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In JoVE (1)
Other Publications (10)
- AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium
- American Journal of Human Genetics
- Pediatric and Developmental Pathology : the Official Journal of the Society for Pediatric Pathology and the Paediatric Pathology Society
- BMC Ecology
- Journal of Animal Science
- Journal of Cancer Education : the Official Journal of the American Association for Cancer Education
- The Journal of Physical Chemistry. A
- Virology
- The Journal of Physical Chemistry. A
- Journal of the American Medical Informatics Association : JAMIA
Articles by Ryan Pacheco in JoVE
JoVE Bioengineering
Synthetic Spider Silk Production on a Laboratory Scale
Department of Biological Sciences, University of the Pacific
Despite the outstanding mechanical and biochemical properties of spider silks, this material cannot be harvested in large quantities by conventional means. Here we describe an efficient strategy to spin artificial spider silk fibers, which is an important process for investigators studying spider silk production and their use as next-generation biomaterials.
Other articles by Ryan Pacheco on PubMed
Analyzing the Heterogeneity and Complexity of Electronic Health Record Oriented Phenotyping Algorithms
The need for formal representations of eligibility criteria for clinical trials - and for phenotyping more generally - has been recognized for some time. Indeed, the availability of a formal computable representation that adequately reflects the types of data and logic evidenced in trial designs is a prerequisite for the automatic identification of study-eligible patients from Electronic Health Records. As part of the wider process of representation development, this paper reports on an analysis of fourteen Electronic Health Record oriented phenotyping algorithms (developed as part of the eMERGE project) in terms of their constituent data elements, types of logic used and temporal characteristics. We discovered that the majority of eMERGE algorithms analyzed include complex, nested boolean logic and negation, with several dependent on cardinality constraints and complex temporal logic. Insights gained from the study will be used to augment the CDISC Protocol Representation Model.
Variants Near FOXE1 Are Associated with Hypothyroidism and Other Thyroid Conditions: Using Electronic Medical Records for Genome- and Phenome-wide Studies
We repurposed existing genotypes in DNA biobanks across the Electronic Medical Records and Genomics network to perform a genome-wide association study for primary hypothyroidism, the most common thyroid disease. Electronic selection algorithms incorporating billing codes, laboratory values, text queries, and medication records identified 1317 cases and 5053 controls of European ancestry within five electronic medical records (EMRs); the algorithms' positive predictive values were 92.4% and 98.5% for cases and controls, respectively. Four single-nucleotide polymorphisms (SNPs) in linkage disequilibrium at 9q22 near FOXE1 were associated with hypothyroidism at genome-wide significance, the strongest being rs7850258 (odds ratio [OR] 0.74, p = 3.96 × 10(-9)). This association was replicated in a set of 263 cases and 1616 controls (OR = 0.60, p = 5.7 × 10(-6)). A phenome-wide association study (PheWAS) that was performed on this locus with 13,617 individuals and more than 200,000 patient-years of billing data identified associations with additional phenotypes: thyroiditis (OR = 0.58, p = 1.4 × 10(-5)), nodular (OR = 0.76, p = 3.1 × 10(-5)) and multinodular (OR = 0.69, p = 3.9 × 10(-5)) goiters, and thyrotoxicosis (OR = 0.76, p = 1.5 × 10(-3)), but not Graves disease (OR = 1.03, p = 0.82). Thyroid cancer, previously associated with this locus, was not significantly associated in the PheWAS (OR = 1.29, p = 0.09). The strongest association in the PheWAS was hypothyroidism (OR = 0.76, p = 2.7 × 10(-13)), which had an odds ratio that was nearly identical to that of the curated case-control population in the primary analysis, providing further validation of the PheWAS method. Our findings indicate that EMR-linked genomic data could allow discovery of genes associated with many diseases without additional genotyping cost.
Rectal Biopsy in Children with Down Syndrome and Chronic Constipation: Hirschsprung Disease Vs. Non-Hirschsprung Disease
Abstract Hirschsprung disease (HD) is reported in patients with Down syndrome (DS) with a frequency between 2% and 10%. The incidence of HD is 2% in our community-based registry that contains > 700 patients with DS. We reviewed rectal biopsy findings in 32 of these patients who had suction rectal biopsy (SRB) performed between 1980 and 2009 to investigate the cause of chronic constipation. We confirmed that 15 patients had diagnostic histological and histochemical features of HD. More challenging were findings in 5/17 patients in whom ganglia co-existed with equivocal acetylcholinesterase reaction patterns and/or hypertrophic submucosal nerves. In this retrospective study, we were able to resolve most of these discrepant findings by demonstrating normal Calretinin positive nerve twigs in the lamina propria and muscularis mucosae, The clinical significance of these unexpected findings in SRB specimens that did not satisfy strict criteria for a tissue diagnosis of HD is unknown. We speculate that a minority of these patients have transition zone morphology or an incomplete/atypical form of HD. Further investigations may help resolve discrepancies that arise when SRB is used to investigate chronic constipation in DS.
