bluuebunny/crossref_metadata_2025_split huggingface dataset:
Instrumentation for Chemiluminescence and Bioluminescence
Authors: Berthold Fritz , Hennecke Manfred , Wulf Jürgen 
Published: October 2010

The most widely used instruments for the measurement of chemiluminescence and bioluminescence are luminometers and low level light imagers.
Luminometers measure single samples in microplates or sample tubes sequentially, while imagers produce quantitative images in one exposure.
The detector of choice for luminometers is the photomultiplier tube, preferably operated as photon counter. To measure flash-type luminescence, luminometers can be equipped with reagent injectors.
CCD's (charge coupled devices) are used in imagers. Besides slow- scan cooled CCD's, modified devices like electron-multiplication CCD's, or CCD's with image intensifier are used in order to obtain higher frame rates.
Imagers are used for objects like small animals, plants, blots, gels, or Petri dishes, but also find use in high- throughput systems, imaging an entire microplate simultaneously.
Fluorescence measuring capabilities are a standard option for imagers, while measurement of bioluminescence and chemiluminescence in single samples is frequently performed in multimode readers, combining luminescence with absorption and different fluorescence measuring capabilities in a single instrument.
Statistical Methods for Categorised Endpoints in In Silico Toxicology
Authors: Rowe P. H. 
Published: October 2010

In this chapter different statistical approaches to analysing categorical data (Discriminant analysis, k-Nearest Neighbours and logistic regression) are discussed, along with recommendations as to the most appropriate methods for a given query. Discriminant functions are equations that use chemical descriptors to generate scores such that different categories of substance (e.g. toxic and non-toxic) yield maximally separated values. A cut-off point for the scores is then chosen. The cut-off may be selected so that compounds are simply separated according to chemical similarity (either more similar to one group or to the other) or account may be taken of the relative frequency of the two classes ('prior likelihood') to minimise the rate of misclassification or finally account may be taken of the relative costs of false positives and negatives to minimise misclassification costs. For dichotomised data, binary logistic regression uses chemical descriptors to predict the probability that a substance will belong to a particular class. The technique can be extended to predict toxicity recorded on a multi-point ordinal scale. The latter may be considerably more powerful than the binary technique.k-Nearest Neighbour (k-NN) analysis predicts toxicity on the basis of closeness to other substances of known toxicity, in multi-dimensional space defined by chemical descriptors. Discriminant and k-NN analyses produce visually intuitive presentations when only two descriptors are used. K-NN analysis can tackle difficult patterns of data such as embedded classes that would otherwise be intractable. Used sensibly, both discriminant analysis and logistic regression can produce models capable of chemical and biological interpretation. Logistic regression is powerful, flexible, reasonably free of onerous statistical requirements and probably has the most attractive combination of characteristics, making it a good first choice.
Expert Systems for Toxicity Prediction
Authors: Dearden J. C. 
Published: October 2010

Expert systems offer the facility to predict a toxicity endpoint, as well sometimes as additional relevant information, simply by inputting the chemical structure of a compound. There is now a number of expert systems available, mostly on a commercial basis although a few are free to use or download. This chapter discusses nineteen currently available expert systems, and their performances (if known). Published studies of consensus predictions with these expert systems indicate that these give better results than do individual expert systems.
A test set of compounds with Tetrahymena pyriformis toxicities has been run through the two expert systems known to predict these toxicities; the predictions were quite good, with standard errors of prediction of 0.395 and 0.433 log unit. A further test set of compounds with local lymph node assay skin sensitisation data has been run through seven expert systems, and it was found that consensus predictions were better than were those from any individual expert system.
Identification of binding partners interacting with the α1-N-propeptide of type V collagen
Authors: Symoens Sofie , Renard Marjolijn , Bonod-Bidaud Christelle , Syx Delfien , Vaganay Elisabeth , Malfait Fransiska , Ricard-Blum Sylvie , Kessler Efrat , Van Laer Lut , Coucke Paul , Ruggiero Florence , De Paepe Anne 
Published: October 2010

