bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maser Source-Finding Methods in HOPS
Authors: Walsh A. J. , Purcell C. , Longmore S. , Jordan C. H. , Lowe V. 
Published: December 2011

AbstractThe H2O Southern Galactic Plane Survey (HOPS) has observed 100 deg2 of the Galactic plane, using the Mopra radio telescope to search for emission from multiple spectral lines in the 12-mm band (19.5–27.5 GHz). Perhaps the most important of these spectral lines is the 22.2-GHz water-maser transition. We describe the methods used to identify water-maser candidates and subsequent confirmation of the sources. Our methods involve a simple determination of likely candidates by searching peak emission maps, utilising the intrinsic nature of water-maser emission, spatially unresolved and spectrally narrow-lined. We estimate completeness limits and compare our method with results from the duchamp source finder. We find that the two methods perform similarly. We conclude that the similarity in performance is due to the intrinsic limitation of the noise characteristics of the data. The advantages of our method are that it is slightly more efficient in eliminating spurious detections and is simple to implement. The disadvantage is that it is a manual method of finding sources and so is not practical on datasets much larger than HOPS, or for datasets with extended emission that needs to be characterised. We outline a two-stage method for the most efficient means of finding masers, using duchamp.
Photo-ribonucleotide reductase β2 by selective cysteine labeling with a radical phototrigger
Authors: Pizano Arturo A. , Lutterman Daniel A. , Holder Patrick G. , Teets Thomas S. , Stubbe JoAnne , Nocera Daniel G. 
Published: December 2011

Photochemical radical initiation is a powerful tool for studying radical initiation and transport in biology. Ribonucleotide reductases (RNRs), which catalyze the conversion of nucleotides to deoxynucleotides in all organisms, are an exemplar of radical mediated transformations in biology. Class Ia RNRs are composed of two subunits: α2 and β2. As a method to initiate radical formation photochemically within β2, a single surface-exposed cysteine of the β2 subunit of
Escherichia coli
Class Ia RNR has been labeled (98%) with a photooxidant ([Re ] = tricarbonyl(1,10-phenanthroline)(methylpyridyl)rhenium(I)). The labeling was achieved by incubation of S355C-β2 with the 4-(bromomethyl)pyridyl derivative of [Re] to yield the labeled species, [Re]-S355C-β2. Steady-state and time-resolved emission experiments reveal that the metal-to-ligand charge transfer (MLCT) excited-state
3
[Re ]
∗
is not significantly perturbed after bioconjugation and is available as a phototrigger of tyrosine radical at position 356 in the β2 subunit; transient absorption spectroscopy reveals that the radical lives for microseconds. The work described herein provides a platform for photochemical radical initiation and study of proton-coupled electron transfer (PCET) in the β2 subunit of RNR, from which radical initiation and transport for this enzyme originates.
Demography of Juvenile and Adult Brown Trout in Streams of Southeastern Minnesota
Authors: Dieterman Douglas J. , Hoxmeier R. John H. 
Published: December 2011

AbstractWe assessed recruitment, survival, emigration, and immigration of brown troutSalmo truttain six interconnected stream reaches to quantitatively estimate how much immigrants contributed to population size in reaches in southeastern Minnesota. We also examined the influence of reach and season on estimates of survival and emigration via mark and recapture of individual trout representing three groups (age‐0 juveniles, age‐1 and age‐2 adults, and age‐3+ large adults). Immigration was calculated as 1 minus emigration. Recruitment varied among the six reaches and 3 years of this study (range, 0–1,292 fish/km). Survival of the age‐0 group and that comprising ages 1 and 2 varied by season but not reach. Survival was highest in winter for both groups but lowest in spring for age‐0 trout and in fall for age‐1 and age ‐2 trout. Emigration varied by season for age‐0 trout but by reach for trout of ages 1 and 2. For age‐3+ trout, survival and emigration only varied by reach. Survival was highest and emigration was lowest in reaches with the most cover, including deep pools. From these demographic characteristics we estimated the proportions of the population that consisted of brown trout that had survived within a reach, recruited into it, or immigrated into it from some other reach. Immigration was predicted to contribute the most for the youngest age‐group (35% or more of the predicted abundance of age‐0 trout in most reaches) and is probably important for genetic purposes or to bolster population units in adjacent reaches. Our results for adult brown trout suggest that within‐reach recruitment and survival contribute a larger proportion of trout to population units in many reaches than do immigrants. This confirms the appropriateness of current management approaches and suggests that maintenance of the exceptional recreational brown trout fishery in southeastern Minnesota is at least solidly dependent on factors promoting recruitment and survival within most managed stream reaches.
Estimating Geographic Variation in Allometric Growth and Body Condition of Blue Suckers with Quantile Regression
Authors: Cade Brian S. , Terrell James W. , Neely Ben C. 
Published: December 2011

