffrey , McNutt Louise-Anne 
Published: July 2007

Objective.To create a clinical tool based on institution-specific risk factors to estimate the probability of carbapenem resistance amongPseudomonas aeruginosaisolates obtained from infected patients. By better estimating the probability of carbapenem resistance on the basis of patient-specific factors, clinicians can refine their empirical therapy forP. aeruginosainfections and potentially maximize clinical outcomes by increasing the likelihood of appropriate empirical antimicrobial therapy.Design.A retrospective, cross-sectional study.Setting.Tertiary care academic hospital.Patients.All adult inpatients who had a respiratory tract infection due toP. aeruginosabetween January 2001 and June 2005.Intervention.Data on demographic characteristics, antibiotic history, and microbiology were collected. Log-binomial regression was employed to identify predictors of carbapenem resistance amongP. aeruginosaisolates and to devise the clinical prediction tool.Results.Among 351 patients withP. aeruginosainfection, 44% were infected with carbapenem-resistant P.aeruginosastrains. Independent predictors of carbapenem resistance were prior receipt of mechanical ventilation for 11 days or more, prior exposure to fluoroquinolones for 3 days or more, and prior exposure to carbapenems for 3 days or more.Conclusions.With carbapenem resistance rates amongP. aeruginosaisolates on the rise at our institution, the challenge was to identify patients for whom carbapenems would remain an effective empirical agent, as well as the patients at greatest risk for infection with carbapenem-resistant strains. The clinical prediction tool accurately estimated carbapenem resistance among this risk-stratified cross-sectional study of patients withP. aeruginosainfection. This tool may be an effective way for clinicians to refine their selection of empirical antibiotic therapy and to maximize clinical outcomes by increasing the likelihood of appropriate antibiotic treatment.
Methicillin-ResistantStaphylococcus aureus: A 5-Year Review of Surveillance Data in a Tertiary Care Hospital in Saudi Arabia
Authors: Balkhy H. H. , Memish Z. A. , Almuneef M. A. , Cunningham G. C. , Francis C. , Fong K. C. , Nazeer Z. B. , Tannous E. 
Published: July 2007

Background.Staphylococcus aureusis an important pathogen that leads to serious infections in the community and in hospitals. Evidence has shown that the prevalence of infection and colonization with drug-resistantS. aureus, such as methicillin-resistantS. aureus(MRSA) and glycopeptide intermediately susceptibleS. aureus, is increasing. Authorities must be aware of the prevalence of MRSA infection and colonization in their country in order to implement and monitor infection control policies that help curtail further emergence of this pathogen.Objectives.To examine the trend of hospital-acquired MRSA infection and colonization in a tertiary care institution in Saudi Arabia during a 5-year period in order to identify specific areas at high risk for MRSA transmission, and to review our MRSA decolonization procedure and outcomes.Methods.Surveillance data prospectively collected from January 1, 2000, through December 31, 2004, on hospital-acquired (HA) MRSA were analyzed, with an emphasis on the trend of HA-MRSA infection and colonization, areas of high transmission, risk factors, and effectiveness of the implemented decolonization policy.Results.During the study period, 442 cases of HA-MRSA infection and colonization were identified. Of these, 51.2% were infections, and 48.8% were colonizations. An increasing trend in the incidence rates of infection and colonization was noticed during the study period, and most cases were identified on the surgical ward (33.3%) and medical ward (32.1%). Of the 34 infected patients who underwent systematic decolonization, 35.3% were successfully decolonized, and of the 11 who underwent topical decolonization, 63.6% were successfully decolonized.Conclusion.The increasing trend of HA-MRSA infections has been a noticeable global problem. We identified a gradual increase in the rates of MRSA colonization and infection in a tertiary care center Saudi Arabia and recognize the importance of abiding by strict infection control policies, including hand hygiene and proper isolation practices. Continued surveillance for MRSA and other emerging multidrug-resistant pathogens is also needed.
Efficacy of Hospital Cleaning Agents and Germicides Against EpidemicClostridium difficileStrains
Authors: Fawley Warren N. , Underwood Sarah , Freeman Jane , Baines Simon D. , Saxton Katie , Stephenson Keith , Owens Robert C. , Wilcox Mark H. 
Published: July 2007

