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1.  International Classification of Diseases Codes and their Use in Dentistry 
The deadline for replacing International Classification of Diseases, 9th edition (ICD-9) code sets with the newer ICD-10 code sets, used for the reporting of medical diagnoses and inpatient hospital procedures, was recently updated to occur at a date no sooner than October 1, 2015; with October 1, 2015 being the likely implementation date. The transition to ICD-10 is mandatory for all entities covered by the Health Insurance Portability Accountability Act (HIPAA). This review will provide a brief history of the development of ICD codes; provide an overview of ICD-9/ICD-9-Clinical Modification (CM) and ICD-10/ ICD-10-CM/Procedural Coding System (PCS) codes; provide information on the conversion of ICD-9-CM to ICD-10-CM/PCS codes; and provide information on the uses of ICD codes in dentistry in the United States.
PMCID: PMC4394630  PMID: 25879045
International Classification of Diseases; ICD 10; ICD 9; Dentistry
2.  A statistical physics perspective on alignment-independent protein sequence comparison 
Bioinformatics  2015;31(15):2469-2474.
Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly.
Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from ‘first passage probability distribution’ to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach.
PMCID: PMC4514925  PMID: 25810434
3.  Smoking as a Risk Factor for Oral Candidiasis in HIV-infected Adults 
We aimed to examine if smoking is an independent predictor of oral candidiasis (OC) among HIV-1 infected persons.
The cross-sectional part of this study evaluated 631 adult dentate HIV-1 seropositive persons examined for OC from 1995 – 2000 at the University of North Carolina Hospitals in Chapel Hill, NC. In the second part, from the above sample, 283 individuals who were free of HIV-associated oral diseases at baseline were followed up for two years to assess incident OC events. Data collected from medical record review, interview questionnaires and clinical examinations were analyzed using chi-square tests and t-tests. Logistic regression models were developed for prevalent OC employing the likelihood ratio test, whereas Poisson regression models were developed for assessing cumulative incidence of OC. These models included a variety of independent variables to adjust for confounding.
Thirteen percent of participants had OC only; 4.6% had OC with Oral Hairy Leukoplakia; and 69.7% had neither. Smoking was associated with OC in all models [prevalent OC - current smokers: logistic regression – Odd Ratio (95% CI) = 2.5 (1.3, 4.8); Incident OC - current smokers: Poisson regression (main effects model) - Incidence Rate Ratio (95% CI) = 1.9 (1.1, 3.8)]. Other Poisson regression models suggested evidence for effect modification between CD4 cell count and incident OC by smoking.
Smoking is an independent risk factor for development of OC in HIV-1 infected persons and the risk of OC is modified by CD4 cell count which measures strength of the immune system.
PMCID: PMC3593773  PMID: 23206208
smoking; HIV; Candida; interaction; regression models
4.  Need for an Ethical Framework for Testing for Systemic Diseases in Dental Clinics 
Testing for systemic diseases in dental clinics is a potentially attractive avenue for oral health professionals and may be viewed as an opportunity to increase professional reach, expand practice, and improve financial returns. However, several ethical questions arise that must be addressed before such activities are adopted. (1) What should be the level of training dentists must acquire to deal with challenges associated with testing? (2) How well are dental practices aware of and compliant with the Health Insurance Portability and Accountability Act and procedures related to informed consent? (3) What is the evidence regarding acceptability and effectiveness of testing? (4) What should be the acceptable standard of practice for conduct of invasive and noninvasive tests? (5) What is the boundary delineating “testing” and “reporting” vis-à-vis counseling? (6) What is the value of testing without counseling? (7) What assurances need to be in place to ensure voluntariness of testing? (8) How would data from testing be used in “research,” especially with the growth of practice based research networks? and (9) Does the American Dental Association Code of Ethics need to incorporate guidance for practicing dentists? We discuss how ethical principles can be used to develop a framework of guidelines for potential testing for systemic diseases in dental clinics..
PMCID: PMC3940436  PMID: 24600534
dental clinic; testing; systemic disease; ethics
5.  Crystal Structure of a Bioactive Pactamycin Analog Bound to the 30S Ribosomal Subunit☆ 
Journal of Molecular Biology  2013;425(20):3907-3910.
Biosynthetically and chemically derived analogs of the antibiotic pactamycin and de-6-methylsalicylyl (MSA)-pactamycin have attracted recent interest as potential antiprotozoal and antitumor drugs. Here, we report a 3.1-Å crystal structure of de-6-MSA-pactamycin bound to its target site on the Thermus thermophilus 30S ribosomal subunit. Although de-6-MSA-pactamycin lacks the MSA moiety, it shares the same binding site as pactamycin and induces a displacement of nucleic acid template bound at the E-site of the 30S. The structure highlights unique interactions between this pactamycin analog and the ribosome, which paves the way for therapeutic development of related compounds.
Graphical abstract
•The potential antitumor drug de-6-MSA-pactamycin retains equivalent biological activity to pactamycin.•We present a 3.1-Å crystal structure of the 30S ribosomal subunit bound to de-6-MSA-pactamycin that describes the interactions between pactamycin analogs and the ribosome.•The structure reveals de-6-MSA-pactamycin functions by disrupting base pairing at the E-site, which can be exploited for therapeutic purposes.
PMCID: PMC3794158  PMID: 23702293
MSA, methylsalicylyl; translation; antibiotic; E-site; mRNA
6.  Seasonal variations of EPG Levels in gastro-intestinal parasitic infection in a southeast asian controlled locale: a statistical analysis 
SpringerPlus  2013;2:205.
