Phenotyping Down syndrome: discovery and predictive modelling with electronic medical records.

BACKGROUND: Individuals with Down syndrome (DS) have a heightened risk for various co-occurring health conditions, including congenital heart disease (CHD). In this two-part study, electronic medical records (EMRs) were leveraged to examine co-occurring health conditions among individuals with DS (Study 1) and to investigate health conditions linked to surgical intervention among DS cases with CHD (Study 2). METHODS: De-identified EMRs were acquired from Vanderbilt University Medical Center and facilitated creating a cohort of N = 2282 DS cases (55% females), along with comparison groups for each study. In Study 1, DS cases were one-by-two sex and age matched with samples of case-controls and of individuals with other intellectual and developmental difficulties (IDDs). The phenome-disease association study (PheDAS) strategy was employed to reveal co-occurring health conditions in DS versus comparison groups, which were then ranked for how often they are discussed in relation to DS using the PubMed database and Novelty Finding Index. In Study 2, a subset of DS individuals with CHD [N = 1098 (48%)] were identified to create longitudinal data for N = 204 cases with surgical intervention (19%) versus 204 case-controls. Data were included in predictive models and assessed which model-based health conditions, when more prevalent, would increase the likelihood of surgical intervention. RESULTS: In Study 1, relative to case-controls and those with other IDDs, co-occurring health conditions among individuals with DS were confirmed to include heart failure, pulmonary heart disease, atrioventricular block, heart transplant/surgery and primary pulmonary hypertension (circulatory); hypothyroidism (endocrine/metabolic); and speech and language disorder and Alzheimer's disease (neurological/mental). Findings also revealed more versus less prevalent co-occurring health conditions in individuals with DS when comparing with those with other IDDs. Findings with high Novelty Finding Index were abnormal electrocardiogram, non-rheumatic aortic valve disorders and heart failure (circulatory); acid-base balance disorder (endocrine/metabolism); and abnormal blood chemistry (symptoms). In Study 2, the predictive models revealed that among individuals with DS and CHD, presence of health conditions such as congestive heart failure (circulatory), valvular heart disease and cardiac shunt (congenital), and pleural effusion and pulmonary collapse (respiratory) were associated with increased likelihood of surgical intervention. CONCLUSIONS: Research efforts using EMRs and rigorous statistical methods could shed light on the complexity in health profile among individuals with DS and other IDDs and motivate precision-care development.

Exploratory Multisite MR Spectroscopic Imaging Shows White Matter Neuroaxonal Loss Associated with Complications of Type 1 Diabetes in Children.

BACKGROUND AND PURPOSE: Type 1 diabetes affects over 200,000 children in the United States and is associated with an increased risk of cognitive dysfunction. Prior single-site, single-voxel MRS case reports and studies have identified associations between reduced NAA/Cr, a marker of neuroaxonal loss, and type 1 diabetes. However, NAA/Cr differences among children with various disease complications or across different brain tissues remain unclear. To better understand this phenomenon and the role of MRS in characterizing it, we conducted a multisite pilot study. MATERIALS AND METHODS: In 25 children, 6-14 years of age, with type 1 diabetes across 3 sites, we acquired T1WI and axial 2D MRSI along with phantom studies to calibrate scanner effects. We quantified tissue-weighted NAA/Cr in WM and deep GM and modeled them against study covariates. RESULTS: We found that MRSI differentiated WM and deep GM by NAA/Cr on the individual level. On the population level, we found significant negative associations of WM NAA/Cr with chronic hyperglycemia quantified by hemoglobin A1c (P < .005) and a history of diabetic ketoacidosis at disease onset (P < .05). We found a statistical interaction (P < .05) between A1c and ketoacidosis, suggesting that neuroaxonal loss from ketoacidosis may outweigh that from poor glucose control. These associations were not present in deep GM. CONCLUSIONS: Our pilot study suggests that MRSI differentiates GM and WM by NAA/Cr in this population, disease complications may lead to neuroaxonal loss in WM in children, and deeper investigation is warranted to further untangle how diabetic ketoacidosis and chronic hyperglycemia affect brain health and cognition in type 1 diabetes.

