bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Spread of Methicillin-Resistant Staphylococcus aureus (MRSA) Outbreaks throughout the Hospitals in Orange County, California
Authors: Lee Bruce Y. , McGlone Sarah M. , Wong Kim F. , Yilmaz S. Levent , Avery Taliser R. , Song Yeohan , Christie Richard , Eubank Stephen , Brown Shawn T. , Epstein Joshua M. , Parker Jon I. , Burke Donald S. , Platt Richard , Huang Susan S. 
Published: May 2011

Background.Since hospitals in a region often share patients, an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infection in one hospital could affect other hospitals.Methods.Using extensive data collected from Orange County (OC), California, we developed a detailed agent-based model to represent patient movement among all OC hospitals. Experiments simulated MRSA outbreaks in various wards, institutions, and regions. Sensitivity analysis varied lengths of stay, intraward transmission coefficients (β), MRSA loss rate, probability of patient transfer or readmission, and time to readmission.Results.Each simulated outbreak eventually affected all of the hospitals in the network, with effects depending on the outbreak size and location. Increasing MRSA prevalence at a single hospital (from 5% to 15%) resulted in a 2.9% average increase in relative prevalence at all other hospitals (ranging from no effect to 46.4%). Single-hospital intensive care unit outbreaks (modeled increase from 5% to 15%) caused a 1.4% average relative increase in all other OC hospitals (ranging from no effect to 12.7%).Conclusion.MRSA outbreaks may rarely be confined to a single hospital but instead may affect all of the hospitals in a region. This suggests that prevention and control strategies and policies should account for the interconnectedness of health care facilities.
Peripheral Venous Catheter-Related Staphylococcus aureus Bacteremia
Authors: Trinh T. Tony , Chan Philip A. , Edwards Omega , Hollenbeck Brian , Huang Brian , Burdick Nancy , Jefferson Julie A. , Mermel Leonard A. 
Published: May 2011

Objective.Better understand the incidence, risk factors, and outcomes of peripheral venous catheter (PVC)-related Staphylococcus aureus bacteremia.Design.Retrospective study of PVC-related S. aureus bacteremias in adult patients from July 2005 through March 2008. A point-prevalence survey was performed January 9, 2008, on adult inpatients to determine PVC utilization; patients with a PVC served as a cohort to assess risk factors for PVC-related S. aureus bacteremia.Setting.Tertiary care teaching hospital.Results.Twenty-four (18 definite and 6 probable) PVC-related S. aureus bacteremias were identified (estimated incidence density, 0.07 per 1,000 catheter-days), with a median duration of catheterization of 3 days (interquartile range, 2-6). Patients with PVC-related S. aureus bacteremia were significantly more likely to have a PVC in the antecubital fossa (odds ratio [OR], 6.5), a PVC placed in the emergency department (OR, 6.0), or a PVC placed at an outside hospital (P = .005), with a longer duration of catheterization (P < .001). These PVCs were significantly less likely to have been inserted in the hand (OR, 0.23) or placed on an inpatient medical unit (OR, 0.17). Mean duration of antibiotic treatment was 19 days (95% confidence interval, 15-23 days); 42% (10/24) of cases encountered complications. We estimate that there may be as many as 10,028 PVC-related S. aureus bacteremias yearly in US adult hospitalized inpatients.Conclusion.PVC-related S. aureus bacteremia is an underrecognized complication. PVCs inserted in the emergency department or at outside institutions, PVCs placed in the antecubital fossa, and those with prolonged dwell times are associated with such infections.
Hand Hygiene, and Not Ertapenem Use, Contributed to Reduction of Carbapenem-Resistant Pseudomonas aeruginosa Rates
Authors: Santos Rodrigo Pires dos , Jacoby Thalita , Machado Denise Pires , Lisboa Thiago , Gastal Sandra Ludwig , Nagel Fabiano Márcio , Kuplich Nádia Mora , Konkewicz Loriane , Lovatto Carem Gorniak , Pires Márcia Rosane , Goldani Luciano Zubaran 
Published: May 2011