Objective.To compare the effects of hospital cleaning agents and germicides on the survival of epidemicClostridium difficilestrains.Methods.We compared the activity of and effects of exposure to 5 cleaning agents and/or germicides (3 containing chlorine, 1 containing only detergent, and 1 containing hydrogen peroxide) on vegetative and spore forms of epidemic and non-epidemicC. difficilestrains (3 of each). We carried out in vitro exposure experiments using a human fecal emulsion to mimic conditions found in situ.Results.Cleaning agent and germicide exposure experiments yielded very different results forC. difficilevegetative cells, compared with those for spores. Working-strength concentrations of all of the agents inhibited the growth ofC. difficilein culture. However, when used at recommended working concentrations, only chlorine-based germicides were able to inactivateC. difficilespores.C. difficileepidemic strains had a greater sporulation rate than nonepidemic strains. The mean sporulation rate, expressed as the proportion of a cell population that is in spore form, was 13% for all strains not exposed to any cleaning agent or germicide, and it was significantly increased by exposure to cleaning agents or germicides containing detergent alone (34%), a combination of detergent and hypochlorite (24%), or hydrogen peroxide (33%). By contrast, the mean sporulation rate did not change substantially after exposure to germicides containing either a combination of detergent and dichloroisocyanurate (9%) or dichloroisocyanurate alone (15%).Conclusions.These results highlight differences in the activity of cleaning agents and germicides againstC. difficilespores and the potential for some of these products to promote sporulation.
Catheter-Associated Bloodstream Infections in General Medical Patients Outside the Intensive Care Unit: A Surveillance Study
Authors: Marschall Jonas , Leone Carole , Jones Marilyn , Nihill Deborah , Fraser Victoria J. , Warren David K. 
Published: July 2007

Objective.To determine the incidence of central venous catheter (CVC)-associated bloodstream infection (CA-BSI) among patients admitted to general medical wards outside the intensive care unit (ICU).Design.Prospective cohort study performed over a 13-month period, from April 1, 2002, through April 30, 2003.Setting.Four selected general medical wards at Barnes-Jewish Hospital, a 1,250-bed teaching hospital in Saint Louis, Missouri.Patients.All patients admitted to 4 general medical wards.Results.A total of 7,337 catheter-days were observed during 33,174 patient-days. The device utilization ratio (defined as the number of catheter-days divided by the number of patient-days) was 0.22 overall and was similar among the 4 wards (0.21, 0.25, 0.19, and 0.24). Forty-two episodes of CA-BSI were identified (rate, 5.7 infections per 1,000 catheter-days). Twenty-four (57%) of the 42 cases of CA-BSI were caused by gram-positive bacteria: 10 isolates (24%) were coagulase-negative staphylococci, 10 (24%) were Enterococcus species, and 3 (7%) were Staphylococcus aureus. Gram-negative bacteria caused 7 infections (17%). Five CA-BSIs (12%) were caused by Candida albicans, and 5 infections (12%) had a polymicrobial etiology. Thirty-five patients (83%) with CA-BSI had nontunneled CVCs in place.Conclusions.Non-ICU medical wards in the study hospital had device utilization rates that were considerably lower than those of medical ICUs, but CA-BSI rates were similar to CA-BSI rates in medical ICUs in the United States. Studies of catheter utilization and on CVC insertion and care should be performed on medical wards. CA-BSI prevention strategies that have been used in ICUs should be studied on medical wards.
Prevalence and Trend in the Use of Hospital-Based Standing Orders Programs for Influenza and Pneumococcal Vaccination
Authors: Pentakota Sri Ram , Halperin William 
Published: July 2007