The predominant form of type V collagen is the [α1(V)]2α2(V) heterotrimer. Mutations in COL5A1 or COL5A2, encoding respectively the α1(V)- and α2(V)-collagen chain, cause classic EDS (Ehlers−Danlos syndrome), a heritable connective tissue disorder, characterized by fragile hyperextensible skin and joint hypermobility. Approximately half of the classic EDS cases remain unexplained. Type V collagen controls collagen fibrillogenesis through its conserved α1(V)-N-propeptide domain. To gain an insight into the role of this domain, a yeast two-hybrid screen among proteins expressed in human dermal fibroblasts was performed utilizing the N-propeptide as a bait. We identified 12 interacting proteins, including extracellular matrix proteins and proteins involved in collagen biosynthesis. Eleven interactions were confirmed by surface plasmon resonance and/or co-immunoprecipitation: α1(I)- and α2(I)-collagen chains, α1(VI)-, α2(VI)- and α3(VI)-collagen chains, tenascin-C, fibronectin, PCPE-1 (procollagen C-proteinase enhancer-1), TIMP-1 (tissue inhibitor of metalloproteinases-1), MMP-2 (matrix metalloproteinase 2) and TGF-β1 (transforming growth factor β1). Solid-phase binding assays confirmed the involvement of the α1(V)-N-propeptide in the interaction between native type V collagen and type VI collagen, suggesting a bridging function of this protein complex in the cell-matrix environment. Enzymatic studies showed that processing of the α1(V)-N-propeptide by BMP-1 (bone morphogenetic protein 1)/procollagen C-proteinase is enhanced by PCPE-1. These interactions are likely to be involved in extracellular matrix homoeostasis and their disruption could explain the pathogenetic mechanism in unresolved classic EDS cases.
PKCζ-interacting protein ZIP3 is generated by intronic polyadenylation, and is expressed in the brain and retina of the rat
Authors: Urbanczyk Andreas , Jünemann Anselm , Enz Ralf 
Published: October 2010

Scaffold proteins contain multiple protein–protein interaction modules that physically assemble functionally related proteins into larger complexes. ZIPs [PKC (protein kinase C) ζ-interacting proteins] link the enzymatic activity of the atypical PKC isoforms PKCλ/ι or PKCζ to target proteins and are associated with neurodegenerative disorders. In the rat, alternative splicing generates three ZIP variants. Previously, we identified the ZIP3 transcript, containing 13 C-terminal amino acids encoded by intron 4, in the rat CNS (central nervous system). In the present study, we identified intronic polyadenylation signals in rat and human ZIP genes [known as SQSTM1 (sequestosome-1) in humans] and detected the corresponding ZIP3-like transcripts. In addition, we generated ZIP3-specific immune sera and observed expression of the protein in the brain and retina of the adult rat. In the retina, ZIP3 is present in nuclear layers where it co-localizes with PKCζ. An immune serum recognizing all three ZIP isoforms labelled the same cells as the newly generated ZIP3-specific antibodies and, in addition, stained both synaptic layers of the retina. There, ZIPs are localized in axon terminals of rod bipolar cells that also contain ZIP-interacting PKCζ and GABAC (γ-aminobutyric acid type C) receptors. In summary, we detected ZIP3-like transcripts in rat- and human-derived samples and describe the expression of ZIP3 in the rat CNS.
Dysfunction of human subcutaneous fat arterioles in obesity alone or obesity associated with Type 2 diabetes
Authors: Georgescu Adriana , Popov Doina , Constantin Anamaria , Nemecz Miruna , Alexandru Nicoleta , Cochior Daniel , Tudor Aura 
Published: October 2010

The aim of the present study was to examine the effects of obesity alone and obesity associated with Type 2 diabetes on the structure, vascular reactivity and response to insulin of isolated human subcutaneous fat arterioles; these effects were correlated with the expression of insulin signalling proteins. Periumbilical subcutaneous adipose tissue was explanted during surgery, small arterioles (internal diameter 220±40 μm) were dissected out and investigated by electron microscopy, myography and immunoblotting. Compared with the subcutaneous arterioles of lean subjects, obesity activated the endothelium, enhanced the accumulation of collagen within vascular wall and increased the sensitivity of adrenergic response; obesity also diminished eNOS (endothelial NO synthase) protein expression, NO production, and endothelium-dependent and insulin-induced vasodilatation, as well as the protein expression of both IRS (insulin receptor substrates)-1 and IRS-2 and of the downstream molecules in the insulin signalling pathway, such as PI3K (phosphoinositide 3-kinase), phospho-Akt and Akt. When obesity was associated with Type 2 diabetes, these changes were significantly augmented. In conclusion, obesity alone or obesity associated with Type 2 diabetes alters human periumbilical adipose tissue arterioles in terms of structure, function and biochemsitry, including diminished eNOS expression and reduced levels of IRS-1, IRS-2, PI3K and Akt in the insulin signalling pathway.
Grain size and strain effects on the optical and electrical properties of hafnium oxide nanocrystalline thin films
Authors: Kamala Bharathi K. , Kalidindi N. R. , Ramana C. V. 
Published: October 2010

