A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log₁₀ increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.

The impact of belatacept on the phenotypic heterogeneity of renal T cell-mediated alloimmune response: The critical role of maintenance treatment and inflammatory load

Belatacept offers superior long-term outcome relative to calcineurin inhibitor (CNI)-based immunosuppression. However, the higher frequency of early T cell-mediated rejection (TCMR) in belatacept-treated patients hampered the widespread adoption of costimulation blockade. Here, we applied gene expression analysis and whole-slide inflammatory cell quantification to assess the impact of belatacept on intragraft immune signature. We studied formalin-fixed, paraffin-embedded renal biopsies from 92 patients stratified by histopathologic diagnosis (TCMR, borderline changes, or normal) and immunosuppression regimen (belatacept, CNI). An interaction model was built to explore maintenance treatment-dependent expression level changes of immune response-related genes across diagnostic categories of normal, borderline changes, and TCMR. Ninety-one percent of genes overexpressed in TCMR showed significant correlation with whole section inflammatory load. There were 27 genes that had a positive association with belatacept treatment. These were mostly related to myeloid cells and innate immunity. Genes negatively associated with costimulation blockade (n = 14) could be linked to B-cell differentiation and proliferation. We concluded that expression levels of genes characteristic of TCMR are strongly interconnected with quantitative changes of the biopsy inflammatory load. Our results might suggest differential involvement of the innate immune system, and an altered B-cell engagement during TCMR in belatacept-treated patients relative to CNI-treated referents.

Reaction Environment Effect on the Kinetics of Radical Thiol-Ene Polymerizations in the Presence of Amines and Thiolate Anions

Because of facile implementation, quantitative conversions, and an insensitivity to oxygen, water, and most organic functional groups, radical-mediated thiol-ene coupling (TEC) reactions have emerged as a valuable tool in macromolecule synthesis. It was recently demonstrated that the kinetics and conversions of thiyl radical-mediated reactions are adversely affected in the presence of basic amines by the formation of retardive thiolate anions. Herein, the performance of TEC polymerizations is evaluated under a variety of reaction environments with the intention to aid in the optimal formulation design of TEC reactions in the presence of amines. Results from both bulk and aqueous-phase network photopolymerizations established that sensitivity to amine basicity and pH is dependent on the thiol acidity, although norbornene-type alkenes exhibit a unique ability to achieve high conversions, where allyl ethers, vinyl ether, and vinyl siloxanes are highly inhibited. Additionally, the protic solvents such as alcohols and acetic acid are established as ideal solvents or additives to suppress or eliminate amine-induced retardation.

Introduction to chemistry for covalent adaptable networks

Christopher Bowman, Filip Du Prez and Julia Kalow introduce the Polymer Chemistry themed collection on chemistry for covalent adaptable networks.

Catalyst-free, aza-Michael polymerization of hydrazides: polymerizability, kinetics, and mechanistic origin of an α-effect

Despite the powerful nature of the aza-Michael reaction for generating C-N linkages and bioactive moieties, the bis-Michael addition of 1° amines remains ineffective for the synthesis of functional, step-growth polymers due to the drastic reduction in reactivity of the resulting 2° amine mono-addition adduct. In this study, a wide range of commercial hydrazides are shown to effectively undergo the bis-Michael reaction with divinyl sulfone (DVS) and 1,6-hexanediol diacrylate (HDA) under catalyst-free, thermal conditions to afford moderate to high molecular weight polymers with M n = 3.8-34.5 kg mol-1. The hydrazide-Michael reactions exhibit two distinctive, conversion-dependent kinetic regimes that are 2nd-order overall, in contrast to the 3rd-order nature of amines previously reported. The mono-addition rate constant was found to be 37-fold greater than that of the bis-addition at 80 °C for the reaction between benzhydrazide and DVS. A significant majority (12 of 15) of the hydrazide derivatives used here show excellent bis-Michael reactivity and achieve >97% conversions after 5 days. This behavior is consistent with calculations that show minimal variance of electron density on the N-nucleophile among the derivatives studied. Reactivity differences between hydrazides and hexylamine are also explored. Overall, the difference in reactivity between hydrazides and amines is attributed to the adjacent nitrogen atom in hydrazides that acts as an efficient hydrogen-bond donor that facilitates intramolecular proton-transfer following the formation of the zwitterion intermediate. This effect not only activates the Michael acceptor but also coordinates with additional Michael acceptors to form an intermolecular reactant complex.

