Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material

BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH. METHODS: In this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use. RESULTS: Our protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method. CONCLUSION: This report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility

Two Stellar Components in the Halo of the Milky Way

The halo of the Milky Way provides unique elemental abundance and kinematic information on the first objects to form in the Universe, which can be used to tightly constrain models of galaxy formation and evolution. Although the halo was once considered a single component, evidence for its dichotomy has slowly emerged in recent years from inspection of small samples of halo objects. Here we show that the halo is indeed clearly divisible into two broadly overlapping structural components -- an inner and an outer halo -- that exhibit different spatial density profiles, stellar orbits and stellar metallicities (abundances of elements heavier than helium). The inner halo has a modest net prograde rotation, whereas the outer halo exhibits a net retrograde rotation and a peak metallicity one-third that of the inner halo. These properties indicate that the individual halo components probably formed in fundamentally different ways, through successive dissipational (inner) and dissipationless (outer) mergers and tidal disruption of proto-Galactic clumps.Comment: Two stand-alone files in manuscript, concatenated together. The first is for the main paper, the second for supplementary information. The version is consistent with the version published in Natur

Kinematics and Dynamics of the Galactic Stellar Halo

The structure, kinematics and dynamics of the Galactic stellar halo are reviewed including evidence of substructure in the spatial distribution and kinematics of halo stars. Implications for galaxy formation theory are subsequently discussed; in particular it is argued that the observed kinematics of stars in the outer Galactic halo can be used as an important constraint on viable galaxy formation scenarios

How many motoric body representations can we grasp?

At present there is a debate on the number of body representations in the brain. The most commonly used dichotomy is based on the body image, thought to underlie perception and proven to be susceptible to bodily illusions, versus the body schema, hypothesized to guide actions and so far proven to be robust against bodily illusions. In this rubber hand illusion study we investigated the susceptibility of the body schema by manipulating the amount of stimulation on the rubber hand and the participant’s hand, adjusting the postural configuration of the hand, and investigating a grasping rather than a pointing response. Observed results showed for the first time altered grasping responses as a consequence of the grip aperture of the rubber hand. This illusion-sensitive motor response challenges one of the foundations on which the dichotomy is based, and addresses the importance of illusion induction versus type of response when investigating body representations

Elucidating a genomic signature associated with behavioral and executive function after moderate to severe pediatric TBI: a systems biology informed approach

This is the final version. Available from Frontiers Media via the DOI in this record. Data availability statement: Data for this project have been deposited into the Federal Interagency Traumatic Brain Injury Research Informatics System (FITBIR) as per funding requirement and can be accessed at the following link: https://fitbir.nih.gov/study_profile/351.Introduction: There is significant unexplained variability in behavioral and executive functioning after pediatric traumatic brain injury (TBI). Prior research indicates that there are likely genetic contributions; however, current research is limited. The purpose of this study is to use a systems biology informed approach to characterize the genomic signature related to behavioral and executive functioning ∼12 months after moderate through severe TBI in children. Methods: Participants were from two prospective cohorts of children with severe TBI (Cohort #1) and moderate-severe TBI and an orthopedic injury (OI) group (Cohort #2). Participants included 196 children (n = 72 and n = 124 total from each respective cohort), ranging in age between 0–17 years at the time of injury. In total, 86 children had severe TBI, 49 had moderate TBI, and 61 had an OI. Global behavioral functioning assessed via the Child Behavior Checklist and executive function assessed via the Behavioral Rating Inventory of Executive Function at ∼ 12 months post injury served as outcomes. To test for a genomic signature, we compared the number of nominally significant (p < 0.05) polymorphisms associated with the outcomes in our systems biology identified genes to a set 10,000 permutations using control genes (e.g., not implicated by systems biology). We used the ToppFun application from Toppgene Suite to identify enriched biologic processes likely to be associated with behavioral and executive function outcomes. Results: At 12 months post injury, injury type (TBI vs OI) by polymorphism interaction was significantly enriched in systems biology selected genes for behavioral and executive function outcomes, suggesting these genes form a genomic signature. Effect sizes of the associations from our genes of interest ranged from.2–.5 for the top 5% of variants. Systems biology analysis of the variants associated with the top 5% effect sizes indicated enrichment in several specific biologic processes and systems. Discussion: Findings indicate that a genomic signature may explain heterogeneity of behavioral and executive outcomes after moderate and severe TBI. This work provides the foundation for constructing genomic signatures and integrating systems biology and genetic information into future recovery, prognostic, and treatment algorithms.National Institutes of HealthNational Institute of Neurologic Disorders and Stroke (NINDS)National Institute of Child Health and Human Development (NICHD)National Center for Advancing Translational Scienc

The merger that led to the formation of the Milky Way's inner stellar halo and thick disk