AbstractIncreasing our understanding of how environmental factors affect fish body condition and improving its utility as a metric of aquatic system health require reliable estimates of spatial variation in condition (weight at length). We used three statistical approaches that varied in how they accounted for heterogeneity in allometric growth to estimate differences in body condition of blue suckers Cycleptus elongatus across 19 large‐river locations in the central USA. Quantile regression of an expanded allometric growth model provided the most comprehensive estimates, including variation in exponents within and among locations (range = 2.88–4.24). Blue suckers from more‐southerly locations had the largest exponents. Mixed‐effects mean regression of a similar expanded allometric growth model allowed exponents to vary among locations (range = 3.03–3.60). Mean relative weights compared across selected intervals of total length (TL = 510–594 and 594–692 mm) in a multiplicative model involved the implicit assumption that allometric exponents within and among locations were similar to the exponent (3.46) for the standard weight equation. Proportionate differences in the quantiles of weight at length for adult blue suckers (TL = 510, 594, 644, and 692 mm) compared with their average across locations ranged from 1.08 to 1.30 for southern locations (Texas, Mississippi) and from 0.84 to 1.00 for northern locations (Montana, North Dakota); proportionate differences for mean weight ranged from 1.13 to 1.17 and from 0.87 to 0.95, respectively, and those for mean relative weight ranged from 1.10 to 1.18 and from 0.86 to 0.98, respectively. Weights for fish at longer lengths varied by 600–700 g within a location and by as much as 2,000 g among southern and northern locations. Estimates for the Wabash River, Indiana (0.96–1.07 times the average; greatest increases for lower weights at shorter TLs), and for the Missouri River from Blair, Nebraska, to Sioux City, Iowa (0.90–1.00 times the average; greatest decreases for lower weights at longer TLs), were examined in detail to explain the additional information provided by quantile estimates.
Modified Live Edwardsiella ictaluri Vaccine, AQUAVAC-ESC, Lacks Multidrug Resistance Plasmids
Authors: LaFrentz Benjamin R. , Welch Timothy J. , Shoemaker Craig A. , Drennan John D. , Klesius Phillip H. 
Published: December 2011

Abstract
Plasmid-mediated antibiotic resistance was first discovered in Edwardsiella ictaluri in the early 1990s, and in 2007 an E. ictaluri isolate harboring an IncA/C plasmid was recovered from a moribund channel catfish Ictalurus punctatus infected with the bacterium. Due to the identification of multidrug resistance plasmids in aquaculture and their potential clinical importance, we sought to determine whether the modified live E. ictaluri vaccine strain in AQUAVAC-ESC harbors such plasmids, so that the use of this vaccine will not directly contribute to the pool of bacteria carrying plasmid-borne resistance. Antimicrobial sensitivity testing of the E. ictaluri parent isolate and vaccine strain demonstrated that both were sensitive to 15 of the 16 antimicrobials tested. Total DNA from each isolate was analyzed by polymerase chain reaction (PCR) using a set of 13 primer pairs specific for conserved regions of the IncA/C plasmid backbone, and no specific products were obtained. PCR-based replicon typing of the parent isolate and vaccine strain demonstrated the absence of the 18 commonly occurring plasmid incompatibility groups. These results demonstrate that the vaccine strain does not carry resistance to commonly used antimicrobials and provide strong support for the absence of IncA/C and other commonly occurring plasmid incompatibility groups. Therefore, its use should not directly contribute to the pool of bacteria carrying plasmid-borne resistance. This work highlights the importance of thoroughly investigating potential vaccine strains for the presence of plasmids or other transmissible elements that may encode resistance to antibiotics.
Received May 6, 2011; accepted July 22, 2011
Use of Medicare Diagnosis and Procedure Codes to Improve Detection of Surgical Site Infections following Hip Arthroplasty, Knee Arthroplasty, and Vascular Surgery
Authors: Calderwood Michael S. , Ma Allen , Khan Yosef M. , Olsen Margaret A. , Bratzler Dale W. , Yokoe Deborah S. , Hooper David C. , Stevenson Kurt , Fraser Victoria J. , Platt Richard , Huang Susan S. ,   CDC Prevention Epicenters Program
Published: December 2011