Data for evaluation of the onshore Cretaceous Zululand Basin in South Africa for geological CO2 storage.

The world has set the goal of reducing CO2 emissions from burning fossil fuels by using carbon capture and storage (CCS) as one of the major solutions. A sudden and complete switch from fossil fuels to renewable resources cannot be achieved immediately. Therefore, CCS remains an essential techniques to reduce CO2. In this work, the 180 - 65 Ma old onshore part of the Zululand Basin in KwaZulu-Natal in South Africa was investigated for geological CO2 sequestration. A total of 160 core samples of sandstone, conglomerate, tuff, rhyolite, breccia, and siltstone were taken from NZA, ZA, ZB, and ZC drill cores. The wells were drilled in the 1960s by the South African Petroleum and Gas Corporation Company for hydrocarbon exploration. In order to examine the basin suitability for CO2 storage, porosity and permeability, mineralogy, geochemistry, geomechanical properties, and H2O-CO2-rock interactions were investigated using geological core logging, spectral scanning, petrography, X-ray diffraction (XRD), X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry, uniaxial compressive stress, and scanning electron microscopy. The basin comprises clastic sedimentary rocks, pyroclastic deposits and carbonates from the Makatini, Mzinene and St. Lucia formations. Aptian and Cenomanian sandstones are identified as CO2 reservoirs, and the siltstone above is considered capstone. The sandstone comprises on average 34.45 wt% quartz, 32.91 wt% clays, 29.53 wt% feldspars, 4.44 wt% carbonates, 3.10 wt% Fe-oxides, 2.40 wt% micas, and 2.00 wt% organic materials as per XRD data, also contains trace amounts of sulphides and sulphates. Geochemical XRF data for sandstone are 29.72 - 62.51 wt% SiO2, 6.95 - 13.44 wt% Al2O3, 3.06 - 48.81 wt%, 1.90 - 4.51 wt% MgO, 1.04 - 2.19 wt% K2O, 1.00 - 3.67 Na2O wt%. The content of TiO2, Cr2O3 and P2O5 is below 0.01 wt% each. Siltstone has similar mineralogy and geochemistry as sandstone, but high clay content, fine-grained, impervious, with porosity <5%. The sandstone and siltstone are geomechanically soft and recorded 15 MPa on the Enerpac P141 device. CO2-H2O-rock interaction experiments performed at 100 °C and 100 bar using autoclaves showed that sandstone and siltstone react with scCO2.

Transcriptomics of cortical gray matter thickness decline during normal aging.

INTRODUCTION: We performed a whole-transcriptome correlation analysis, followed by the pathway enrichment and testing of innate immune response pathway analyses to evaluate the hypothesis that transcriptional activity can predict cortical gray matter thickness (GMT) variability during normal cerebral aging. METHODS: Transcriptome and GMT data were available for 379 individuals (age range=28-85) community-dwelling members of large extended Mexican American families. Collection of transcriptome data preceded that of neuroimaging data by 17 years. Genome-wide gene transcriptome data consisted of 20,413 heritable lymphocytes-based transcripts. GMT measurements were performed from high-resolution (isotropic 800 µm) T1-weighted MRI. Transcriptome-wide and pathway enrichment analysis was used to classify genes correlated with GMT. Transcripts for sixty genes from seven innate immune pathways were tested as specific predictors of GMT variability. RESULTS: Transcripts for eight genes (IGFBP3, LRRN3, CRIP2, SCD, IDS, TCF4, GATA3, and HN1) passed the transcriptome-wide significance threshold. Four orthogonal factors extracted from this set predicted 31.9% of the variability in the whole-brain and between 23.4 and 35% of regional GMT measurements. Pathway enrichment analysis identified six functional categories including cellular proliferation, aggregation, differentiation, viral infection, and metabolism. The integrin signaling pathway was significantly (p<10(-6)) enriched with GMT. Finally, three innate immune pathways (complement signaling, toll-receptors and scavenger and immunoglobulins) were significantly associated with GMT. CONCLUSION: Expression activity for the genes that regulate cellular proliferation, adhesion, differentiation and inflammation can explain a significant proportion of individual variability in cortical GMT. Our findings suggest that normal cerebral aging is the product of a progressive decline in regenerative capacity and increased neuroinflammation.

