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1.  Practical implementation of an existing smoking detection pipeline and reduced support vector machine training corpus requirements 
This study aimed to reduce reliance on large training datasets in support vector machine (SVM)-based clinical text analysis by categorizing keyword features. An enhanced Mayo smoking status detection pipeline was deployed. We used a corpus of 709 annotated patient narratives. The pipeline was optimized for local data entry practice and lexicon. SVM classifier retraining used a grouped keyword approach for better efficiency. Accuracy, precision, and F-measure of the unaltered and optimized pipelines were evaluated using k-fold cross-validation. Initial accuracy of the clinical Text Analysis and Knowledge Extraction System (cTAKES) package was 0.69. Localization and keyword grouping improved system accuracy to 0.9 and 0.92, respectively. F-measures for current and past smoker classes improved from 0.43 to 0.81 and 0.71 to 0.91, respectively. Non-smoker and unknown-class F-measures were 0.96 and 0.98, respectively. Keyword grouping had no negative effect on performance, and decreased training time. Grouping keywords is a practical method to reduce training corpus size.
PMCID: PMC3912731  PMID: 23921192
Classification/methods; Medical Records Systems, Computerized; Natural Language Processing; Smoking
2.  Muscle Spindle Traffic in Functionally Unstable Ankles During Ligamentous Stress 
Journal of Athletic Training  2013;48(2):192-202.
Ankle sprains are common in athletes, with functional ankle instability (FAI) developing in approximately half of cases. The relationship between laxity and FAI has been inconclusive, suggesting that instability may be caused by insufficient sensorimotor function and dynamic restraint. Research has suggested that deafferentation of peripheral mechanoreceptors potentially causes FAI; however, direct evidence confirming peripheral sensory deficits has been elusive because previous investigators relied upon subjective proprioceptive tests.
To develop a method for simultaneously recording peripheral sensory traffic, joint forces, and laxity and to quantify differences between healthy ankles and those with reported instability.
Case-control study.
University laboratory.
Patients or Other Participants:
A total of 29 participants (age = 20.9 ± 2.2 years, height = 173.1 ± 8.9 cm, mass = 74.5 ± 12.7 kg) stratified as having healthy (HA, n = 19) or unstable ankles (UA, n = 10).
Sensory traffic from muscle spindle afferents in the peroneal nerve was recorded with microneurography while anterior (AP) and inversion (IE) stress was applied to ligamentous structures using an ankle arthrometer under test and sham conditions.
Main Outcome Measure(s):
Laxity (millimeters or degrees) and amplitude of sensory traffic (percentage) were determined at 0, 30, 60, 90, and 125 N of AP force and at 0, 1, 2, 3, and 4 Nm of IE torque. Two-factor repeated-measures analyses of variance were used to determine differences between groups and conditions.
No differences in laxity were observed between groups (P > .05). Afferent traffic increased with increased force and torque in test trials (P < .001). The UA group displayed decreased afferent activity at 30 N of AP force compared with the HA group (HA: 30.2% ± 9.9%, UA: 17.1% ± 16.1%, P < .05).
The amplitude of sensory traffic increased simultaneously with greater ankle motion and loading, providing evidence of the integrated role of capsuloligamentous and musculotendinous mechanoreceptors in maintaining joint sensation. Unstable ankles demonstrated diminished afferent traffic at low levels of force, suggesting the early detection of joint loading may be compromised.
PMCID: PMC3600921  PMID: 23672383
functional ankle instability; microneurography; ankle arthrometry
3.  Three years in vivo wear: core-ceramic, veneers, and enamel antagonists 
Test the hypotheses that there are equivalent wear rates for enamel-versus-enamel and ceramic-versus-enamel, analyzing the in vivo wear of crown ceramics, their natural enamel antagonists, and the corresponding two contralateral teeth; and, that bite force does not correlate with the wear.