Objective.To evaluate the use of routinely collected electronic health data in Medicare claims to identify surgical site infections (SSIs) following hip arthroplasty, knee arthroplasty, and vascular surgery.Design.Retrospective cohort study.Setting.Four academic hospitals that perform prospective SSI surveillance.Methods.We developed lists of International Classification of Diseases, Ninth Revision, and Current Procedural Terminology diagnosis and procedure codes to identify potential SSIs. We then screened for these codes in Medicare claims submitted by each hospital on patients older than 65 years of age who had undergone 1 of the study procedures during 2007. Each site reviewed medical records of patients identified by either claims codes or traditional infection control surveillance to confirm SSI using Centers for Disease Control and Prevention/ National Healthcare Safety Network criteria. We assessed the performance of both methods against all chart-confirmed SSIs identified by either method.Results.Claims-based surveillance detected 1.8–4.7-fold more SSIs than traditional surveillance, including detection of all previously identified cases. For hip and vascular surgery, there was a 5-fold and 1.6-fold increase in detection of deep and organ/space infections, respectively, with no increased detection of deep and organ/space infections following knee surgery. Use of claims to trigger chart review led to confirmation of SSI in 1 out of 3 charts for hip arthroplasty, 1 out of 5 charts for knee arthroplasty, and 1 out of 2 charts for vascular surgery.Conclusion.Claims-based SSI surveillance markedly increased the number of SSIs detected following hip arthroplasty, knee arthroplasty, and vascular surgery. It deserves consideration as a more effective approach to target chart reviews for identifying SSIs.Infect Control Hosp Epidemiol 2012;33(1):40-49
Frequent Hospital Readmissions for Clostridium difficile Infection and the Impact on Estimates of Hospital-Associated C. difficile Burden
Authors: Murphy Courtney R. , Avery Taliser R. , Dubberke Erik R. , Huang Susan S. 
Published: December 2011

Objective.Clostridium difficile infection (CDI) is associated with hospitalization and may cause readmission following admission for any reason. We aimed to measure the incidence of readmissions due to CDI.Design.Retrospective cohort study.Patients.Adult inpatients in Orange County, California, who presented with new-onset CDI within 12 weeks of discharge.Methods.We assessed mandatory 2000–2007 hospital discharge data for trends in hospital-associated CDI (HA-CDI) incidence, with and without inclusion of postdischarge CDI (PD-CDI) events resulting in rehospitalization within 12 weeks of discharge. We measured the effect of including PD-CDI events on hospital-specific CDI incidence, a mandatory reporting measure in California, and on relative hospital ranks by CDI incidence.Results.From 2000 to 2007, countywide hospital-onset CDI (HO-CDI) incidence increased from 15 per 10,000 to 22 per 10,000 admissions. When including PD-CDI events, HA-CDI incidence doubled (29 per 10,000 in 2000 and 52 per 10,000 in 2007). Overall, including PD-CDI events resulted in significantly higher hospital-specific CDI incidence, although hospitals had disproportionate amounts of HA-CDI occurring postdischarge. This resulted in substantial shifts in some hospitals' rankings by CDI incidence. In multivariate models, both HO and PD-CDI were associated with increasing age, higher length of stay, and select comorbidities. Race and Hispanic ethnicity were predictive of PD-CDI but not HO-CDI.Conclusions.PD-CDI events associated with rehospitalization are increasingly common. The majority of HA-CDI cases may be occurring postdischarge, raising important questions about both accurate reporting and effective prevention strategies. Some risk factors for PD-CDI may be different than those for HO-CDI, allowing additional identification of high-risk groups before discharge.Infect Control Hosp Epidemiol 2012;33(1):20-28
Assessment of a Mandatory Tetanus, Diphtheria, and Pertussis Vaccination Requirement on Vaccine Uptake over Time
Authors: Weber David J. , Consoli Stephanie A. , Sickbert-Bennett Emily , Rutala William A. 
Published: December 2011

