bluuebunny/crossref_metadata_2025_split huggingface dataset:
In VivoGrowth Rates Are Poorly Correlated with Phage Therapy Success in a Mouse Infection Model
Authors: Bull J. J. , Otto G. , Molineux I. J. 
Published: November 2011

ABSTRACTTwo classes of phages yield profoundly different levels of recovery in mice experimentally infected with anEscherichia coliO18:K1:H7 strain. Phages requiring the K1 capsule for infection (K1-dep) rescue virtually all infected mice, whereas phages not requiring the capsule (K1-ind) rescue modest numbers (∼30%). To rescue infected mice, K1-ind phages require at least a 106-fold-higher inoculum than K1-dep phages. Yet theirin vivogrowth dynamics are only modestly inferior to those of K1-dep phages, and competition between the two phage types in the same mouse reveals only a slight growth advantage for the K1-dep phage. Thein vivogrowth rate seems unlikely to be the primary determinant of phage therapy success. An alternative explanation is that the success of K1-dep phages is due substantially to their proteomic composition. They encode an enzyme that degrades the K1 capsule, which has been shown in other work to be sufficient to cure infection in the complete absence of phages.
Comparison of Asymptomatic Bacteriuria Escherichia coli Isolates from Healthy Individuals versus Those from Hospital Patients Shows that Long-Term Bladder Colonization Selects for Attenuated Virulence Phenotypes
Authors: Salvador Ellaine , Wagenlehner Florian , Köhler Christian-Daniel , Mellmann Alexander , Hacker Jörg , Svanborg Catharina , Dobrindt Ulrich 
Published: November 2011

ABSTRACTAsymptomatic bacteriuria (ABU) is a condition where bacteria stably colonize the urinary tract, in a manner closely resembling commensalism at other mucosal sites. The patients carry >105CFU/ml for extended periods of time and rarely develop symptoms. Contrasting the properties of ABU strains to those of uropathogenic isolates causing symptomatic infection is therefore highly relevant to understand mechanisms of bacterial adaptation. The prototype ABU strainEscherichia coli83972 has a smaller genome than uropathogenicE. coli(UPEC) strains with deletions or point mutations in several virulence genes, suggesting that ABU strains undergo a programmed reductive evolution within human hosts. This study addressed if these observations can be generalized. Strains causing ABU in outpatients or hospitalized patients after catheterization or other invasive procedures were compared to commensalE. coliisolates from the intestinal flora of healthy individuals. Notably, clonal complex 73 (CC73) was a prominent phylogenetic lineage dominated by ABU isolates. ABU isolates from outpatients and hospitalized patients had a similar overall virulence gene repertoire, which distinguished them from many commensals, but typical UPEC virulence genes were less frequently attenuated in hospital strains than in outpatient strains or commensals. The decreased virulence potential of outpatient ABU isolates relative to that of ABU strains from hospitalized patients supports the hypothesis that loss of expression or decay of virulence genes facilitates long-term carriage and adaptation to host environments.
Circulating Insulin-Like Growth Factors and IGF-Binding Proteins in PSA-Detected Prostate Cancer: The Large Case–Control Study ProtecT
Authors: Rowlands Mari-Anne , Holly Jeff M.P. , Gunnell David , Donovan Jenny , Lane J. Athene , Hamdy Freddie , Neal David E. , Oliver Steven , Smith George Davey , Martin Richard M. 
Published: November 2011