A controlled, clinical trial was conducted involving patients needing full coverage crowns opposing enamel antagonists. Bite forces were measured using a bilateral gnathodynamometer. Single-unit restorations of metal/ceramic (Argedent 62, Argen Corp/IPS d.SIGN veneer); or, core-ceramic/veneer from either, Empress2/Eris, or e.maxPress core/e.maxCeram glaze (ceramics: Ivoclar Vivadent, USA) were randomly assigned, fabricated and cemented. Impressions were made of the ceramic crowns, as well as each maxillary and mandibular quadrant at one week (baseline) and one, two and three years. Resulting models were scanned (3D laser scanner). Maximum wear was calculated by superimposing baseline with annual images.
There were a total of thirty-six crowns required for thirty-one patients. Each restoration had three associated enamel teeth; 1) crown, 2) antagonist, 3) contralateral, and 4) contralateral-antagonist. SAS PROC MIXED (α=0.05) indicated no statistical significance for mean maximum wear among crown ceramics, enamel antagonists and contralaterals. However, enamel wear was statistically significant in relation to intraoral location (p=0.04) and among years (p<0.02). Analyzed alone, the enamel contralateral-antagonist exhibited significantly greater wear (p<0.001). Considering all wear sites, there was no correlation with bite force (p=0.15).
The ceramics and their antagonists exhibited in vivo wear rates within the range of normal enamel. Future studies should examine the wear implications of the contralateral-antagonist enamel.
PMCID: PMC3570123  PMID: 22410113
ceramic wear; enamel wear; core ceramic; clinical; in vivo; antagonists
4.  Randomized, Controlled Clinical Trial of Bilayer Ceramic and Metal-Ceramic Crown Performance 
Analyzing the clinical performance of restorative materials is important, as there is an expectation that these materials and procedures will restore teeth and do no harm. The objective of this research study was to characterize the clinical performance of metal-ceramic crowns, core ceramic crowns, and core ceramic/veneer ceramic crowns based on 11 clinical criteria.
Materials and Methods
An IRB-approved, randomized, controlled clinical trial was conducted as a single-blind pilot study. The following three types of full crowns were fabricated: (1) metal-ceramic crown (MC) made from a Pd-Au-Ag-Sn-In alloy (Argedent 62) and a glass-ceramic veneer (IPS d.SIGN veneer); (2) non-veneered (glazed) lithium disilicate glass-ceramic crown (LDC) (IPS e.max Press core and e.max Ceram Glaze); and (3) veneered lithia disilicate glass-ceramic crown (LDC/V) with glass-ceramic veneer (IPS Empress 2 core and IPS Eris). Single-unit crowns were randomly assigned. Patients were recalled for each of 3 years and were evaluated by two calibrated clinicians. Thirty-six crowns were placed in 31 patients. A total of 12 crowns of each of the three crown types were studied. Eleven criteria were evaluated: tissue health, marginal integrity, secondary caries, proximal contact, anatomic contour, occlusion, surface texture, cracks/chips (fractures), color match, tooth sensitivity, and wear (of crowns and opposing enamel). Numerical rankings ranged from 1 to 4, with 4 being excellent, and 1 indicating a need for immediate replacement. Statistical analysis of the numerical rankings was performed using a Fisher’s exact test.
There was no statistically significant difference between performance of the core ceramic crowns and the two veneered crowns at year 1 and year 2 (p > 0.05). All crowns were rated either as excellent or good for each of the clinical criteria; however, between years 2 and 3, gradual roughening of the occlusal surface occurred in some of the ceramic-ceramic crowns, possibly caused by dissolution and wear of the glaze. Statistically significant differences in surface texture (p = 0.0013) and crown wear (p = 0.0078) were found at year 3 between the metal-ceramic crowns and the lithium-disilicate-based crowns.
Based on the 11 criteria, the clinical performance of ceramic-ceramic crowns was comparable to that of the metal-ceramic crowns after 2 years; however, gradual roughening occurred between years 2 and 3, which resulted in differences in surface texture and wear.
