bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Modulations of the Active MJO Cycle Characterized by Nonlinear Principal Component Analysis
Authors: Jenkner Johannes , Hsieh William W. , Cannon Alex J. 
Published: January 2011

Abstract
A novel methodology is presented for the identification of the mean cycle of the Madden–Julian oscillation (MJO) along the equator. The methodology is based on a nonlinear principal component (NLPC) computed with a neural network model. The bandpass-filtered input data encompass 30 yr with zonal winds at 850 and 200 hPa plus outgoing longwave radiation (OLR). The NLPC is conditioned on a sufficiently strong MJO activity and is computed both for the pooled dataset and for the dataset stratified into seasons. The NLPC for all data depicts a circular mode formed by the first two linear principal components (LPCs) with marginal contributions by the higher-order LPCs. Hence, the mean MJO cycle throughout the year is effectively captured by the amplitude of the leading two LPCs varying in quadrature. The NLPC for individual seasons shows additional variability, which mainly arises from a subordinate oscillation of the second pair of LPCs superimposed on the annual MJO signal. In reference to the all-year solution, the difference in resolved variability approximately accounts for 9% in solstitial seasons and 3% in equinoctial seasons. The phasing of the third LPC is such that convective activity oscillations over the Maritime Continent as well as wind oscillations over the Indian Ocean appear enhanced (suppressed) during boreal winter (summer). Also, convective activity oscillations appear more pronounced at the date line during both winter and summer. The phasing of the fourth LPC is such that upper-level westerlies over the Atlantic region are more persistent during boreal spring than during other seasons.
Infections and Patellar Tendon Ruptures After Anterior Cruciate Ligament Reconstruction
Authors: Benner Rodney W. , Shelbourne K. Donald , Freeman Heather 
Published: January 2011

Background: No studies document the incidence or results of infections and patellar tendon ruptures after anterior cruciate ligament reconstruction with a contralateral patellar tendon autograft. Purpose: To determine the results of patients who have infections and patellar tendon ruptures after anterior cruciate ligament reconstruction with a patellar tendon autograft and compare the results between ipsilateral and contralateral grafts. Study Design: Cohort study; Level of evidence, 3. Methods: The authors determined the incidence of infections requiring surgical intervention and complete patellar tendon ruptures after surgery. Data were analyzed in 2 groups based on the graft source: ipsilateral (n = 2553) or contralateral (n = 2811). Data reviewed included range of motion, quadriceps strength, and subjective evaluations. Results: Infections occurred in 9 ipsilateral patients (0.35%) and 4 contralateral patients (0.14%) ( P = .12). At final follow-up, less than normal knee extension was found in 4 ipsilateral patients and 1 contralateral patient; less than normal flexion was found in 4 ipsilateral patients and 2 contralateral patients. Patellar tendon ruptures occurred in 6 ipsilateral patients (0.24%) and 7 contralateral patients (0.25%) ( P = .92). At 1 month after patellar tendon repair, mean motion (degree of hyperextension–degree short of 0° extension–degree of flexion) in the contralateral group was 5-0-137 in the reconstructed knee and 5-0-118 in the graft-donor knee, which was greater than 5-0-98 found in the ipsilateral group for the reconstructed knee ( P < .05). The mean Noyes subjective score at a mean of 4 years postoperatively for the tendon-ruptured knee was 87 points in the ipsilateral group and 93 points in the contralateral group ( P = .32), which is comparable with the published normative data for the Noyes score reporting a mean score of 93.6 ± 8.3 points. Conclusion: There were no significant differences in the incidence of infection or patellar tendon rupture between the ipsilateral and contralateral groups. Patients with complications after anterior cruciate ligament reconstruction with a patellar tendon autograft may have less difficulty obtaining full knee motion when the graft is harvested from the contralateral knee.
Staphylococcus aureus harbouring Enterotoxin A as a possible risk factor for multiple sclerosis exacerbations
Authors: Mulvey Michael R , Doupe Malcolm , Prout Michael , Leong Christine , Hizon Romeo , Grossberndt Amy , Klowak Meghann , Gupta Aneri , Melanson Maria , Gomori Andrew , Esfahani Farid , Klassen Loressa , Frost Emma E , Namaka Michael 
Published: January 2011