Tetanus, diphtheria, and pertussis (Tdap) vaccine is recommended for all healthcare personnel who provide direct patient care unless medically contraindicated. Our university hospital made employment conditional upon receipt of Tdap vaccine. Implementation for newly hired employees quickly resulted in complete compliance, but achieving adherence among current workers required setting a termination date for noncompliance.Infect Control Hosp Epidemiol 2012;33(1):81-83
Association between Contact Precautions and Delirium at a Tertiary Care Center
Authors: Day Hannah R. , Perencevich Eli N. , Harris Anthony D. , Gruber-Baldini Ann L. , Himelhoch Seth S. , Brown Clayton H. , Dotter Emily , Morgan Daniel J. 
Published: December 2011

Objective.To investigate the relationship between contact precautions and delirium among inpatients, adjusting for other factors.Design.Retrospective cohort study.Setting.A 662-bed tertiary care center.Patients.All nonpyschiatric adult patients admitted to a tertiary care center from 2007 through 2009.Methods.Generalized estimating equations were used to estimate the association between contact precautions and delirium in a retrospective cohort of 2 years of admissions to a tertiary care center.Results.During the 2-year period, 60,151 admissions occurred in 45,266 unique nonpsychiatric patients. After adjusting for comorbid conditions, age, sex, intensive care unit status, and length of hospitalization, contact precautions were significantly associated with delirium (as denned byInternational Classification of Diseases, Ninth Revision),medication, or restraint exposure (adjusted odds ratio [OR], 1.40 [95% confidence interval {CI}, 1.24–1.51]). The association between contact precautions and delirium was seen only in patients who were newly placed under contact precautions during the course of their stay (adjusted OR, 1.75 [95% CI, 1.60–1.92];P< .01) and was not seen in patients who were already under contact precautions at admission (adjusted OR, 0.97 [95% CI, 0.86–1.09];P= .60).Conclusions.Although delirium was more common in patients who were newly placed under contact precautions during the course of their hospital admission, delirium was not associated with contact precautions started at hospital admission. Patients newly placed under contact precautions after admission but during hospitalization appear to be at a higher risk and may benefit from proven delirium-prevention strategies.Infect Control Hosp Epidemiol2012;33(1):34-39
The Antimicrobial Efficacy of Copper Alloy Furnishing in the Clinical Environment: A Crossover Study
Authors: Karpanen T. J. , Casey A. L. , Lambert P. A. , Cookson B. D. , Nightingale P. , Miruszenko L. , Elliott T. S. J. 
Published: December 2011

Objective.To determine whether copper incorporated into hospital ward furnishings and equipment can reduce their surface microbial load.Design.A crossover study.Setting.Acute care medical ward with 19 beds at a large university hospital.Methods.Fourteen types of frequent-touch items made of copper alloy were installed in various locations on an acute care medical ward. These included door handles and push plates, toilet seats and flush handles, grab rails, light switches and pull cord toggles, sockets, overbed tables, dressing trolleys, commodes, taps, and sink fittings. Their surfaces and those of equivalent standard items on the same ward were sampled once weekly for 24 weeks. The copper and standard items were switched over after 12 weeks of sampling to reduce bias in usage patterns. The total aerobic microbial counts and the presence of indicator microorganisms were determined.Results.Eight of the 14 copper item types had microbial counts on their surfaces that were significantly lower than counts on standard materials. The other 6 copper item types had reduced microbial numbers on their surfaces, compared with microbial counts on standard items, but the reduction did not reach statistical significance. Indicator microorganisms were recovered from both types of surfaces; however, significantly fewer copper surfaces were contaminated with vancomycin-resistant enterococci, methicillin-susceptible Staphylococcus aureus, and coliforms, compared with standard surfaces.Conclusions.Copper alloys (greater than or equal to 58% copper), when incorporated into various hospital furnishings and fittings, reduce the surface microorganisms. The use of copper in combination with optimal infection-prevention strategies may therefore further reduce the risk that patients will acquire infection in healthcare environments.Infect Control Hosp Epidemiol 2012;33(1):3-9
seeQTL: a searchable database for human eQTLs
Authors: Xia Kai , Shabalin Andrey A. , Huang Shunping , Madar Vered , Zhou Yi-Hui , Wang Wei , Zou Fei , Sun Wei , Sullivan Patrick F. , Wright Fred A. 
Published: December 2011