MON-001 Assessment of Endocrine Clinic Attendance Rates to Guide Interventions to Reduce Patient No-Show Rates

As a part of our endocrine fellowship quality improvement training, we sought to improve patient access to endocrine outpatient clinic appointments at our institution. From the physician perspective, patients who do not show up for a 30-45 minute new patient visit slot disrupt clinic flow and limits access for other patients. Therefore, we decided to focus our attention on reducing the new patient no-show rate. Here, we assessed the efficacy of our current scheduling system from 2014-2016. This analysis was performed as part of a quality improvement project to inform future interventions. Previously, only a few studies have attempted to identify baseline no-show rates (1,2). Our institution utilizes an automated telephone appointment reminder system (Televox) which calls patients three to four business days prior to a scheduled appointment and gives the patient an opportunity to confirm or cancel the appointment. Televox data for 7,556 patients over 34 months (1/2014-10/2016) revealed a 95% show frequency for patients who confirmed their appointment, 82% show frequency for patients for which there was no response to the Televox reminder, and 78% show frequency of patients who were not reached (Televox call not made). P-Chart of the show frequencies of patients who did not respond or were not reached fluctuated between 70-90% over this period. This analysis shows that new patients who did not respond or were not reached are a potential target for intervention. By identifying this cohort early, we will be able to implement intervention and reschedule patients in a timely manner to improve clinic flow and clinic access. References: 1. Mohamed, K., Mustafa, A., Tahtamouni, S., Taha, E., Hassan, R. A Quality Improvement Project to Reduce the ‘No Show’ Rate in a Paediatric Neurology Clinic. BMJ Quality Improvement Reports. pii: u209266.w3789, 2016. PMID: 27651897 2. Santiago, V.A., Warwick, K., Ratnakumarasuriyar, S., Oyewumi, A., Robinson, S., Sockalingam, S. Evaluation of a Patient-Care Planning Intervention to Improve Appointment Attendance by Adults After Bariatric Surgery. Canadian Journal of Diabetes, pii: S1499-2671(17)31001-8, 2018. PMID: 30121163 Sources of Research Support: None

Physically principled reflection models applied to filtered camera imaging inversions in metal walled fusion machines

Ray-tracing techniques are applied to filtered divertor imaging, a diagnostic that has long suffered from artifacts due to the polluting effect of reflected light in metal walled fusion machines. Physically realistic surface reflections were modeled using a Cook-Torrance micro-facet bi-directional reflection distribution function applied to a high resolution mesh of the vessel geometry. In the absence of gonioreflectometer measurements, a technique was developed to fit the free parameters of the Cook-Torrance model against images of the JET in-vessel light sources. By coupling this model with high fidelity plasma fluid simulations, photo-realistic renderings of a number of tokamak plasma emission scenarios were generated. Finally, a sensitivity matrix describing the optical coupling of a JET divertor camera and the emission profile of the plasma was obtained, including full reflection effects. These matrices are used to perform inversions on measured data and shown to reduce the level of artifacts in inverted emission profiles.

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2

Low-grade astrocytomas (LGAs) carry neomorphic mutations in isocitrate dehydrogenase (IDH) concurrently with P53 and ATRX loss. To model LGA formation, we introduced R132H IDH1, P53 shRNA, and ATRX shRNA into human neural stem cells (NSCs). These oncogenic hits blocked NSC differentiation, increased invasiveness in vivo, and led to a DNA methylation and transcriptional profile resembling IDH1 mutant human LGAs. The differentiation block was caused by transcriptional silencing of the transcription factor SOX2 secondary to disassociation of its promoter from a putative enhancer. This occurred because of reduced binding of the chromatin organizer CTCF to its DNA motifs and disrupted chromatin looping. Our human model of IDH mutant LGA formation implicates impaired NSC differentiation because of repression of SOX2 as an early driver of gliomagenesis.