Abstract
Circulating insulin-like growth factor-I (IGF-I) has been studied extensively in prostate cancer, but there is still little information about IGFs and IGF-binding proteins (IGFBP) in cancers detected by the prostate-specific antigen (PSA) test. Here, we report the findings of a U.K.-based case–control study to investigate circulating IGFs and IGFBPs in PSA-detected prostate cancer with regard to their potential associations with different cancer stages or grades. PSA testing was offered to 110,000 men aged 50 to 69 years from 2002 to 2009. Participants with an elevated level of PSA (≥3.0 ng/mL) underwent prostate biopsy and measurements of blood serum IGF-I, IGF-II, IGFBP-2, and IGFBP-3 obtained at recruitment. We found that serum levels of IGF-II (OR per SD increase: 1.16; 95% CI: 1.08–1.24; Ptrend &lt; 0.001), IGFBP-2 (1.18; 1.06–1.31; Ptrend &lt; 0.01) and IGFBP-3 (1.27; 1.19–1.36; Ptrend &lt; 0.001), but not IGF-I (0.99; 0.93–1.04; Ptrend = 0.62), were associated with PSA-detected prostate cancer. After controlling for IGFBP-3, IGF-II was no longer associated (0.99; 0.91–1.08; Ptrend = 0.62) and IGF-I was inversely associated (0.85; 0.79–0.91; Ptrend &lt; 0.001) with prostate cancer. In addition, no strong associations existed with cancer stage or grade. Overall, these findings suggest potentially important roles for circulating IGF-II, IGFBP-2, and IGFBP-3 in PSA-detected prostate cancer, in support of recent in vitro evidence. Although our findings for IGF-I agree with previous results from PSA screening trials, they contrast with positive associations in routinely detected disease, suggesting that reducing levels of circulating IGF-I might not prevent the initiation of prostate cancer but might, nonetheless, prevent its progression. Cancer Res; 72(2); 503–15. ©2011 AACR.
Assessing the Performance of Multiple Regional Climate Model Simulations for Seasonal Mountain Snow in the Upper Colorado River Basin
Authors: Salzmann Nadine , Mearns Linda O. 
Published: November 2011

Abstract
This study assesses the performance of the regional climate model (RCM) simulations from the North American Regional Climate Change Assessment Program (NARCCAP) for the Upper Colorado River basin (UCRB), U.S. Rocky Mountains. The UCRB is a major contributor to the Colorado River’s runoff. Its significant snow-dominated hydrological regime makes it highly sensitive to climatic changes, and future water shortage in this region is likely. The RCMs are evaluated with a clear RCM output user’s perspective and a main focus on snow. Snow water equivalent (SWE) and snow duration, as well as air temperature and precipitation from five RCMs, are compared with snowpack telemetry (SNOTEL) observations, with National Centers for Environmental Prediction (NCEP)–National Center for Atmospheric Research (NCAR) Reanalysis II (R2), which provides the boundary conditions for the RCM simulations, and with North American Regional Reanalysis (NARR). Overall, most RCMs were able to significantly improve on the results from the NCEP–NCAR reanalysis. However, in comparison with spatially aggregated point observations and NARR, the RCMs are generally too dry, too warm, simulate too little SWE, and have a too-short snow cover duration with a too-late start and a too-early end of a significant snow cover. The intermodel biases found are partly associated with inadequately resolved topography (at the spatial resolution of the RCMs), imperfect observational data, different forcing techniques (spectral nudging versus no nudging), and the different land surface schemes (LSS). Attributing the found biases to specific features of the RCMs remains difficult or even impossible without detailed knowledge of the physical and technical specification of the models.
Development and Validation of a Virtual Reality Simulator
Authors: Johnson Sheena Joanne , Guediri Sara M. , Kilkenny Caroline , Clough Peter J. 
Published: November 2011

Objective: This study developed and validated a virtual reality (VR) simulator for use by interventional radiologists. Background: Research in the area of skill acquisition reports practice as essential to become a task expert. Studies on simulation show skills learned in VR can be successfully transferred to a real-world task. Recently, with improvements in technology, VR simulators have been developed to allow complex medical procedures to be practiced without risking the patient. Method: Three studies are reported. In Study 1, 35 consultant interventional radiologists took part in a cognitive task analysis to empirically establish the key competencies of the Seldinger procedure. In Study 2, 62 participants performed one simulated procedure, and their performance was compared by expertise. In Study 3, the transferability of simulator training to a real-world procedure was assessed with 14 trainees. Results: Study 1 produced 23 key competencies that were implemented as performance measures in the simulator. Study 2 showed the simulator had both face and construct validity, although some issues were identified. Study 3 showed the group that had undergone simulator training received significantly higher mean performance ratings on a subsequent patient procedure. Conclusion: The findings of this study support the centrality of validation in the successful design of simulators and show the utility of simulators as a training device. Application: The studies show the key elements of a validation program for a simulator. In addition to task analysis and face and construct validities, the authors highlight the importance of transfer of training in validation studies.
Continuously Informing Vibrotactile Displays in Support of Attention Management and Multitasking in Anesthesiology
Authors: Ferris Thomas K. , Sarter Nadine 
Published: November 2011