Objective.To evaluate the impact of ertapenem use in Pseudomonas aeruginosa carbapenem resistance, taking into account the volume of antimicrobial consumption, the consumption by the entire hospital of alcohol-based antiseptic hand rub, and the density rate of invasive practices.Design.Before-and-after trial.Setting.A tertiary care university hospital in southern Brazil.Methods.Ertapenem was first added to the hospital formulary in June 2006, and it was excluded in February 2009. We evaluated Pseudomonas aeruginosa resistance rates through 3 study periods: period 1, before ertapenem use (17 months); period 2, during ertapenem use (33 months); and period 3, after exclusion of ertapenem (15 months).Results.After introduction of ertapenem, there was a significant decrease in median consumption of imipenem or meropenem, from 2.6 to 2.2 defined daily doses (DDDs) per 100 patient-days (level change from 0.04 to -1.08; P < .01), and an increase in the use of these medications after ertapenem exclusion, from 2.2 to 3.3 DDDs per 100 patient-days (level change from -0.14 to 0.91; P < .01), by segmented regression analysis. There was no difference in the incidence density of carbapenem-resistant P. aeruginosa infection related to ertapenem use throughout the study periods. However, by multiple regression analysis, the reduction in the rate of carbapenem-resistant P. aeruginosa infection correlated significantly with the increase in the volume of alcohol used as hand sanitizer, which was from 660.7 mL per 100 patient-days in period 1 to 2,955.1 mL per 100 patient-days in period 3 (P = .04). Ertapenem use did not impact the rate of carbapenem-resistant P. aeruginosa infection.Conclusions.Use of alcohol-based hand gel, rather than ertapenem, was associated with a reduction in the rates of carbapenem-resistant P. aeruginosa infection. Measures to reduce resistance must include factors other than just antimicrobial stewardship programs alone.
Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data
Authors: Bedo Justin , Kowalczyk Adam 
Published: May 2011

Abstract
Motivation: Many ChIP-Seq experiments are aimed at developing gold standards for determining the locations of various genomic features such as transcription start or transcription factor binding sites on the whole genome. Many such pioneering experiments lack rigorous testing methods and adequate ‘gold standard’ annotations to compare against as they themselves are the most reliable source of empirical data available. To overcome this problem, we propose a self-consistency test whereby a dataset is tested against itself. It relies on a supervised machine learning style protocol for in silico annotation of a genome and accuracy estimation to guarantee, at least, self-consistency.
Results: The main results use a novel performance metric (a calibrated precision) in order to assess and compare the robustness of the proposed supervised learning method across different test sets. As a proof of principle, we applied the whole protocol to two recent ChIP-Seq ENCODE datasets of STAT1 and Pol-II binding sites. STAT1 is benchmarked against in silico detection of binding sites using available position weight matrices. Pol-II, the main focus of this paper, is benchmarked against 17 algorithms for the closely related and well-studied problem of in silico transcription start site (TSS) prediction. Our results also demonstrate the feasibility of in silico genome annotation extension with encouraging results from a small portion of annotated genome to the remainder.
Availability: Available from http://www.genomics.csse.unimelb.edu.au/gat.
Contact: justin.bedo@nicta.com.au; adam.kowalczyk@nicta.com.au
Supplementary Information: Supplementary data are available at Bioinformatics online.
Resistant Starch and Starch Thermal Characteristics in Exotic Corn Lines Grown in Temperate and Tropical Environments
Authors: Pollak Linda M. , Scott M. Paul , Duvick Susan A. 
Published: May 2011

ABSTRACTCorn as a food that is heated and cooled to allow starch retrogradation has higher levels of resistant starch (RS). Increasing the amount of RS can make corn an even healthier food and may be accomplished by breeding and selection, especially by using exotic germplasm. Sixty breeding lines of introgressed exotic germplasm backgrounds, selected for high yield, were grown in three tropical and temperate locations and analyzed for starch thermal characteristics and RS levels. Although actual values for all starch characteristics were within normal levels, most characteristics had significant genotypic effects, and all had significant location effects. Thermal properties of retrograded starch were more influenced by the environment than the thermal properties of raw starch, making retrograded starch traits more heritable than raw starch traits. This suggests that a breeding strategy based on retrograded starch traits will have a better chance of success than a breeding strategy based on raw starch traits. A significant genotype effect for RS levels indicates that genotypic selection to raise the level of RS and increase the healthful aspects of corn food should be successful. Significant location effects indicate that breeders using winter nurseries to accelerate their breeding progress need to be careful when making selections using RS data collected on seed grown in the tropics. A small but highly significant correlation between RS and some thermal characteristics, especially percentage of retrogradation, indicates that we may be able to select promising genotypes for RS selection based on our extensive database of thermal characteristics collected on a wide number of diverse corn lines.
Functional Incorporation of Sorghum Small Subunit Increases the Catalytic Turnover Rate of Rubisco in Transgenic Rice
Authors: Ishikawa Chie , Hatanaka Tomoko , Misoo Shuji , Miyake Chikahiro , Fukayama Hiroshi 
Published: May 2011