Background: Staphylococcus aureus may produce superantigens that can non-specifically activate CD4+ cells to potentially target the myelin basic protein. Objective: This study examined the association between individuals with multiple sclerosis (MS) and colonization with S. aureus harbouring superantigens. Methods: Nasal swabs were collected from non-MS subjects and patients with MS who had not experienced a relapse in the past six months (MS stable group) and who had suffered a relapse within 30 days of study recruitment (MS exacerbation group). S. aureus was isolated from the anterior nares of participants following standard procedures and staphylococcal superantigen genes ( sea, seb, and tsst-1) were detected using standard laboratory PCR techniques. Results: The study enrolled 204 patients, 80 in the non-MS and MS stable groups and 44 patients in the MS exacerbation group. Overall, 27.0% of patients were colonized with S. aureus with no significant differences identified between study groups. Amongst individuals colonized with S. aureus, the prevalence of sea was significantly greater in the MS exacerbation versus non-MS study group ( p < 0.05; odds ratio 7.9; 95% confidence interval 1.2–49.5). Conclusions: The ability to rapidly screen patients for the presence of S. aureus producing sea may serve as a useful marker of a potential MS exacerbation.
Some ABCA3 mutations elevate ER stress and initiate apoptosis of lung epithelial cells
Authors: Weichert Nina , Kaltenborn Eva , Hector Andreas , Woischnik Markus , Schams Andrea , Holzinger Andreas , Kern Sunčana , Griese Matthias 
Published: January 2011

Abstract

Background
ABCA3 transporter (ATP-binding cassette transporter of the A subfamily) is localized to the limiting membrane of lamellar bodies, organelles for assembly and storage of pulmonary surfactant in alveolar epithelial type II cells (AECII). It transports surfactant phospholipids into lamellar bodies and absence of ABCA3 function disrupts lamellar body biogenesis. Mutations of the ABCA3 gene lead to fatal neonatal surfactant deficiency and chronic interstitial lung disease (ILD) of children. ABCA3 mutations can result in either functional defects of the correctly localized ABCA3 or trafficking/folding defects where mutated ABCA3 remains in the endoplasmic reticulum (ER).

Methods
Human alveolar epithelial A549 cells were transfected with vectors expressing wild-type ABCA3 or one of the three ABCA3 mutant forms, R43L, R280C and L101P, C-terminally tagged with YFP or hemagglutinin-tag. Localization/trafficking properties were analyzed by immunofluorescence and ABCA3 deglycosylation. Uptake of fluorescent NBD-labeled lipids into lamellar bodies was used as a functional assay. ER stress and apoptotic signaling were examined through RT-PCR based analyses of XBP1 splicing, immunoblotting or FACS analyses of stress/apoptosis proteins, Annexin V surface staining and determination of the intracellular glutathion level.

Results
We demonstrate that two ABCA3 mutations, which affect ABCA3 protein trafficking/folding and lead to partial (R280C) or complete (L101P) retention of ABCA3 in the ER compartment, can elevate ER stress and susceptibility to it and induce apoptotic markers in the cultured lung epithelial A549 cells. R43L mutation, resulting in a functional defect of the properly localized ABCA3, had no effect on intracellular stress and apoptotic signaling.

Conclusion
Our data suggest that expression of partially or completely ER localized ABCA3 mutant proteins can increase the apoptotic cell death of the affected cells, which are factors that might contribute to the pathogenesis of genetic ILD.
Flexible taxonomic assignment of ambiguous sequencing reads
Authors: Clemente José C , Jansson Jesper , Valiente Gabriel 
Published: January 2011

Abstract

Background
To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it.

Results
We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed.