PMCID: PMC3625457  PMID: 22978697
Bilayer ceramics; clinical research; clinical performance; metal-ceramic; prosthodontics
5.  A TLR 9 cytoplasmic tyrosine motif is selectively required for proinflammatory cytokine production1 
Compartmentalization of nucleic acid sensing TLR9 has been implicated as a mechanism to prevent recognition of self nucleic acid structures. Furthermore, recognition of CpG DNA in different endosomal compartments leads to the production of the proinflammatory cytokine TNF-α, or type I IFN. We previously characterized a tyrosine-based motif at amino acid 888–891 in the cytoplasmic tail of TLR9 important for appropriate intracellular localization. Here we show that this motif is selectively required for the production of TNF, but not IFN. In response to CpG DNA stimulation, the proteolytically processed 80 kDa fragment is tyrosine phosphorylated. Although tyrosine 888 is not itself phosphorylated, the structure of this motif is necessary for both TLR9 phosphorylation and TNF-α production in response to CpG DNA. We conclude that bifurcation in TLR9 signaling is regulated by a critical tyrosine motif in the cytoplasmic tail.
PMCID: PMC3253180  PMID: 22174451
6.  Multifunctional role of dextran sulfate sodium for in vivo modeling of intestinal diseases 
BMC Immunology  2012;13:41.
Inflammatory bowel diseases (IBDs) are chronic, relapsing disorders that affect the gastrointestinal tract of millions of people and continue to increase in incidence each year. While several factors have been associated with development of IBDs, the exact etiology is unknown. Research using animal models of IBDs is beginning to provide insights into how the different factors contribute to disease development. Oral administration of dextran sulfate sodium (DSS) to mice induces a reproducible experimental colitis that models several intestinal lesions associated with IBDs. The murine DSS colitis model can also be adapted to quantify intestinal repair following injury. Understanding the mechanistic basis behind intestinal repair is critical to development of new therapeutics for IBDs because of their chronic relapsing nature.
The murine DSS colitis model was adapted to provide a system enabling the quantification of severe intestinal injury with impaired wound healing or mild intestinal injury with rapid restoration of mucosal integrity, by altering DSS concentrations and including a recovery phase. We showed that through a novel format for presentation of the clinical disease data, the temporal progression of intestinal lesions can be quantified on an individual mouse basis. Additionally, parameters for quantification of DSS-induced alterations in epithelial cell populations are included to provide insights into mechanisms underlying the development of these lesions. For example, the use of the two different model systems showed that toll-like receptor 9, a nucleic acid-sensing pattern recognition receptor, is important for protection only following mild intestinal damage and suggests that this model is superior for identifying proteins necessary for intestinal repair.
We showed that using a murine DSS-induced experimental colitis model system, and presenting data in a longitudinal manner on a per mouse basis, enhanced the usefulness of this model, and provided novel insights into the role of an innate immune receptor in intestinal repair. By elucidating the mechanistic basis of intestinal injury and repair, we can begin to understand the etiology of IBDs, enabling development of novel therapeutics or prophylactics.
PMCID: PMC3488029  PMID: 22853702
Dextran sulfate sodium; Inflammatory bowel disease; Intestinal repair; Toll-like receptor 9
7.  Commensal Bacteria Modulate Innate Immune Responses of Vaginal Epithelial Cell Multilayer Cultures 
PLoS ONE  2012;7(3):e32728.