Objective: A novel vibrotactile display type was investigated to determine the potential benefits for supporting the attention and task management of anesthesiologists. Background: Recent research has shown physiological monitoring and multitasking performance can benefit from displaying patient data via alarm-like tactile notifications and via continuously informing auditory displays (e.g., sonifications). The current study investigated a novel combination of these two approaches: continuously informing tactile displays. Method: A tactile alarm and two continuously informing tactile display designs were evaluated in an anesthesia induction simulation with anesthesiologists as participants. Several performance measures were collected for two tasks: physiological monitoring and anesthesia induction. A multi-task performance score equivalently weighted components from each task, normalized across experimental scenarios. Subjective rankings of the displays were also collected. Results: Compared to the baseline (visual and auditory only) display configuration, each tactile display significantly improved performance in several objective measures, including multitask performance score. The continuously informing display that encoded the severity of patient health into the salience of its signals supported significantly better performance than the other two tactile displays. Contrasting the objective results, participants subjectively ranked the tactile alarm display highest. Conclusion: Continuously informing tactile displays with alarm-like properties (e.g., salience mapping) can better support anesthesiologists’ physiological monitoring and multitasking performance under the high task demands of anesthesia induction. Adaptive display mechanisms may improve user acceptance. Application: This study can inform display design to support multitasking performance of anesthesiologists in the clinical setting and other supervisory control operators in work domains characterized by high demands for visual and auditory resources.
Against the odds: Foster carers’ perceptions of family, commitment and belonging in successful placements
Authors: Oke Nicholas , Rostill-Brookes Helen , Larkin Michael 
Published: November 2011

This study examines carer attributes associated with placement stability for teenagers growing up in long term foster care, focusing on unexpected placement success. We explored experiences and perceptions relating to family, belonging and commitment in a group of foster carers providing a stable placement for a young person who had not been expected to settle. These placements showed positive outcome, despite factors in the child’s history that might have predicted otherwise. Seven foster carers were interviewed following a semi-structured guide, which covered their ideas about their relationship with the child in question, about the foster family, and the child’s sense of belonging in foster and birth family. Analysis of carers’ accounts of placements which had succeeded ‘against the odds’ revealed four major themes, described under the headings My Child—emotional bonding, the carers’ enlarged view of family and their parental regard for the young person; Jam in the Sandwich—working within a ‘compromised space’ between Local Authority and birth family; Repair and Rebuild—the craft of fostering including managing the foster/birth family boundary; Sticking with It—resilience, tenacity and maintaining hopefulness. The carers’ accounts offer pointers towards the ingredients of successful placements and prompt reflection on how these may be supported and promoted. They also highlight tensions inherent in the foster carer task relating to carers’ parental functioning for young people in long-term foster care.
EUS-guided drainage and stent placement for postoperative intra-abdominal and pelvic fluid collections in oncological surgery
Authors: Ulla-Rocha Jose Luis , Vilar-Cao Zenaida , Sardina-Ferreiro Raquel 
Published: November 2011

Objectives: The objective of this study was to evaluate the role and benefits of endoscopic ultrasonography (EUS) in the management of postoperative intra-abdominal fluid collections after attempted curative surgery for abdominal cancer. Methods: The authors retrospectively analysed the Endobase from 1 July 2007 to 30 January 2011 for patients with a postoperative intra-abdominal fluid collection who had undergone EUS-guided drainage and the placement of a stent. The data analysed included the demographics, type of surgery and clinical indications of each patient as well as their clinical and radiological findings. Results: Six patients (three men and three women; mean age, 61.8 years [range, 38–78 years]) with intra-abdominal and pelvic fluid collections after abdominal surgery for cancer had undergone EUS-guided internal drainage. All procedures had been performed using linear EUS guidance and 8-Fr stent drainage catheters (‘one step device’, Giovannini, NWOA system Needle-Wire, Cook). The collection types included perigastric abscess ( n = 3), perigastric hematoma and rectal hematoma ( n = 1), perirectal biloma ( n = 1), and perirectal abscess ( n = 1). Patients had undergone the following types of surgery: lower-anterior rectal resection ( n = 2), Whipple’s duodenopancreatectomy type ( n = 1), total gastrectomy ( n = 1), splenectomy ( n = 1), and distal pancreatectomy ( n = 1). The number of stents inserted for each collection was one (five patients) and two (one patient). Conclusions: EUS-guided drainage and stenting provide another option for the management of postoperative collections. It allows access to areas that are difficult to reach with the CT-guided approach and it can be performed accurately, efficiently and safely. In addition to this, the internal nature of the drainage offers patients more comfort.
Identification and correction of systematic error in high-throughput sequence data
Authors: Meacham Frazer , Boffelli Dario , Dhahbi Joseph , Martin David IK , Singer Meromit , Pachter Lior 
Published: November 2011

Abstract

Background
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed "next-gen" sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of systematic error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations.

Results
We characterize and describe systematic errors using overlapping paired reads from high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that they are highly replicable across experiments. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq), and can be used with single-end datasets.

Conclusions
Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments.
eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Authors: Sinha Amit U , Merrill Emily , Armstrong Scott A , Clark Tim W , Das Sudeshna 
Published: November 2011

Abstract

Background
Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.

Results
We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.

Conclusion
The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.
Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection
Authors: Ahmad Riaz , Parfitt Dan E , Fass Joseph , Ogundiwin Ebenezer , Dhingra Amit , Gradziel Thomas M , Lin Dawei , Joshi Nikhil A , Martinez-Garcia Pedro J , Crisosto Carlos H 
Published: November 2011

Abstract

Background
The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery.

Description
The sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly.

Conclusion
The eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.
Clinical outcome of pneumococcal meningitis during the emergence of pencillin-resistant Streptococcus pneumoniae: an observational study
Authors: Gouveia Edilane L , Reis Joice N , Flannery Brendan , Cordeiro Soraia M , Lima Josilene BT , Pinheiro Ricardo M , Salgado Kátia , Mascarenhas Ana Veronica , Carvalho M Gloria , Beall Bernard W , Reis Mitermayer G , Ko Albert I 
Published: November 2011

AbstractBackgroundPrior to the availability of generic third-generation cephalosporins, penicillins were widely used for treatment of pneumococcal meningitis in developing countries despite concerns about rising levels of penicillin resistance among pneumococcal isolates. We examined the impact of penicillin resistance on outcomes of pneumococcal meningitis over a ten year period in an infectious diseases hospital in Brazil.MethodsClinical presentation, antimicrobial therapy and outcomes were reviewed for 548 patients with culture-confirmed pneumococcal meningitis from December, 1995, to November, 2005. Pneumococcal isolates from meningitis patients were defined as penicillin-resistant if Minimum Inhibitory Concentrations for penicillin were greater than 0.06 μg/ml. Proportional hazards regression was used to identify risk factors for fatal outcomes.ResultsDuring the ten-year period, ceftriaxone replaced ampicillin as first-line therapy for suspected bacterial meningitis. In hospital case-fatality for pneumococcal meningitis was 37%. Of 548 pneumococcal isolates from meningitis cases, 92 (17%) were resistant to penicillin. After controlling for age and severity of disease at admission, penicillin resistance was associated with higher case-fatality (Hazard Ratio [HR], 1.62; 95% Confidence Interval [CI], 1.08-2.43). Penicillin-resistance remained associated with higher case-fatality when initial therapy included ceftriaxone (HR, 1.68; 95% CI 1.02-2.76).ConclusionsFindings support the use of third generation cephalosporin antibiotics for treatment of suspected pneumococcal meningitis even at low prevalence of pneumococcal resistance to penicillins.