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1.  Visualizing Hyolaryngeal Mechanics in Swallowing Using Dynamic MRI 
Coordinates of anatomical landmarks are captured using dynamic MRI to explore whether a proposed two-sling mechanism underlies hyolaryngeal elevation in pharyngeal swallowing. A principal components analysis (PCA) is applied to coordinates to determine the covariant function of the proposed mechanism.
Dynamic MRI (dMRI) data were acquired from eleven healthy subjects during a repeated swallows task. Coordinates mapping the proposed mechanism are collected from each dynamic (frame) of a dynamic MRI swallowing series of a randomly selected subject in order to demonstrate shape changes in a single subject. Coordinates representing minimum and maximum hyolaryngeal elevation of all 11 subjects were also mapped to demonstrate shape changes of the system among all subjects. MophoJ software was used to perform PCA and determine vectors of shape change (eigenvectors) for elements of the two-sling mechanism of hyolaryngeal elevation.
For both single subject and group PCAs, hyolaryngeal elevation accounted for the first principal component of variation. For the single subject PCA, the first principal component accounted for 81.5% of the variance. For the between subjects PCA, the first principal component accounted for 58.5% of the variance. Eigenvectors and shape changes associated with this first principal component are reported.
Eigenvectors indicate that two-muscle slings and associated skeletal elements function as components of a covariant mechanism to elevate the hyolaryngeal complex. Morphological analysis is useful to model shape changes in the two-sling mechanism of hyolaryngeal elevation.
PMCID: PMC4108173  PMID: 25090608
Imaging and Visualization in Biomechanics; Medical Imaging and Visualization; Deglutition; Morphometrics; Hyolaryngeal complex
2.  Selecting the Right Similarity-Scoring Matrix 
Protein sequence similarity searching programs like BLASTP, SSEARCH (UNIT 3.10), and FASTA use scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 for BLAST, BLOSUM50 for SEARCH and FASTA). Different similarity scoring matrices are most effective at different evolutionary distances. “Deep” scoring matrices like BLOSUM62 and BLOSUM50 target alignments with 20 – 30% identity, while “shallow” scoring matrices (e.g. VTML10 – VTML80), target alignments that share 90 – 50% identity, reflecting much less evolutionary change. While “deep” matrices provide very sensitive similarity searches, they also require longer sequence alignments and can sometimes produce alignment overextension into non-homologous regions. Shallower scoring matrices are more effective when searching for short protein domains, or when the goal is to limit the scope of the search to sequences that are likely to be orthologous between recently diverged organisms. Likewise, in DNA searches, the match and mismatch parameters set evolutionary look-back times and domain boundaries. In this unit, we will discuss the theoretical foundations that drive practical choices of protein and DNA similarity scoring matrices and gap penalties. Deep scoring matrices (BLOSUM62 and BLOSUM50) should be used for sensitive searches with full-length protein sequences, but short domains or restricted evolutionary look-back require shallower scoring matrices.
PMCID: PMC3848038  PMID: 24509512
similarity scoring matrices; PAM matrices; BLOSUM matrices; sequence alignment
3.  Image-based Measurement of Post-Swallow Residue: The Normalized Residue Ratio Scale 
Dysphagia  2012;28(2):167-177.
Post-swallow residue is considered a sign of swallowing impairment. Existing methods for capturing post-swallow residue (perceptual and quantitative) have inherent limitations. We employed several different perceptual and quantitative (ratio) methods for measuring post-swallow residue on the same 40 swallows and addressed the following questions: (1) Do perceptual and quantitative methods demonstrate good agreement? (2) What differences in precision are apparent by measurement method (one-dimensional, two-dimensional, and circumscribed area ratios)? (3) Do residue ratios agree strongly with residue area measures that are anatomically normalized? Based on the findings of this series of questions, a new method for capturing residue is proposed: the Normalized Residue Ratio Scale (NRRS). The NRRS is a continuous measurement that incorporates both the ratio of residue relative to the available pharyngeal space and the residue proportionate to the size of the individual. A demonstration of this method is presented to illustrate the added precision of the NRRS measurement in comparison to other approaches for measuring residue severity.