Conclusions
The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.
Stroke awareness decreases prehospital delay after acute ischemic stroke in korea
Authors: Kim Young Seo , Park Sang-Soon , Bae Hee-Joon , Cho A-Hyun , Cho Yong-Jin , Han Moon-Ku , Heo Ji Hoe , Kang Kyusik , Kim Dong-Eog , Kim Hahn Young , Kim Gyeong-Moon , Kwon Sun Uk , Kwon Hyung-Min , Lee Byung-Chul , Lee Kyung Bok , Lee Seung-Hoon , Lee Su-Ho , Lee Yong-Seok , Nam Hyo Suk , Oh Mi-Sun , Park Jong-Moo , Rha Joung-Ho , Yu Kyung-Ho , Yoon Byung-Woo 
Published: January 2011

Abstract

Background
Delayed arrival at hospital is one of the major obstacles in enhancing the rate of thrombolysis therapy in patients with acute ischemic stroke. Our study aimed to investigate factors associated with prehospital delay after acute ischemic stroke in Korea.

Methods
A prospective, multicenter study was conducted at 14 tertiary hospitals in Korea from March 2009 to July 2009. We interviewed 500 consecutive patients with acute ischemic stroke who arrived within 48 hours. Univariate and multivariate analyses were performed to evaluate factors influencing prehospital delay.

Results
Among the 500 patients (median 67 years, 62% men), the median time interval from symptom onset to arrival was 474 minutes (interquartile range, 170-1313). Early arrival within 3 hours of symptom onset was significantly associated with the following factors: high National Institutes of Health Stroke Scale (NIHSS) score, previous stroke, atrial fibrillation, use of ambulance, knowledge about thrombolysis and awareness of the patient/bystander that the initial symptom was a stroke. Multivariable logistic regression analysis indicated that awareness of the patient/bystander that the initial symptom was a stroke (OR 4.438, 95% CI 2.669-7.381), knowledge about thrombolysis (OR 2.002, 95% CI 1.104-3.633) and use of ambulance (OR 1.961, 95% CI 1.176-3.270) were significantly associated with early arrival.

Conclusions
In Korea, stroke awareness not only on the part of patients, but also of bystanders, had a great impact on early arrival at hospital. To increase the rate of thrombolysis therapy and the incidence of favorable outcomes, extensive general public education including how to recognize stroke symptoms would be important.
Preventing hospital admissions by reviewing medication (PHARM) in primary care: design of the cluster randomised, controlled, multi-centre PHARM-study
Authors: Leendertse Anne J , de Koning Fred HP , Goudswaard Alex N , Jonkhoff Andries R , van den Bogert Sander CA , de Gier Han J , Egberts Toine CG , van den Bemt Patricia MLA 
Published: January 2011

Abstract

Background
Medication can be effective but can also be harmful and even cause hospital admissions. Medication review or pharmacotherapy review has often been proposed as a solution to prevent these admissions and to improve the effectiveness and safety of pharmacotherapy. However, most published randomised controlled trials on pharmacotherapy reviews showed no or little effect on morbidity and mortality. Therefore we designed the PHARM (Preventing Hospital Admissions by Reviewing Medication)-study with the objective to study the effect of the total pharmaceutical care process on medication related hospital admissions and on adverse drug events, survival and quality of life.

Methods/Design
The PHARM-study is designed as a cluster randomised, controlled, multi-centre study in an integrated primary care setting. Patients with a high risk of a medication related hospital admission are included in the study with randomisation at GP (general practitioner) level. We aim to include 14200 patients, 7100 in each arm, from at least 142 pharmacy practices.
The intervention consists of a patient-centred, structured, pharmaceutical care process. This process consists of several steps, is continuous and occurrs over multiple encounters of patients and clinicians. The steps of this pharmaceutical care process are a pharmaceutical anamnesis, a review of the patient's pharmacotherapy, the formulation and execution of a pharmaceutical care plan combined with the monitoring and follow up evaluation of the care plan and pharmacotherapy. The patient's own pharmacist and GP carry out the intervention. The control group receives usual care.
The primary outcome of the study is the frequency of hospital admissions related to medication within the study period of 12 months of each patient. The secondary outcomes are survival, quality of life, adverse drug events and severe adverse drug events. The outcomes will be analysed by using mixed-effects Cox models.

