bluuebunny/crossref_metadata_2025_split huggingface dataset:
ω‐3 Fatty Acids Infusions as Adjuvant Therapy in Rheumatoid Arthritis
Authors: Bahadori Babak , Uitz Elisabeth , Thonhofer Rene , Trummer Markus , Pestemer‐Lach Iris , McCarty Mark , Krejs Guenter J. 
Published: April 2010

Background:The present study investigated the efficacy and safety of parenteral ω‐3 fatty acids (ω‐3 FA) in patients with active rheumatoid arthritis (RA).Methods:We performed a double‐blind, randomized, placebo‐controlled study in 23 patients with moderate to severe RA. Patients received either 0.2 g of fish oil emulsion/kg (active) or 0.9% saline (placebo) infusion intravenously for 14 consecutive days, followed by 20 weeks of 0.05 g of fish oil/kg (active) or paraffin wax (placebo) ingested orally as capsules. A decrease in swollen and tender joint counts was the primary efficacy measure.Results:At baseline, both swollen and tender joint counts were not significantly different between patients in the treatment and placebo groups. Twenty patients completed the infusion portion of the study, and 13 completed the oral portion. Swollen joint count was significantly lower in the ω‐3 FA group compared with the placebo group after 1 week of infusion (P = .002) as well as after 2 weeks of infusion (P = .046). Tender joint count also tended to be lower in the ω‐3 FA group, although this did not reach statistical significance. Both swollen and tender joint counts were significantly lower in the ω‐3 FA group compared with the placebo group during and at the end of oral treatment.Conclusion:Our pilot study indicates that parenteral ω‐3 FAs are well tolerated and improve clinical symptoms of RA. Subsequent oral administration of ω‐3 FAs may prolong the beneficial effects of the infusion therapy. These results warrant validation in larger multicenter studies.
Nutrition Markers in Patients After Heart Surgery
Authors: Racca Vittorio , Castiglioni Paolo , Ripamonti Vittorino , Bertoli Simona , Calvo Maria Gaetana , Ferratini Maurizio 
Published: April 2010

Background:Nutrition support is an important aspect of multidisciplinary approaches in cardiology rehabilitation. However, little is known about the impact of a patient's nutrition status on recovery after elective heart surgery. The authors assessed changes in nutrition markers in patients undergoing postsurgical rehabilitation, and tested their correlation with systemic inflammatory responses and clinical outcomes to determine the adequacy of the prescribed dietary regimen.Methods:Plasma concentrations of nutrition biomarkers were measured in 50 nondiabetic patients upon admission to a cardiology rehabilitation unit after coronary artery bypass grafting or mitral and/or aortic valve replacement (D0), and again 16 days later (D16).Results:On D16, low plasma albumin increased, anemia improved, and high levels of inflammation markers declined. Vitamins remained stable within normal values, with the exception of vitamin B12, which decreased significantly from 516 ± 341 to 445 ± 212 ng/mL (P = .007). Blood glucose was >110 mg/dL in 51% of the patients at baseline; this proportion did not decline after rehabilitation. Overweight patients (body mass index >25 kg/m2) were prevalent (58%). They showed a slightly but not significantly greater inflammatory response and had a higher incidence of infective complications than the normal‐weight group, but similar levels of nutrition markers.Conclusions:The standard dietary regimen followed during cardiological rehabilitation after major cardiovascular surgery aids recovery from surgical insult, but fails to normalize high glucose levels. Vitamin B12 supplementation should be encouraged because of its substantial reduction during the rehabilitation period.
Using jackknife to assess the quality of gene order phylogenies
Authors: Shi Jian , Zhang Yiwei , Luo Haiwei , Tang Jijun 
Published: April 2010

Abstract

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to determine the confidence level of a phylogeny obtained from gene orders and a jackknife rate of 40% should be used. However, although a branch with support value of 85% can be trusted, low support branches require careful investigation before being discarded.

Conclusions
Our experiments show that jackknife is indeed necessary and useful for gene order data, yet some caution should be taken when the results are interpreted.
The Alveolate Perkinsus marinus: Biological Insights from EST Gene Discovery
Authors: Joseph Sandeep J , Fernández-Robledo José A , Gardner Malcolm J , El-Sayed Najib M , Kuo Chih-Horng , Schott Eric J , Wang Haiming , Kissinger Jessica C , Vasta Gerardo R 
Published: April 2010

Abstract

Background

Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism) within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date.

Results
To gain insight into the biological basis of the parasite's virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated >31,000 5' expressed sequence tags (ESTs) derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-value ≤ 1e-5). Some sequences are similar to those proven to be targets for effective intervention in other protozoan parasites, and include not only proteases, antioxidant enzymes, and heat shock proteins, but also those associated with relict plastids, such as acetyl-CoA carboxylase and methyl erythrithol phosphate pathway components, and those involved in glycan assembly, protein folding/secretion, and parasite-host interactions.

