bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter Evaluation of the Staphylococcus QuickFISH Method for Simultaneous Identification of Staphylococcus aureus and Coagulase-Negative Staphylococci Directly from Blood Culture Bottles in Less than 30 Minutes
Authors: Deck Melissa K. , Anderson Erica S. , Buckner Rebecca J. , Colasante Georgia , Coull James M. , Crystal Benjamin , Latta Phyllis Della , Fuchs Martin , Fuller Deanna , Harris Will , Hazen Kevin , Klimas Lisa L. , Lindao Daniel , Meltzer Michelle C. , Morgan Margie , Shepard Janeen , Stevens Sharon , Wu Fann , Fiandaca Mark J. 
Published: April 2012

ABSTRACT

A novel rapid peptide nucleic acid fluorescence
in situ
hybridization (FISH) method,
Staphylococcus Quick
FISH, for the direct detection of
Staphylococcus
species from positive blood culture bottles was evaluated in a multicenter clinical study. The method utilizes a microscope slide with predeposited positive- and negative-control organisms and a self-reporting 15-min hybridization step, which eliminates the need for a wash step. Five clinical laboratories tested 722 positive blood culture bottles containing Gram-positive cocci in clusters. The sensitivities for detection of
Staphylococcus aureus
and coagulase-negative staphylococci (CoNS) were 99.5% (217/218) and 98.8% (487/493), respectively, and the combined specificity of the assay was 89.5% (17/19). The combined positive and negative predictive values of the assay were 99.7% (696/698) and 70.8% (17/24), respectively. Studies were also performed on spiked cultures to establish the specificity and performance sensitivity of the method.
Staphylococcus Quick
FISH has a turnaround time (TAT) of <30 min and a hands-on time (HOT) of <5 min. The ease and speed of the method have the potential to improve the accuracy of therapeutic intervention by providing
S. aureus
/CoNS identification simultaneously with Gram stain results.
Impact of Results of a Rapid Staphylococcus aureus Diagnostic Test on Prescribing of Antibiotics for Patients with Clustered Gram-Positive Cocci in Blood Cultures
Authors: Davies Jane , Gordon Claire L. , Tong Steven Y. C. , Baird Robert W. , Davis Joshua S. 
Published: April 2012

ABSTRACT

In tropical northern Australia, approximately 20% of
Staphylococcus aureus
bacteremia is caused by methicillin-resistant
Staphylococcus aureus
(MRSA). We prospectively evaluated the impact on clinician antibiotic prescribing of the results obtained from performing the GeneXpert MRSA/SA test on 151 positive blood cultures with clustered Gram-positive cocci. The GeneXpert result led to earlier appropriate prescription of vancomycin for 54% of patients with MRSA; 25% of patients avoided vancomycin, and 16% of patients had all antibiotics ceased.
GFDL’s ESM2 Global Coupled Climate–Carbon Earth System Models. Part I: Physical Formulation and Baseline Simulation Characteristics
Authors: Dunne John P. , John Jasmin G. , Adcroft Alistair J. , Griffies Stephen M. , Hallberg Robert W. , Shevliakova Elena , Stouffer Ronald J. , Cooke William , Dunne Krista A. , Harrison Matthew J. , Krasting John P. , Malyshev Sergey L. , Milly P. C. D. , Phillipps Peter J. , Sentman Lori T. , Samuels Bonita L. , Spelman Michael J. , Winton Michael , Wittenberg Andrew T. , Zadeh Niki 
Published: April 2012

Abstract
The physical climate formulation and simulation characteristics of two new global coupled carbon–climate Earth System Models, ESM2M and ESM2G, are described. These models demonstrate similar climate fidelity as the Geophysical Fluid Dynamics Laboratory’s previous Climate Model version 2.1 (CM2.1) while incorporating explicit and consistent carbon dynamics. The two models differ exclusively in the physical ocean component; ESM2M uses Modular Ocean Model version 4p1 with vertical pressure layers while ESM2G uses Generalized Ocean Layer Dynamics with a bulk mixed layer and interior isopycnal layers. Differences in the ocean mean state include the thermocline depth being relatively deep in ESM2M and relatively shallow in ESM2G compared to observations. The crucial role of ocean dynamics on climate variability is highlighted in El Niño–Southern Oscillation being overly strong in ESM2M and overly weak in ESM2G relative to observations. Thus, while ESM2G might better represent climate changes relating to total heat content variability given its lack of long-term drift, gyre circulation, and ventilation in the North Pacific, tropical Atlantic, and Indian Oceans, and depth structure in the overturning and abyssal flows, ESM2M might better represent climate changes relating to surface circulation given its superior surface temperature, salinity, and height patterns, tropical Pacific circulation and variability, and Southern Ocean dynamics. The overall assessment is that neither model is fundamentally superior to the other, and that both models achieve sufficient fidelity to allow meaningful climate and earth system modeling applications. This affords the ability to assess the role of ocean configuration on earth system interactions in the context of two state-of-the-art coupled carbon–climate models.
Influence of the Kuroshio in the East China Sea on the Early Summer (Baiu) Rain
Authors: Sasaki Yoshi N. , Minobe S. , Asai T. , Inatsu M. 
Published: April 2012