PMCID: PMC3584199  PMID: 23089830
Deglutition; Dysphagia; Swallowing; Videofluoroscopy; Residue; Deglutition disorders
4.  An Introduction to Sequence Similarity (“Homology”) Searching 
Sequence similarity searching, typically with BLAST (units 3.3, 3.4), is the most widely used, and most reliable, strategy for characterizing newly determined sequences. Sequence similarity searches can identify ”homologous” proteins or genes by detecting excess similarity – statistically significant similarity that reflects common ancestry. This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs.
PMCID: PMC3820096  PMID: 23749753
sequence similarity; homology; orthlogy; paralogy; sequence alignment; multiple alignment; sequence evolution; Bioinformatics; Bioinformatics Fundamentals; Finding Similarities and Inferring Homologies
5.  Evaluating Swallowing Muscles Essential for Hyolaryngeal Elevation by Using Muscle Functional Magnetic Resonance Imaging 
Elevation of the larynx is critical to swallowing function, an observation supported by the fact that radiation therapy-induced dysphagia is associated with reduced laryngeal elevation. We investigated muscles underlying hyolaryngeal elevation by using muscle functional MRI. We acquired scans from 11 healthy subjects to determine whole-muscle T2 signal profiles pre-swallowing, post-swallowing, and after performing swallowing exercises. Results demonstrate muscles essential to laryngeal elevation and exercises that target them.
Reduced hyolaryngeal elevation, a critical event in swallowing, is associated with radiation therapy. Two muscle groups that suspend the hyoid, larynx, and pharynx have been proposed to elevate the hyolaryngeal complex: the suprahyoid and longitudinal pharyngeal muscles. Thought to assist both groups is the thyrohyoid, a muscle intrinsic to the hyolaryngeal complex. Intensity modulated radiation therapy guidelines designed to preserve structures important to swallowing currently exclude the suprahyoid and thyrohyoid muscles. This study used muscle functional magnetic resonance imaging (mfMRI) in normal healthy adults to determine whether both muscle groups are active in swallowing and to test therapeutic exercises thought to be specific to hyolaryngeal elevation.
Methods and Materials
mfMRI data were acquired from 11 healthy subjects before and after normal swallowing and after swallowing exercise regimens (the Mendelsohn maneuver and effortful pitch glide). Whole-muscle transverse relaxation time (T2 signal, measured in milliseconds) profiles of 7 test muscles were used to evaluate the physiologic response of each muscle to each condition. Changes in effect size (using the Cohen d measure) of whole-muscle T2 profiles were used to determine which muscles underlie swallowing and swallowing exercises.
Post-swallowing effect size changes (where a d value of >0.20 indicates significant activity during swallowing) for the T2 signal profile of the thyrohyoid was a d value of 0.09; a d value of 0.40 for the mylohyoid, 0.80 for the geniohyoid, 0.04 for the anterior digastric, and 0.25 for the posterior digastric-stylohyoid in the suprahyoid muscle group; and d values of 0.47 for the palatopharyngeus and 0.28 for the stylopharyngeus muscles in the longitudinal pharyngeal muscle group. The Mendelsohn maneuver and effortful pitch glide swallowing exercises showed significant effect size changes for all muscles tested, except for the thyrohyoid.
Muscles of both the suprahyoid and the longitudinal pharyngeal muscle groups are active in swallowing, and both swallowing exercises effectively target muscles elevating the hyolaryngeal complex. mfMRI is useful in testing swallowing muscle function.
PMCID: PMC3563921  PMID: 22995662
6.  State-Based Medicaid Costs for Pediatric Asthma Emergency Department Visits 
The prevalence of childhood asthma in the United States increased from 8.7% in 2001 to 9.5% in 2011. This increased prevalence adds to the costs incurred by state Medicaid programs. We provide state-based cost estimates of pediatric asthma emergency department (ED) visits and highlight an opportunity for states to reduce these costs through a recently changed Centers for Medicare and Medicaid Services (CMS) regulation.
We used a cross-sectional design across multiple data sets to produce state-based cost estimates for asthma-related ED visits among children younger than 18, where Medicaid/CHIP (Children’s Health Insurance Program) was the primary payer.
