bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonization and Transmission of Methicillin-Resistant Staphylococcus aureus ST398 in Nursery Piglets
Authors: Crombé Florence , Vanderhaeghen Wannes , Dewulf Jeroen , Hermans Katleen , Haesebrouck Freddy , Butaye Patrick 
Published: December 2011

ABSTRACT

A transmission experiment was performed to evaluate the spread of methicillin-resistant
Staphylococcus aureus
(MRSA) ST398 in nursery piglets. Reproduction ratios (R
0
) in three experimental groups were found to vary between 3.92 and 52.54, indicating that after introduction, MRSA ST398 will spread easily among weaned piglets, with a tendency to become established.
Vascular Incorporation of Endothelial Colony-Forming Cells Is Essential for Functional Recovery of Murine Ischemic Tissue Following Cell Therapy
Authors: Schwarz Theresa M. , Leicht Simon F. , Radic Tamara , Rodriguez-Arabaolaza Iker , Hermann Patrick C. , Berger Frank , Saif Jaimy , Böcker Wolfgang , Ellwart Joachim W. , Aicher Alexandra , Heeschen Christopher 
Published: December 2011

Objective—
Cord blood–derived human endothelial colony-forming cells (ECFCs) bear a high proliferative capacity and potently enhance tissue neovascularization in vivo. Here, we investigated whether the leading mechanism for the functional improvement relates to their physical vascular incorporation or perivascular paracrine effects and whether the effects can be further enhanced by dual-cell–based therapy, including mesenchymal stem cells (MSCs).

Methods and Results—

ECFCs or MSCs were lentivirally transduced with thymidine kinase suicide gene driven by the endothelial-specific vascular endothelial growth factor 2 (kinase insert domain receptor) promoter and evaluated in a hindlimb ischemia model. ECFCs and MSCs enhanced neovascularization after ischemic events to a similar extent. Dual therapy using ECFCs and MSCs further enhanced neovascularization. Mechanistically, 3 weeks after induction of ischemia followed by cell therapy, ganciclovir-mediated elimination of kinase insert domain receptor
+
cells completely reversed the therapeutic effect of ECFCs but not that of MSCs. Histological analysis revealed that ganciclovir effectively eliminated ECFCs incorporated into the vasculature.

Conclusion—
Endothelial-specific suicide gene technology demonstrates distinct mechanisms for ECFCs and MSCs, with complete abolishment of ECFC-mediated effects, whereas MSC-mediated effects remained unaffected. These data strengthen the notion that a dual-cell–based therapy represents a promising approach for vascular regeneration of ischemic tissue.
Matrix Metalloproteinase-2 Proteolysis of Calponin-1 Contributes to Vascular Hypocontractility in Endotoxemic Rats
Authors: Castro Michele M. , Cena Jonathan , Cho Woo Jung , Walsh Michael P. , Schulz Richard 
Published: December 2011

Objective—
Matrix metalloproteinase (MMP)-2 is activated in aorta during endotoxemia and plays a role in the hypocontractility to vasoconstrictors. Calponin-1 is a regulator of vascular smooth muscle tone with similarities to troponin, a cardiac myocyte protein that is cleaved by MMP-2 in myocardial oxidative stress injuries. We hypothesized that calponin-1 may be proteolyzed by MMP-2 in endotoxemia-induced vascular hypocontractility.

Methods and Results—
Rats were given a nonlethal dose of bacterial lipopolysaccharide (LPS) or vehicle. Some rats were given the MMP inhibitors ONO-4817 or doxycycline. Six hours later, plasma nitrate+nitrite increased >15-fold in LPS-treated rats, an effect unchanged by doxycycline. Both ONO-4817 and doxycycline prevented LPS-induced aortic hypocontractility to phenylephrine. LPS activated MMP-2 in the aorta by S-glutathiolation. Calponin-1 levels decreased by 25% in endotoxemic aortae, which was prevented by doxycycline. Calponin-1 and MMP-2 coimmunoprecipitated and both exhibited uniform cytosolic staining in medial vascular smooth muscle cells. In vitro incubation of calponin-1 with MMP-2 led to calponin-1 degradation and appearance of its cleavage product.

Conclusion—
Calponin-1 is a target of MMP-2, which contributes to endotoxemia-induced vascular hypocontractility.
Gene selection and classification for cancer microarray data based on machine learning and similarity measures
Authors: Liu Qingzhong , Sung Andrew H , Chen Zhongxue , Liu Jianzhong , Chen Lei , Qiao Mengyu , Wang Zhaohui , Huang Xudong , Deng Youping 
Published: December 2011

Abstract

Background
Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease status, and how to determine the final gene set that is best for classification. Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money.