Nanocrystalline hafnium oxide (HfO2) thin films with an average crystal size ∼5–50 nm have been produced under controlled temperature and pressure and their structural, optical and electrical properties have been evaluated. Structural investigations indicate that the monoclinic HfO2 nanocrystals are highly oriented along the (1¯11) direction. The lattice expansion increases with a reduction in size while minimum strain energy occurs at maximum lattice expansion. The strain factor increases linearly from 2.4% to 4% with increasing HfO2 crystal dimensions from 10 to 40 nm. The optical absorption measurements indicate that the band gap (Eg) changes are not very significant with size reduction. The interband absorption corresponding to O 2p→Hf 5d transitions dominate the optical absorption edge at E∼6.25 eV; Eg varied in the range 5.42–5.60 eV for a variation in crystal dimension in the range 10–40 nm. Room temperature electrical conductivity increases from 1.08×10−3 to 1.7×10−3 (Ω cm)−1 with increasing size from 10 to 40 nm. The frequency dispersion of the electrical resistivity reveals the hopping conduction mechanism. The functional relationship derived between geometric and electronic structure for HfO2 suggest that tuning properties for desired applications can be achieved by controlling the grain size and, hence, the strain at the nanoscale dimensions.
At the request of the authors, this article is being retracted effective 31 May 2011.
Chlorhexidine-Impregnated Cloths to Prevent Skin and Soft-Tissue Infection in Marine Recruits: A Cluster-Randomized, Double-Blind, Controlled Effectiveness Trial
Authors: Whitman Timothy J. , Herlihy Rachel K. , Schlett Carey D. , Murray Patrick R. , Grandits Greg A. , Ganesan Anuradha , Brown Maya , Mancuso James D. , Adams William B. , Tribble David R. 
Published: October 2010

Background.Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causes skin and soft-tissue infection (SSTI) in military recruits.Objective.To evaluate the effectiveness of 2% Chlorhexidine gluconate (CHG)-impregnated cloths in reducing rates of SSTI and S. aureus colonization among military recruits.Design.A cluster-randomized (by platoon), double-blind, controlled effectiveness trial.Setting.Marine Officer Candidate School, Quantico, Virginia, 2007.Participants.Military recruits.Intervention.Application of CHG-impregnated or control (Comfort Bath; Sage) cloths applied over entire body thrice weekly.Measurements.Recruits were monitored daily for SSTI. Baseline and serial nasal and/or axillary swabs were collected to assess S. aureus colonization.Results.Of 1,562 subjects enrolled, 781 (from 23 platoons) underwent CHG-impregnated cloth application and 781 (from 21 platoons) underwent control cloth application. The rate of compliance (defined as application of 50% or more of wipes) at 2 weeks was similar (CHG group, 63%; control group, 67%) and decreased over the 6-week period. The mean 6-week SSTI rate in the CHG-impregnated cloth group was 0.094, compared with 0.071 in the control group (analysis of variance model rate difference, 0.025 ± 0.016; P = .14). At baseline, 43% of subjects were colonized with methicillin-susceptible S. aureus (MSSA), and 2.1% were colonized with MRSA. The mean incidence of colonization with MSSA was 50% and 61% (P = .026) and with MRSA was 2.6% and 6.0% (P = .034) for the CHG-impregnated and control cloth groups, respectively.Conclusions.CHG-impregnated cloths applied thrice weekly did not reduce rates of SSTI among recruits. S. aureus colonization rates increased in both groups but to a lesser extent in those assigned to the CHG-impregnated cloth Intervention. Antecedent S. aureus colonization was not a risk factor for SSTI. Additional studies are needed to identify effective measures for preventing SSTI among military recruits.Clinical Trials Registration.ClinicalTrials.gov identifier: NCT00475930.
Ertapenem-Resistant Enterobacteriaceae Risk Factors for Acquisition and Outcomes
Authors: Hyle E. P. , Ferraro M. J. , Silver M. , Lee H. , Hooper D. C. 
Published: October 2010