Discussion
The PHARM-study is one of the largest controlled trials to study the effectiveness of the total pharmaceutical care process. The study should therefore provide evidence as to whether such a pharmaceutical care process should be implemented in the primary care setting.

Trial Registration
Trial number: NTR 2647
Barriers and facilitators to the dissemination of DECISION+, a continuing medical education program for optimizing decisions about antibiotics for acute respiratory infections in primary care: A study protocol
Authors: Allaire Anne-Sophie , Labrecque Michel , Giguère Anik , Gagnon Marie-Pierre , Grimshaw Jeremy , Légaré France 
Published: January 2011

Abstract

Background
In North America, acute respiratory infections are the main reason for doctors' visits in primary care. Family physicians and their patients overuse antibiotics for treating acute respiratory infections. In a pilot clustered randomized trial, we showed that DECISION+, a continuing medical education program in shared decision making, has the potential to reduce the overuse of antibiotics for treating acute respiratory infections. DECISION+ learning activities consisted of three interactive sessions of three hours each, reminders at the point of care, and feedback to doctors on their agreement with patients about comfort with the decision whether to use antibiotics. The objective of this study is to identify the barriers and facilitators to physicians' participation in DECISION+ with the goal of disseminating DECISION+ on a larger scale.

Methods/design
This descriptive study will use mixed methods and retrospective and prospective components. All analyses will be based on an adapted version of the Ottawa Model of Research Use. First, we will use qualitative methods to analyze the following retrospective data from the pilot study: the logbooks of eight research assistants, the transcriptions of 15 training sessions, and 27 participant evaluations of the DECISION+ training sessions. Second, we will collect prospective data in semi-structured focus groups composed of family physicians to identify barriers and facilitators to the dissemination of a future training program similar to DECISION+. All 39 family physicians exposed to DECISION+ during the pilot project will be eligible to participate. We will use a self-administered questionnaire based on Azjen's Theory of Planned Behaviour to assess participants' intention to take part in future training programs similar to DECISION+.

Discussion
Barriers and facilitators identified in this project will guide modifications to DECISION+, a continuing medical education program in shared decision making regarding the use of antibiotics in acute respiratory infections, to facilitate its dissemination in primary care on a large scale. Our results should help continuing medical educators develop a continuing medical education program in shared decision making for other clinically relevant topics. This will help optimize clinical decisions in primary care.
The efficacy of four-slice helical CT in evaluating pancreatic trauma: a single institution experience
Authors: Lee Wei-Jing , Foo Ning-Ping , Lin Hung-Jung , Huang Yen-Chang , Chen Kuo-Tai 
Published: January 2011

AbstractStudy objectiveTo assess the efficacy of computed tomography (CT) in evaluating patients with pancreatic trauma.MethodsWe undertook a retrospective review of all blunt trauma patients admitted to the Chi-Mei Medical Center from January 2004 to June 2006. Every patients underwent abdominal CT scan in emergency department and the CT scans were obtained with a four-slice helical CT. Diagnosis of a pancreatic injury in these patients was by surgical observation or by CT findings. Radiographic pancreatic injuries were classified as deep or superficial lesions. Deep lesions were defined as the hematomas or lacerations >50% thickness of the pancreas. Superficial lesions were described as the hematomas or lacerations <50% thickness of the pancreas; pancreatic edema; and focal fluid accumulation around the pancreasResultsNineteen patients with pancreatic trauma, fourteen males and five females, average age 40.6 ± 21.4 years, were included. Most patients (73.7%) with pancreatic trauma had associated organ injuries. CT was performed in all patients and laparotomy in 14 patients. CT was 78.9% sensitive in detecting pancreatic trauma. All deep pancreatic lesions revealed on CT required surgical treatment, and complication was discovered in two patients undergoing delayed surgery. Superficial lesions were managed conservatively.ConclusionFour-slice helical CT can detect most pancreatic trauma and provide practical therapeutic guidance. Delayed operation might result in complications and is associated with prolonged hospital stays.
Paradoxical ventilator associated pneumonia incidences among selective digestive decontamination studies versus other studies of mechanically ventilated patients: benchmarking the evidence base
Authors: Hurley James C 
Published: January 2011