Regional differences in diffusion tensor imaging measurements: assessment of intrarater and interrater variability.

BACKGROUND AND PURPOSE: Diffusion tensor imaging (DTI) has become a valuable tool in both the research and clinical evaluation of subjects. We sought to quantify interobserver and intraobserver variability of diffusivity and diffusion anisotropy measurements with regard to specific regions of interest (ROIs). MATERIALS AND METHODS: The subject group consisted of 5 healthy control subjects and 7 study subjects (all males; 16-19 years old; mean age = 17.5 years), as part of a protocol for closed head injury. Two whole-brain DTI scans were acquired on a 3T scanner for each subject. Analysis was performed using a ROI approach. Two independent observers analyzed the apparent diffusion coefficient (ADC) and fractional anisotropy (FA) indices in the corpus callosum, cortical spinal tract, internal capsules (ICs), basal ganglia, and centrum semiovale (CSO). Intraobserver and interobserver variability were calculated for the mean ADC, FA, and ordered eigenvalues of the diffusion tensor (lambda(1), lambda(2), and lambda(3)). RESULTS: The overall kappa statistic for intraobserver variability for both observers showed slight-to-substantial agreement (kappa = 0.02-0.69), however FA values in the CSO showed only slight agreement. Interobserver agreement was also slight to substantial for these DTI measurements with high variability in FA values in the IC and CSO. CONCLUSIONS: When one is comparing 2 DTI measurements, it is important to assess intraobserver and interobserver variability. We recommend caution in the analysis of DTI contrasts in the IC and CSO, because we have found the widest range of variability in measurements within these structures.

ROBUST MAXIMUM LIKELIHOOD ESTIMATION IN Q-SPACE MRI.

Q-space imaging is an emerging diffusion weighted MR imaging technique to estimate molecular diffusion probability density functions (PDF's) without the need to assume a Gaussian distribution. We present a robust M-estimator, Q-space Estimation by Maximizing Rician Likelihood (QEMRL), for diffusion PDF's based on maximum likelihood. PDF's are modeled by constrained Gaussian mixtures. In QEMRL, robust likelihood measures mitigate the impacts of imaging artifacts. In simulation and in vivo human spinal cord, the method improves reliability of estimated PDF's and increases tissue contrast. QEMRL enables more detailed exploration of the PDF properties than prior approaches and may allow acquisitions at higher spatial resolution.

Ways to improve the biosecurity of bovine semen.

Semen production and trade is a worldwide industry. A framework, based on international standards is awaiting international and national regulation. In the perspective of biosecurity of the final product, critical notes can be made according to the semen production regulation and product safety. Process description brings the obligatory health standards for the production bulls, collection and processing of semen, identification, registration, worldwide distribution and insemination into discussion. Test frequency, test quality and demands, way of sampling and test consistency can influence product safety. New scientific knowledge can influence the value of the regulation. Whether a country is free of notifiable disease should influence decisions regarding necessary tests for the production bulls. The biosecurity of the semen production process is influenced by several factors. The effectiveness of the antibiotics used is questionable. The extenders for cryopreservation added to the semen can affect product safety. The way materials and storage containers have to be disinfected must be clear. In modern industry, tracking and tracing is an important issue. Worldwide differences in ways of identification of straws do not benefit a proper identification and registration throughout the process. Regulation could help improve the transparency of production and trade. Before anything concerning biohazard is implemented in regulation, each rule should be thoroughly based on scientific research where possible and furthermore it must be possible to enforce the regulation. The effort it takes to enforce the regulation should be in balance with the benefit it provides. An approach to alter regulation quickly is advisable. To produce a safe product that is accepted for international trade is of vital interest for the survival of artificial insemination (AI) in cattle.