Abstract
Influence of the Kuroshio in the East China Sea on the baiu rainband is examined using satellite observations, a reanalysis dataset, and a regional atmospheric model from 2003 to 2008. Satellite observations and reanalysis data reveal that precipitation over the Kuroshio is the highest in early summer (June), when the baiu rainband covers the East China Sea. The high rainfall is collocated with the warm sea surface temperature (SST) tongue of the Kuroshio. This locally enhanced precipitation is embedded in the large-scale baiu rainband, so that the amplitude of precipitation over the Kuroshio is twice as large as that in its surrounding area. The Kuroshio is also accompanied by high surface wind speed, energetic evaporation, and wind convergence. This wind convergence likely results from the SST influence on atmospheric pressure through not only temperature changes, but also humidity changes. Furthermore, the Kuroshio anchors the ascent motion and large diabatic heating with a peak in the midtroposphere, suggesting that the influence of the Kuroshio extends to the upper troposphere. It is also found that the East China Sea in June is the region of the strongest deep atmospheric response to western boundary currents along with the Gulf Stream region in summer.
The observational results are well reproduced by the regional atmospheric model. The model indicates that when the SST tongue of the Kuroshio is smoothed, the enhanced precipitation, the energetic evaporation, and the wind convergence over the Kuroshio disappear, although the large-scale structure of the baiu rainband is not essentially changed.
Verification and Calibration of Neighborhood and Object-Based Probabilistic Precipitation Forecasts from a Multimodel Convection-Allowing Ensemble
Authors: Johnson Aaron , Wang Xuguang 
Published: April 2012

Abstract
Neighborhood and object-based probabilistic precipitation forecasts from a convection-allowing ensemble are verified and calibrated. Calibration methods include logistic regression, one- and two-parameter reliability-based calibration, and cumulative distribution function (CDF)-based bias adjustment. Newly proposed object-based probabilistic forecasts for the occurrence of a forecast object are derived from the percentage of ensemble members with a matching object. Verification and calibration of single- and multimodel subensembles are performed to explore the effect of using multiple models.
The uncalibrated neighborhood-based probabilistic forecasts have skill minima during the afternoon convective maximum. Calibration generally improves the skill, especially during the skill minima, resulting in positive skill. In general all calibration methods perform similarly, with a slight advantage of logistic regression (one-parameter reliability based) calibration for 1-h (6 h) accumulations.
The uncalibrated object-based probabilistic forecasts are, in general, less skillful than the uncalibrated neighborhood-based probabilistic forecasts. Object-based calibration also results in positive skill at all lead times. For object-based calibration the skill is significantly different among the calibration methods, with the logistic regression performing the best and CDF-based bias adjustment performing the worst.
For both the neighborhood and object-based probabilistic forecasts, the impact of using 10 or 25 days of training data for calibration is generally small and is most significant for the two-parameter reliability-based method. An uncalibrated Advanced Research Weather Research and Forecasting Model (ARW-WRF) subensemble is significantly more skillful than an uncalibrated WRF Nonhydrostatic Mesoscale Model (NMM) subensemble. The difference is reduced by calibration. The multimodel subensemble only shows an advantage for the neighborhood-based forecasts beyond 1-day lead time and shows no advantage for the object-based forecasts.
Hypothyroidism maintained reactive oxygen species–steady state in the kidney of rats intoxicated with ethylene glycol: effect related to an increase in the glutathione that maintains the redox environment
Authors: Estévez-Carmona María Mirian , Meléndez-Camargo Estela , Ortiz-Butron Rocio , Pineda-Reynoso Marisol , Franco-Colin Margarita , Cano-Europa Edgar 
Published: April 2012

