bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Bloodstream Infection Rates: The Effect of Indicator Specifications in the Evaluation of Processes and Indicators in Infection Control (EPIC) Study
Authors: Braun Barbara I. , Kritchevsky Stephen B. , Kusek Linda , Wong Edward S. , Solomon Steven L. , Steele Lynn , Richards Cheryl L. , Gaynes Robert P. , Simmons Bryan ,   Evaluation of Processes and Indicators in Infection Control (EPIC) Study Group
Published: January 2006

Objective.Bloodstream infection (BSI) rates are used as comparative clinical performance indicators; however, variations in definitions and data-collection approaches make it difficult to compare and interpret rates. To determine the extent to which variation in indicator specifications affected infection rates and hospital performance rankings, we compared absolute rates and relative rankings of hospitals across 5 BSI indicators.Design.Multicenter observational study. BSI rate specifications varied by data source (clinical data, administrative data, or both), scope (hospital wide or intensive care unit specific), and inclusion/exclusion criteria. As appropriate, hospital-specific infection rates and rankings were calculated by processing data from each site according to 2-5 different specifications.Setting.A total of 28 hospitals participating in the EPIC study.Participants.Hospitals submitted deidentified information about all patients with BSIs from January through September 1999.Results.Median BSI rates for 2 indicators based on intensive care unit surveillance data ranged from 2.23 to 2.91 BSIs per 1000 central-line days. In contrast, median rates for indicators based on administrative data varied from 0.046 to 7.03 BSIs per 100 patients. Hospital-specific rates and rankings varied substantially as different specifications were applied; the rates of 8 of 10 hospitals were both greater than and less than the mean. Correlations of hospital rankings among indicator pairs were generally low (rs = 0-0.45), except when both indicators were based on intensive care unit surveillance (rs = 0.83).Conclusions.Although BSI rates seem to be a logical indicator of clinical performance, the use of various indicator specifications can produce remarkably different judgments of absolute and relative performance for a given hospital. Recent national initiatives continue to mix methods for specifying BSI rates; this practice is likely to limit the usefulness of such information for comparing and improving performance.
Fungal Contamination in Hospital Environments
Authors: Perdelli F. , Cristina M. L. , Sartini M. , Spagnolo A. M. , Dallera M. , Ottria G. , Lombardi R. , Grimaldi M. , Orlando P. 
Published: January 2006

Objectives.To assess the degree of fungal contamination in hospital environments and to evaluate the ability of air conditioning systems to reduce such contamination.Methods.We monitored airborne microbial concentrations in various environments in 10 hospitals equipped with air conditioning. Sampling was performed with a portable Surface Air System impactor with replicate organism detection and counting plates containing a fungus-selective medium. The total fungal concentration was determined 72-120 hours after sampling. The genera most involved in infection were identified by macroscopic and microscopic observation.Results.The mean concentration of airborne fungi in the set of environments examined was 19 ± 19 colony-forming units (cfu) per cubic meter. Analysis of the fungal concentration in the different types of environments revealed different levels of contamination: the lowest mean values (12 ± 14 cfu/m3) were recorded in operating theaters, and the highest (45 ± 37 cfu/m3) were recorded in kitchens. Analyses revealed statistically significant differences between median values for the various environments. The fungal genus most commonly encountered was Penicillium, which, in kitchens, displayed the highest mean airborne concentration (8 ± 2.4 cfu/m3). The percentage (35%) of Aspergillus documented in the wards was higher than that in any of the other environments monitored.Conclusions.The fungal concentrations recorded in the present study are comparable to those recorded in other studies conducted in hospital environments and are considerably lower than those seen in other indoor environments that are not air conditioned. These findings demonstrate the effectiveness of air-handling systems in reducing fungal contamination.
Risk Factors and Outcomes Associated With Non–Enterococcus faecalis, Non–Enterococcus faeciumEnterococcal Bacteremia
Authors: Perio Marie A. de , Yarnold Paul R. , Warren John , Noskin Gary A. 
Published: January 2006