We present a data based statistical study on the effects of seasonal variations in the growth rates of the gastro-intestinal (GI) parasitic infection in livestock. The alluded growth rate is estimated through the variation in the number of eggs per gram (EPG) of faeces in animals. In accordance with earlier studies, our analysis too shows that rainfall is the dominant variable in determining EPG infection rates compared to other macro-parameters like temperature and humidity. Our statistical analysis clearly indicates an oscillatory dependence of EPG levels on rainfall fluctuations. Monsoon recorded the highest infection with a comparative increase of at least 2.5 times compared to the next most infected period (summer). A least square fit of the EPG versus rainfall data indicates an approach towards a super diffusive (i. e. root mean square displacement growing faster than the square root of the elapsed time as obtained for simple diffusion) infection growth pattern regime for low rainfall regimes (technically defined as zeroth level dependence) that gets remarkably augmented for large rainfall zones. Our analysis further indicates that for low fluctuations in temperature (true on the bulk data), EPG level saturates beyond a critical value of the rainfall, a threshold that is expected to indicate the onset of the nonlinear regime. The probability density functions (PDFs) of the EPG data show oscillatory behavior in the large rainfall regime (greater than 500 mm), the frequency of oscillation, once again, being determined by the ambient wetness (rainfall, and humidity). Data recorded over three pilot projects spanning three measures of rainfall and humidity bear testimony to the universality of this statistical argument.
PMCID: PMC4082254  PMID: 25013746
EPG; anthelmintic; strongyle; coccidia; least square fit; histogram; Probability Density Function (PDF)
7.  Pilot survey of oral health-related quality of life: a cross-sectional study of adults in Benin City, Edo State, Nigeria 
BMC Oral Health  2005;5:7.
Oral health studies conducted so far in Nigeria have documented prevalence and incidence of dental disease using traditional clinical measures. However none have investigated the use of an oral health-related quality of life (OHRQoL) instrument to document oral health outcomes. The aims of this study are: to describe how oral health affects and impacts quality of life (QoL) and to explore the association between these affects and the oral health care seeking behavior of adults in Benin City, Edo State, Nigeria.
A cross-sectional survey recruited 356 adults aged 18–64 years from two large hospital outpatient departments and from members of a university community. Closed-ended oral health questionnaire with "effect and impact" item-questions from OHQoL-UK© instrument was administered by trained interviewers. Collected data included sociodemographic, dental visits, and effects and impact of oral health on QoL. Univariate and bivariable analyses were done and a chi-square test was used to test differences in proportions. Multivariable analyses using ANOVA examined the association between QoL factors and visits to a dentist.
Complete data was available for 83% of the participants. About 62% of participants perceived their oral health as affecting their QoL. Overall, 82%, 63%, and 77% of participants perceived that oral health has an effect on their eating or enjoyment of food, sleep or ability to relax, and smiling or laughing, respectively. Some 46%, 36%, and 25% of participants reported that oral health impact their daily activities, social activities, and talking to people, respectively. Dental visits within the last year was significantly associated with eating, speech, and finance (P < 0.05). The summary score for the oral health effects on QoL ranged from 33 to 80 with a median value of 61 (95% CI: 60, 62) and interquartile range of 52–70. Multivariable modeling suggested a model containing only education (F = 6.5, pr>F = 0.0111). The mean of effects sum score for those with secondary/tertiary education levels (mean = 61.8; 95% CI: 60.6, 62.9) was significantly higher than those with less than secondary level of education (mean = 57.2; 95% CI: 57.2, 60.6).
Most adults in the study reported that oral health affects their life quality, and have little/no impact on their quality of life. Dental visits within the last year were associated with eating, speech, and finance.
PMCID: PMC1190187  PMID: 16042806
8.  Salivary Secretory Leukocyte Protease Inhibitor and Oral Candidiasis in Human Immunodeficiency Virus Type 1-Infected Persons  
Infection and Immunity  2004;72(4):1956-1963.
Oropharyngeal candidiasis, typically caused by Candida albicans, is the most common oral disease associated with human immunodeficiency virus type 1 (HIV-1) infection. Secretory leukocyte protease inhibitor (SLPI), a 12-kDa antiprotease, suppresses the growth of C. albicans in vitro. To determine whether the mucosal protein plays a role in protecting oral tissues against fungal infection, we conducted a cross-sectional study investigating the oral and systemic health and salivary SLPI levels in 91 dentate HIV-1-infected adults receiving medical care in the southeastern United States. Participants with a self-reported history of clinical oropharyngeal candidiasis during the previous 2 years constituted the test group (n = 52), while the comparison group (n = 39) had no oropharyngeal candidiasis during that period. Data collected from medical records, oral examination, and SLPI enzyme-linked immunosorbent assay quantitation of whole saliva were analyzed by t test, analysis of variance, linear regression, and unconditional logistic regression. The test group had a significantly higher mean salivary SLPI level than the comparison group (1.9 μg/ml versus 1.1 μg/ml, P < 0.05). Linear regression modeling identified CD4 cell count and history of oropharyngeal candidiasis as key predictors of salivary SLPI and revealed a significant interaction (P < 0.05) between immunosuppression (CD4 cell count below 200 cells/μl) and positive history of oropharyngeal candidiasis in predicting salivary SLPI level. By logistic regression modeling, a salivary SLPI level exceeding 2.1 μg/ml, low CD4 count, antiretroviral monotherapy, and smoking were key predictors of oropharyngeal candidiasis. These data support a key role for SLPI in the oral mucosal defense against C. albicans. The antimicrobial mucosal protein may serve as an indicator of previous oropharyngeal candidiasis infection among immunosuppressed persons.
PMCID: PMC375171  PMID: 15039315

Results 1-8 (8)