Our objective was to determine whether hypothyroidism protects against ethylene glycol (EG)-induced renal damage and whether the redox environment participates in the protection process. We used 36 male Wistar rats divided into four groups: (1) euthyroid, (2) euthyroid + 0.75% EG, (3) hypothyroid, and (4) hypothyroid + 0.75% EG. Hypothyroidism occurred 2 weeks after thyroidectomy. The parathyroid gland was reimplanted. EG was administrated for 21 days in drinking water. On day 21, the renal function was assessed and then the rats were decapitated. The left kidney was processed for histology, and the right kidney was used to determine the redox environment, oxidative stress, and the testing of the antioxidant enzymatic system. EG in euthyroid rats reduced the hydric and electrolytic balance and it also caused oxidative stress and renal damage. Hypothyroidism per se modifies the renal function causing a low osmolal and potassium clearance and the filtered load of potassium and sodium. In addition, there was an enhanced redox state because hypothyroidism increases the reduced glutathione concentration caused by a high activity of γ-glutamylcysteine synthase. Hypothyroidism is a protective state against EG because the changes in the renal function were smaller than in the euthyroid state. The oxidative stress and cellular damage were ameliorated by the hypothyroid condition. Also, the hypothyroidism-enhanced redox environment protects against EG-induced oxidative stress, renal damage, and renal dysfunction.
Breaking Through the Glass Ceiling in the Ivory Tower
Authors: Murray Niki , Tremaine Marianne , Fountaine Susan 
Published: April 2012

The Problem. Universities are patriarchal institutions. More males reach upper levels of the academic hierarchy than females. The authors were concerned that their university had a marginally lower percentage of female professors than others in their country and used a survey and interviews to explore the facts behind the figures. The Solution. Statistics showed that though fewer females applied for promotion, proportionately more female applicants were successful. The authors researched what helped female professors and associate professors gain promotion and explored views on the spillover between work and family/community roles. Promotion enhancement factors included encouragement from department heads and senior colleagues. Family/community roles were seen to spillover positively to work, though work could negatively affect time for family and community involvement. The Stakeholders. These findings could encourage proactive mentoring of female academic staff by managers, and increase HR and HRD support for family-friendly policies and training programs.
Systems analysis of inflammatory bowel disease based on comprehensive gene information
Authors: Suzuki Satoru , Takai-Igarashi Takako , Fukuoka Yutaka , Wall Dennis P , Tanaka Hiroshi , Tonellato Peter J 
Published: April 2012

Abstract

Background
The rise of systems biology and availability of highly curated gene and molecular information resources has promoted a comprehensive approach to study disease as the cumulative deleterious function of a collection of individual genes and networks of molecules acting in concert. These "human disease networks" (HDN) have revealed novel candidate genes and pharmaceutical targets for many diseases and identified fundamental HDN features conserved across diseases. A network-based analysis is particularly vital for a study on polygenic diseases where many interactions between molecules should be simultaneously examined and elucidated. We employ a new knowledge driven HDN gene and molecular database systems approach to analyze Inflammatory Bowel Disease (IBD), whose pathogenesis remains largely unknown.

Methods and Results
Based on drug indications for IBD, we determined sibling diseases of mild and severe states of IBD. Approximately 1,000 genes associated with the sibling diseases were retrieved from four databases. After ranking the genes by the frequency of records in the databases, we obtained 250 and 253 genes highly associated with the mild and severe IBD states, respectively. We then calculated functional similarities of these genes with known drug targets and examined and presented their interactions as PPI networks.

Conclusions
The results demonstrate that this knowledge-based systems approach, predicated on functionally similar genes important to sibling diseases is an effective method to identify important components of the IBD human disease network. Our approach elucidates a previously unknown biological distinction between mild and severe IBD states.
Biomass pretreatment affects Ustilago maydis in producing itaconic acid
Authors: Klement Tobias , Milker Sofia , Jäger Gernot , Grande Philipp M , Domínguez de María Pablo , Büchs Jochen 
Published: April 2012

Abstract

Background
In the last years, the biotechnological production of platform chemicals for fuel components has become a major focus of interest. Although ligno-cellulosic material is considered as suitable feedstock, the almost inevitable pretreatment of this recalcitrant material may interfere with the subsequent fermentation steps. In this study, the fungus Ustilago maydis was used to produce itaconic acid as platform chemical for the synthesis of potential biofuels such as 3-methyltetrahydrofuran. No studies, however, have investigated how pretreatment of ligno-cellulosic biomass precisely influences the subsequent fermentation by U. maydis. Thus, this current study aims to first characterize U. maydis in shake flasks and then to evaluate the influence of three exemplary pretreatment methods on the cultivation and itaconic acid production of this fungus. Cellulose enzymatically hydrolysed in seawater and salt-assisted organic-acid catalysed cellulose were investigated as substrates. Lastly, hydrolysed hemicellulose from fractionated beech wood was applied as substrate.