Abstract PR01: A DNA methylation-based classifier for accurate molecular diagnosis of bone sarcomas

Background: Bone sarcomas present a unique diagnostic challenge because of the considerable morphologic overlap between different entities. The choice of optimal treatment, however, is dependent upon accurate diagnosis. Genome-wide DNA methylation profiling has emerged as a new approach to aid in the diagnosis of brain tumors, with diagnostic accuracy exceeding standard histopathology. In this work we developed and validated a methylation-based classifier to differentiate between osteosarcoma, Ewing's sarcoma, and synovial sarcoma.

Methods: DNA methylation status of 482,421 CpG sites in 15 osteosarcoma, 10 Ewing's sarcoma, and 11 synovial sarcoma samples were measured using the Illumina HumanMethylation450 array. From this training set of 36 sarcoma samples we developed a random forest classifier from the 400 most differentially methylated CpG sites (FDR q value <0.001). This classifier was then validated on 10 synovial sarcoma samples from The Cancer Genome Atlas (TCGA), 86 osteosarcoma samples from TARGET-OS, and 15 Ewing's sarcoma from a recently published series. (Huertas-Martinez et al., Cancer Lett 2016)

Results: Methylation profiling revealed three distinct molecular clusters, each enriched with a single sarcoma subtype. Within the validation cohorts, all samples from TCGA were accurately classified as synovial sarcoma (10/10, sensitivity and specificity 100%). All but one sample from TARGET-OS were classified as osteosarcoma (85/86, sensitivity 98%, specificity 100%) and all but one sample from the Ewing's sarcoma series was classified as Ewing's (14/15, sensitivity 93%, specificity 100%). The single misclassified osteosarcoma sample was classified as a Ewing's sarcoma, and later determined to be a misdiagnosed Ewing's sarcoma based on RNA-seq data demonstrating high EWRS1 and ETV1 expression. An additional clinical sample that was misdiagnosed as a synovial sarcoma based on initial histopathology was accurately recognized as osteosarcoma by the methylation classifier. Pathway analysis with MSigDB (Broad Institute) identified targets of polycomb group proteins SUZ12 and EED, possessing the H3K27 trimethylated mark, as highly enriched within classifier genes

Conclusions: Osteosarcoma, Ewing's sarcoma, and synovial sarcoma have distinct epigenetic profiles. Our validated methylation-based classifier provides increased diagnostic accuracy, including in cases where standard histopathology is inconclusive.

This abstract is also being presented as Poster A01.

Citation Format: Shengyang Wu, Benjamin Cooper, Fang Bu, Christopher Bowman, Jonathan K. Killian, Shiyang Wang, Twana Jackson, Daniel Gorovets, Richard Gorlick, Kristen Thomas, Matthias Karajannis, Matija Snuderl. A DNA methylation-based classifier for accurate molecular diagnosis of bone sarcomas [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR01.

Ketoacidosis With Canagliflozin Prescribed for Phosphoinositide 3-Kinase Inhibitor-Induced Hyperglycemia: A Case Report

Context. Many phosphoinositide-3-kinase (PI3K) inhibitors are under trial for cancer treatment. We present a patient taking taselisib who developed ketoacidosis within 1 week of starting canagliflozin. Case Description. A 69-year-old female patient with no previous history of diabetes mellitus was enrolled in a clinical trial for taselisib therapy in stage IV breast cancer. Hyperglycemia treatment with metformin was insufficient and not tolerated. The addition of canagliflozin daily resulted in ketoacidosis and hospitalization within 1 week. Conclusions. This case report brings together 2 poorly understood and relatively understudied disorders of glucose homeostasis: hyperglycemia due to PI3K inhibition and euglycemic ketoacidosis due to dehydration/SGLT2 inhibition. It demonstrates the complexities of glucose management in the setting of PI3K inhibition. PI3K stimulation (via insulin) in this setting is counterintuitive; therefore, non–insulin-mediated therapies (eg, metformin, thiazolidinediones) might be favored over insulin-mediated therapies.