Abstract
Rubisco limits photosynthetic CO2 fixation because of its low catalytic turnover rate (k cat) and competing oxygenase reaction. Previous attempts to improve the catalytic efficiency of Rubisco by genetic engineering have gained little progress. Here we demonstrate that the introduction of the small subunit (RbcS) of high k cat Rubisco from the C4 plant sorghum (Sorghum bicolor) significantly enhances k cat of Rubisco in transgenic rice (Oryza sativa). Three independent transgenic lines expressed sorghum RbcS at a high level, accounting for 30%, 44%, and 79% of the total RbcS. Rubisco was likely present as a chimera of sorghum and rice RbcS, and showed 1.32- to 1.50-fold higher k cat than in nontransgenic rice. Rubisco from transgenic lines showed a higher K m for CO2 and slightly lower specificity for CO2 than nontransgenic controls. These results suggest that Rubisco in rice transformed with sorghum RbcS partially acquires the catalytic properties of sorghum Rubisco. Rubisco content in transgenic lines was significantly increased over wild-type levels but Rubisco activation was slightly decreased. The expression of sorghum RbcS did not affect CO2 assimilation rates under a range of CO2 partial pressures. The J max/V cmax ratio was significantly lower in transgenic line compared to the nontransgenic plants. These observations suggest that the capacity of electron transport is not sufficient to support the increased Rubisco capacity in transgenic rice. Although the photosynthetic rate was not enhanced, the strategy presented here opens the way to engineering Rubisco for improvement of photosynthesis and productivity in the future.
Nitric Oxide Regulates DELLA Content and PIF Expression to Promote Photomorphogenesis in Arabidopsis
Authors: Lozano-Juste Jorge , León José 
Published: May 2011

Abstract
The transition from etiolated to green seedlings involves a shift from hypocotyl growth-promoting conditions to growth restraint. These changes occur through a complex light-driven process involving multiple and tightly coordinated hormonal signaling pathways. Nitric oxide (NO) has been lately characterized as a regulator of plant development interacting with hormone signaling. Here, we show that Arabidopsis (Arabidopsis thaliana) NO-deficient mutant hypocotyls are longer than those from wild-type seedlings under red light but not under blue or far-red light. Accordingly, exogenous treatment with the NO donor sodium nitroprusside and mutant plants with increased endogenous NO levels resulted in reduced hypocotyl length. In addition to increased hypocotyl elongation, NO deficiency led to increased anthocyanin levels and reduced PHYB content under red light, all processes governed by phytochrome-interacting factors (PIFs). NO-deficient plants accordingly showed an enhanced expression of PIF3, PIF1, and PIF4. Moreover, exogenous NO increased the levels of the gibberellin (GA)-regulated DELLA proteins and shortened hypocotyls, likely through the negative regulation of the GA Insensitive Dwarf1 (GID1)-Sleepy1 (SLY1) module. Consequently, NO-deficient seedlings displayed up-regulation of SLY1, defective DELLA accumulation, and altered GA sensitivity, thus resulting in defective deetiolation under red light. Accumulation of NO in wild-type seedlings undergoing red light-triggered deetiolation and elevated levels of NO in the GA-deficient ga1-3 mutant in darkness suggest a mutual NO-GA antagonism in controlling photomorphogenesis. PHYB-dependent NO production promotes photomorphogenesis by a GID1-GA-SLY1-mediated mechanism based on the coordinated repression of growth-promoting PIF genes and the increase in the content of DELLA proteins.
Advances in the prognostication and management of advanced MDS in children
Authors: Hasle Henrik , Niemeyer Charlotte M. 
Published: May 2011