Conclusions
Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence for the presence of a relict plastid. Further, although P. marinus sequences display significant similarity to those from both apicomplexans and dinoflagellates, the presence of trans-spliced transcripts confirms the previously established affinities with the latter. The EST analysis reported herein, together with the recently completed sequence of the P. marinus genome and the development of transfection methodology, should result in improved intervention strategies against dermo disease.
Adhesion to and biofilm formation on IB3-1 bronchial cells by Stenotrophomonas maltophilia isolates from cystic fibrosis patients
Authors: Pompilio Arianna , Crocetta Valentina , Confalone Pamela , Nicoletti Mauro , Petrucca Andrea , Guarnieri Simone , Fiscarelli Ersilia , Savini Vincenzo , Piccolomini Raffaele , Di Bonaventura Giovanni 
Published: April 2010

Abstract

Background

Stenotrophomonas maltophilia has recently gained considerable attention as an important emerging pathogen in cystic fibrosis (CF) patients. However, the role of this microorganism in the pathophysiology of CF lung disease remains largely unexplored. In the present study for the first time we assessed the ability of S. maltophilia CF isolates to adhere to and form biofilm in experimental infection experiments using the CF-derived bronchial epithelial IB3-1cell line. The role of flagella on the adhesiveness of S. maltophilia to IB3-1 cell monolayers was also assessed by using fliI mutant derivative strains.

Results
All S. maltophilia CF isolates tested in the present study were able, although at different levels, to adhere to and form biofilm on IB3-1 cell monolayers. Scanning electron and confocal microscopy revealed S. maltophilia structures typical of biofilm formation on bronchial IB3-1 cells. The loss of flagella significantly (P < 0.001) decreased bacterial adhesiveness, if compared to that of their parental flagellated strains. S. maltophilia CF isolates were also able to invade IB3-1 cells, albeit at a very low level (internalization rate ranged from 0.01 to 4.94%). Pre-exposure of IB3-1 cells to P. aeruginosa PAO1 significantly increased S. maltophilia adhesiveness. Further, the presence of S. maltophilia negatively influenced P. aeruginosa PAO1 adhesiveness.

Conclusions
The main contribution of the present study is the finding that S. maltophilia is able to form biofilm on and invade CF-derived IB3-1 bronchial epithelial cells, thus posing a rationale for the persistence and the systemic spread of this opportunistic pathogen in CF patients. Experiments using in vivo models which more closely mimic CF pulmonary tissues will certainly be needed to validate the relevance of our results.
Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study data
Authors: Ma Li , Yang Jing , Runesha H Birali , Tanaka Toshiko , Ferrucci Luigi , Bandinelli Stefania , Da Yang 
Published: April 2010

AbstractBackgroundCholesterol concentrations in blood are related to cardiovascular diseases. Recent genome-wide association studies (GWAS) of cholesterol levels identified a number of single-locus effects on total cholesterol (TC) and high-density lipoprotein cholesterol (HDL-C) levels. Here, we report single-locus and epistasis SNP effects on TC and HDL-C using the Framingham Heart Study (FHS) data.ResultsSingle-locus effects and pairwise epistasis effects of 432,096 SNP markers were tested for their significance on log-transformed TC and HDL-C levels. Twenty nine additive SNP effects reached single-locus genome-wide significance (p < 7.2 × 10-8) and no dominance effect reached genome-wide significance. Two new gene regions were detected, theRAB3GAP1-R3HDM1-LCT-MCM6region of chr02 for TC identified by six new SNPs, and theOSBPL8-ZDHHC17region (chr12) for HDL-C identified by one new SNP. The remaining 22 single-locus SNP effects confirmed previously reported genes or gene regions. For TC, three SNPs identified two gene regions that were tightly linked with previously reported genes associated with TC, including rs599839 that was 10 bases downstreamPSRC1and 3.498 kb downstreamCELSR2, rs4970834 inCELSR2, and rs4245791 inABCG8that slightly overlapped withABCG5. For HDL-C,LPLwas confirmed by 12 SNPs 8-45 kb downstream,CETPby two SNPs 0.5-11 kb upstream, and theLIPG-ACAA2region by five SNPs inside this region. Two epistasis effects on TC and thirteen epistasis effects on HDL-C reached the significance of "suggestive linkage". The most significant epistasis effect (p = 5.72 × 10-13) was close to reaching "significant linkage" and was a dominance × dominance effect of HDL-C betweenLMBRD1(chr06) and theLRIG3region (chr12), and this pair of gene regions had six other D × D effects with "suggestive linkage".ConclusionsGenome-wide association analysis of the FHS data detected two new gene regions with genome-wide significance, detected epistatic SNP effects on TC and HDL-C with the significance of suggestive linkage in seven pairs of gene regions, and confirmed some previously reported gene regions associated with TC and HDL-C.
A prospective, randomized, double-blinded single-site control study comparing blood loss prevention of tranexamic acid (TXA) to epsilon aminocaproic acid (EACA) for corrective spinal surgery
Authors: Verma Kushagra , Errico Thomas J , Vaz Kenneth M , Lonner Baron S 
Published: April 2010