A DNA methylation-based classifier for accurate molecular diagnosis of bone sarcomas

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Background: Bone sarcomas present a unique diagnostic challenge because of the considerable morphologic overlap between different entities. The choice of optimal treatment, however, is dependent upon accurate diagnosis. Genome-wide DNA methylation profiling has emerged as a new approach to aid in the diagnosis of brain tumors, with diagnostic accuracy exceeding standard histopathology. In this work we developed and validated a methylation based classifier to differentiate between osteosarcoma, Ewing’s sarcoma, and synovial sarcoma. Methods: DNA methylation status of 482,421 CpG sites in 15 osteosarcoma, 10 Ewing’s sarcoma, and 11 synovial sarcoma samples were measured using the Illumina HumanMethylation450 array. From this training set of 36 samples we developed a random forest classifier using the 400 most differentially methylated CpG sites (FDR q value < 0.001). This classifier was then validated on 10 synovial sarcoma samples from TCGA, 86 osteosarcoma samples from TARGET-OS, and 15 Ewing’s sarcoma from a recently published series (Huertas-Martinez et al., Cancer Letters 2016). Results: Methylation profiling revealed three distinct molecular clusters, each enriched with a single sarcoma subtype. Within the validation cohorts, all samples from TCGA were correctly classified as synovial sarcoma (10/10, sensitivity and specificity 100%). All but one sample from TARGET-OS were classified as osteosarcoma (85/86, sensitivity 98%, specificity 100%) and all but one sample from the Ewing’s sarcoma series was classified as Ewing’s sarcoma (14/15, sensitivity 93%, specificity 100%). The single misclassified osteosarcoma sample was classified as Ewing’s sarcoma, and was later determined to be a misdiagnosed Ewing’s sarcoma based on RNA-Seq demonstrating high EWRS1 and ETV1 expression. An additional clinical sample that was misdiagnosed as a synovial sarcoma by initial histolopathology, was accurately recognized as osteosarcoma by the methylation classifier. Conclusions: Osteosarcoma, Ewing’s sarcoma and synovial sarcoma have distinct epigenetic profiles. Our validated methylation-based classifier can be used to provide an accurate diagnosis when histological and standard techniques are inconclusive.

The development and validation of a meta-tool for quality appraisal of public health evidence: Meta Quality Appraisal Tool (MetaQAT)

OBJECTIVES

Most quality appraisal tools were developed for clinical medicine and tend to be study-specific with a strong emphasis on risk of bias. In order to be more relevant to public health, an appropriate quality appraisal tool needs to be less reliant on the evidence hierarchy and consider practice applicability. Given the broad range of study designs used in public health, the objective of this study was to develop and validate a meta-tool that combines public health-focused principles of appraisal coupled with a set of design-specific companion tools.

STUDY DESIGN

Several design methods were used to develop and validate the tool including literature review, synthesis, and validation with a reference standard.

METHODS

A search of critical appraisal tools relevant to public health was conducted; core concepts were collated. The resulting framework was piloted during three feedback sessions with public health practitioners. Following subsequent revisions, the final meta-tool, the Meta Quality Appraisal Tool (MetaQAT), was then validated through a content analysis of appraisals conducted by two groups of experienced public health researchers (MetaQAT vs generic appraisal form).

RESULTS

The MetaQAT framework consists of four domains: relevancy, reliability, validity, and applicability. In addition, a companion tool was assembled from existing critical appraisal tools to provide study design-specific guidance on validity appraisal. Content analysis showed similar methodological and generalizability concerns were raised by both groups; however, the MetaQAT appraisers commented more extensively on applicability to public health practice.

CONCLUSIONS

Critical appraisal tools designed for clinical medicine have limitations for use in the context of public health. The meta-tool structure of the MetaQAT allows for rigorous appraisal, while allowing users to simultaneously appraise the multitude of study designs relevant to public health research and assess non-standard domains, such as applicability.