Plant and Animal Endemism in the Eastern Andean Slope: Challenges to Conservation
ABSTRACT: BACKGROUND: The Andes-Amazon basin of Peru and Bolivia is one of the most data-poor, biologically rich, and rapidly changing areas of the world. Conservation scientists agree that this area hosts extremely high endemism, perhaps the highest in the world, yet we know little about the geographic distributions of these species and ecosystems within country boundaries. To address this need, we have developed conservation data on endemic biodiversity (~800 species of birds, mammals, and amphibians) and terrestrial ecological systems (~90; groups of vegetation communities resulting the action of ecological processes, substrates, and/or environmental gradients) with which we conducted a fine scale conservation prioritization across the Amazon watershed of Peru and Bolivia. We modelled the geographic distributions of 435 endemic plants and all 347 endemic vertebrate species, from existing museum and herbaria specimens at a regional conservation practitioner's scale (1:250,000-1:1,000,000), based on the best available tools and geographic data. We mapped ecological systems, endemic species concentrations, and irreplaceable areas with respect to national level protected areas. RESULTS: We found that sizes of endemic species distributions ranged widely (< 20 km2 to > 200,000 km2) across the study area. Bird and mammal endemic species richness was greatest within a narrow 2500-3000 m elevation band along the length of the Andes Mountains. Endemic amphibian richness was highest at 1000-1500 m elevation and concentrated in the southern half of the study area. Geographical distribution of plant endemism was highly taxon-dependent. Irreplaceable areas, defined as locations with the highest number of species with narrow ranges, overlapped slightly with areas of high endemism, yet generally exhibited unique patterns across the study area by species group. We found that many endemic species and ecological systems are lacking national-level protection; a third of endemic species have distributions completely outside of national protected areas. Protected areas cover only 20% of areas of high endemism and 20% of irreplaceable areas. Almost 40% of the 91 ecological systems are in serious need of protection (=< 2% of their ranges protected). CONCLUSIONS: We identify for the first time, areas of high endemic species concentrations and high irreplaceability that have only been roughly indicated in the past at the continental scale. We conclude that new complementary protected areas are needed to safeguard these endemics and ecosystems. An expansion in protected areas will be challenged by geographically isolated micro-endemics, varied endemic patterns among taxa, increasing deforestation, resource extraction, and changes in climate. Relying on pre-existing collections, publically accessible datasets and tools, this working framework is exportable to other regions plagued by incomplete conservation data.
Effects of Feeding a Multivalent Polyclonal Antibody Preparation on Feedlot Performance, Carcass Characteristics, Rumenitis and Blood Gas Profile in Bos Indicus Biotype Yearling Bulls
The objective of this study was to evaluate effects of feeding monensin (MON) or a multivalent polyclonal antibody preparation (PAP) against several rumen microorganisms on feedlot performance, carcass characteristics, blood gas profile, and rumenitis of Bos indicus biotype (BT) yearling bulls. The study was designed as a completely randomized design with a 3 × 2 factorial arrangement, replicated four times, in which 32 yearling bulls of each of three BT evaluated (3-way-cross, TC; Canchim, CC; and Nellore, NE) were fed diets containing either MON at 300 mg•d(-1) or PAP at 10 mL•d(-1 )across three different periods. No significant (P > 0.10) feed additive (FA) main effects were observed for any of the feedlot performance variables and carcass characteristics with the exception of dressing percentage. Yearling bulls receiving PAP had a decreased (P = 0.047) dressing percentage when compared with yearling bulls receiving MON. Significant (P < 0.05) BT main effects were observed for all feedlot performance variables and carcass characteristics with the exception of kidney-pelvic fat expressed in kg (P = 0.49) and LM lipids content (P = 0.45). Crossbred yearling bulls (TC and CC) had greater (P < 0.001) ADG, DMI in kg, DMI as % of BW, and improved (P = 0.001) G:F when compared with NE yearling bulls. A tendency (P = 0.072) for a FA main effect was observed for rumenitis scores, in which yearling bulls receiving PAP had lesser rumenitis scores than those receiving MON. When the data was disposed as frequency percent, 55.6% and 45.7% of the rumens from yearling bulls fed PAP and MON were scored between 0 and 1, respectively (0 = no lesions, 10 = severe lesions). Likewise, a significant BT main effect was observed (P = 0.008), where NE yearling bulls had greater rumenitis scores than those of crossbred yearling bulls (TC and CC). No significant FA main effects were observed (P > 0.10) for any of the fatty acids measured in the subcutaneous adipose tissue, with the exception that yearling bulls receiving MON had greater (P < 0.05) concentrations of palmitic acid (16:0), margaric acid (17:0), docosapentaenoic acid (22:5) and docosahexaenoic acid (22:6) than those yearling bulls receiving PAP. Feeding PAP tended to decrease incidence of rumen lesions and led to similar feedlot performance compared with feeding MON. Thus, PAP is a new technology that presents a possible alternative for ionophores.