Results

U. maydis was characterized on shake flask level regarding its itaconic acid production on glucose. Nitrogen limitation was shown to be a crucial condition for the production of itaconic acid. For itaconic acid concentrations above 25 g/L, a significant product inhibition was observed. Performing experiments that simulated influences of possible pretreatment methods, U. maydis was only slightly affected by high osmolarities up to 3.5 osmol/L as well as of 0.1 M oxalic acid. The production of itaconic acid was achieved on pretreated cellulose in seawater and on the hydrolysed hemicellulosic fraction of pretreated beech wood.

Conclusion
The fungus U. maydis is a promising producer of itaconic acid, since it grows as single cells (yeast-like) in submerged cultivations and it is extremely robust in high osmotic media and real seawater. Moreover, U. maydis can grow on the hemicellulosic fraction of pretreated beech wood. Thereby, this fungus combines important advantages of yeasts and filamentous fungi. Nevertheless, the biomass pretreatment does indeed affect the subsequent itaconic acid production. Although U. maydis is insusceptible to most possible impurities from pretreatment, high amounts of salts or residues of organic acids can slow microbial growth and decrease the production. Consequently, the pretreatment step needs to fit the prerequisites defined by the actual microorganisms applied for fermentation.
Synthesis of Diblock copolymer poly-3-hydroxybutyrate -block-poly-3-hydroxyhexanoate [PHB-b-PHHx] by a β-oxidation weakened Pseudomonas putida KT2442
Authors: Tripathi Lakshmi , Wu Lin-Ping , Chen Jinchun , Chen Guo-Qiang 
Published: April 2012

Abstract

Background
Block polyhydroxyalkanoates (PHA) were reported to be resistant against polymer aging that negatively affects polymer properties. Recently, more and more attempts have been directed to make PHA block copolymers. Diblock copolymers PHB-b-PHHx consisting of poly-3-hydroxybutyrate (PHB) block covalently bonded with poly-3-hydroxyhexanoate (PHHx) block were for the first time produced successfully by a recombinant Pseudomonas putida KT2442 with its β-oxidation cycle deleted to its maximum.

Results
The chloroform extracted polymers were characterized by nuclear magnetic resonance (NMR), thermo- and mechanical analysis. NMR confirmed the existence of diblock copolymers consisting of 58 mol% PHB as the short chain length block with 42 mol% PHHx as the medium chain length block. The block copolymers had two glass transition temperatures (T

g
) at 2.7°C and −16.4°C, one melting temperature (T

m
) at 172.1°C and one cool crystallization temperature (T

c
) at 69.1°C as revealed by differential scanning calorimetry (DSC), respectively. This is the first microbial short-chain-length (scl) and medium-chain-length (mcl) PHA block copolymer reported.

Conclusions
It is possible to produce PHA block copolymers of various kinds using the recombinant Pseudomonas putida KT2442 with its β-oxidation cycle deleted to its maximum. In comparison to a random copolymer poly-3-hydroxybutyrate-co-3-hydroxyhexanoate (P(HB-co-HHx)) and a blend sample of PHB and PHHx, the PHB-b-PHHx showed improved structural related mechanical properties.
Digitoxin and its analogs as novel cancer therapeutics
Authors: Elbaz Hosam A , Stueckle Todd A , Tse William , Rojanasakul Yon , Dinu Cerasela Zoica 
Published: April 2012