Results
To deal with redundant information and improve classification, we propose a gene selection method, Recursive Feature Addition, which combines supervised learning and statistical similarity measures. To determine the final optimal gene set for prediction and classification, we propose an algorithm, Lagging Prediction Peephole Optimization. By using six benchmark microarray gene expression data sets, we compared Recursive Feature Addition with recently developed gene selection methods: Support Vector Machine Recursive Feature Elimination, Leave-One-Out Calculation Sequential Forward Selection and several others.

Conclusions
On average, with the use of popular learning machines including Nearest Mean Scaled Classifier, Support Vector Machine, Naive Bayes Classifier and Random Forest, Recursive Feature Addition outperformed other methods. Our studies also showed that Lagging Prediction Peephole Optimization is superior to random strategy; Recursive Feature Addition with Lagging Prediction Peephole Optimization obtained better testing accuracies than the gene selection method varSelRF.
Changes in predicted protein disorder tendency may contribute to disease risk
Authors: Hu Yang , Liu Yunlong , Jung Jeesun , Dunker A Keith , Wang Yadong 
Published: December 2011

Abstract

Background
Recent studies suggest that many proteins or regions of proteins lack 3D structure. Defined as intrinsically disordered proteins, these proteins/peptides are functionally important. Recent advances in next generation sequencing technologies enable genome-wide identification of novel nucleotide variations in a specific population or cohort.

Results
Using the exonic single nucleotide variations (SNVs) identified in the 1,000 Genomes Project and distributed by the Genetic Analysis Workshop 17, we systematically analysed the genetic and predicted disorder potential features of the non-synonymous variations. The result of experiments suggests that a significant change in the tendency of a protein region to be structured or disordered caused by SNVs may lead to malfunction of such a protein and contribute to disease risk.

Conclusions
After validation with functional SNVs on the traits distributed by GAW17, we conclude that it is valuable to consider structure/disorder tendencies while prioritizing and predicting mechanistic effects arising from novel genetic variations.
Parallel progressive multiple sequence alignment on reconfigurable meshes
Authors: Nguyen Ken D , Pan Yi , Nong Ge 
Published: December 2011

Abstract

Background
One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.

Results
We design O(1) run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align m sequences with max length n, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from O(m × n
4) to O(m) using O(m × n
3) processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes O(m × n
4) processing units and completes in O(m) time.

Conclusions
To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with O(m) run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS) with O(1) run-time using O(n
3) processing units. This is a big improvement over the current best constant-time algorithm that uses O(n
4) processing units.
Maximizing biomarker discovery by minimizing gene signatures
Authors: Chang Chang , Wang Junwei , Zhao Chen , Fostel Jennifer , Tong Weida , Bushel Pierre R , Deng Youping , Pusztai Lajos , Symmans W Fraser , Shi Tieliu 
Published: December 2011

Abstract

Background
The use of gene signatures can potentially be of considerable value in the field of clinical diagnosis. However, gene signatures defined with different methods can be quite various even when applied the same disease and the same endpoint. Previous studies have shown that the correct selection of subsets of genes from microarray data is key for the accurate classification of disease phenotypes, and a number of methods have been proposed for the purpose. However, these methods refine the subsets by only considering each single feature, and they do not confirm the association between the genes identified in each gene signature and the phenotype of the disease. We proposed an innovative new method termed Minimize Feature's Size (MFS) based on multiple level similarity analyses and association between the genes and disease for breast cancer endpoints by comparing classifier models generated from the second phase of MicroArray Quality Control (MAQC-II), trying to develop effective meta-analysis strategies to transform the MAQC-II signatures into a robust and reliable set of biomarker for clinical applications.

Results
We analyzed the similarity of the multiple gene signatures in an endpoint and between the two endpoints of breast cancer at probe and gene levels, the results indicate that disease-related genes can be preferably selected as the components of gene signature, and that the gene signatures for the two endpoints could be interchangeable. The minimized signatures were built at probe level by using MFS for each endpoint. By applying the approach, we generated a much smaller set of gene signature with the similar predictive power compared with those gene signatures from MAQC-II.

Conclusions
Our results indicate that gene signatures of both large and small sizes could perform equally well in clinical applications. Besides, consistency and biological significances can be detected among different gene signatures, reflecting the studying endpoints. New classifiers built with MFS exhibit improved performance with both internal and external validation, suggesting that MFS method generally reduces redundancies for features within gene signatures and improves the performance of the model. Consequently, our strategy will be beneficial for the microarray-based clinical applications.
Global host metabolic response to Plasmodium vivax infection: a 1H NMR based urinary metabonomic study
Authors: Sengupta Arjun , Ghosh Soumita , Basant Angika , Malusare Suhas , Johri Parul , Pathak Sulabha , Sharma Shobhona , Sonawat Haripalsingh M 
Published: December 2011

Abstract

Background

Plasmodium vivax is responsible for the majority of malarial infection in the Indian subcontinent. This species of the parasite is generally believed to cause a relatively benign form of the disease. However, recent reports from different parts of the world indicate that vivax malaria can also have severe manifestation. Host response to the parasite invasion is thought to be an important factor in determining the severity of manifestation. In this paper, attempt was made to determine the host metabolic response associated with P. vivax infection by means of NMR spectroscopy-based metabonomic techniques in an attempt to better understand the disease pathology.