Background and Objective.Carbapenem resistance among Enterobacteriaceae is of concern because of increasing prevalence and limited therapeutic options. Limited research has been focused on understanding ertapenem resistance as a more sensitive marker for resistance to other carbapenems. We sought to determine risk factors for acquisition of ertapenem-resistant, meropenem-susceptible, or intermediate Enterobacteriaceae and to assess associated patient outcomes.Design.Retrospective case-control study among adult hospitalized inpatients.Setting.A 902-bed quaternary care urban hospital.Results.Sixty-two cases of ertapenem-resistant Enterobacteriaceae were identified from March 14, 2006, through October 31, 2007, and 62 unmatched control patients were randomly selected from other inpatients with cultures positive for ertapenem-susceptible Enterobacteriaceae. Thirty-seven (60%) of case patient isolates were Enterobacter cloacae, 20 (32%) were Klebsiella pneumoniae, and 5 (8%) were other species of Enterobacteriaceae. Risk factors for ertapenem-resistant Enterobacteriaceae infection included intensive care unit stay (odds ratio [OR], 4.6 [95% confidence interval {CI}, 2.0–10.3]), vancomycin-resistant Enterococcus colonization (OR, 7.1 [95% CI, 2.4–21.4]), prior central venous catheter use (OR, 10.0 [95% CI, 3.0–33.1]), prior receipt of mechanical ventilation (OR, 5.8 [95% CI, 2.1–16.2]), exposure to any antibiotic during the 30 days prior to a positive culture result (OR, 18.5 [95% CI, 4.9–69.9]), use of a β-lactam during the 30 days prior to a positive culture result (OR, 6.9 [95% CI, 3.0–16.0], and use of a carbapenem during the 30 days prior to a positive culture result (OR, 18.2 [95% CI, 2.6–130.0]). For the 62 case patients, 30-day outcomes from the time of positive culture result were 24 discharges (39%), 10 deaths (16%), and 28 continued hospitalizations (44%). The final end point of the hospitalization was discharge for 44 patients (71%) and death for 18 patients (29%).Conclusions.Ertapenem-resistant Enterobacteriaceae are important nosocomial pathogens. Multiple mechanisms of resistance maybe in operation. Additional study of ertapenem resistance is needed.
Impact of International Nosocomial Infection Control Consortium (INICC) Strategy on Central Line–Associated Bloodstream Infection Rates in the Intensive Care Units of 15 Developing Countries
Authors: Rosenthal Victor D. , Maki Dennis G. , Rodrigues Camila , Álvarez-Moreno Carlos , Leblebicioglu Hakan , Sobreyra-Oropeza Martha , Berba Regina , Madani Naoufel , Medeiros Eduardo A. , Cuéllar Luis E. , Mitrev Zan , Dueñas Lourdes , Guanche-Garcell Humberto , Mapp Trudell , Kanj Souha S. , Fernández-Hidalgo Rosalía ,   International Nosocomial Infection Control Consortium Investigators
Published: October 2010

Background.The International Nosocomial Infection Control Consortium (INICC) was established in 15 developing countries to reduce infection rates in resource-limited hospitals by focusing on education and feedback of outcome surveillance (infection rates) and process surveillance (adherence to infection control measures). We report a time-sequence analysis of the effectiveness of this approach in reducing rates of central line–associated bloodstream infection (CLABSI) and associated deaths in 86 intensive care units with a minimum of 6-month INICC membership.Methods.Pooled CLABSI rates during the first 3 months (baseline) were compared with rates at 6-month intervals during the first 24 months in 53,719 patients (190,905 central line–days). Process surveillance results at baseline were compared with intervention period data.Results.During the first 6 months, CLABSI incidence decreased by 33% (from 14.5 to 9.7 CLABSIs per 1,000 central line–days). Over the first 24 months there was a cumulative reduction from baseline of 54% (from 16.0 to 7.4 CLABSIs per 1,000 central line–days; relative risk, 0.46 [95% confidence interval, 0.33–0.63];P<.001). The number of deaths in patients with CLABSI decreased by 58%. During the intervention period, hand hygiene adherence improved from 50% to 60% (P<.001); the percentage of intensive care units that used maximal sterile barriers at insertion increased from 45% to 85% (P< .001), that adopted Chlorhexidine for antisepsis increased from 7% to 27% (P= .018), and that sought to remove unneeded catheters increased from 37% to 83% (P= .004); and the duration of central line placement decreased from 4.1 to 3.5 days (P< .001).Conclusions.Education, performance feedback, and outcome and process surveillance of CLABSI rates significantly improved infection control adherence, reducing the CLABSI incidence by 54% and the number of CLABSI-associated deaths by 58% in INICC hospitals during the first 2 years.
Improving Efficiency in Active Surveillance for Methicillin-Resistant Staphylococcus aureus or Vancomycin-Resistant Enterococcus at Hospital Admission
Authors: Morgan Daniel J. , Day Hannah R. , Furuno Jon P , Young Atlisa , Johnson J. Kristie , Bradham Douglas D. , Perencevich Eli N. 
Published: October 2010