Objectives.To compare risk factors, clinical features, and outcomes in patients withEnterococcus avium,Enterococcus casseliflavus,Enterococcus durans,Enterococcus gallinarum, andEnterococcus mundtiibacteremia (cases) with those in patients withEnterococcus faecalisbacteremia (controls).Design.A retrospective case-control study.Setting.A 725-bed, university-affiliated, academic medical center.Patients.The clinical microbiology database at Northwestern Memorial Hospital from January 1994 to May 2003 was searched to identify cases; each case was matched to one control on the basis of date of admission.Results.Thirty-three cases were identified and matched with 33 controls. The mean duration of hospital stay was longer (29.7 vs 17.2 days;P= .03) and the mean time to acquisition of bacteremia was greater (16.5 vs 6.3 days;P= .003) for cases than controls. Cases were more likely to have underlying hematologic malignancies (P< .001), to have been treated with corticosteroids (P= .02), and to be neutropenic (P= .003). Controls were more likely to have an indwelling bladder catheter (P= .01), and cases were more likely to have the gastrointestinal tract as a source of infection (P= .007) and to have concurrent cholangitis (P= .002). There were no differences in severity of illness or in mortality rates.Conclusions.Compared with patients withE. faecalisbacteremia, patients with non-E. faecalis, non-Enterococcus faeciumenterococcal bacteremia were more likely to have a hematologic malignancy, prior treatment with corticosteroids, neutropenia, and cholangitis; longer duration of hospital stay was also identified as a clinical feature. However, non-E. faecalis, non-E. faeciumspecies are not associated with any differences in mortality.
APETALA2Regulates the Stem Cell Niche in theArabidopsisShoot Meristem
Authors: Würschum Tobias , Groß-Hardt Rita , Laux Thomas 
Published: December 2005

AbstractPostembryonic organ formation in higher plants relies on the activity of stem cell niches in shoot and root meristems where differentiation of the resident cells is repressed by signals from surrounding cells. We searched for mutations affecting stem cell maintenance and isolated the semidominant l28 mutant, which displays premature termination of the shoot meristem and differentiation of the stem cells. Allele competition experiments suggest that l28 is a dominant-negative allele of the APETALA2 (AP2) gene, which previously has been implicated in floral patterning and seed development. Expression of both WUSCHEL (WUS) and CLAVATA3 (CLV3) genes, which regulate stem cell maintenance in the wild type, were disrupted in l28 shoot apices from early stages on. Unlike in floral patterning, AP2 mRNA is active in the center of the shoot meristem and acts via a mechanism independent of AGAMOUS, which is a repressor of WUS and stem cell maintenance in the floral meristem. Genetic analysis shows that termination of the primary shoot meristem in l28 mutants requires an active CLV signaling pathway, indicating that AP2 functions in stem cell maintenance by modifying the WUS-CLV3 feedback loop.
Regulation of Phosphate Homeostasis by MicroRNA in Arabidopsis
Authors: Chiou Tzyy-Jen , Aung Kyaw , Lin Shu-I , Wu Chia-Chune , Chiang Su-Fen , Su Chun-lin 
Published: December 2005

Abstract
In this study, we reveal a mechanism by which plants regulate inorganic phosphate (Pi) homeostasis to adapt to environmental changes in Pi availability. This mechanism involves the suppression of a ubiquitin-conjugating E2 enzyme by a specific microRNA, miR399. Upon Pi starvation, the miR399 is upregulated and its target gene, a ubiquitin-conjugating E2 enzyme, is downregulated in Arabidopsis thaliana. Accumulation of the E2 transcript is suppressed in transgenic Arabidopsis overexpressing miR399. Transgenic plants accumulated five to six times the normal Pi level in shoots and displayed Pi toxicity symptoms that were phenocopied by a loss-of-function E2 mutant. Pi toxicity was caused by increased Pi uptake and by translocation of Pi from roots to shoots and retention of Pi in the shoots. Moreover, unlike wild-type plants, in which Pi in old leaves was readily retranslocated to other developing young tissues, remobilization of Pi in miR399-overexpressing plants was impaired. These results provide evidence that miRNA controls Pi homeostasis by regulating the expression of a component of the proteolysis machinery in plants.
Association of HLA DQ4‐DR8 haplotype with papillary thyroid carcinomas
Authors: Porto Teresa , Coelho Ibraim , Boavida José , Pereira Clara , Nunes José M. , Mendonça Denisa , Martins Berta , Sobrinho Luís G. , Leite Valeriano 
Published: January 2006