Methods
NMR spectroscopy of urine samples from P. vivax- infected patients, healthy individuals and non-malarial fever patients were carried out followed by multivariate statistical analysis. Two data analysis techniques were employed, namely, Principal Component Analysis [PCA] and Orthogonal Projection to Latent Structure Discriminant Analysis [OPLS-DA]. Several NMR signals from the urinary metabolites were further selected for univariate comparison among the classes.

Results
The urine metabolic profiles of P. vivax- infected patients were distinct from those of healthy individuals as well as of non-malarial fever patients. A highly predictive model was constructed from urine profile of malarial and non-malarial fever patients. Several metabolites were found to be varying significantly across these cohorts. Urinary ornithine seems to have the potential to be used as biomarkers of vivax malaria. An increasing trend in pipecolic acid was also observed. The results suggest impairment in the functioning of liver as well as impairment in urea cycle.

Conclusions
The results open up a possibility of non-invasive analysis and diagnosis of P. vivax using urine metabolic profile. Distinct variations in certain metabolites were recorded, and amongst these, ornithine may have the potential of being used as biomarker of malaria. Pipecolic acid also showed increasing trend in the malaria patient compared to the other groups.
Effect of yoghurt containing Bifidobacterium lactis Bb12®on faecal excretion of secretory immunoglobulin A and human beta-defensin 2 in healthy adult volunteers
Authors: Kabeerdoss Jayakanthan , Devi R Shobana , Mary R Regina , Prabhavathi D , Vidya R , Mechenro John , Mahendri NV , Pugazhendhi Srinivasan , Ramakrishna Balakrishnan S 
Published: December 2011

Abstract

Background
Probiotics are used to provide health benefits. The present study tested the effect of a probiotic yoghurt on faecal output of beta-defensin and immunoglobulin A in a group of young healthy women eating a defined diet.

Findings
26 women aged 18-21 (median 19) years residing in a hostel were given 200 ml normal yoghurt every day for a week, followed by probiotic yoghurt containing Bifidobacterium lactis Bb12® (109 in 200 ml) for three weeks, followed again by normal yoghurt for four weeks. Stool samples were collected at 0, 4 and 8 weeks and assayed for immunoglobulin A and human beta-defensin-2 by ELISA. All participants tolerated both normal and probiotic yoghurt well. Human beta-defensin-2 levels in faeces were not altered during the course of the study. On the other hand, compared to the basal sample, faecal IgA increased during probiotic feeding (P = 0.0184) and returned to normal after cessation of probiotic yoghurt intake.

Conclusions

Bifidobacterium lactis Bb12® increased secretory IgA output in faeces. This property may explain the ability of probiotics to prevent gastrointestinal and lower respiratory tract infections.
The peroxisome proliferator-activated receptor delta +294T > C polymorphism and alcohol consumption on serum lipid levels
Authors: Wei Xian-Liang , Yin Rui-Xing , Miao Lin , Wu Dong-Feng 
Published: December 2011

Abstract

Background
The single nucleotide polymorphism (SNP) of peroxisome proliferator-activated receptor delta (PPARD) gene affects serum lipid profiles, but to what extent alcohol consumption interferes with this association remains unknown. The present study was undertaken to compare the association of PPARD +294T > C (rs2016520) polymorphism and serum lipid levels in the nondrinkers and drinkers.

Methods
A total of 685 unrelated nondrinkers and 497 drinkers aged 15-82 were randomly selected from our previous stratified randomized cluster samples. Genotyping of the PPARD +294T > C was performed by polymerase chain reaction and restriction fragment length polymorphism. Interactions of the PPARD +294T > C genotypes and alcohol consumption on serum lipid levels were detected by using a factorial regression analysis after controlling for potential confounders.