SummaryAdvanced myelodysplastic syndrome (MDS) in children includes refractory anaemia with excess blasts (RAEB) and RAEB in transformation (RAEB‐T) according to the paediatric modification of the World Health Organization classification. Clinical features and cytogenetics are essential to make a diagnosis because blast count alone is insufficient to differentiate MDS from acute myeloid leukaemia (AML). Little is known about molecular genetics in paediatric MDS but hypermethylation seem to be frequent. Monosomy 7 is the most common cytogenetic aberration but prognostic neutral whereas those with structural complex karyotype have a very poor outcome. Haematopoietic stem cell transplantation (HSCT) is the treatment of choice and results in cure rates of around 60%. Intensive chemotherapy prior to HSCT provides no survival benefit for children with RAEB and RAEB‐T and can generally not be recommended. Intensive chemotherapy before HSCT should be considered in patients with myelodysplasia‐related‐AML (MDR‐AML).
Co‐parenting quality among adoptive mothers: contributions of socioeconomic status, child demands and adult relationship characteristics
Authors: Hock Robert M. , Mooradian John K. 
Published: May 2011

ABSTRACTDespite the growing emphasis on co‐parenting in family life, little is known about the co‐parenting relationships of adoptive parents. This study examined the contributions of socioeconomic status (SES), child demands and couple relationship characteristics to reported co‐parenting quality among adoptive mothers. Mail questionnaires were administered to 94 adoptive mothers in a Midwestern state. Regression results revealed that SES and child demands were largely unrelated to co‐parenting quality, while couple relationship characteristics (dyadic coping, dyadic adjustment and conflict resolution) contributed significantly to co‐parenting quality. Further, the co‐parenting dimensions revealed different patterns of relatedness with the independent variables, providing support for the notion that co‐parenting is a multidimensional construct. Implications for social work research and practice are discussed.
Defendants with intellectual disabilities and mental health diagnoses: faring in a mental health court
Authors: Burke M. M. , Griggs M. , Dykens E. M. , Hodapp R. M. 
Published: May 2011

AbstractBackground  Begun in the late 1990s, mental health courts are specialty criminal courts developed to address the needs of persons with mental illness.Methods  As many persons with intellectual disabilities (IDs) may overlap in the mental health court system, we used mental health court records to examine the phenomenology and outcomes of 224 defendants with and without co‐occurring IDs in the mental health court. This study had two goals: (1) to examine the prevalence of defendants with IDs in the court and (2) to compare defendants with dual diagnoses with defendants with lone mental health disorders.Results  Approximately 11% of defendants in the mental health court also had IDs. Compared with individuals with mental health disorders alone, individuals with dual diagnoses were more likely to be younger, male, African‐American and less well‐educated; these defendants were also more likely to show externalising, ‘turning‐against‐others’ symptoms, less likely to show internalising, ‘turning‐against‐self’ symptoms. Defendants with IDs (vs. those without) more often received behavioural, vocational rehabilitation and other services, although the two groups did not differ on most outcome variables.Conclusion  Directions for future research are discussed.
Nitrosative damage to free and zinc‐bound cysteine thiols underlies nitric oxide toxicity in wild‐type Borrelia burgdorferi
Authors: Bourret Travis J. , Boylan Julie A. , Lawrence Kevin A. , Gherardini Frank C. 
Published: May 2011

Summary Borrelia burgdorferi encounters potentially harmful reactive nitrogen species (RNS) throughout its infective cycle. In this study, diethylamine NONOate (DEA/NO) was used to characterize the lethal effects of RNS on B. burgdorferi. RNS produce a variety of DNA lesions in a broad spectrum of microbial pathogens; however, levels of the DNA deamination product, deoxyinosine, and the numbers of apurinic/apyrimidinic (AP) sites were identical in DNA isolated from untreated and DEA/NO‐treated B. burgdorferi cells. Strains with mutations in the nucleotide excision repair (NER) pathway genes uvrC or uvrB treated with DEA/NO had significantly higher spontaneous mutation frequencies, increased numbers of AP sites in DNA and reduced survival compared with wild‐type controls. Polyunsaturated fatty acids in B. burgdorferi cell membranes, which are susceptible to peroxidation by reactive oxygen species (ROS), were not sensitive to RNS‐mediated lipid peroxidation. However, treatment of B. burgdorferi cells with DEA/NO resulted in nitrosative damage to several proteins, including the zinc‐dependent glycolytic enzyme fructose‐1,6‐bisphosphate aldolase (BB0445), the Borrelia oxidative stress regulator (BosR) and neutrophil‐activating protein (NapA). Collectively, these data suggested that nitrosative damage to proteins harbouring free or zinc‐bound cysteine thiols, rather than DNA or membrane lipids underlies RNS toxicity in wild‐type B. burgdorferi.
Phloroglucinol mediates cross‐talk between the pyoluteorin and 2,4‐diacetylphloroglucinol biosynthetic pathways in Pseudomonas fluorescens Pf‐5
Authors: Kidarsa Teresa A. , Goebel Neal C. , Zabriskie T. Mark , Loper Joyce E. 
Published: May 2011