AbstractBackgroundMultilevel spinal fusion surgery has typically been associated with significant blood loss. To limit both the need for transfusions and co-morbidities associated with blood loss, the use of anti-fibrinolytic agents has been proposed. While there is some literature comparing the effectiveness of tranexamic acid (TXA) to epsilon aminocaproic acid (EACA) in cardiac procedures, there is currently no literature directly comparing TXA to EACA in orthopedic surgery.Methods/DesignHere we propose a prospective, randomized, double-blinded control study evaluating the effects of TXA, EACA, and placebo for treatment of adolescent idiopathic scoliosis (AIS), neuromuscular scoliosis (NMS), and adult deformity (AD) via corrective spinal surgery. Efficacy will be determined by intraoperative and postoperative blood loss. Other clinical outcomes that will be compared include transfusion rates, preoperative and postoperative hemodynamic values, and length of hospital stay after the procedure.DiscussionThe primary goal of the study is to determine perioperative blood loss as a measure of the efficacy of TXA, EACA, and placebo. Based on current literature and the mechanism by which the medications act, we hypothesize that TXA will be more effective at reducing blood loss than EACA or placebo and result in improved patient outcomes.Trial RegistrationClinicalTrials.gov ID: NCT00958581
Building capacity in health facility management: guiding principles for skills transfer in Liberia
Authors: Rowe Laura A , Brillant Sister Barbara , Cleveland Emily , Dahn Bernice T , Ramanadhan Shoba , Podesta Mae , Bradley Elizabeth H 
Published: April 2010

Abstract

Background
Management training is fundamental to developing human resources for health. Particularly as Liberia revives its health delivery system, facility and county health team managers are central to progress. Nevertheless, such management skills are rarely prioritized in health training, and sustained capacity building in this area is limited. We describe a health management delivery program in which a north and south institution collaborated to integrate classroom and field-based training in health management and to transfer the capacity for sustained management development in Liberia.

Methods
We developed and implemented a 6-month training program in health management skills (i.e. strategic problem solving, financial management, human resource management and leadership) delivered by Yale University and Mother Patern College from Liberia, with support from the Clinton HIV/AIDS Initiative. Over three 6-month cycles, responsibility for course instruction was transferred from the north institution to the south institution. A self-administered survey was conducted of all participants completing the course to measure changes in self-rated management skills, the degree to which the course was helpful and met its stated objectives, and faculty members' responsiveness to participant needs as the transfer process occurred.

Results
Respondents (n = 93, response rate 95.9%) reported substantial improvement in self-reported management skills, and rated the helpfulness of the course and the degree to which the course met its objectives highly. Levels of improvement and course ratings were similar over the three cohorts as the course was transferred to the south institution. We suggest a framework of five elements for implementing successful management training programs that can be transferred and sustained in resource-limited settings, including: 1) use a short-course format focusing on four key skill areas with practical tools; 2) include didactic training, on-site projects, and on-site mentoring; 3) collaborate with an in-country academic institution, willing and able to scale-up and maintain the training; 4) provide training for the in-country academic faculty; and 5) secure Ministry-level support to ensure participation.

Conclusion
Our findings demonstrate key elements for scaling up and replicating educational initiatives that address management skills essential for long-term health systems strengthening in resource-poor settings.
A novel and safe technique in closed tube thoracostomy
Authors: Dural Koray , Gulbahar Gultekin , Kocer Bulent , Sakinci Unal 
Published: April 2010

Abstract

Background
Tube thoracostomy (TT) is the most commonly performed surgical procedure in thoracic surgery clinics. The procedure might have to be repeated due to ineffective drainage in patients with tube malposition (TM), in whom the drain is not directed to the apex or located in the fissure. Trocar technique, which is used to prevent TM, is not recommended because of its potential for severe complications.

Methods
The study involved 180 patients who required TT application for any etiology within one year. The patients were divided into two groups as Group A, who had undergone classical surgical technique (n = 90) and Group B, who had undergone a combination of surgery and trocar techniques (n = 90). The groups were compared for TM, the effect of TM on the drain removal, and other insertion related complications.