Methylation profiling of locally advanced rectal cancer (LARC): Exploration of potential predictive markers for neoadjuvant chemoradiation (NACR)

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Background: NACR followed by total mesorectal excision (TME) is standard of care for LARC. However, only 10-20% of patients achieve complete pathologic response with associated optimal clinical outcome. No predictive biomarker is currently available. Aberrant DNA methylation is well known for its key role in the pathogenesis of colorectal cancer. Previous rectal cancer methylation studies were conducted in patients without NACR or inconclusive. We hypothesized a correlation between methylation status and pathologic outcome following NACR. Methods: This is an IRB approved, retrospective, translational study of patients with LARC who received identical NACR before TME at New York University hospitals. Ten micron sections from FFPE tissue blocks underwent laser capture microdissection (LCM) followed by genome DNA isolation. Illumina Infinium 450k methylation array was used to assess 485,000 methylation sites. Methylation profiles and copy number changes were analyzed using in-house bioinformatics. Histone H3K27me, a global methylation marker, was assessed using immunohistochemistry (IHC) and expression quantified in carcinoma cells, normal epithelium, inflammatory cells, stromal cells and endothelial cells. Results: Tumor specimens from 52 patients were collected. Analyzed specimens of stromal and cancer cells showed distinct methylation profiles pre- and post- therapy. The histone H3K27me3 mark was markedly increased in carcinoma compared to normal epithelium and strong trimethyl mark expression persisted in invasive carcinoma after the therapy including single cells. We obtained adequate DNA to demonstrate differences between pre- and post- NACR specimens and tissue sites. Full data set, including the known clinical and pathologic results, is to be presented. Conclusions: This is the first study to combine LCM and high throughput quantitative methylation profiling in rectal cancer to correlate with NACR outcome. Histone H3K27me3 IHC can be used to identify high-grade and invasive carcinoma with high specificity. Data from our annotated clinical cohort and correlative molecular results can inform a future prospective trial.

A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers

Monomethylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and promoters, although its function is unknown. Here, we uncover roles for H3K4me1 in diverse cell types. Remarkably, we find that MLL3/4 provokes monomethylation of promoter regions and the conditional repression of muscle and inflammatory response genes in myoblasts. During myogenesis, muscle genes are activated, lose MLL3 occupancy, and become H3K4-trimethylated through an alternative COMPASS complex. Monomethylation-mediated repression was not restricted to skeletal muscle. Together with H3K27me3 and H4K20me1, H3K4me1 was associated with transcriptional silencing in embryonic fibroblasts, macrophages, and human embryonic stem cells (ESCs). On promoters of active genes, we find that H3K4me1 spatially demarcates the recruitment of factors that interact with H3K4me3, including ING1, which, in turn, recruits Sin3A. Our findings point to a unique role for H3K4 monomethylation in establishing boundaries that restrict the recruitment of chromatin-modifying enzymes to defined regions within promoters.

Colorectal cancer is reliably excluded in the frail and elderly population by minimal preparation CT

BACKGROUND

This study aimed to retrospectively assess the accuracy of minimal preparation computed tomography (MPCT) in the detection of colorectal cancer (CRC) within the frail and elderly population and to evaluate the relevance of extra-colonic findings (ECF).

METHODS

Radiology reports, clinical notes and follow-up reports from 207 patients who underwent MPCT to investigate for CRC between 2005 and 2009 were analysed. Patients were scanned following the administration of oral contrast for 48 h, without bowel preparation or colonic insufflation. MPCT results were measured against patient outcomes, with a minimum of 2 years of follow-up.

RESULTS

Twelve cases of clinically relevant CRC were confirmed (5.8 %). MPCT correctly identified 11 of these lesions (sensitivity 91.6 %). Thirty-one patients had a possible CRC identified by MPCT, which was not confirmed by further examination (specificity 84.1 %). This results in a positive predictive value of 26.2 % and a negative predictive value of 99.4 %. Five of the patients with colon cancer underwent curative surgery. Sixty-eight clinically relevant ECF were confirmed, including 14 previously undiagnosed extra-colonic malignancies. ECF were considered to account for the presenting complaint in 15.0 % (31/207) of all patients.

CONCLUSIONS

Minimal preparation computed tomography is an effective and reliable investigation for the exclusion of clinically relevant CRC in this population. It provides clinicians with a valuable and pragmatic alternative to colonoscopy and CT colonography when invasive examination or cathartic bowel preparation will be poorly tolerated and small polyps are of limited significance. MPCT has an advantage over purely luminal imaging in the detection of extra-colonic pathology and appears to have an equally important role in the detection of CRC.

Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1

To identify the compendium of distal regulatory elements that govern myogenic differentiation, we generated chromatin state maps based on histone modifications and recruitment of factors that typify enhancers in myoblasts and myotubes. We found a striking concordance between the locations of these newly defined enhancers, MyoD1-binding events, and noncoding RNA transcripts. These enhancers recruit several sequence-specific transcription factors in a spatially constrained manner around MyoD1-binding sites. Remarkably, MyoD1-null myoblasts show a wholesale loss of recruitment of these factors as well as diminished monomethylation of H3K4 (H3K4me1) and acetylation of H3K27 (H3K27ac) and reduced recruitment of Set7, an H3K4 monomethylase. Surprisingly, we found that H3K4me1, but not H3K27ac, could be restored by re-expression of MyoD1 in MyoD1(-/-) myoblasts, although re-expression of this factor in MyoD1-null myotubes restored both histone modifications. Our studies identified a role for MyoD1 in condition-specific enhancer assembly through recruitment of transcription factors and histone-modifying enzymes that shape muscle differentiation.

Comparison of cleaning efficacy between in-use disinfectant and electrolysed water in an English residential care home

BACKGROUND

Infection control in hospitals and care homes remains a key issue. They are regularly inspected regarding standards of hygiene, but visual assessment does not necessarily correlate with microbial cleanliness. Pathogens can persist in the inanimate environment for extended periods of time.

AIM

This prospective study compared the effectiveness of a novel sanitizer containing electrolysed water, in which the active ingredient is stabilized hypochlorous acid (Aqualution™), with the effectiveness of the quaternary ammonium disinfectant in current use for microbial removal from hand-touch surfaces in a care home. The study had a two-period crossover design.

METHODS

Five surfaces were cleaned daily over a four-week period, with screening swabs taken before and after cleaning. Swabs were cultured in order to compare levels of surface microbial contamination [colony-forming units (cfu)/cm(2)] before and after cleaning with each product.

FINDINGS

Cleaning with electrolysed water reduced the mean surface bacterial load from 2.6 [interquartile range (IQR) 0.30-30.40] cfu/cm(2) to 0.10 (IQR 0.10-1.40) cfu/cm(2) [mean log(10) reduction factor 1.042, 95% confidence interval (CI) 0.79-1.30]. Cleaning with the in-use quaternary ammonium disinfectant increased the bacterial load from 0.90 (IQR 0.10-8.50) cfu/cm(2) to 93.30 (IQR 9.85-363.65) cfu/cm(2) (mean log(10) reduction -1.499, 95% CI -1.87 to -1.12) (P < 0.0001). Using two proposed benchmark standards for surface microbial levels in hospitals, electrolysed water resulted in a higher 'pass rate' than the in-use quaternary ammonium disinfectant (80-86% vs 15-21%, P < 0.0001).

CONCLUSION

Electrolysed water exerts a more effective bacterial kill than the in-use quaternary ammonium disinfectant, which suggests that it may be useful as a surface sanitizer in environments such as care homes.

A model for rewarding professional growth in the diagnostic molecular oncology laboratory

The University of Texas M.D. Anderson Cancer Center (UTMDACC), Department of Pathology and Laboratory Medicine is committed to the endless pursuit of innovative research, education, training and administration for the prevention, diagnosis and clinical management of cancer and associated diseases. The molecular genetic technology professional development model promotes personal development, recognizes increased competencies, and sets high standards for all skills and services provided. There are four competency levels that comprise our Professional Development Model (PDM): Discovery, Application, Maturation, and Expert. The skill, knowledge, education, and certification requirements for each level are defined based on the business needs of each lab. When a genetic technologist successfully completes all skills, knowledge, proficiency, education and certification requirements within the appropriate time frame for a particular competency level, his/her salary would be adjusted to the entry point for the competency level he/she has completed.