Objective.Mandatory active surveillance culturing of all patients admitted to Veterans Affairs (VA) hospitals carries substantial economic costs. Clinical prediction rules have been used elsewhere to identify patients at high risk of colonization with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant enterococci (VRE). We aimed to derive and evaluate the clinical efficacy of prediction rules for MRSA and VRE colonization in a VA hospital.Design and Setting.Prospective cohort of adult inpatients admitted to the medical and surgical wards of a 119-bed tertiary care VA hospital.Methods.Within 48 hours after admission, patients gave consent, completed a 44-item risk factor questionnaire, and provided nasal culture samples for MRSA testing. A subset provided perirectal culture samples for VRE testing.Results.Of 598 patients enrolled from August 30, 2007, through October 30, 2009, 585 provided nares samples and 239 provided perirectal samples. The prevalence of MRSA was 10.4% (61 of 585) (15.0% in patients with and 5.6% in patients without electronic medical record (EMR)-documented antibiotic use during the past year; P < .01). The prevalence of VRE was 6.3% (15 of 239) (11.3% in patients with and 0.9% in patients without EMR-documented antibiotic use; P < .01 ). The use of EMR-documented antibiotic use during the past year as the predictive rule for screening identified 242.8 (84%) of 290.6 subsequent days of exposure to MRSA and 60.0 (98%) of 61.0 subsequent days of exposure to VRE, respectively. EMR documentation of antibiotic use during the past year identified 301 (51%) of 585 patients as high-risk patients for whom additional testing with active surveillance culturing would be appropriate.Conclusions.EMR documentation of antibiotic use during the year prior to admission identifies most MRSA and nearly all VRE transmission risk with surveillance culture sampling of only 51% of patients. This approach has substantial cost savings compared with the practice of universal active surveillance.
Investigation of Increased Rates of Isolation ofBacillusSpecies
Authors: Meites Elissa , Taur Ying , Marino Leslie , Schaefer Melissa , Eagan Janet , Jensen Bette , Williams Margaret , Kamboj Mini , Srinivasan Arjun 
Published: October 2010

Background.In 2007–2008, several US hospitals reported summertime increases in the number of clinical blood cultures positive forBacillusspecies, which are common environmental bacteria.Objective.To investigate increased rates of isolation ofBacillusspecies from blood cultures, identify risk factors, and recommend control strategies.Design.Survey and case-control study.Setting.Multiple hospitals, including a cancer center.Methods.We surveyed 24 facilities that reported increases. We also conducted a field investigation at a hospital with a high rate, reviewing charts, collecting clinical and environmental isolates, and observing infection control procedures. A case-control study compared inpatient case patients who had any blood culture positive forBacilluswith unmatched control patients who had a blood culture with no growth during June-August 2008.Results.Among surveyed facilities, mean monthly rates rose from 25 to a peak of 75Bacillus-positive blood cultures per 10,000 blood cultures performed during the period June-August. At the hospital where the case-control investigation was conducted, for most case patients (75%), theBacillus-positive blood cultures represented contamination or device colonization rather than infection. We enrolled 48 case patients and 48 control patients; in multivariate analysis, only central venous access device use was significantly associated with case status (odds ratio, 14.0;P< .01). Laboratory testing identified at least 12 differentBacillusspecies (non-anthracis) among the isolates. Observation of infection control procedures revealed variability in central line care and blood sample collection techniques.Conclusions.Periodic increases in the environmental load ofBacillusspecies may occur in hospitals. Our investigation indicated that at one facility, these increases likely represented a pseudo-outbreak ofBacillusspecies colonizing central venous lines or their accessories, such as needleless connector devices. Vigilant attention should be paid to infection control practices when collecting blood samples for culture, to minimize the risk of contamination by environmental microorganisms.