SummaryObjective  The association of the human leucocyte antigen (HLA) system with thyroid carcinomas is not clear. We sought to relate HLA alleles to susceptibility to papillary thyroid carcinoma (PTC) and also to clinical and pathological characteristics of PTC patients.Design and patients  The distribution of HLA in 181 unrelated Caucasian patients with PTC was compared to the HLA distribution in 315 normal controls, 31 patients with follicular carcinoma (FTC), 29 patients with lymphocytic thyroiditis (LT) and 50 patients with multinodular goitre (MNG), using a microlymphocytotoxicity assay.Results  Compared to normal controls, patients with PTC showed a significantly increased frequency of HLA‐DQ4 [12·8%vs. 3·5%, P = 0·0005, Pcorrected (Pc) = 0·0032, odds ratio (OR) = 4·058, 95% confidence interval (95% CI) = 1·820–9·045] and HLA‐DR8 (10·9%vs. 4·3%, P = 0·013, Pc > 0·05, OR = 2·752, 95% CI = 1·275–5·940). DQ4 and DR8 were also significantly increased in patients with MNG (DQ4, 16·3%; DR8, 16·3%) compared to controls (DQ4, P = 0·0019, Pc = 0·011, OR = 5·420, 95% CI = 1·978–14·852; DR8, P = 0·0044, Pc = 0·062). Linkage disequilibrium (LD) for these two alleles was present in controls (D = 0·0130, P = 9·7e‐57) and in MNG patients (D = 0·0730, P = 4·6e‐19) but not in PTC patients (D = 0·038, P > 0·05). In the subgroup of PTC subjects with concomitant nonthyroidal neoplasias (n = 27), there was a significant (P < 0·05) increase in the frequency of B57 (18·5%), DR11 (56·5%) and DQ3 (81·8%) compared to PTC patients without coexistent neoplasias (2·0%, 21% and 47%, respectively). No significant differences of HLA allele distribution was found in relation to PTC histology, age at diagnosis (> 45 or ≤ 45 years), gender or tumour–node–metastasis (TNM) staging. In patients with FTC, the frequency of DR17 (FTC = 51·6%; controls = 22·5%; P = 0·0009; Pc = 0·0138) was significantly increased compared to controls. Patients with LT showed a higher frequency of the DR11 allele (48·3%) than controls (DR11 = 21·3%; P = 0·0028, Pc = 0·039, OR = 3·445, 95% CI = 1·568–7·567).Conclusions  We have typed the largest series of patients with thyroid carcinomas reported to date, and found that DR8 and DQ4 are independent susceptibility markers for PTC.
Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation
Authors: VIANNA JULIANA A. , BONDE ROBERT K. , CABALLERO SUSANA , GIRALDO JUAN PABLO , LIMA RÉGIS P. , CLARK ANNMARIE , MARMONTEL MÍRIAM , MORALES‐VELA BENJAMÍN , DE SOUZA MARIA JOSÉ , PARR LESLEE , RODRÍGUEZ‐LOPEZ MARTA A. , MIGNUCCI‐GIANNONI ANTONIO A. , POWELL JAMES A. , SANTOS FABRÍCIO R. 
Published: January 2006

AbstractThe three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.
Inferring colonization history from analyses of spatial genetic structure within populations of Pinus strobus and Quercus rubra
Authors: JONES F. A. , HAMRICK J. L. , PETERSON C. J. , SQUIERS E. R. 
Published: January 2006