Breast Cancer Screening Beliefs and Behaviors Among American Indian Women in Kansas and Missouri: a Qualitative Inquiry
American Indian women have rising incidence and disproportionate mortality rates due to breast cancer. Using a community-based participatory research approach, we conducted ten focus groups with American Indian women in Kansas and Missouri to understand their barriers to mammography and identify ways to intervene to improve screening rates. Focus groups were stratified by screening status, including women who were up to date with current screening mammography recommendations (mammogram within the last 2 years, N = 7 groups, 66 participants) and women who were not (N = 3 groups, 18 participants). While many similarities were identified across strata, some differences emerged, particularly descriptions of prior negative experiences with the health care system among women who were not up to date with screening recommendations. Primary areas identified by participants for intervention included culturally appropriate educational materials and interventions directed specifically at improving American Indian women's trust in Western medicine and alleviating feelings of discrimination.
"Pump-probe" Atom-centered Density Matrix Propagation Studies to Gauge Anharmonicity and Energy Repartitioning in Atmospheric Reactive Adducts: Case Study of the OH + Isoprene and OH + Butadiene Reaction Intermediates
Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.
Role of Arginine-56 Within the Structural Protein VP3 of Foot-and-mouth Disease Virus (FMDV) O1 Campos in Virus Virulence
FMDV O1 subtype undergoes antigenic variation under diverse growth conditions. Of particular interest is the amino acid variation observed at position 56 within the structural protein VP3. Selective pressures influence whether histidine (H) or arginine (R) is present at this position, ultimately influencing in vitro plaque morphology and in vivo pathogenesis in cattle. Using reverse genetics techniques, we have constructed FMDV type O1 Campos variants differing only at VP3 position 56, possessing either an H or R (O1Ca-VP3-56H and O1Ca-VP3-56R, respectively), and characterized their in vitro phenotype and virulence in the natural host. Both viruses showed similar growth kinetics in vitro. Conversely, they had distinct temperature-sensitivity (ts) and displayed significantly different pathogenic profiles in cattle and swine. O1Ca-VP3-56H was thermo stable and induced typical clinical signs of FMD, whereas O1Ca-VP3-56R presented a ts phenotype and was nonpathogenic unless VP3 position 56 reverted in vivo to either H or cysteine (C).
Influence of Water on Anharmonicity, Stability, and Vibrational Energy Distribution of Hydrogen-bonded Adducts in Atmospheric Reactions: Case Study of the OH + Isoprene Reaction Intermediate Using Ab Initio Molecular Dynamics
The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.
Use of Diverse Electronic Medical Record Systems to Identify Genetic Risk for Type 2 Diabetes Within a Genome-wide Association Study
Objective Genome-wide association studies (GWAS) require high specificity and large numbers of subjects to identify genotype-phenotype correlations accurately. The aim of this study was to identify type 2 diabetes (T2D) cases and controls for a GWAS, using data captured through routine clinical care across five institutions using different electronic medical record (EMR) systems. Materials and Methods An algorithm was developed to identify T2D cases and controls based on a combination of diagnoses, medications, and laboratory results. The performance of the algorithm was validated at three of the five participating institutions compared against clinician review. A GWAS was subsequently performed using cases and controls identified by the algorithm, with samples pooled across all five institutions. Results The algorithm achieved 98% and 100% positive predictive values for the identification of diabetic cases and controls, respectively, as compared against clinician review. By standardizing and applying the algorithm across institutions, 3353 cases and 3352 controls were identified. Subsequent GWAS using data from five institutions replicated the TCF7L2 gene variant (rs7903146) previously associated with T2D. Discussion By applying stringent criteria to EMR data collected through routine clinical care, cases and controls for a GWAS were identified that subsequently replicated a known genetic variant. The use of standard terminologies to define data elements enabled pooling of subjects and data across five different institutions to achieve the robust numbers required for GWAS. Conclusions An algorithm using commonly available data from five different EMR can accurately identify T2D cases and controls for genetic study across multiple institutions.