The assembly process of our Galaxy can be retrieved using the motions and chemistry of individual stars. Chemo-dynamical studies of the nearby halo have long hinted at the presence of multiple components such as streams, clumps, duality and correlations between the stars' chemical abundances and orbital parameters. More recently, the analysis of two large stellar surveys have revealed the presence of a well-populated chemical elemental abundance sequence, of two distinct sequences in the colour-magnitude diagram, and of a prominent slightly retrograde kinematic structure all in the nearby halo, which may trace an important accretion event experienced by the Galaxy. Here report an analysis of the kinematics, chemistry, age and spatial distribution of stars in a relatively large volume around the Sun that are mainly linked to two major Galactic components, the thick disk and the stellar halo. We demonstrate that the inner halo is dominated by debris from an object which at infall was slightly more massive than the Small Magellanic Cloud, and which we refer to as Gaia-Enceladus. The stars originating in Gaia-Enceladus cover nearly the full sky, their motions reveal the presence of streams and slightly retrograde and elongated trajectories. Hundreds of RR Lyrae stars and thirteen globular clusters following a consistent age-metallicity relation can be associated to Gaia-Enceladus on the basis of their orbits. With an estimated 4:1 mass-ratio, the merger with Gaia-Enceladus must have led to the dynamical heating of the precursor of the Galactic thick disk and therefore contributed to the formation of this component approximately 10 Gyr ago. These findings are in line with simulations of galaxy formation, which predict that the inner stellar halo should be dominated by debris from just a few massive progenitors.Comment: 19 pages, 8 figures. Published in Nature in the issue of Nov. 1st, 2018. This is the authors' version before final edit

The stellar halo of the Galaxy

Stellar halos may hold some of the best preserved fossils of the formation history of galaxies. They are a natural product of the merging processes that probably take place during the assembly of a galaxy, and hence may well be the most ubiquitous component of galaxies, independently of their Hubble type. This review focuses on our current understanding of the spatial structure, the kinematics and chemistry of halo stars in the Milky Way. In recent years, we have experienced a change in paradigm thanks to the discovery of large amounts of substructure, especially in the outer halo. I discuss the implications of the currently available observational constraints and fold them into several possible formation scenarios. Unraveling the formation of the Galactic halo will be possible in the near future through a combination of large wide field photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes. Full-resolution version available at http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd

Prevalence of inappropriate medication using Beers criteria in Japanese long-term care facilities

BACKGROUND: The prevalence and risk factors of potentially inappropriate medication use among the elderly patients have been studied in various countries, but because of the difficulty of obtaining data on patient characteristics and medications they have not been studied in Japan. METHODS: We conducted a retrospective cross-sectional study in 17 Japanese long-term care (LTC) facilities by collecting data from the comprehensive MDS assessment forms for 1669 patients aged 65 years and over who were assessed between January and July of 2002. Potentially inappropriate medications were identified on the basis of the 2003 Beers criteria. RESULTS: The patients in the sample were similar in terms of demographic characteristics to those in the national survey. Our study revealed that 356 (21.1%) of the patients were treated with potentially inappropriate medication independent of disease or condition. The most commonly inappropriately prescribed medication was ticlopidine, which had been prescribed for 107 patients (6.3%). There were 300 (18.0%) patients treated with at least 1 inappropriate medication dependent on the disease or condition. The highest prevalence of inappropriate medication use dependent on the disease or condition was found in patients with chronic constipation. Multiple logistic regression analysis revealed psychotropic drug use (OR = 1.511), medication cost of per day (OR = 1.173), number of medications (OR = 1.140), and age (OR = 0.981) as factors related to inappropriate medication use independent of disease or condition. Neither patient characteristics nor facility characteristics emerged as predictors of inappropriate prescription. CONCLUSION: The prevalence and predictors of inappropriate medication use in Japanese LTC facilities were similar to those in other countries

APOGEE chemical abundances of globular cluster giants in the inner Galaxy

We report chemical abundances obtained by Sloan Digital Sky Survey (SDSS)-III/Apache Point Observatory Galactic Evolution Experiment for giant stars in five globular clusters located within 2.2 kpc of the Galactic Centre. We detect the presence of multiple stellar populations in four of those clusters (NGC 6553, NGC 6528, Terzan 5 and Palomar 6) and find strong evidence for their presence in NGC 6522. All clusters with a large enough sample present a significant spread in the abundances of N, C, Na and Al, with the usual correlations and anticorrelations between various abundances seen in other globular clusters. Our results provide important quantitative constraints on theoretical models for self-enrichment of globular clusters, by testing their predictions for the dependence of yields of elements such as Na, N, C and Al on metallicity. They also confirm that, under the assumption that field N-rich stars originate from globular cluster destruction, they can be used as tracers of their parental systems in the high-metallicity regime

Homogeneous analysis of globular clusters from the APOGEE survey with the BACCHUS code – II. The Southern clusters and overview

We investigate the Fe, C, N, O, Mg, Al, Si, K, Ca, Ce, and Nd abundances of 2283 red giant stars in 31 globular clusters from high-resolution spectra observed in both the Northern and Southern hemisphere by the SDSS-IV APOGEE-2 survey. This unprecedented homogeneous data set, largest to date, allows us to discuss the intrinsic Fe spread, the shape, and statistics of Al-Mg and N-C anti-correlations as a function of cluster mass, luminosity, age, and metallicity for all 31 clusters. We find that the Fe spread does not depend on these parameters within our uncertainties including cluster metallicity, contradicting earlier observations. We do not confirm the metallicity variations previously observed in M22 and NGC 1851. Some clusters show a bimodal Al distribution, while others exhibit a continuous distribution as has been previously reported in the literature. We confirm more than two populations in ω Cen and NGC 6752, and find new ones in M79. We discuss the scatter of Al by implementing a correction to the standard chemical evolution of Al in the Milky Way. After correction, its dependence on cluster mass is increased suggesting that the extent of Al enrichment as a function of mass was suppressed before the correction. We observe a turnover in the Mg-Al anticorrelation at very low Mg in ω Cen, similar to the pattern previously reported in M15 and M92. ω Cen may also have a weak K-Mg anticorrelation, and if confirmed, it would be only the third cluster known to show such a pattern