Results
In Group A, 23 patients had TM, 4 of whom developed associated ineffective drainage, while the patients in Group B had no insertion related complications (p = 0.001). The mean drain removal time of the patients with TM was 5 ± 2.25 days. In the patients who did not develop TM, it was 3.39 ± 1.18 days (p = 0.001).

Conclusions
The modified combination technique is a reliable method in preventing TM and its potential complications.
Applying mass spectrometry based proteomic technology to advance the understanding of multiple myeloma
Authors: Micallef Johann , Dharsee Moyez , Chen Jian , Ackloo Suzanne , Evans Ken , Qiu Luqui , Chang Hong 
Published: April 2010

AbstractMultiple myeloma (MM) is the second most common hematological malignancy in adults. It is characterized by clonal proliferation of terminally differentiated B lymphocytes and over-production of monoclonal immunoglobulins. Recurrent genomic aberrations have been identified to contribute to the aggressiveness of this cancer. Despite a wealth of knowledge describing the molecular biology of MM as well as significant advances in therapeutics, this disease remains fatal. The identification of biomarkers, especially through the use of mass spectrometry, however, holds great promise to increasing our understanding of this disease. In particular, novel biomarkers will help in the diagnosis, prognosis and therapeutic stratification of MM. To date, results from mass spectrometry studies of MM have provided valuable information with regards to MM diagnosis and response to therapy. In addition, mass spectrometry was employed to study relevant signaling pathways activated in MM. This review will focus on how mass spectrometry has been applied to increase our understanding of MM.
A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region
Authors: McInnes L Alison , Nakamine Alisa , Pilorge Marion , Brandt Tracy , Jiménez González Patricia , Fallas Marietha , Manghi Elina R , Edelmann Lisa , Glessner Joseph , Hakonarson Hakon , Betancur Catalina , Buxbaum Joseph D 
Published: April 2010

Abstract

Background
The 15q24 microdeletion syndrome has been recently described as a recurrent, submicroscopic genomic imbalance found in individuals with intellectual disability, typical facial appearance, hypotonia, and digital and genital abnormalities. Gene dosage abnormalities, including copy number variations (CNVs), have been identified in a significant fraction of individuals with autism spectrum disorders (ASDs). In this study we surveyed two ASD cohorts for 15q24 abnormalities to assess the frequency of genomic imbalances in this interval.

Methods
We screened 173 unrelated subjects with ASD from the Central Valley of Costa Rica and 1336 subjects with ASD from 785 independent families registered with the Autism Genetic Resource Exchange (AGRE) for CNVs across 15q24 using oligonucleotide arrays. Rearrangements were confirmed by array comparative genomic hybridization and quantitative PCR.

Results
Among the patients from Costa Rica, an atypical de novo deletion of 3.06 Mb in 15q23-q24.1 was detected in a boy with autism sharing many features with the other 13 subjects with the 15q24 microdeletion syndrome described to date. He exhibited intellectual disability, constant smiling, characteristic facial features (high anterior hairline, broad medial eyebrows, epicanthal folds, hypertelorism, full lower lip and protuberant, posteriorly rotated ears), single palmar crease, toe syndactyly and congenital nystagmus. The deletion breakpoints are atypical and lie outside previously characterized low copy repeats (69,838-72,897 Mb). Genotyping data revealed that the deletion had occurred in the paternal chromosome. Among the AGRE families, no large 15q24 deletions were observed.

Conclusions
From the current and previous studies, deletions in the 15q24 region represent rare causes of ASDs with an estimated frequency of 0.1 to 0.2% in individuals ascertained for ASDs, although the proportion might be higher in sporadic cases. These rates compare with a frequency of about 0.3% in patients ascertained for unexplained intellectual disability and congenital anomalies. This atypical deletion reduces the minimal interval for the syndrome from 1.75 Mb to 766 kb, implicating a reduced number of genes (15 versus 38). Sequencing of genes in the 15q24 interval in large ASD and intellectual disability samples may identify mutations of etiologic importance in the development of these disorders.
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data
Authors: Hendrix David , Levine Michael , Shi Weiyang 
Published: April 2010

AbstractMicroRNAs (miRs) have been broadly implicated in animal development and disease. We developed a novel computational strategy for the systematic, whole-genome identification of miRs from high throughput sequencing information. This method, miRTRAP, incorporates the mechanisms of miR biogenesis and includes additional criteria regarding the prevalence and quality of small RNAs arising from the antisense strand and neighboring loci. This program was applied to the simple chordate Ciona intestinalis and identified nearly 400 putative miR loci.