There were approximately 629,000 ED visits for pediatric asthma for Medicaid/CHIP enrollees, which cost $272 million in 2010. The average cost per visit was $433. Costs ranged from $282,000 in Alaska to more than $25 million in California.
Costs to states for pediatric asthma ED visits vary widely. Effective January 1, 2014, the CMS rule expanded which type of providers can be reimbursed for providing preventive services to Medicaid/CHIP beneficiaries. This rule change, in combination with existing flexibility for states to define practice setting, allows state Medicaid programs to reimburse for asthma interventions that use nontraditional providers (such as community health workers or certified asthma educators) in a nonclinical setting, as long as the service was initially recommended by a physician or other licensed practitioner. The rule change may help states reduce Medicaid costs of asthma treatment and the severity of pediatric asthma.
PMCID: PMC4075488  PMID: 24967830
7.  The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes 
Nucleic Acids Research  2013;42(Database issue):D485-D489.
Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) ( published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface.
PMCID: PMC3964973  PMID: 24319146
8.  Structural Analysis of Muscles Elevating the Hyolaryngeal Complex 
Dysphagia  2012;27(4):445-451.
A critical event of pharyngeal swallowing is the elevation of the hyolaryngeal complex to open the upper esophageal sphincter. Current swallowing theory assigns this function to the submental and thyrohyoid muscles. However, the attachments of the long pharyngeal muscles indicate that they could contribute to this function, yet their role is uninvestigated in humans. In addition, there is evidence the posterior digastric and stylohyoid contribute to hyoid elevation. A cadaver model was used to document the structural properties of muscles. These properties were used to model muscle groups as force vectors and analyze their potential for hyolaryngeal elevation. Vector magnitude was determined using physiological cross-sectional areas (PCSAs) of muscles calculated from structural properties of muscle taken from 12 hemisected cadaver specimens. Vector direction (lines of action) was calculated from the three-dimensional coordinates of muscle attachment sites. Unit force vectors in the superior direction of submental, suprahyoid (which includes the submental muscles), long pharyngeal, and thyrohyoid muscles were derived and compared by an analysis of variance (ANOVA) to document each muscle’s potential contribution to hyolaryngeal elevation. An ANOVA with Tukey HSD post hoc analysis of unit force vectors showed no statistically significant difference between the submental (0.92 ± 0.24 cm2) and long pharyngeal (0.73 ± 0.20 cm2) muscles. Both demonstrated greater potential to elevate the hyolaryngeal complex than the thyrohyoid (0.49 ± 0.18 cm2), with P < 0.01 and P < 0.05, respectively. The suprahyoid muscles (1.52 ± 0.35 cm2) demonstrated the greatest potential to elevate the hyolaryngeal complex: greater than both the long pharyngeal muscles (P < 0.01) and the thyrohyoid (P < 0.01). The submental and thyrohyoid muscles by convention are thought to elevate the hyolaryngeal complex. This study demonstrates that structurally the long pharyngeal muscles have similar potential to contribute to this critical function, with the suprahyoid muscles having the greatest potential. If verified by functional data, these findings would amend current swallowing theory.
PMCID: PMC3350616  PMID: 22278076
Deglutition; Laryngeal elevation; Physiological cross-sectional area; Structural properties; Hyolaryngeal complex; Deglutition disorders
9.  Adjusting scoring matrices to correct overextended alignments 
Bioinformatics  2013;29(23):3007-3013.
Motivation: Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (<33%) alignments. Although such scoring matrices can effectively identify distant homologs, they can also produce local alignments that extend beyond the homologous regions.
Results: We measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended. Overextended alignments include non-homologous sequences; they occur most frequently between sequences that are more closely related (>33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment. Realigning with the predicted scoring matrix corrected 37% of all overextended alignments, resulting in more correct alignments than using BLOSUM62 alone.