The human vaginal microbiome plays a critical but poorly defined role in reproductive health. Vaginal microbiome alterations are associated with increased susceptibility to sexually-transmitted infections (STI) possibly due to related changes in innate defense responses from epithelial cells. Study of the impact of commensal bacteria on the vaginal mucosal surface has been hindered by current vaginal epithelial cell (VEC) culture systems that lack an appropriate interface between the apical surface of stratified squamous epithelium and the air-filled vaginal lumen. Therefore we developed a reproducible multilayer VEC culture system with an apical (luminal) air-interface that supported colonization with selected commensal bacteria. Multilayer VEC developed tight-junctions and other hallmarks of the vaginal mucosa including predictable proinflammatory cytokine secretion following TLR stimulation. Colonization of multilayers by common vaginal commensals including Lactobacillus crispatus, L. jensenii, and L. rhamnosus led to intimate associations with the VEC exclusively on the apical surface. Vaginal commensals did not trigger cytokine secretion but Staphylococcus epidermidis, a skin commensal, was inflammatory. Lactobacilli reduced cytokine secretion in an isolate-specific fashion following TLR stimulation. This tempering of inflammation offers a potential explanation for increased susceptibility to STI in the absence of common commensals and has implications for testing of potential STI preventatives.
PMCID: PMC3296736  PMID: 22412914
8.  Comparison of methods for kinematic identification of footstrike and toe-off during overground and treadmill running 
When analysing gait, the identification of the period of stance is often needed. Forceplates are typically used, but in their absence kinematic data can be employed. Five kinematic methods have been previously described in the literature. However, these methods have not been compared to each other for overground or treadmill running. Therefore, the purpose of this study was to compare these five kinematic methods of identifying the stance phase with vertical ground reaction force data both during overground and treadmill running. We recruited forty recreational runners (20 males) for this study. Twenty runners underwent an instrumented gait analysis during overground running, and twenty were tested during instrumented treadmill running. All runners ran at 3.35 m·s−1. Each kinematic method was compared with stance identified from the vertical ground reaction force (gold standard) for overground running. This method was then repeated for treadmill running. Two methods were found to be valid and reliable for determining footstrike. These were the time when the distal heel marker reached a minimum vertical position, and when the vertical velocity of this same marker changed from negative to positive. These methods had absolute errors that ranged from 22.4 ms to 24.6 ms for both modes of running. Toe-off was best identified using peak knee extension, with absolute errors of 4.9 ms for overground running and 5.2 ms for treadmill running. Utilising automated kinematic methods of determining stance will aid researchers studying running when forceplates are unavailable.
PMCID: PMC3266867  PMID: 20478742
9.  Heterogeneous Interleukin-15 Inducibilities in Murine B16 Melanoma and RM-1 Prostate Carcinoma by Interferon-α Treatment 
Long-term treatment of mouse cancer cells with interferon-α (IFN-α) converts parental B16 melanoma cells to B16α vaccine cells. Inoculation of syngeneic mice with UV-irradiated B16α vaccine cells triggers immunity to the parental B16 tumor that is mediated by host macrophages, T cells, and NK cells. Lymph node cells from mice inoculated with irradiated B16α vaccine cells, but not with irradiated parental cells, proliferate when cultured in vitro, suggesting long-term in vivo activation of lymphoid cells. Both IL-15 mRNA and IL-15 protein are highly induced in B16α vaccine cells. The bulk of the induced IL-15 is shown to be cell-associated, either cytoplasmic or membranous. The current study investigated the feasibility of applying the B16α vaccination protocol to generate a cancer vaccine against murine RM-1 prostate carcinoma. In comparison to B16α vaccine cells, long-term IFN-α–treated RM-1 cells (RM-1α vaccine cells) showed significant IL-15 mRNA induction but relatively low IL-15 protein up-regulation. When UV-irradiated, a 3-fold increase in intracellular IL-15 was observed in RM-1α vaccine cells, suggesting UV damage may have negated a possible control mechanism for IL-15 synthesis. Efficacy of in vivo vaccination of syngeneic mice with UV-irradiated RM-1α and B16α vaccine cells showed correlation between high IL-15 level and high vaccine efficacy in B16α cells compared to low IL-15 level and low vaccine efficacy in RM-1α cells. This supports the concept that the induction of IL-15 in tumor cells can be useful for creating whole-cell cancer vaccines.
