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1.  CTGF is a central mediator of tissue remodeling and fibrosis and its inhibition can reverse the process of fibrosis 
Fibrogenesis & Tissue Repair  2012;5(Suppl 1):S24.
CTGF is a secreted matricellular protein with very complex biology. It has been shown to modulate many signaling pathways leading to cell adhesion and migration, angiogenesis, myofibroblast activation, and extracellular matrix deposition and remodeling, which together lead to tissue remodeling and fibrosis. It has been reported in the literature that inhibition of CTGF expression by siRNA prevents CCl4-induced liver fibrosis and can reverse fibrosis when administered after significant collagen deposition is observed. A monoclonal antibody to CTGF that is currently in clinical development (FG-3019) has demonstrated the ability to reverse vascular stiffening and improve cardiac function in a rat model of diabetic complications. FG-3019 has also exhibited activity in a murine radiation-induced pulmonary fibrosis model. When FG-3019 was administered to mice after a significant radiation-induced increase in lung density could be observed by CT imaging, the density of the lungs was observed to decrease over the period during which the antibody was administered and to remain stable after therapy had ceased. When considered together, these data indicate that inhibition of CTGF can prevent and reverse the process of fibrosis.
PMCID: PMC3368796  PMID: 23259531
2.  Ensemble learning algorithms for classification of mtDNA into haplogroups 
Briefings in Bioinformatics  2010;12(1):1-9.
Classification of mitochondrial DNA (mtDNA) into their respective haplogroups allows the addressing of various anthropologic and forensic issues. Unique to mtDNA is its abundance and non-recombining uni-parental mode of inheritance; consequently, mutations are the only changes observed in the genetic material. These individual mutations are classified into their cladistic haplogroups allowing the tracing of different genetic branch points in human (and other organisms) evolution. Due to the large number of samples, it becomes necessary to automate the classification process. Using 5-fold cross-validation, we investigated two classification techniques on the consented database of 21 141 samples published by the Genographic project. The support vector machines (SVM) algorithm achieved a macro-accuracy of 88.06% and micro-accuracy of 96.59%, while the random forest (RF) algorithm achieved a macro-accuracy of 87.35% and micro-accuracy of 96.19%. In addition to being faster and more memory-economic in making predictions, SVM and RF are better than or comparable to the nearest-neighbor method employed by the Genographic project in terms of prediction accuracy.
PMCID: PMC3030810  PMID: 20203074
mitochondrial DNA; ensemble learning; classification algorithms; support vector machines; random forest; genographic project
3.  Size Dependent Elemental Composition of Road-Associated Particles 
The Science of the total environment  2008;398(1-3):145-153.
Stormwater particles often provide transport for metals and other contaminants, however only larger particles are effectively removed by typical best management practices. Fine particles and their associated constituents are more likely to reach receiving waters; this merits further investigation regarding the metal contribution of fine (dp<10 μm) and very fine (dp <1.5 μm) particles. Road associated particles were collected by vacuuming a road surface and by collecting highway stormwater runoff. A cell sorter was employed to sort road associated particles into four size ranges: 0.1–0.3, 0.3–0.5, 0.5–1.0, and 1.0–1.5 μm. These very fine particles, along with six particle size ranges (total range <2–63 μm) separated using a settling column, were analyzed for Al, Mn, Fe, Cr, Ni, Cu, Zn, and Pb using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Enrichment factors (EFs), calculated using Al as a basis to represent crustal contributions, were similar for the vacuumed road dust and the stormwater runoff. Fe and Mn were minimally depleted (0.1x) or near unity for all size ranges (Fe EF range 0.01–3.7; Mn EF range 0.02–10.6). Cr, Ni, Cu, Zn, and Pb were moderately (10x) to considerably (>100x) enriched for most size ranges; these metals were most enriched in the very fine fractions (max EF~4900 in Zn, 0.1–0.3 μm). Based on this preliminary study, a cell sorter is an acceptable means of fractionating aqueous particles of diameter 0.1–1.5 μm. In spite of their minimal relative mass contribution, the very fine particles are environmentally relevant due to their mobility and enrichment in potentially toxic metals..
PMCID: PMC2702324  PMID: 18433840
stormwater; particles; metals; enrichment factor
4.  Assessment of the Validity of the Sections in Musa (Musaceae) using AFLP 
Annals of Botany  2002;90(2):231-238.