Availability: RefProtDom2 (RPD2) sequences and the FASTA software are available from
PMCID: PMC3834790  PMID: 23995390
10.  Adult Caregivers in the United States: Characteristics and Differences in Well-being, by Caregiver Age and Caregiving Status 
We examined the characteristics of adults providing regular care or assistance to friends or family members who have health problems, long-term illnesses, or disabilities (ie, caregivers). We used data from the 2009 Behavioral Risk Factor Surveillance System (BRFSS) to examine caregiver characteristics, by age and caregiving status, and compare these characteristics with those of noncaregivers. Approximately 24.7% (95% confidence interval, 24.4%–25.0%) of respondents were caregivers. Compared with younger caregivers, older caregivers reported more fair or poor health and physical distress but more satisfaction with life and lower mental distress. Understanding the characteristics of caregivers can help enhance strategies that support their role in providing long-term care.
PMCID: PMC3748279  PMID: 23948336
11.  Emergency Department Visits for Traumatic Brain Injury in Older Adults in the United States: 2006–08 
Traumatic brain injury (TBI) can be complicated among older adults due to age-related frailty, a greater prevalence of chronic conditions and the use of anticoagulants. We conducted this study using the latest available, nationally-representative emergency department (ED) data to characterize visits for TBI among older adults.
We used the 2006–2008 National Hospital Ambulatory Medical Care – Emergency Department (NHAMCS-ED) data to examine ED visits for TBI among older adults. Population-level estimates of triage immediacy, receipt of a head computed tomography (CT) and/or head magnetic resonance imaging (MRI), and hospital admission by type were used to characterize 1,561 sample visits, stratified by age <65 and ≥65 years of age.
Of ED visits made by persons ≥65 years of age, 29.1% required attention from a physician within 15 minutes of arrival; 82.1% required a head CT, and 20.9% required hospitalization. Persons ≥65 years of age were 3 times more likely to receive a head CT or MRI compared to younger patients presenting with TBI (adjusted odds ratio [aOR] 3.2; 95% confidence interval [CI], 1.8–5.8), and were 4 times more likely to be admitted to an intensive care unit, step-down unit, or surgery (aOR 4.1; 95% CI 2.1–8.0) compared to younger patients presenting with TBI, while controlling for sex and race.
Results demonstrate increased emergent service delivery for older persons presenting with TBI. As the United States population ages and continues to grow, TBI will become an even more important public health issue that will place a greater demand on the healthcare system.
PMCID: PMC3426370  PMID: 22928058
12.  PSI-Search: iterative HOE-reduced profile SSEARCH searching 
Bioinformatics  2012;28(12):1650-1651.
Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains—homologous over-extension (HOE). PSI-Search combines an optimal Smith–Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive.
Availability and implementation: PSI-Search is available from the authors as a standalone implementation written in Perl for Linux-compatible platforms. It is also available through a web interface ( and SOAP and REST Web Services (
PMCID: PMC3371869  PMID: 22539666
13.  Cumulative Childhood Stress and Autoimmune Diseases in Adults 
Psychosomatic Medicine  2009;71(2):243-250.
To examine whether childhood traumatic stress increased the risk of developing autoimmune diseases as an adult.
Retrospective cohort study of 15,357 adult health maintenance organization members enrolled in the Adverse Childhood Experiences (ACEs) Study from 1995 to 1997 in San Diego, California, and eligible for follow-up through 2005. ACEs included childhood physical, emotional, or sexual abuse; witnessing domestic violence; growing up with household substance abuse, mental illness, parental divorce, and/or an incarcerated household member. The total number of ACEs (ACE Score range = 0–8) was used as a measure of cumulative childhood stress. The outcome was hospitalizations for any of 21 selected autoimmune diseases and 4 immunopathology groupings: T- helper 1 (Th1) (e.g., idiopathic myocarditis); T-helper 2 (Th2) (e.g., myasthenia gravis); Th2 rheumatic (e.g., rheumatoid arthritis); and mixed Th1/Th2 (e.g., autoimmune hemolytic anemia).
Sixty-four percent reported at least one ACE. The event rate (per 10,000 person-years) for a first hospitalization with any autoimmune disease was 31.4 in women and 34.4 in men. First hospitalizations for any autoimmune disease increased with increasing number of ACEs (p < .05). Compared with persons with no ACEs, persons with ≥2 ACEs were at a 70% increased risk for hospitalizations with Th1, 80% increased risk for Th2, and 100% increased risk for rheumatic diseases (p < .05).