PMCID: PMC3096523  PMID: 19642895
10.  Discovery of anticancer agents of diverse natural origin* 
A collaborative multidisciplinary research project is described in which new natural product anticancer drug leads are obtained from a diverse group of organisms, constituted by tropical plants, aquatic cyanobacteria, and filamentous fungi. Information is provided on how these organisms are collected and processed. The types of bioassays are indicated in which crude extracts of these acquisitions are tested. Progress made in the isolation of lead bioactive secondary metabolites from three tropical plants is discussed.
PMCID: PMC2765058  PMID: 20046887
natural products; plants; cyanobacteria; fungi; anticancer activity
11.  FSL-1, a bacterial-derived toll-like receptor 2/6 agonist, enhances resistance to experimental HSV-2 infection 
Virology Journal  2009;6:195.
Herpes simplex virus type 2 (HSV-2) is a leading cause of genital ulceration that can predispose individuals to an increased risk of acquiring other sexually transmitted infections. There are no approved HSV-2 vaccines and current suppressive therapies require daily compound administration that does not prevent all recurrences. A promising experimental strategy is the use of toll-like receptor (TLR) agonists to induce an innate immune response that provides resistance to HSV-2 infection. Previous studies showed that anti-herpetic activity varied based on origin of the agonists and activation of different TLR indicating that activity likely occurs through elaboration of a specific innate immune response. To test the hypothesis, we evaluated the ability of a bacterial-derived TLR2/6 agonist (FSL-1) to increase resistance to experimental genital HSV-2 infection.
Vaginal application of FSL-1 at selected doses and times was evaluated to identify potential increased resistance to genital HSV-2 infection in the mouse model. The FSL-1 induced cytokine profile was quantified using kinetically collected vaginal lavages. Additionally, cytokine elaboration and organ weights were evaluated after single or multiple FSL-1 doses to establish a preliminary safety profile. Human vaginal EC cultures were used to confirm the mouse model outcomes.
The results showed that vaginally-applied FSL-1 created an environment resistant to a 25-fold higher HSV-2 challenge dose. Mechanistically, vaginal FSL-1 application led to transient elaboration of cytokines linked to anti-herpetic innate immune responses. No gross local or peripheral immunotoxicity was observed even after multiple dosing. FSL-1 also created an anti-herpetic environment in cultures of human vaginal epithelial cells (EC).
The results showed, for the first time, that the bacterial-derived TLR2/6 agonist FSL-1 induced significant resistance to HSV-2 infection when applied in mice or human vaginal EC cultures. Cytokine evaluation illustrated that anti-herpetic activity correlated with induction of a specific profile. The identified anti-herpetic profile provides an invaluable resource for the future design of novel compounds to reduce genital HSV-2 transmission and improves understanding of the complex innate immune response to potential pathogens elicited by the vaginal mucosa.
PMCID: PMC2780411  PMID: 19903337
12.  Alvaradoins E-N, Antitumor and Cytotoxic Anthracenone C-glycosides from the Leaves of Alvaradoa haitiensis 
Journal of natural products  2007;70(6):954-961.
Bioactivity-directed fractionation of an extract of the leaves of Alvaradoa haitiensis, using the KB (human oral epidermoid carcinoma) cell line, led to the isolation and identification of 10 new anthracenone C-glycosides, alvaradoins E-N (1–10), along with the known compound, chrysophanol (11). The cytotoxicity of all compounds was evaluated, and preliminary structure-activity relationships are suggested. The most potent compounds in the in vitro assays (1 and 2) were evaluated in vivo vs. the P388 (murine lymphocytic leukemia) model, and alvaradoin E (1) showed antileukemic activity (125% T/C) at a dose of 0.2 mg kg−1 per injection when administered intraperitoneally.
PMCID: PMC2442713  PMID: 17552563
13.  The Amino Acids in Nutrition * 
PMCID: PMC2606433  PMID: 21433533
18.  A Case of Double Hare-Lip in a Man Aged 32 
British Medical Journal  1883;1(1153):202-203.
PMCID: PMC2372083  PMID: 20750489

Results 1-19 (19)