Musa L. (Musaceae) is currently separated into five sections (Musa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on chromosome numbers and morphological characters. However, the validation of this classification system is questioned due to the common occurrence of hybridizations across sections and the system not accommodating anomalous species. This study employed amplified fragment length polymorphism (AFLP) in a phenetic examination of the relationships among four sections (material of sect. Ingentimusa was not available) to evaluate whether their genetic differences justify distinction into separate groups. Using eight primer combinations, a total of 276 bands was scored, of which 275 were polymorphic. Among the monomorphic bands, 11 unique markers were identified that revealed the distinct separation of the 11‐chromosome species from the 10‐chromosome species. AFLP results suggest that species of sect. Rhodochlamys should be combined into a single section with species of sect. Musa, and likewise for species of sect. Australimusa to be merged with those of sect. Callimusa.
PMCID: PMC4240415  PMID: 12197520
Banana; Musa; Musaceae; section; Rhodochlamys; Callimusa; Australimusa; AFLP; DNA fingerprinting
5.  Performance Evaluation of the VERSANT HCV RNA Qualitative Assay by Using Transcription-Mediated Amplification 
Journal of Clinical Microbiology  2003;41(1):310-317.
A preclinical evaluation of a qualitative assay for the detection of hepatitis C virus (HCV) RNA by transcription-mediated amplification (TMA) was conducted according to the guidelines of the National Committee for Clinical Laboratory Standards and the U.S. Food and Drug Administration. Our results showed that this assay, HCV TMA, detected 95% of samples with HCV RNA concentrations of 5.3 IU/ml and 29 copies/ml. HCV TMA showed an overall specificity of 99.6% and was highly reproducible, detecting 99.3% of samples with HCV RNA concentrations of 50 copies/ml across seven different lots of reagents. Experiments with clinical samples showed that HCV TMA detected all HCV genotypes with similar efficiencies, detecting ≥95% of samples at 50 HCV RNA copies/ml from patients infected with HCV genotypes 1a, 2b, 3a, 4a, 5a, and 6a. In experiments with RNA transcripts, HCV TMA detected ≥96.6% of transcripts derived from HCV genotypes 1a, 1b, 2a, 2c, 3a, 4a, 5a, and 6a at 50 HCV RNA copies/ml. Detection of transcripts derived from HCV genotype 2b was slightly lower (88.4%) at 50 copies/ml but was 97.0% at 75 copies/ml. In addition, HCV TMA exhibited robust performance in detecting HCV RNA in samples subjected to various conditions commonly encountered in a clinical laboratory, including long-term storage, multiple freeze-thaw cycles, different collection tubes, and the presence of endogenous substances, commonly prescribed drugs, or other microorganisms and viruses. With its high sensitivity, specificity, reproducibility, and equivalent genotype reactivity, HCV TMA may provide an attractive alternative for routine qualitative HCV RNA testing in clinical laboratories.
PMCID: PMC149605  PMID: 12517866
6.  ICAP-1, a Novel β1 Integrin Cytoplasmic Domain–associated Protein, Binds to a Conserved and Functionally Important NPXY Sequence Motif of β1 Integrin  
The Journal of Cell Biology  1997;138(5):1149-1157.
The cytoplasmic domains of integrins are essential for cell adhesion. We report identification of a novel protein, ICAP-1 (integrin cytoplasmic domain– associated protein-1), which binds to the β1 integrin cytoplasmic domain. The interaction between ICAP-1 and β1 integrins is highly specific, as demonstrated by the lack of interaction between ICAP-1 and the cytoplasmic domains of other β integrins, and requires a conserved and functionally important NPXY sequence motif found in the COOH-terminal region of the β1 integrin cytoplasmic domain. Mutational studies reveal that Asn and Tyr of the NPXY motif and a Val residue located NH2-terminal to this motif are critical for the ICAP-1 binding. Two isoforms of ICAP-1, a 200–amino acid protein (ICAP-1α) and a shorter 150–amino acid protein (ICAP-1β), derived from alternatively spliced mRNA, are expressed in most cells. ICAP-1α is a phosphoprotein and the extent of its phosphorylation is regulated by the cell–matrix interaction. First, an enhancement of ICAP-1α phosphorylation is observed when cells were plated on fibronectin-coated but not on nonspecific poly-l-lysine–coated surface. Second, the expression of a constitutively activated RhoA protein that disrupts the cell–matrix interaction results in dephosphorylation of ICAP-1α. The regulation of ICAP-1α phosphorylation by the cell–matrix interaction suggests an important role of ICAP-1 during integrin-dependent cell adhesion.
PMCID: PMC2136751  PMID: 9281591

Results 1-6 (6)