Childhood traumatic stress increased the likelihood of hospitalization with a diagnosed autoimmune disease decades into adulthood. These findings are consistent with recent biological studies on the impact of early life stress on subsequent inflammatory responses.
PMCID: PMC3318917  PMID: 19188532
childhood abuse; traumatic stress; autoimmune diseases; stress; inflammatory response
14.  Evaluating the Structural Properties of Suprahyoid Muscles and their Potential for Moving the Hyoid 
Dysphagia  2010;26(4):345-351.
Superior and anterior hyoid movements are important events in pharyngeal deglutition. This cross-sectional study uses a cadaver model to document the structural properties of the muscles underlying these movements in an effort to understand how their morphology influences function. Measurements to determine physiological cross-sectional areas (PCSAs) of swallowing muscles were taken from hemisected head and neck formalin-fixed cadaver specimens (n = 13). Coordinates of muscle attachment sites and PCSAs were used to calculate î and ĵ unit force vectors, where î and ĵ represent anterior-posterior and superior-inferior directions, respectively. The suprahyoid muscle subsamples were grouped for analysis as follows: digastric (DG), geniohyoid (GH), mylohyoid (MH), and stylohyoid (SH). The ANOVA with Tukey HSD post hoc analysis of unit force vectors showed the following results: GH (−0.44 ± 0.15 cm2) >MH (−0.02 ± 0.21 cm2), DG (−0.05 ± 0.11 cm2), SH (0.14 ± 0.04 cm2), with negative values representing the anterior direction (p < 0.01); and MH (0.91 ± 0.28 cm2) >DG (0.29 ± 0.14 cm2), SH (0.22 ± 0.08 cm2), GH (12 ± 0.08 cm2), with positive values representing the superior direction (p < 0.01). The morphology of the suprahyoid muscles suggests that based on structural properties, the geniohyoid has the most potential to displace the hyoid in the anterior direction and the mylohyoid has the most potential to displace the hyoid in the superior direction. These data in complement with physiological findings may provide greater insight into these movements for those developing novel treatments for dysphagia.
PMCID: PMC3154991  PMID: 21069388
Deglutition; Suprahyoid muscles; Hyoid movement; Physiological cross-sectional area; Structural properties; Deglutition disorders
15.  MACiE: exploring the diversity of biochemical reactions 
Nucleic Acids Research  2011;40(Database issue):D783-D789.
MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from This article presents the release of Version 3 of MACiE, which not only extends the dataset to 335 entries, covering 182 of the EC sub-subclasses with a crystal structure available (∼90%), but also incorporates greater chemical and structural detail. This version of MACiE represents a shift in emphasis for new entries, from non-homologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life. We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts.
PMCID: PMC3244993  PMID: 22058127
16.  Globally, unrelated protein sequences appear random 
Bioinformatics  2009;26(3):310-318.
Motivation: To test whether protein folding constraints and secondary structure sequence preferences significantly reduce the space of amino acid words in proteins, we compared the frequencies of four- and five-amino acid word clumps (independent words) in proteins to the frequencies predicted by four random sequence models.
Results: While the human proteome has many overrepresented word clumps, these words come from large protein families with biased compositions (e.g. Zn-fingers). In contrast, in a non-redundant sample of Pfam-AB, only 1% of four-amino acid word clumps (4.7% of 5mer words) are 2-fold overrepresented compared with our simplest random model [MC(0)], and 0.1% (4mers) to 0.5% (5mers) are 2-fold overrepresented compared with a window-shuffled random model. Using a false discovery rate q-value analysis, the number of exceptional four- or five-letter words in real proteins is similar to the number found when comparing words from one random model to another. Consensus overrepresented words are not enriched in conserved regions of proteins, but four-letter words are enriched 1.18- to 1.56-fold in α-helical secondary structures (but not β-strands). Five-residue consensus exceptional words are enriched for α-helix 1.43- to 1.61-fold. Protein word preferences in regular secondary structure do not appear to significantly restrict the use of sequence words in unrelated proteins, although the consensus exceptional words have a secondary structure bias for α-helix. Globally, words in protein sequences appear to be under very few constraints; for the most part, they appear to be random.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2852211  PMID: 19948773
17.  An Analysis of Language as a Barrier to Receiving Influenza Vaccinations among an Elderly Hispanic Population in the United States 
Background. The Hispanic population in the United States is growing, and disparities in the receipt of healthcare services as a result of limited English proficiency have been demonstrated. We set out to determine if Spanish language preference was a barrier to receiving influenza vaccinations among Hispanic persons 65 years and older in the USA. Methods. Differences in the receipt of vaccinations by language preference were tested with both Chi-square analyses and adjusted logistic regression analyses. Results. Findings suggest that elderly Hispanic persons, 65 years of age and older, who prefer to communicate in Spanish instead of English, are significantly less likely to have received influenza vaccinations when compared to their Hispanic counterparts who prefer to communicate in English. Conclusions. Influenza infections can more often be fatal in older persons and may disparately affect minority populations such as Hispanic persons. Therefore, understanding barriers to the receipt of effective preventive health measures is necessary.