Results
The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), apolipoprotein (Apo) A1, and the ratio of ApoA1 to ApoB were higher in drinkers than in nondrinkers (P < 0.05-0.001). There were no significant differences in the levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and ApoB between the two groups (P > 0.05 for all). The frequencies of TT, TC and CC genotypes were 56.0%, 36.4% and 7.6% in nondrinkers, and 57.2%, 38.0% and 4.8% in drinkers (P > 0.05); respectively. The frequencies of T and C alleles were 74.2% and 25.8% in nondrinkers, and 76.2% and 23.8% in drinkers (P > 0.05); respectively. There was also no significant difference in the genotypic and allelic frequencies between males and females in both groups (P > 0.05 for all). The levels of TC in nondrinkers were different among the three genotypes (P = 0.01), the C allele carriers had higher serum TC levels than the C allele noncarriers. The levels of all seven lipid traits in drinkers were not different among the three genotypes (P > 0.05 for all). The interactions of PPARD +294T > C genotypes and alcohol consumption on serum lipid levels were not detected in the drinkers (P > 0.05 for all). Multiple linear regression analysis showed that serum TC, HDL-C, LDL-C, ApoA1, and ApoB levels were correlated with genotypes in drinkers but not in nondrinkers (P < 0.05-0.01).

Conclusions
These results suggest that the great majority of our study populations are beneficial from alcohol consumption. But there is no interaction between the PPARD +294T > C genotypes and alcohol consumption on serum lipid levels in the drinkers.
Polytomy identification in microbial phylogenetic reconstruction
Authors: Lin Guan Ning , Zhang Chao , Xu Dong 
Published: December 2011

Abstract

Background
A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating branches) may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties.

Results
PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression) classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate), 'IntraR' (Intra-subset branch rate) and 'InterR' (Inter-subset branch rate), all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall) of 81% with about 0.9 area under the curve (AUC) of ROC.

Conclusions
PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.
Mass segmentation using a combined method for cancer detection
Authors: Liu Jun , Chen Jianxun , Liu Xiaoming , Chun Lei , Tang Jinshan , Deng Youping 
Published: December 2011

Abstract

Background
Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breast cancer, computer aided technology has been introduced. In computer aided cancer detection, the detection and segmentation of mass are very important. The shape of mass can be used as one of the factors to determine whether the mass is malignant or benign. However, many of the current methods are semi-automatic. In this paper, we investigate fully automatic segmentation method.

Results
In this paper, a new mass segmentation algorithm is proposed. In the proposed algorithm, a fully automatic marker-controlled watershed transform is proposed to segment the mass region roughly, and then a level set is used to refine the segmentation. For over-segmentation caused by watershed, we also investigated different noise reduction technologies. Images from DDSM were used in the experiments and the results show that the new algorithm can improve the accuracy of mass segmentation.

Conclusions
The new algorithm combines the advantages of both methods. The combination of the watershed based segmentation and level set method can improve the efficiency of the segmentation. Besides, the introduction of noise reduction technologies can reduce over-segmentation.
High fat diet enhances cardiac abnormalities in SHR rats: Protective role of heme oxygenase-adiponectin axis
Authors: Cao Jian , Sodhi Komal , Puri Nitin , Monu Sumit R , Rezzani Rita , Abraham Nader G 
Published: December 2011

Abstract

Background
High dietary fat intake is a major risk factor for development of cardiovascular and metabolic dysfunction including obesity, cardiomyopathy and hypertension.

Methods
The present study was designed to examine effect of high fat (HF) diet on cardio-vascular structure and function in spontaneously hypertensive rats (SHR), fed HF diet for 15 weeks, a phenotype designed to mimic metabolic syndrome.

Results
Development of metabolic syndrome like phenotype was confirmed using parameters, including body weight, total cholesterol and blood pressure levels. High fat diet impaired vascular relaxation by acetylcholine and exacerbated cardiac dysfunction in SHRs as evidenced by lower left ventricular function, and higher coronary resistance (CR) as compared to controls (p < 0.05). The histological examination revealed significant myocardial and peri-vascular fibrosis in hearts from SHRs on HF diet. This cardiac dysfunction was associated with increased levels of inflammatory cytokines, COX-2, NOX-2, TxB2 expression and increase in superoxide (O2
-) levels in SHR fed a HF diet (p < 0.05). HO-1 induction via cobalt-protoporphyrin (CoPP,3 mg/kg), in HF fed rats, not only improved cardiac performance parameters, but also prevented myocardial and perivascular fibrosis. These effects of CoPP were accompanied by enhanced levels of cardiac adiponectin levels, pAMPK, peNOS and iNOS expression; otherwise significantly attenuated (p < 0.05) in HF fed SHRs. Prevention of such beneficial effects of CoPP by the concurrent administration of the HO inhibitor stannic mesoporphyrin (SnMP) corroborates the role of HO system in mediating such effects.

Conclusion
In conclusion, this novel study demonstrates that up-regulation of HO-1 improves cardiac and vascular dysfunction by blunting oxidative stress, COX-2 levels and increasing adiponectin levels in hypertensive rats on HF diet.