Speckle reduction and lesion segmentation of OCT tooth images for early caries detection

The significance of identifying early non-cavitated carious lesions and monitoring the lesion extent has led to increasing prospects for prevention, early diagnosis, and implementation of conservative treatments. This paper emphasizes the importance of speckle reduction and possible lesion segmentation options of optical coherence tomography (OCT) images prior to caries detection. First, a comparison of popular speckle reduction filters is presented. These filtering algorithms were evaluated to measure the ability of different methods for reducing background noise from raw images. Both qualitative and quantitative results (signal-to-noise ratio, contrast-to-noise ratio) are reported. Image segmentation is then applied to multiple tooth images. With proper thresholding, high intensity response regions are outlined with the possibility of assessing caries and monitoring its regression. Our results show that a rotating kernel transformation (RKT) filter with 9x9 kernel size provides a good compromise between noise reduction yet preserving the pathological features of interest as required for subsequent feature segmentation analyses.

(Meth)Acrylate Vinyl Ester Hybrid Polymerizations

In this study vinyl ester monomers were synthesized by an amine catalyzed Michael addition reaction between a multifunctional thiol and the acrylate double bond of vinyl acrylate. The copolymerization behavior of both methacrylate/vinyl ester and acrylate/vinyl ester systems was studied with near-infrared spectroscopy. In acrylate/vinyl ester systems, the acrylate groups polymerize faster than the vinyl ester groups resulting in an overall conversion of 80% for acrylate double bonds in the acrylate/vinyl ester system relative to only 50% in the bulk acrylate system. In the methacrylate/vinyl ester systems, the difference in reactivity is even more pronounced resulting in two distinguishable polymerization regimes, one dominated by methacrylate polymerization and a second dominated by vinyl ester polymerization. A faster polymerization rate and higher overall conversion of the methacrylate double bonds is thus achieved relative to polymerization of the pure methacrylate system. The methacrylate conversion in the methacrylate/vinyl ester system is near 100% compared to only ~60% in the pure methacrylate system. Utilizing hydrophilic vinyl ester and hydrophobic methacrylate monomers, polymerization-induced phase separation is observed. The phase separated domain size is on the order of ~1 μm under the polymerization conditions. The phase separated domains become larger and more distinct with slower polymerization and correspondingly increased time for diffusion.

Using multiple data features improved the validity of osteoporosis case ascertainment from administrative databases

OBJECTIVES

The aim was to construct and validate algorithms for osteoporosis case ascertainment from administrative databases and to estimate the population prevalence of osteoporosis for these algorithms.

STUDY DESIGN AND SETTING

Artificial neural networks, classification trees, and logistic regression were applied to hospital, physician, and pharmacy data from Manitoba, Canada. Discriminative performance and calibration (i.e., error) were compared for algorithms defined from different sets of diagnosis, prescription drug, comorbidity, and demographic variables. Algorithms were validated against a regional bone mineral density testing program.

RESULTS

Discriminative performance and calibration were poorer and sensitivity was generally lower for algorithms based on diagnosis codes alone than for algorithms based on an expanded set of data features that included osteoporosis prescriptions and age. Validation measures were similar for neural networks and classification trees, but prevalence estimates were lower for the former model.

CONCLUSION

Multiple features of administrative data generally resulted in improved sensitivity of osteoporosis case-detection algorithm without loss of specificity. However, prevalence estimates using an expanded set of features were still slightly lower than estimates from a population-based study with primary data collection. The classification methods developed in this study can be extended to other chronic diseases for which there may be multiple markers in administrative data.

A mathematical model for assessing control strategies against West Nile virus

Since its incursion into North America in 1999, West Nile virus (WNV) has spread rapidly across the continent resulting in numerous human infections and deaths. Owing to the absence of an effective diagnostic test and therapeutic treatment against WNV, public health officials have focussed on the use of preventive measures in an attempt to halt the spread of WNV in humans. The aim of this paper is to use mathematical modelling and analysis to assess two main anti-WNV preventive strategies, namely: mosquito reduction strategies and personal protection. We propose a single-season ordinary differential equation model for the transmission dynamics of WNV in a mosquito-bird-human community, with birds as reservoir hosts and culicine mosquitoes as vectors. The model exhibits two equilibria; namely the disease-free equilibrium and a unique endemic equilibrium. Stability analysis of the model shows that the disease-free equilibrium is globally asymptotically stable if a certain threshold quantity (R0), which depends solely on parameters associated with the mosquito-bird cycle, is less than unity. The public health implication of this is that WNV can be eradicated from the mosquito-bird cycle (and, consequently, from the human population) if the adopted mosquito reduction strategy (or strategies) can make R0<1. On the other hand, it is shown, using a novel and robust technique that is based on the theory of monotone dynamical systems coupled with a regular perturbation argument and a Liapunov function, that if R0>1, then the unique endemic equilibrium is globally stable for small WNV-induced avian mortality. Thus, in this case, WNV persists in the mosquito-bird population.

