Evaluation of atlas based mouse brain segmentation

Magentic Reasonance Imaging for mouse phenotype study is one of the important tools to understand human diseases. In this paper, we present a fully automatic pipeline for the process of morphometric mouse brain analysis. The method is based on atlas-based tissue and regional segmentation, which was originally developed for the human brain. To evaluate our method, we conduct a qualitative and quantitative validation study as well as compare of b-spline and fluid registration methods as components in the pipeline. The validation study includes visual inspection, shape and volumetric measurements and stability of the registration methods against various parameter settings in the processing pipeline. The result shows both fluid and b-spline registration methods work well in murine settings, but the fluid registration is more stable. Additionally, we evaluated our segmentation methods by comparing volume differences between Fmr1 FXS in FVB background vs C57BL/6J mouse strains

Executive function predictors of science achievement in middle-school students

Cognitive flexibility as measured by the Wisconsin Card Sort Task (WCST) has long been associated with frontal lobe function. More recently, this construct has been associated with executive function (EF), which shares overlapping neural correlates. Here, we investigate the relationship between EF, cognitive flexibility, and science achievement in adolescents. This is important because there are fewer educational neuroscience studies of scientific reasoning than of other academically relevant forms of cognition (i.e., mathematical thinking and language understanding). Eighth grade students at a diverse middle school in the Midwestern US completed classroom-adapted measures of three EFs (shifting, inhibition, and updating) and the WCST. Science achievement was indexed by students’ standardized test scores and their end-of-the-year science class grades. Among the EF measures, updating was strongly predictive of science achievement. The association between cognitive flexibility and science achievement was comparatively weaker. These findings illuminate the relationship between EF, cognitive flexibility, and science achievement. A methodological contribution was the development of paper-and-pencil based versions of standard EF and cognitive flexibility measures suitable for classroom administration. We expect these materials to help support future classroom-based studies of EF and cognitive flexibility, and whether training these abilities in adolescent learners improves their science achievement

Association of endocrine active environmental compounds with body mass index and weight loss following bariatric surgery

IntroductionThe objective of this study was to study associations of a wide range of halogenated biphenyls, dibenzo‐p‐dioxins, dibenzofurans, and diphenylethers with body mass index (BMI) and evaluate changes in their concentration following bariatric surgery.MethodsSubcutaneous fat, visceral fat, and liver tissue samples were collected from 106 patients undergoing Roux‐en‐Y gastric bypass surgery for weight loss or patients who were undergoing abdominal surgery for non‐bariatric reasons. We measured concentrations of an extensive panel of chlorinated and brominated biphenyls, dioxins, and furans, and brominated diphenylethers in the samples. We conducted linear regression to examine associations with BMI, adjusting for age and gender. Changes in concentration for indicator chemicals were evaluated in samples collected following bariatric surgery in a small sub‐population.ResultsAfter adjustments for age and gender and correction for multiple testing, seven ortho‐chlorinated biphenyls, one non‐ortho‐chlorinated biphenyl, four PCDD/F’s and one ortho‐brominated biphenyl were associated with BMI. The strongest associations between BMI and lipid‐adjusted concentrations were seen with PCB‐105 in subcutaneous fat (beta=16.838 P‐val=1.45E‐06) PCB‐126 in visceral fat (beta=15.067 P‐val=7.72E‐06) and PCB‐118 (beta=14.101 P‐val=2.66E‐05) in liver. The concentrations of sum PCBs, chlorinated toxic equivalent quantity (TEQ's) and brominated compounds increased significantly with weight loss in subcutaneous fat in a group of ten individuals resampled up to five years after bariatric surgery and substantial weight loss.ConclusionWe show that selected polychlorinated biphenyls PCBs and structurally related polychlorinated dibenzo‐p‐dioxins dibenzofurans (PCDD/Fs) were associated with BMI. Concentrations of these lipophilic compounds in subcutaneous fat increased following bariatric surgery

Evaluation of atlas based mouse brain segmentation

Magentic Reasonance Imaging for mouse phenotype study is one of the important tools to understand human diseases. In this paper, we present a fully automatic pipeline for the process of morphometric mouse brain analysis. The method is based on atlas-based tissue and regional segmentation, which was originally developed for the human brain. To evaluate our method, we conduct a qualitative and quantitative validation study as well as compare of b-spline and fluid registration methods as components in the pipeline. The validation study includes visual inspection, shape and volumetric measurements and stability of the registration methods against various parameter settings in the processing pipeline. The result shows both fluid and b-spline registration methods work well in murine settings, but the fluid registration is more stable. Additionally, we evaluated our segmentation methods by comparing volume differences between Fmr1 FXS in FVB background vs C57BL/6J mouse strains