Abstract
Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots.
Availability and implementation: seeQTL is freely available for non-commercial use at http://www.bios.unc.edu/research/genomic_software/seeQTL/.
Contact: fred_wright@unc.edu; kxia@bios.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Function of RH22, a DEAD RNA Helicase, in the Biogenesis of the 50S Ribosomal Subunits of Arabidopsis Chloroplasts
Authors: Chi Wei , He Baoye , Mao Juan , Li Qiannan , Ma Jinfang , Ji Daili , Zou Meijuan , Zhang Lixin 
Published: December 2011

Abstract
The chloroplast ribosome is a large and dynamic ribonucleoprotein machine that is composed of the 30S and 50S subunits. Although the components of the chloroplast ribosome have been identified in the last decade, the molecular mechanisms driving chloroplast ribosome biogenesis remain largely elusive. Here, we show that RNA helicase 22 (RH22), a putative DEAD RNA helicase, is involved in chloroplast ribosome assembly in Arabidopsis (Arabidopsis thaliana). A loss of RH22 was lethal, whereas a knockdown of RH22 expression resulted in virescent seedlings with clear defects in chloroplast ribosomal RNA (rRNA) accumulation. The precursors of 23S and 4.5S, but not 16S, rRNA accumulated in rh22 mutants. Further analysis showed that RH22 was associated with the precursors of 50S ribosomal subunits. These results suggest that RH22 may function in the assembly of 50S ribosomal subunits in chloroplasts. In addition, RH22 interacted with the 50S ribosomal protein RPL24 through yeast two-hybrid and pull-down assays, and it was also bound to a small 23S rRNA fragment encompassing RPL24-binding sites. This action of RH22 may be similar to, but distinct from, that of SrmB, a DEAD RNA helicase that is involved in the ribosomal assembly in Escherichia coli, which suggests that DEAD RNA helicases and rRNA structures may have coevolved with respect to ribosomal assembly and function.
Histone modifications in herpesvirus infections
Authors: Van Opdenbosch Nina , Favoreel Herman , Van de Walle Gerlinde R. 
Published: December 2011

AbstractIn eukaryotic cells, gene expression is not only regulated by transcription factors but also by several epigenetic mechanisms including post‐translational modifications of histone proteins. There are numerous histone modifications described to date and methylation, acetylation, ubiquitination and phosphorylation are amongst the best studied. In parallel, certain viruses interact with the very same regulatory mechanisms, hereby manipulating the normal epigenetic landscape of the host cell, to fit their own replication needs. This review concentrates on herpesviruses specifically and how they interfere with the histone‐modifying enzymes to regulate their replication cycles. Herpesviruses vary greatly with respect to the cell types they infect and the clinical diseases they cause, yet they share various common features including their capacity to encode viral proteins which affect and interfere with the normal functions of histone‐modifying enzymes. Studying the epigenetic manipulation/dysregulation of herpesvirus–host interactions not only generates novel insights into the pathogenesis of these viruses but may also have important therapeutic implications.
The oncogenic TBC domain protein USP6/TRE17 regulates cell migration and cytokinesis
Authors: Rueckert Christine , Haucke Volker 
Published: December 2011

AbstractBackground informationCancer cells are characterized by their intrinsic ability to rapidly divide and migrate and to invade other tissues. How these processes are regulated at a molecular level is largely unknown.ResultsHere, we identify the oncogenic TBC (Tre‐2/Bub2/Cdc16) domain protein USP6 (also termed TRE17) as a regulator of both cell migration and division. We show that manipulating USP6 expression levels alters the ability of cells to migrate and to divide. Furthermore, we observe that cell proliferation and progression through cytokinesis depend on USP6 expression via a pathway that involves the small GTPase Arf6 and its GTPase‐activating protein ACAP1.ConclusionsOur data suggest a model whereby the oncogenic potential of USP6 is linked to its ability to integrate cell migration and cytokinesis by regulating Arf6/ACAP1.