PMCID: PMC3169338  PMID: 21991435
18.  RefProtDom: a protein database with improved domain boundaries and homology relationships 
Bioinformatics  2010;26(18):2361-2362.
Summary: RefProtDom provides a set of divergent query domains, originally selected from Pfam, and full-length proteins containing their homologous domains, with diverse architectures, for evaluating pair-wise and iterative sequence similarity searches. Pfam homology and domain boundary annotations in the target library were supplemented using local and semi-global searches, PSI-BLAST searches, and SCOP and CATH classifications.
Availability: RefProtDom is available from
PMCID: PMC2935417  PMID: 20693322
19.  Analysis of five-year trends in self-reported language preference and issues of item non-response among Hispanic persons in a large cross-sectional health survey: implications for the measurement of an ethnic minority population 
Significant differences in health outcomes have been documented among Hispanic persons, the fastest-growing demographic segment of the United States. The objective of this study was to examine trends in population growth and the collection of health data among Hispanic persons, including issues of language preference and survey completion using a national health survey to highlight issues of measurement of an increasingly important demographic segment of the United States.
Data from the 2003-2007 United States Census and the Behavioral Risk Factor Surveillance System were used to compare trends in population growth and survey sample size as well as differences in survey response based on language preference among a Hispanic population. Percentages of item non-response on selected survey questions were compared for Hispanic respondents choosing to complete the survey in Spanish and those choosing to complete the survey in English. The mean number of attempts to complete the survey was also compared based on language preference among Hispanic respondents.
The sample size of Hispanic persons in the Behavioral Risk Factor Surveillance System saw little growth compared to the actual growth of the Hispanic population in the United States. Significant differences in survey item non-response for nine of 15 survey questions were seen based on language preference. Hispanic respondents choosing to complete the survey in Spanish had a significantly fewer number of call attempts for survey completion compared to their Hispanic counterparts choosing to communicate in English.
Including additional measures of acculturation and increasing the sample size of Hispanic persons in a national health survey such as the Behavioral Risk Factor Surveillance System may result in more precise findings that could be used to better target prevention and health care needs for an ethnic minority population.
PMCID: PMC2873928  PMID: 20412575
20.  The limits of protein sequence comparison? 
Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized.
PMCID: PMC2845305  PMID: 15919194
21.  Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments 
BMC Bioinformatics  2010;11:146.
While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate.
We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values < 10-5) and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph) according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The model can also be used to generate novel alignments by using the probabilities in lieu of a scoring matrix. These alignments are typically better than the optimal sequence alignment, and include novel correct structural edges. We find that the probA alignments sample a larger variety of alignments than the Zuker set, which more frequently results in alignments that are closer to the structural alignments, but that using the probA alignments as input to the regression model does not increase performance.
The pool of suboptimal pairwise protein sequence alignments substantially overlaps structure-based alignments for pairs with statistically significant similarity, and a regression model based on information contained in this alignment pool improves the accuracy of pairwise alignments with respect to structure-based alignments.
PMCID: PMC2850363  PMID: 20307279
22.  Visualization of near-optimal sequence alignments 
Bioinformatics (Oxford, England)  2004;20(6):953-958.
Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.
We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.