Abstract
A growing body of evidence indicates that digitoxin cardiac glycoside is a promising anticancer agent when used at therapeutic concentrations. Digitoxin has a prolonged half-life and a well-established clinical profile. New scientific avenues have shown that manipulating the chemical structure of the saccharide moiety of digitoxin leads to synthetic analogs with increased cytotoxic activity. However, the anticancer mechanism of digitoxin or synthetic analogs is still subject to study while concerns about digitoxin's cardiotoxicity preclude its clinical application in cancer therapeutics. This review focuses on digitoxin and its analogs, and their cytotoxicity against cancer cells. Moreover, a new perspective on the pharmacological aspects of digitoxin and its analogs is provided to emphasize new research directions for developing potent chemotherapeutic drugs.
Tamoxifen Alters the Plasma Concentration of Molecules Associated with Cardiovascular Risk in Women with Breast Cancer Undergoing Chemotherapy
Authors: Romero Walckiria G. , Da Silva Fabrício B. , Borgo Mariana V. , Bissoli Nazaré S. , Gouvêa Sonia A. , Abreu Gláucia R. 
Published: April 2012

Abstract

Objectives.
The objective of this study was to evaluate the effect of tamoxifen on blood markers that are associated with cardiovascular risk, such as C-reactive protein (CRP), apolipoprotein A-1 (Apo-A), and apolipoprotein B-100 (Apo-B), in women undergoing chemotherapy for breast cancer.

Methods.
Over a period of 12 months, we followed 60 women with breast cancer. The women were divided into the following groups: a group that received only chemotherapy (n = 23), a group that received chemotherapy plus tamoxifen (n = 21), and a group that received only tamoxifen (n = 16). Plasma CRP levels were assessed at 0, 3, 6, and 12 months, and Apo-A and Apo B levels as well as the Apo-B/Apo-A ratio were assessed at 0 and 12 months.

Results.
We found increases in the plasma concentration of CRP in the chemotherapy alone and chemotherapy plus tamoxifen groups after 3 and 6 months of treatment (before the introduction of tamoxifen). However, after 12 months of treatment, women who used tamoxifen (the chemotherapy plus tamoxifen and tamoxifen alone groups) showed a significant reduction in CRP and Apo-B levels and a decrease in the Apo-B/Apo-A ratio. A significant increase in serum Apo-A levels was observed in the group receiving chemotherapy alone as a treatment for breast cancer.

Conclusion.
The use of tamoxifen after chemotherapy for the treatment of breast cancer significantly reduces the levels of cardiovascular disease risk markers (CRP, Apo-B, and the Apo-B/Apo-A ratio).
Analysis of the Solidification and Properties of Plaster Cast Al Based Composites
Authors: Egizabal P. , Romero A. , Torregaray A. 
Published: April 2012

Analysis of the Solidification and Properties of Plaster Cast Al Based CompositesThe present work deals with aspects related to the solidification and properties of an Al-Si10Mg/SiC20palloy cast in plaster moulds. Several strategies were followed to shorten its solidification time such as embedding copper tubes into the mould to make circulate cooling fluids immediately after the casting step. The analysis of cooling curves provided valuable information on the effect of the particles on solidification events. The precipitation of different phases of the MMC takes place at higher temperatures and earlier than in the case of the non reinforced alloy. Particles affect the solidification pattern of the alloy and play a noticeable role in the precipitation of the phases. This fact should be taken into account to design the filling and feeding systems correctly and for modelling and processing parameters as well as in thermal treatments. Eventually samples were obtained under the highest solidification rate conditions to analyse the microstructure and tensile properties of the MMC material.
Co-Mo and Co-Mo-C Alloys Deposited in a Magnetic Field of High Intensity and their Electrocatalytic Properties
Authors: Żabiński P. , Mech K. , Kowalik R. 
Published: April 2012

Co-Mo and Co-Mo-C Alloys Deposited in a Magnetic Field of High Intensity and their Electrocatalytic PropertiesThe article presents results of tests on electrodeposition in a magnetic field of Co-Mo and Co-Mo-C alloys characterised by low overvoltage of hydrogen evolution. Addition of molybdenum and carbon was to lower the values of overvoltage of hydrogen evolution on cobalt. The influence of a magnetic field of high intensity (1 - 12 T) on the deposits composition, structure and morphology was determined. The deposition was conducted in a magnetic field of parallel orientation of the magnetic field forces lines in relation to the working electrode. Electrocatalytic properties of the obtained alloy coatings within the range of hydrogen evolution were tested in a concentrated solution of NaOH. The obtained alloys were analysed with the XRD method, their composition was tested with the WDXRF technique and they underwent observation applying scanning electron microscopy (SEM). The comparison of electrocatalytic properties of Co-Mo alloys with properties of Co-Mo-C ones enabled determining the influence of carbon presence in cathodic deposits on the overvoltage value of hydrogen evolution on them.