AbstractMany factors interact to determine genetic structure within populations including adult density, the mating system, colonization history, natural selection, and the mechanism and spatial patterns of gene dispersal. We examined spatial genetic structure within colonizing populations of Quercus rubra seedlings and Pinus strobus juveniles and adults in an aspen–white pine forest in northern Michigan, USA. A 20‐year spatially explicit demographic study of the forest enables us to interpret the results in light of recent colonization of the site for both species. We assayed 217 Q. rubra seedlings and 171 P. strobus individuals at 11 polymorphic loci using nine allozyme systems. Plant genotypes and locations were used in an analysis of spatial genetic structure. Q. rubra and P. strobus showed similar observed levels of heterozygosity, but Q. rubra seedlings have less heterozygosity than expected. Q. rubra seedlings show spatial genetic clumping of individuals on a scale to 25 m and levels of genetic relatedness expected from the clumped dispersion of half‐siblings. In contrast, P. strobus has low levels of genetic relatedness at the smallest distance class and positive spatial genetic structure at scales < 10 m within the plot. The low density of adult Q. rubra outside the study plot and limited, spatially clumped rodent dispersal of acorns is likely responsible for the observed pattern of spatial genetic structure and the observed heterozygote deficit (i.e. a Wahlund effect). We attribute weaker patterns observed in P. strobus to the longer dispersal distance of seeds and the historical overlap of seed shadows from adults outside of the plot coupled with the overlap of seed shadows from younger, more recently established reproductive adults. The study demonstrates the utility of long‐term demographic data in interpreting mechanisms responsible for generating contemporary patterns of genetic structure within populations.
Iron‐sulphur clusters and the problem with oxygen
Authors: Imlay James A. 
Published: January 2006

SummaryDuring the first billion years of life on the Earth, the environment was anaerobic. Iron and sulphur were plentiful, and they were recruited in the formation of iron‐sulphur (Fe‐S) clusters within ancient proteins. These clusters provided many enzymes with the ability to transfer electrons; to others they offered a cationic feature that tightly bound oxyanionic and nitrogenous metabolites. Still others acquired a crystallizing surface around which polypeptide could fold to establish a three‐dimensional structure. However, the subsequent oxygenation of the Earth's atmosphere by photosynthetic organisms created a threat to cluster‐dependent proteins that still has not been fully resolved. By oxidizing environmental iron, oxygen limits its bioavailability, requiring that organisms employ complex schemes with which to satisfy their iron requirement. More directly, oxygen species convert exposed Fe‐S clusters to unstable forms that quickly decompose. Some microbes responded to this dilemma by retreating to anaerobic habitats. Others abandoned the use of low‐potential electron‐transfer pathways, which rely upon the least stable cluster enzymes, and developed antioxidant strategies to protect the remainder. These adjustments were only partially successful: largely because of their reliance upon Fe‐S clusters, aerobes remain vulnerable to iron restriction and oxidative stress, features that higher organisms exploit in defending themselves against bacterial pathogens. Thus, the history of Fe‐S clusters is an unusual one that has profoundly shaped contemporary microbial ecology.
Predicting metals sensed by ArsR‐SmtB repressors: allosteric interference by a non‐effector metal
Authors: Harvie Duncan R. , Andreini Claudia , Cavallaro Gabriele , Meng Wenmao , Connolly Bernard A. , Yoshida Ken‐ichi , Fujita Yasutaro , Harwood Colin R. , Radford David S. , Tottey Stephen , Cavet Jennifer S. , Robinson Nigel J. 
Published: January 2006