Development and Psychometric Properties of an Assessment for Persons With Intellectual Disability—The interRAI ID

This paper describes the development of the interRAI-Intellectual Disability (interRAI ID), a comprehensive instrument that assesses all key domains of interest to service providers relative to a person with an intellectual disability (ID). The authors report on the reliability and validity of embedded scales for cognition, self-care, aggression, and depression. Four provider agencies volunteered to participate and assessed a total of 160 community-dwelling adults with ID using the interRAI ID, Dementia Questionnaire for Persons with Mental Retardation, and Reiss Screen for Maladaptive Behavior. All scales had acceptable levels of internal consistency (Cronbach’s alpha 0.74–0.93) and good relationships with the criterion measures ( r  = 0.50–0.93, p  < 0.0001). The development of the interRAI ID represents an important and successful first step toward an integrated, comprehensive, and standardized assessment of adults with ID. Use of this instrument may lead to more appropriate support planning, enhanced communication between various professionals supporting persons with ID, and a more seamless approach to supports across the health and social service systems.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75618/1/j.1741-1130.2006.00094.x.pd

3D of brain shape and volume after cranial vault remodeling surgery for craniosynostosis correction in infants

ABSTRACT The skull of young children is made up of bony plates that enable growth. Craniosynostosis is a birth defect that causes one or more sutures on an infant&apos;s skull to close prematurely. Corrective surgery focuses on cranial and orbital rim shaping to return the skull to a more normal shape. Functional problems caused by craniosynostosis such as speech and motor delay can improve after surgical correction, but a post-surgical analysis of brain development in comparison with age-matched healthy controls is necessary to assess surgical outcome. Full brain segmentations obtained from pre-and post-operative computed tomography (CT) scans of 8 patients with single suture sagittal (n=5) and metopic (n=3), nonsyndromic craniosynostosis from 41 to 452 days-of-age were included in this study. Age-matched controls obtained via 4D acceleration-based regression of a cohort of 402 full brain segmentations from healthy controls magnetic resonance images (MRI) were also used for comparison (ages 38 to 825 days). 3D point-based models of patient and control cohorts were obtained using SPHARM-PDM shape analysis tool. From a full dataset of regressed shapes, 240 healthy regressed shapes between 30 and 588 days-of-age (time step = 2.34 days) were selected. Volumes and shape metrics were obtained for craniosynostosis and healthy age-matched subjects. Volumes and shape metrics in single suture craniosynostosis patients were larger than age-matched controls for pre-and post-surgery. The use of 3D shape and volumetric measurements show that brain growth is not normal in patients with single suture craniosynostosis

Brain bases of morphological processing in Chineseâ English bilingual children

Can bilingual exposure impact children’s neural circuitry for learning to read? To answer this question, we investigated the brain bases of morphological awareness, one of the key spoken language abilities for learning to read in English and Chinese. Bilingual Chineseâ English and monolingual English children (N = 22, ages 7â 12) completed morphological tasks that best characterize each of their languages: compound morphology in Chinese (e.g. basket + ball = basketball) and derivational morphology in English (e.g. re + do = redo). In contrast to monolinguals, bilinguals showed greater activation in the left middle temporal region, suggesting that bilingual exposure to Chinese impacts the functionality of brain regions supporting semantic abilities. Similar to monolinguals, bilinguals showed greater activation in the left inferior frontal region [BA 45] in English than Chinese, suggesting that young bilinguals form languageâ specific neural representations. The findings offer new insights to inform bilingual and crossâ linguistic models of language and literacy acquisition.The study investigated the impact of bilingual exposure on children’s language and reading abilities. During auditory morphological awareness tasks, young Chineseâ English bilinguals showed monolingualâ like competence as well as languageâ specific patterns of brain activation in left inferior frontal gyrus (IFG). This activation was greater for English than for Chinese in left IFG BA 45, but similar across languages in left IFG BA 47. Relative to English monolinguals, the bilinguals showed greater activation in left MTG region and this activation was significantly correlated with bilingualsâ English literacy. The findings suggest that bilingual exposure to a language with rich lexical morphology, such as Chinese, impacts the functionality of bilingualsâ left temporal regions typically associated with lexicoâ semantic processing and the ability to link word meanings to their orthographic forms.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138272/1/desc12449_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138272/2/desc12449.pd

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio