bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Electronic Health Information to Risk-Stratify Rates of Clostridium difficile Infection in US Hospitals
Authors: Zilberberg Marya D. , Tabak Ying P. , Sievert Dawn M. , Derby Karen G. , Johannes Richard S. , Sun Xiaowu , McDonald L. Clifford 
Published: June 2011

Background.Expanding hospitalized patients' risk stratification for Clostridium difficile infection (CDI) is important for improving patient safety. We applied definitions for hospital-onset (HO) and community-onset (CO) CDI to electronic data from 85 hospitals between January 2007 and June 2008 to identify factors associated with higher HO CDI rates.Methods.Nonrecurrent CDI cases were identified among adult (≥18-year-old) inpatients by a positive C. difficile toxin assay result more than 8 weeks after any previous positive result. Case categories included HO, CO-hospital associated (CO-HA), CO-indeterminate hospital association (CO-IN), and CO–non–hospital associated (CO-NHA). C. difficile testing intensity (CDTI) was defined as the total number of C. difficile tests performed, normalized to the number of patients with at least 1 C. difficile toxin test recorded. We calculated both the incidence density and the prevalence of CDI where appropriate. We fitted a multivariable Poisson model to identify factors associated with higher HO CDI rates.Results.Among 1,351,156 unique patients with 2,022,213 admissions, 9,803 cases of CDI were identified; of these, 50.6% were HO, 17.4% were CO-HA, 9.0% were CO-IN, and 23.0% were CO-NHA. The incidence density of HO was 6.3 per 10,000 patient-days. The prevalence of CO CDI on admission was, per 10,000 admissions, 8.4 for CO-HA, 4.4 for CO-IN, and 11.1 for CO-NHA. Factors associated (P< .0001) with higher HO CDI rates included older age, higher CO-NHA prevalence on admission, and increased CDTI.Conclusion.Electronic health information can be leveraged to risk-stratify HO CDI rates by patient age and CO-NHA prevalence on admission. Hospitals should optimize diagnostic testing to improve patient care and measured CDI rates.
RNASAlign: RNA Structural Alignment System
Authors: Wong Thomas K. F. , Wan Kwok-Lung , Hsu Bay-Yuan , Cheung Brenda W. Y. , Hon Wing-Kai , Lam Tak-Wah , Yiu Siu-Ming 
Published: June 2011

Abstract
Motivation: Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appropriate algoirthm to use which limits the usage of structural alignment in identifying novel ncRNAs.
Results: We implemented the first web server, RNASAlign, which can automatically identify the pseudoknot type of a secondary structure and perform structural alignment of a folded RNA with every region of a target DNA/RNA sequence. Regions with high similarity scores and low e-values, together with the detailed alignments will be reported to the user. Experiments on more than 350 ncRNA families show that RNASAlign is effective.
Availability: http://www.bio8.cs.hku.hk/RNASAlign.
Contact: smyiu@cs.hku.hk
mapDamage: testing for damage patterns in ancient DNA sequences
Authors: Ginolhac Aurelien , Rasmussen Morten , Gilbert M. Thomas P. , Willerslev Eske , Orlando Ludovic 
Published: June 2011

Abstract
Summary: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences.
Availability and implementation: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems.
Contact: aginolhac@snm.ku.dk
Supplementary information: Supplementary data available at Bioinformatics online
Noninvasive versus invasive ventilation for acute respiratory failure in patients with hematologic malignancies: A 5-year multicenter observational survey*
Authors: Gristina Giuseppe R. , Antonelli Massimo , Conti Giorgio , Ciarlone Alessia , Rogante Silvia , Rossi Carlotta , Bertolini Guido 
Published: June 2011

Background:
Mortality is high among patients with hematologic malignancies admitted to intensive care units for acute respiratory failure. Early noninvasive mechanical ventilation seems to improve outcomes.

Objective:
To characterize noninvasive mechanical ventilation use in Italian intensive care units for acute respiratory failure patients with hematologic malignancies and its impact on outcomes vs. invasive mechanical ventilation.

Design, Setting, Participants:
Retrospective analysis of observational data prospectively collected in 2002–2006 on 1,302 patients with hematologic malignancies admitted with acute respiratory failure to 158 Italian intensive care units.

Measurements:
Mortality (intensive care unit and hospital) was assessed in patients treated initially with noninvasive mechanical ventilation vs. invasive mechanical ventilation and in those treated with invasive mechanical ventilation ab initio vs. after noninvasive mechanical ventilation failure. Findings were adjusted for propensity scores reflecting the probability of initial treatment with noninvasive mechanical ventilation.

Results:
Few patients (21%) initially received noninvasive mechanical ventilation; 46% of these later required invasive mechanical ventilation. Better outcomes were associated with successful noninvasive mechanical ventilation (vs. invasive mechanical ventilation ab initio and vs. invasive mechanical ventilation after noninvasive mechanical ventilation failure), particularly in patients with acute lung injury/adult respiratory distress syndrome (mortality: 42% vs. 69% and 77%, respectively). Delayed vs. immediate invasive mechanical ventilation was associated with slightly but not significantly higher hospital mortality (65% vs. 58%, p = .12). After propensity-score adjustment, noninvasive mechanical ventilation was associated with significantly lower mortality than invasive mechanical ventilation.

Limitations:
The population could not be stratified according to specific hematologic diagnoses. Furthermore, the study was observational, and treatment groups may have included unaccounted for differences in covariates although the risk of this bias was minimized with propensity score regression adjustment.

Conclusions:
In patients with hematologic malignancies, acute respiratory failure should probably be managed initially with noninvasive mechanical ventilation. Further study is needed to determine whether immediate invasive mechanical ventilation might offer some benefits for those with acute lung injury/adult respiratory distress syndrome.
Pleural effusion complicates monitoring of respiratory mechanics*
Authors: Graf Jeronimo , Formenti Paolo , Santos Arnoldo , Gard Kenneth , Adams Alexander , Tashjian Joseph , Dries David , Marini John J. 
Published: June 2011

Objectives:
Although pleural effusion reduces respiratory system compliance by restricting the lungs, the effusion volume is partially accommodated by chest wall expansion. The implications for these opposing volume changes on airway pressure monitoring in ventilated patients with pleural effusion are unreported. We investigated the interactions among pleural effusion, positive end-expiratory pressure, and indices of respiratory mechanics in a swine model.

Design:
Interventional animal model.

Setting:
Hospital animal research facility.

Subjects:
Nine deeply anesthetized swine.

Interventions:
The preparation included tracheostomy, arterial/venous catheter placement, and chest tube insertion. Animals were ventilated throughout the study at 9 mL/kg, and frequency was adjusted to maintain normocapnia (inspiratory:expiratory = 1:2, Fio2 = 0.5) and positive end-expiratory pressure of 1 cm H2O and 10 cm H2O. Fluid was instilled into the right pleural space to simulate effusions of 13 mL/kg (pleural effusion 1) and 26 mL/kg (pleural effusion 2).

Measurements and Main Results:
Quantitative computerized tomography studies (in five animals) and functional residual capacity volumes (wash-in/wash-out technique) were obtained for each pleural effusion/positive end-expiratory pressure combination. Mean functional residual capacity compared to baseline at positive end-expiratory pressure of 1 cm H2O was decreased by pleural effusion 1 and pleural effusion 2 (−42%, −64%) and restored by positive end-expiratory pressure of 10 cm H2O (moderate) to +23% of baseline for pleural effusion 1 and +1% for pleural effusion 2. Plateau pressure increased and compliance decreased in response to pleural effusion 1 and pleural effusion 2. Moderate positive end-expiratory pressure applied during both pleural effusion quantities restored plateau pressure and tidal compliance to prepleural effusion values. Computed tomography studies revealed lung compression and tidal derecruitment cycles occurring with pleural effusion at positive end-expiratory pressure of 1 cm H2O, whereas a moderate positive end-expiratory pressure restored prepleural effusion functional residual capacity and prevented lung and intratidal derecruitment.

Conclusions:
When pleural effusion is present, respiratory mechanics must be interpreted cautiously and sufficient positive end-expiratory pressure should be applied to prevent extensive collapse and intratidal cycles of recruitment/derecruitment.
Solitary fibrous tumour: a diagnostic challenge for the cytopathologist
Authors: Gupta N. , Barwad A. , Katamuthu K. , Rajwanshi A. , Radotra B. D. , Nijhawan R. , Dey P. 
Published: June 2011

N. Gupta, A. Barwad, K. Katamuthu, A. Rajwanshi, B. D. Radotra, R. Nijhawan and P. DeySolitary fibrous tumour: a diagnostic challenge for the cytopathologistBackground:  Solitary fibrous tumour (SFT) is an uncommon spindle cell tumour that can occur in a variety of locations. Cytological features of this tumour have only rarely been reported in the literature. We describe the cytomorphological features of SFT with an emphasis on diagnostic pitfalls.Methods:  We retrieved nine cases of histopathologically proven SFT. Three cases had sampling error with inadequate smears and, therefore, six cases with adequate cellularity were analysed for cytological findings. The cytomorphological features and the differential diagnoses on fine needle aspiration cytology (FNAC) are discussed.Results:  No definitive cyto‐diagnosis of any of these cases was possible because of the morphological overlap with various soft tissue tumours and other tumour types. There was one false‐positive case, in which the possibility of sarcoma was suggested due to the presence of scattered atypical cells. Cytologically, the smears from the SFTs showed spindle to plump cells embedded in metachromatically staining dense ropy collagen material. The cells usually had oval to spindle shaped nuclei, bland chromatin and wavy elongated pale staining cytoplasm.Conclusion:  A diagnosis of SFT on cytology smears is challenging. Careful attention given to certain cytological features in an appropriate clinicoradiological setting and application of immunochemistry, including CD34 and CD99 immunostaining on cytological samples, can help in the diagnosis of SFT in some cases. It is important to consider cytological overlaps of this tumour in order to avoid false‐negative or false‐positive results.
Predictability of anthrax infection in the Serengeti, Tanzania
Authors: Hampson Katie , Lembo Tiziana , Bessell Paul , Auty Harriet , Packer Craig , Halliday Jo , Beesley Cari A. , Fyumagwa Robert , Hoare Richard , Ernest Eblate , Mentzel Christine , Metzger Kristine L. , Mlengeya Titus , Stamey Karen , Roberts Keith , Wilkins Patricia P. , Cleaveland Sarah 
Published: June 2011

Summary1. Anthrax is endemic throughout Africa, causing considerable livestock and wildlife losses and severe, sometimes fatal, infection in humans. Predicting the risk of infection is therefore important for public health, wildlife conservation and livestock economies. However, because of the intermittent and variable nature of anthrax outbreaks, associated environmental and climatic conditions, and diversity of species affected, the ecology of this multihost pathogen is poorly understood.2. We explored records of anthrax from the Serengeti ecosystem in north‐west Tanzania where the disease has been documented in humans, domestic animals and a range of wildlife. Using spatial and temporal case‐detection and seroprevalence data from wild and domestic animals, we investigated spatial, environmental, climatic and species‐specific associations in exposure and disease.3. Anthrax was detected annually in numerous species, but large outbreaks were spatially localized, mostly affecting a few focal herbivores.4. Soil alkalinity and cumulative weather extremes were identified as useful spatial and temporal predictors of exposure and infection risk, and for triggering the onset of large outbreaks.5. Interacting ecological and behavioural factors, specifically functional groups and spatiotemporal overlap, helped to explain the variable patterns of infection and exposure among species.6. Synthesis and applications. Our results shed light on ecological drivers of anthrax infection and suggest that soil alkalinity and prolonged droughts or rains are useful predictors of disease occurrence that could guide risk‐based surveillance. These insights should inform strategies for managing anthrax including prophylactic livestock vaccination, timing of public health warnings and antibiotic provision in high‐risk areas. However, this research highlights the need for greater surveillance (environmental, serological and case‐detection‐orientated) to determine the mechanisms underlying anthrax dynamics.
Rural surgeons’ attitudes towards and usage of evidence‐based medicine in rural surgical practice
Authors: Kitto Simon C. , Peller Jennifer C. , Villanueva Elmer V. , Gruen Russell L. , Smith Julian A. 
Published: June 2011

AbstractIntroduction Rural and remote surgical practice presents unique barriers to the uptake of the evidence‐based medicine (EBM) paradigm. As medical and education institutions around Australia develop practices and support for EBM, there are growing questions about how EBM is situated in the rural and remote context. The Monash University Department of Surgery at Monash Medical Centre implemented a study to explore the current understandings, attitudes and practices of rural surgeons towards the EBM paradigm.Methods Descriptive survey of rural surgeons based in a tertiary care environment.Results The overall results of the survey demonstrate that: (1) rural surgeons have a good understanding of EBM; (2) EBM evidence is somewhat useful but not very important to clinical decision making; and (3) while rural surgeons are relatively confident in most sources listed, they are most confident in their own judgment and clinical practice guidelines, and least confident in telephone contact with colleagues. Rural surgeons’ understanding, usage and confidence in EBM purports that rural surgeons have contradictory, ambivalent and complex views of the EBM paradigm and its place in rural surgical practice.Discussion Professional isolation and context specificity are important to consider when extending the EBM paradigm to rural surgical practice and understanding the EBM uptake in the rural surgery context.
Interplay between calcium signalling and early signalling elements during defence responses to microbe‐ or damage‐associated molecular patterns
Authors: Ranf Stefanie , Eschen‐Lippold Lennart , Pecher Pascal , Lee Justin , Scheel Dierk 
Published: June 2011

SummaryWhile diverse microbe‐ or damage‐associated molecular patterns (MAMPs/DAMPs) typically trigger a common set of intracellular signalling events, comparative analysis between the MAMPs flg22 and elf18 revealed MAMP‐specific differences in Ca2+ signalling, defence gene expression and MAMP‐mediated growth arrest in Arabidopsis thaliana. Such MAMP‐specific differences are, in part, controlled by BAK1, a kinase associated with several receptors. Whereas defence gene expression and growth inhibition mediated by flg22 were reduced in bak1 mutants, BAK1 had no or minor effects on the same responses elicited by elf18. As the residual Ca2+ elevations induced by diverse MAMPs/DAMPs (flg22, elf18 and Pep1) were virtually identical in bak1 mutants, a differential BAK1‐mediated signal amplification to attain MAMP/DAMP‐specific Ca2+ amplitudes in wild‐type plants may be hypothesized. Furthermore, abrogation of reactive oxygen species (ROS) accumulation, either in the rbohD mutant or through inhibitor application, led to loss of a second Ca2+ peak, demonstrating a feedback effect of ROS on Ca2+ signalling. Conversely, mpk3 mutants showed a prolonged accumulation of ROS but this did not significantly impinge on the overall Ca2+ response. Thus, fine‐tuning of MAMP/DAMP responses involves interplay between diverse signalling elements functioning both up‐ or downstream of Ca2+ signalling.
Prevalence of immunoglobulin A deficiency in Chinese blood donors and evaluation of anaphylactic transfusion reaction risk
Authors: Feng M. L. , Zhao Y. L. , Shen T. , Huang H. , Yin B. , Liu R. Z. , Qian K. C. , Liu D‐Z. 
Published: June 2011

Objectives/Aims: We investigated the incidence of immunoglobulin A (IgA) deficiency in Chinese population.Background: The frequency of IgA deficiency, defined as a serum IgA level of <0·05 mg dL−1, has been broadly studied in different ethnic groups. Individuals with IgA deficiency may form specific antibodies against IgA, which can cause an anaphylactic response when the patient receives an IgA‐containing blood transfusion.Methods: A sandwich enzyme‐linked immunosorbent assay was performed to screen for IgA deficiency and particle gel immunoassay used for confirmation. IgA antibodies were further detected by the DiaMed anti‐IgA test in IgA‐deficient blood donors.Results: Of the total 22 609 healthy blood donors screened, only seven cases were confirmed as having IgA deficiency (<0·05 mg dL−1). Another seven cases displayed relative IgA deficiencies, with mean IgA concentrations ranging from 0·39 to 3·70 mg dL−1. Anti‐IgA was identified in 2 of the 14 IgA‐deficient blood donors whose IgA levels were <5 mg dL−1. Estimation of the theoretical risk for IgA anaphylactic transfusion reaction was 0·009%.Conclusion: The prevalence of IgA deficiency in Chinese is low. However, potential risks exist in performing blood transfusion to IgA‐deficient persons, and measures should be taken to reduce IgA anaphylaxis.
Effects of a short‐term increase in the nutritional plane before the mating period on metabolic and endocrine parameters, hepatic gene expression and reproduction in primiparous beef cows on grazing conditions
Authors: Astessiano A. L. , Pérez‐Clariget R. , Quintans G. , Soca P. , Carriquiry M. 
Published: June 2011

SummarySixty‐four spring‐calved primiparous crossbred cows paired by calving date and body condition score (BCS) at calving were used to study the effect of a short‐term increase in the nutritional plane before the mating period on cow and calf performance, changes in metabolic and endocrine parameters and hepatic gene expression. At 48 ± 10 days post‐partum (onset of nutritional treatment = day 0), cows were assigned to two treatments during 23 days: control (grazing of native pastures; NP; n = 31) and increased nutritional plane (NP improved with Lotus subbiflorous cv Rincon; IP; n = 33). Cow body weight (BW), BCS and total protein and albumin concentrations increased while urea and non‐esterified fatty acids levels decreased from the beginning of the nutritional treatment in both groups, indicating the animal positive energy balance as forage growth and availability of pastures increased during spring. In addition, cow BW and BCS, as well as calf average daily gain and BW, were greater in IP than in NP cows groups. Insulin concentrations were less in IP than in NP (1.37 vs. 2.25 ± 0.26 μU/ml) because insulin increased owing to nutritional treatment only in NP cows. Hepatic insulin receptor mRNA at day 23 tended to be 1.5‐fold greater, while insulin growth factor binding protein‐3 mRNA expression was 1.7‐fold greater in NP than in IP cows. Reproductive responses were not affected by nutritional treatment, but days to initiation of ovarian ciclicity (108 ± 10 days) were positively correlated with insulin concentrations. Grazing of improved NP for 23 days before the mating period did not improve cow reproductive performance but modified metabolic, endocrine and gene expression parameters, in agreement with greater nutrient and energy partitioning towards milk production, reflected in better calf performance.
Factors that influence cecal intubation rate during colonoscopy in deeply sedated patients
Authors: Hsu Chen‐Ming , Lin Wei‐Pin , Su Ming‐Yao , Chiu Cheng‐Tang , Ho Yu‐Pin , Chen Pang‐Chi 
Published: June 2011

AbstractBackground and Aim:  The technical performance of colonoscopy performed in deeply sedated patients differs from that performed without sedation or under minimal to moderate sedation. The aim of this study is to evaluate the factors affecting cecal intubation during colonoscopy performed under deep sedation.Methods:  A total of 5352 consecutive subjects who underwent a screening colonoscopy as part of a health check‐up between January 2008 and December 2008 at an academic hospital were reviewed. All endoscopies were performed with deep sedation using combination propofol or propofol alone. Data collected included characteristics of the patients (age, gender, body mass index, bowel habits, history of abdominal or pelvic surgery, quality of bowel preparation, and presence/absence of colonic diverticula) and characteristics of the colonoscopists (experience level, colonoscopy procedure volume, and instrument handling method). These factors were analyzed to evaluate their impact on cecal intubation rates.Results:  The crude cecal intubation rate was 98% and the adjusted cecal intubation rate was 98.3%. The mean cecal intubation time was 5.6 ± 3.2 min. Multivariate logistic regression analysis demonstrated that patient age greater than 60 years, constipation, poor colon preparation and a two‐person colonoscopy procedure were independently associated with lower cecal intubation rates.Conclusions:  Colonoscopy performed under deep sedation by experienced colonoscopists results in high cecal intubation rates. Among the significant patient‐related predictors influencing the cecal intubation, the quality of the bowel preparation was the only modifiable factor. When performed by experienced hands, the one‐person method was associated with higher cecal intubation rates than the two‐person method.