Available at noptalign. For source code contact the authors at
PMCID: PMC2836811  PMID: 14751975
23.  Homologous over-extension: a challenge for iterative similarity searches 
Nucleic Acids Research  2010;38(7):2177-2189.
We have characterized a novel type of PSI-BLAST error, homologous over-extension (HOE), using embedded PFAM domain queries on searches against a reference library containing Pfam-annotated UniProt sequences and random synthetic sequences. PSI-BLAST makes two types of errors: alignments to non-homologous regions and HOE alignments that begin in a homologous region, but extend beyond the homology into neighboring sequence regions. When the neighboring sequence region contains a non-homologous domain, PSI-BLAST can incorporate the unrelated sequence into its position specific scoring matrix, which then finds non-homologous proteins with significant expectation values. HOE accounts for the largest fraction of the initial false positive (FP) errors, and the largest fraction of FPs at iteration 5. In searches against complete protein sequences, 5–9% of alignments at iteration 5 are non-homologous. HOE frequently begins in a partial protein domain; when partial domains are removed from the library, HOE errors decrease from 16 to 3% of weighted coverage (hard queries; 35–5% for sampled queries) and no-error searches increase from 2 to 58% weighed coverage (hard; 16–78% sampled). When HOE is reduced by not extending previously found sequences, PSI-BLAST specificity improves 4–8-fold, with little loss in sensitivity.
PMCID: PMC2853128  PMID: 20064877
24.  State and Metropolitan Variation in Lack of Health Insurance Among Working-Age Adults, Behavioral Risk Factor Surveillance System, 2006 
Public Health Reports  2009;124(1):34-41.
Lack of health insurance coverage for working-age adults is one of the most pressing issues facing the U.S. population, and it continues to be a concern for a large number of people. In the absence of a national solution, the states and municipalities are left to address this need. We examined the disparities in uninsurance prevalence by state and metropolitan areas in the U.S. and among racial/ethnic groups.
Data from the 2006 Behavioral Risk Factor Surveillance System (BRFSS) were analyzed for working-age adults 18 to 64 years of age.
In 2006, according to the BRFSS data, overall 18.6% (standard error = 0.20) of working-age adults were without health insurance coverage; by state, this proportion ranged from 9.7% to 29.0%. Health insurance coverage varied by state and metropolitan area and racial/ethnic group, and a higher age-adjusted prevalence of uninsurance was observed for non-Hispanic black and Hispanic respondents.
A substantial proportion of working-age Americans remain without health insurance coverage. Disparities in health insurance coverage were observed by population and geographic groups. Overall, black and Hispanic populations fared far worse in terms of lack of health-care coverage than working-age white Americans.
PMCID: PMC2602929  PMID: 19413026
25.  The impact of obesity on time spent with the provider and number of medications managed during office-based physician visits using a cross-sectional, national health survey 
BMC Public Health  2009;9:436.
Obesity is associated with morbidity, mortality, and increased health care costs. Few studies have examined the impact of obesity on outpatient office visits. The purpose of this study was to determine if outpatient visits by obese persons required more time with the provider and more prescription medication management compared to visits made by non-obese persons.
Obesity status was determined for 9,280 patient visits made by persons aged 18 years or older in the 2006 National Ambulatory Medical Care Survey. Multivariate analyses compared obese and non-obese visits, stratified by sex, for duration of the visit and the number of medications mentioned at the visit.
Average duration of visit was higher among visits with patients determined to be obese. However, these differences were not considered significant after statistical testing. Visits made by obese female patients were significantly more likely to involve more than two prescription medications (OR 1.26, 95% CI 1.05 - 1.51) and visits made by obese male patients were significantly more likely to involve more than two prescription medications (OR 1.46, 95% CI 1.16 - 1.83) as compared to visits made by non-obese patients.
Time spent with the provider was found to be greater among visits with obese patients, but not significantly different from visits with non-obese patients. The number of medications for each visit was found to be significantly greater for visits where the patient was considered to be obese. Increased time for the visit and increased numbers of medication for each visit translate into increased costs. These findings document the impact of obesity on our health care system and have great implications on medical care cost and planning.
PMCID: PMC2792229  PMID: 19948026

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