Background.In 2002, federal regulations authorized the use of standing orders programs (SOPs) for promoting influenza and pneumococcal vaccination. In 2003, the New Jersey Hospital Association conducted a demonstration project illustrating the efficacy of SOPs, and the state health department informed healthcare facilities of their benefits. We describe the prevalence of reported use of SOPs in New Jersey hospitals in 2003 and 2005 and identify hospital characteristics associated with the use of SOPs.Methods.A survey was mailed to the directors of infection control at 117 New Jersey hospitals during the period from January to May 2005 (response rate, 90.6%). Data on hospital characteristics were obtained from hospital directories and online resources.Results.The prevalence of use of SOPs for influenza vaccination was 50% (95% confidence interval [CI], 40.1%-59.9%) in 2003, and it increased to 78.3% (95% CI, 69.2%-85.7%) in 2005. The prevalence of SOP use for pneumococcal vaccination was similar. In 2005, the reported rate of use of SOPs for inpatients (influenza vaccination, 76.4%; pneumococcal vaccination, 75.5%) was significantly higher than that for outpatients (influenza vaccination, 9.4%; pneumococcal vaccination, 8.5%). Prevalence ratios for SOP use comparing acute care and non-acute care hospitals were 1.71 (95% CI, 1.2-2.5) for influenza vaccination SOPs and 1.8 for (95% CI, 1.2-2.7) pneumococcal vaccination SOPs. Acute care hospitals with a ratio of admissions to total beds greater than 36.7 reported greater use of SOPs for pneumococcal vaccination, compared with those that had a ratio of less than 36.7.Conclusion.The increase in the prevalence of reported use of SOPs among New Jersey hospitals in 2005, compared with 2003, was contemporaneous with SOP-related actions taken by the federal government, the state government, and the New Jersey Hospital Association. Opportunities persist for increased use of SOPs among non-acute care hospitals and for outpatients.
Successful Control of Widespread Methicillin-ResistantStaphylococcus aureusColonization and Infection in a Large Teaching Hospital in The Netherlands
Authors: van Trijp M. J. C. A. , Melles D. C. , Hendriks W. D. H. , Parlevliet G. A. , Gommans M. , Ott A. 
Published: July 2007

Objective.The low prevalence of infection and colonization with methicillin-resistantStaphylococcus aureus(MRSA) in The Netherlands is ascribed to a national “search-and-destroy” policy. We describe the measures that were implemented to control widespread MRSA colonization and infection in a Dutch hospital.Design.Descriptive intervention study.Setting.Teaching medical center with a capacity of 679 beds, including 16 intensive care beds.Interventions.MRSA colonization and infection were identified using conventional culture with a selective broth. Isolates were typed using pulsed-field gel electrophoresis. Measures to control the epidemic included screening of contacts (patients and hospital staff), screening of patients at readmission or discharge, strict isolation of MRSA-positive patients, decolonization of colonized staff and patients, the development of an electronic signal identifying MRSA-positive patients, and the development of a culture information-system for hospital personnel.Results.Awareness of uncontrolled dissemination of MRSA began in November 2001. Because the clone involved had a low minimum inhibitory concentration for oxacillin, at first it was not recognized as MRSA. In February 2002, when major screening efforts started, it appeared that MRSA had spread all over the hospital and that many staff members were colonized. By the end of December 2005, a total of 600 patients and 135 staff members were found to be newly colonized. The yearly incidence of cases of MRSA colonization and infection decreased from 351 in 2002 to 56 in 2005. Typing of the isolates showed that 3 MRSA clones were predominant. Outbreaks of colonization involving these clones did not occur after 2003.Conclusion.Our observations show that strict application of “search-and-destroy” measures can effectively control a huge epidemic of MRSA colonization and infection.
Altered kelp (Laminariales) phlorotannins and growth under elevated carbon dioxide and ultraviolet‐B treatments can influence associated intertidal food webs
Authors: SWANSON ANDREW K. , FOX CAROLINE H. 
Published: July 2007

AbstractDue to the importance of brown algae, such as kelp (Laminariales, Phaeophyta), within most cool nearshore environments, any direct responses of kelp to multiple global changes could alter the integrity of future coastal marine systems. Fifty‐five‐day manipulation of carbon dioxide (CO2) and ultraviolet light (UVB) within outdoor sea‐tanks, approximating past, present and two predicted future levels, examined the direct influences on Saccharina latissima (=Laminaria saccharina) and Nereocystis luetkeana development and biochemistry, as well as the indirect influences on a marine herbivore (Tegula funebralis; Gastropoda, Mollusca) and on naturally occurring intertidal detritivores. Kelp species displayed variable directional (negative and positive growth) and scale responses to CO2 and UVB manipulations, which was influenced by interactions. Kelp phlorotannin (phenolic) production in blade tissues was induced by elevated UVB levels, and especially enhanced (additively) by elevated CO2, further suggesting that some actively growing kelp species are carbon limited in typical nearshore environments. Negative indirect effects upon detritivore consumers fed CO2‐manipulated kelp blade tissues were detected, however, no statistical relationships existed among UVB‐treated tissues, and test herbivores did not distinguish between phlorotannin‐altered CO2: UVB‐treated kelp blade tissues. Results suggest that past and future conditions differentially benefit these kelp species, which implies a potential for shifts in species abundance and community composition. Higher CO2 conditions can indirectly impede marine decay processes delaying access to recycled trace nutrients, which may be disruptive to the seasonal regrowth of algae and/or higher trophic levels of nearshore ecosystems.