Abstract
Introduction
Selective digestive decontamination (SDD) appears to have a more compelling evidence base than non-antimicrobial methods for the prevention of ventilator associated pneumonia (VAP). However, the striking variability in ventilator associated pneumonia-incidence proportion (VAP-IP) among the SDD studies remains unexplained and a postulated contextual effect remains untested for.

Methods
Nine reviews were used to source 45 observational (benchmark) groups and 137 component (control and intervention) groups of studies of SDD and studies of three non-antimicrobial methods of VAP prevention. The logit VAP-IP data were summarized by meta-analysis using random effects methods and the associated heterogeneity (tau2) was measured. As group level predictors of logit VAP-IP, the mode of VAP diagnosis, proportion of trauma admissions, the proportion receiving prolonged ventilation and the intervention method under study were examined in meta-regression models containing the benchmark groups together with either the control (models 1 to 3) or intervention (models 4 to 6) groups of the prevention studies.

Results
The VAP-IP benchmark derived here is 22.1% (95% confidence interval; 95% CI; 19.2 to 25.5; tau2 0.34) whereas the mean VAP-IP of control groups from studies of SDD and of non-antimicrobial methods, is 35.7 (29.7 to 41.8; tau2 0.63) versus 20.4 (17.2 to 24.0; tau2 0.41), respectively (P < 0.001). The disparity between the benchmark groups and the control groups of the SDD studies, which was most apparent for the highest quality studies, could not be explained in the meta-regression models after adjusting for various group level factors. The mean VAP-IP (95% CI) of intervention groups is 16.0 (12.6 to 20.3; tau2 0.59) and 17.1 (14.2 to 20.3; tau2 0.35) for SDD studies versus studies of non-antimicrobial methods, respectively.

Conclusions
The VAP-IP among the intervention groups within the SDD evidence base is less variable and more similar to the benchmark than among the control groups. These paradoxical observations cannot readily be explained. The interpretation of the SDD evidence base cannot proceed without further consideration of this contextual effect.
On some Fano–Enriques threefolds
Authors: Karzhemanov Ilya 
Published: January 2011

Abstract
We give a classification of Fano threefolds X with canonical Gorenstein singularities such that X possess a regular involution which acts freely on some smooth surface in |– KX
|, and such that the linear system |– KX
| gives a morphism which is not an embedding. From this classification one gets, in particular, a description of some natural class of Fano–Enriques threefolds.
Polarities of Schellhammer planes
Authors: Poppitz Steffen , Stroppel Markus 
Published: January 2011

Abstract
We construct polarities for projective planes admitting a group of automorphisms that acts regularly on the complements of an anti-flag in the point and line set. In particular, we determine all polarities of the compact connected planes studied by I. Schellhammer and by P. Sperner. For both classes of planes we solve the conjugacy problem, and determine the set of absolute points for each one of the polarities. Among these polarities we find the first examples of elliptic polarities in non-Moufang compact projective planes.
On the local structure and the homology of CAT(κ) spaces and euclidean buildings
Authors: Kramer Linus 
Published: January 2011

Abstract
We prove that every open subset of a euclidean building is a finite-dimensional absolute neighborhood retract. This implies in particular that such a set has the homotopy type of a finite dimensional simplicial complex. We also include a proof for the rigidity of homeomorphisms of euclidean buildings. A key step in our approach to this result is the following: the space of directions ∑
oX of a CAT(κ) space X is homotopy equivalent to a small punctured disk Bɛ
(X, o) – o. The second ingredient is the local homology sheaf of X. Along the way, we prove some results about the local structure of CAT(κ)-spaces which may be of independent interest.