Latent S alleles are widespread in cultivated self-compatible Brassica napus

The genetic control of self-incompatibility in Brassica napus was investigated using crosses between resynthesized lines of B. napus and cultivars of oilseed rape. These crosses introduced eight C-genome S alleles from Brassica oleracea (S16, S22, S23, S25, S29, S35, S60, and S63) and one A-genome S allele from Brassica rapa (SRM29) into winter oilseed rape. The inheritance of S alleles was monitored using genetic markers and S phenotypes were determined in the F1, F2, first backcross (B1), and testcross (T1) generations. Two different F1 hybrids were used to develop populations of doubled haploid lines that were subjected to genetic mapping and scored for S phenotype. These investigations identified a latent S allele in at least two oilseed rape cultivars and indicated that the S phenotype of these latent alleles was masked by a suppressor system common to oilseed rape. These latent S alleles may be widespread in oilseed rape varieties and are possibly associated with the highly conserved C-genome S locus of these crop types. Segregation for S phenotype in subpopulations uniform for S genotype suggests the existence of suppressor loci that influenced the expression of the S phenotype. These suppressor loci were not linked to the S loci and possessed suppressing alleles in oilseed rape and non-suppressing alleles in the diploid parents of resynthesized B. napus lines.

Molecular classification of scrapie strains in mice using gene expression profiling

Transmissible spongiform encephalopathy strains demonstrate specific prion characteristics, each with specific incubation times, and strain-specific patterns of deposition of the misfolded isoform of prion, PrPSc, in the brains of infected individuals. Different biochemical properties, including glycosylation profiles and the degree of proteinase resistance, have been shown to be strain-specific. However, no relationship between these properties and the phenotypic differences in the subsequent diseases has as yet been determined. Here we explore the utility of gene expression profiles to identify differences in the host response to different strains of prion agent. We identify 114 genes that exhibit significantly different levels of expression in mice infected with three strains of scrapie. These genes represent a pool of genes involved in a strain-specific response to prion disease. We have identified the most discriminatory genes from this list utilizing a wrapper-based feature selection algorithm with external cross-validation.

Identification of central nervous system genes involved in the host response to the scrapie agent during preclinical and clinical infection

Genes that are expressed differentially in the central nervous system of mice during infection with mouse-adapted scrapie agents were identified in this study. cDNA microarrays were used to examine gene-expression profiles at early, middle (preclinical) and late (clinical) time points after inoculation. A number of genes that showed significant changes in expression during the clinical stage of disease were identified. Of these, 138 were upregulated and 20 were downregulated. A smaller number of genes showed differential expression at the early and middle stages of the disease time course. These genes are interesting, as they may reflect biological processes that are involved in the molecular pathogenesis of the prion agent. At present, little is known about the early events in the disease process that trigger neurodegeneration. Perhaps most interestingly, one group of genes that exhibited decreased expression in all tested stages of the disease was identified in this study. This cluster included four transcripts representing haematopoietic system-related genes, which suggests that the haematopoietic system is involved in the disease process from an early stage.

Unsupervised feature dimension reduction for classification of MR spectra

We present an unsupervised feature dimension reduction method for the classification of magnetic resonance spectra. The technique preserves spectral information, important for disease profiling. We propose to use this technique as a preprocessing step for computationally demanding wrapper-based feature subset selection. We show that the classification accuracy on an independent test set can be sustained while achieving considerable feature reduction. Our method is applicable to other classification techniques, such as neural networks, support vector machines, etc.