SummaryMany bacterial genomes encode multiple metal‐sensing ArsR‐SmtB transcriptional repressors. There is interest in understanding and predicting their metal specificities. Here we analyse twoarsR‐smtBgenes,ydeTandyozA(nowaseRandczrA) fromBacillus subtilis. Purified AseR and CzrA formed complexes in gel‐retardation and fluorescence‐anisotropy assays with fragments of promoters that were derepressed in ΔaseRand ΔczrAcells. Candidate (i) partly thiolate, α3‐helix (for AseR) and (ii) tetrahedral, non‐thiolate, α5‐helix (for CzrA) metal binding sites were predicted then testedin vitroand/orin vivo. The precedents are for such sites to sense arsenite/antimonite (α3) and zinc (α5). This correlated with the respective metal inducers of AseR and CzrA repressed promoters inB. subtilisand matched the metals that impaired formation of protein–DNA complexesin vitro. The putative sensory sites of 1024 ArsR‐SmtB homologues are reported. Although AseR did not sense zincin vivo, it bound zincin vitroexploiting α3 thiols, but AseR DNA binding was not impaired by zinc. If selectivity relies on discriminatory triggering of allostery not just selective metal binding, then tight non‐effector metal complexes could theoretically inhibit metal sensing. AseR remained arsenite‐sensitive in equimolar zinc, while CzrA remained zinc‐sensitive in equimolar arsenitein vitro. However, cupric ions did not impair CzrA–DNA complex formation but did inhibit zinc‐mediated allosteryin vitroand prevent zinc binding. Access to copper must be controlledin vivoto avoid formation of cupric CzrA.
Effects of Curcumin on Tumour Necrosis Factor‐α and Interleukin‐6 in the Late Phase of Experimental Acute Pancreatitis
Authors: Gulcubuk A. , Altunatmaz K. , Sonmez K. , Haktanir‐Yatkin D. , Uzun H. , Gurel A. , Aydin S. 
Published: January 2006

SummaryInflammatory cytokines have been demonstrated to play an important role in the induction and severity of acute pancreatitis (AP) in the recent studies. The aim of this study was to investigate the effects of curcumin on inflammatory cytokines, such as tumour necrosis factor (TNF)‐α and interleukin (IL)‐6 in the late phase of AP. The study was conducted on 40 male Wistar Albino rats. The animals were divided randomly into four equal groups. AP was induced by the infusion of 3% sodium taurocholate into the biliopancreatic duct (in groups I and II). Starting on day 20 prior to the induction of AP, rats in group I received daily dose of 100 mg/kg of curcumin, dissolved in 9% ethanol via an intragastric tube. The same procedure was repeated for 6 days following the onset of AP. Group III was infused only on saline solution. Group IV (curcumin control group) received 9% ethanol via an intragastric tube, during the experimental period (totally 26 days). All the animals were sacrificed on day 6 after the collection of blood samples and serum TNF‐α and IL‐6 levels were determined. Tissue samples were taken from pancreas, mesenteric lymph nodes, liver, lungs, spleen and the kidneys for histopathological evaluation. Serum TNF‐α and IL‐6 levels in the group, which received curcumin (group I), were determined to be significantly lower than those of the untreated group (group II) (P<0.05). No statistically significant difference was detected in terms of total histopathological scores in the treatment group versus untreated group. Curcumin has been shown to markedly reduce serum TNF‐α and IL‐6 levels in the late phase of AP, but failed in the prevention of tissue injury.
Conferring cadmium resistance to mature tobacco plants through metal‐adsorbing particles of tomato mosaic virus vector
Authors: Shingu Yoshinori , Yokomizo Satoko , Kimura Makoto , Ono Yoshiro , Yamaguchi Isamu , Hamamoto Hiroshi 
Published: January 2006

SummaryTomato mosaic virus vectors were designed that produced, by a translational readthrough, a fusion protein consisting of coat protein and metal‐binding peptide, as a result of which particles were expected to present the metal‐binding peptides on their surface. When inoculated in plants, they were expected to replicate and form a metal‐adsorbing artificial sink in the cytoplasm, so as to reduce metal toxicity. Vectors were constructed harbouring sequences encoding various lengths of polyhistidine as a metal‐binding peptide. One of the vectors, TLRT6His, which contains a 6 × histidine sequence, moved systemically in tobacco plants, and its particles were shown to retain cadmium ions by an in vitro assay. When a toxic amount of cadmium was applied, the toxic effect was much reduced in TLRT6His‐inoculated tobacco plants, probably as a result of cadmium adsorption by TLRT6His particles in the cytosol. This shows the possible use of an artificial sink for metal tolerance and the advantage of employing a plant viral vector for phytoremediation.