SummaryThe antibiotics pyoluteorin and 2,4‐diacetylphloroglucinol (DAPG) contribute to the biological control of soilborne plant diseases by some strains of Pseudomonas fluorescens, including Pf‐5. These secondary metabolites also have signalling functions with each compound reported to induce its own production and repress the other's production. The first step in DAPG biosynthesis is production of phloroglucinol (PG) by PhlD. In this study, we show that PG is required at nanomolar concentrations for pyoluteorin production in Pf‐5. At higher concentrations, PG is responsible for the inhibition of pyoluteorin production previously attributed to DAPG. DAPG had no effect on pyoluteorin production, and monoacetylphloroglucinol showed both stimulatory and inhibitory activities but at concentrations 100‐fold greater than the levels of PG required for similar effects. We also demonstrate that PG regulates pyoluteorin production in P. aeruginosa and that a phlD gene adjacent to the pyoluteorin biosynthetic gene cluster in P. aeruginosa strain LESB58 can restore pyoluteorin biosynthesis to a ΔphlD mutant of Pf‐5. Bioinformatic analyses show that the dual role of PhlD in the biosynthesis of DAPG and the regulation of pyoluteorin production could have arisen within the pseudomonads during the assembly of these biosynthetic gene clusters from genes and gene subclusters of diverse origins.
Cutting out the φC31 prophage
Authors: Stark W. Marshall 
Published: May 2011

SummaryTo establish a lysogenic lifestyle, the temperate bacteriophage φC31 integrates its genome into the chromosome of its Streptomyces host, by site‐specific recombination between attP (the attachment site in the phage DNA) and attB (the chromosomal attachment site). This reaction is promoted by a phage‐encoded serine recombinase Int. To return to the lytic lifestyle, the prophage excises its DNA by a similar Int‐mediated reaction between the recombinant sites flanking the prophage, attL and attR. φC31 Int has been developed into a popular experimental tool for integration of transgenic DNA into the genomes of eukaryotic organisms. However, until now it has not been possible to use Int to promote the reverse reaction, excision. In many other phages, the presence of a recombination directionality factor (RDF) protein biases the phage‐encoded integrase towards prophage excision, whereas absence of the RDF favours integration; but the φC31 RDF had proved elusive. In this issue of Molecular Microbiology, Khaleel et al. (2011) report the identification and purification of the φC31 RDF, and show that it both promotes excision and inhibits integration by direct protein‐protein interactions with Int itself.
Septum‐directed secretion in the filamentous fungus Aspergillus oryzae
Authors: Hayakawa Yugo , Ishikawa Eri , Shoji Jun‐ya , Nakano Hiroyuki , Kitamoto Katsuhiko 
Published: May 2011

SummaryAlthough exocytosis in fungal cells takes place at hyphal tips, there also seems a line of circumstantial evidence suggesting the occurrence of exocytosis at other sites of cells, such as septa. To investigate whether exocytosis takes place at fungal septa, we monitored dynamics of EGFP‐fused α‐amylase (AmyB–EGFP), the representative secretory enzyme of the filamentous fungus Aspergillus oryzae. We found that AmyB–EGFP accumulates in Spitzenkörper at hyphal tips as well as septal periplasm between the plasma membrane and cell walls. The septal accumulation of AmyB–EGFP was a rapid process, and required microtubules but not F‐actin. Thus, this process is independent of exocytosis at hyphal tips that requires both microtubules and F‐actin. In addition, fluorescence recovery after photobleaching (FRAP) analysis of EGFP‐fused AoSnc1 revealed that secretory vesicles constitutively fuse with the septal plasma membrane. These results demonstrated that exocytosis takes place at septa in addition to hyphal tips. Analysis of two plasma membrane transporters, AoUapC and AoGap1, revealed that they preferentially accumulate at septa and the lateral plasma membrane with no clear accumulation at apical Spitzenkörper, suggesting that non‐tip directed exocytosis is important for delivery of these proteins.