Programming Heterogeneous Parallel Machines Using Refactoring and Monte-Carlo Tree Search

Funding: This work was supported by the EU Horizon 2020 project, TeamPlay, Grant Number 779882, and UK EPSRC Discovery, Grant Number EP/P020631/1.This paper presents a new technique for introducing and tuning parallelism for heterogeneous shared-memory systems (comprising a mixture of CPUs and GPUs), using a combination of algorithmic skeletons (such as farms and pipelines), Monte–Carlo tree search for deriving mappings of tasks to available hardware resources, and refactoring tool support for applying the patterns and mappings in an easy and effective way. Using our approach, we demonstrate easily obtainable, significant and scalable speedups on a number of case studies showing speedups of up to 41 over the sequential code on a 24-core machine with one GPU. We also demonstrate that the speedups obtained by mappings derived by the MCTS algorithm are within 5–15% of the best-obtained manual parallelisation.Publisher PDFPeer reviewe

Individual, Environmental, and Meteorological Predictors of Daily Personal Ultraviolet Radiation Exposure Measurements in a United States Cohort Study

Background Individual exposure to ultraviolet radiation (UVR) is challenging to measure, particularly for diseases with substantial latency periods between first exposure and diagnosis of outcome, such as cancer. To guide the choice of surrogates for long-term UVR exposure in epidemiologic studies, we assessed how well stable sun-related individual characteristics and environmental/meteorological factors predicted daily personal UVR exposure measurements. Methods We evaluated 123 United States Radiologic Technologists subjects who wore personal UVR dosimeters for 8 hours daily for up to 7 days (N = 837 days). Potential predictors of personal UVR derived from a self-administered questionnaire, and public databases that provided daily estimates of ambient UVR and weather conditions. Factors potentially related to personal UVR exposure were tested individually and in a model including all significant variables. Results The strongest predictors of daily personal UVR exposure in the full model were ambient UVR, latitude, daily rainfall, and skin reaction to prolonged sunlight (R2 = 0.30). In a model containing only environmental and meteorological variables, ambient UVR, latitude, and daily rainfall were the strongest predictors of daily personal UVR exposure (R2 = 0.25). Conclusions In the absence of feasible measures of individual longitudinal sun exposure history, stable personal characteristics, ambient UVR, and weather parameters may help estimate long-term personal UVR exposure

Progression in behavioral variant frontotemporal dementia:A longitudinal study

Importance: A gap in the literature exists regarding progression in behavioral variant frontotemporal dementia (BVFTD). Guidance is needed concerning markers that will enable clinicians to discriminate FTD more effectively from phenocopies and to identify factors that determine progression and thereby prognosis.  Objectives: To observe longitudinal outcomes and progression in probable and possible BVFTD in accordance with international diagnostic criteria and to identify features that may aid clinicians to prognosticate better in cases of possible BVFTD.  Design, Setting, and Participants: Longitudinal cohort study performed in a specialist tertiary FTD research clinic. Fifty-eight consecutive patients were followed up longitudinally from January 1, 2008, through December 31, 2013, and classified as having possible, probable, or definite BVFTD at presentation and latest review. Final follow-up was completed on December 31, 2013, and data were analyzed from January 1 to August 1, 2014.  Main Outcomes and Measures: Clinical, pathological, genetic, neuropsychological, and neuroimaging data were analyzed to categorize patients, to compare differences between groups with changed and unchanged diagnoses, to determine rates of progression in BVFTD, and to identify prognostic features in possible BVFTD.  Results: At presentation, 38 of the 58 patients fulfilled criteria for probable BVFTD; of these, 36 continued to satisfy probable criteria or underwent conversion to definite criteria over time. The remaining 20 patients satisfied possible criteria only, and 11 of these patients changed categories over time to probable or definite BVFTD and showed progression on cognitive and functional measures (termed changed status). Of these 11 patients, 8 (73%) carried the C9orf72 expansion. A positive family history, memory impairment, and clinical abnormalities at presentation were key features of progression (P < .05). A continuum of neuropsychological scores, progression rates, and atrophy severity emerged across patients in probable, possible, changed status, and nonchanged status groups; patients with probable BVFTD exhibited the most severe abnormalities.  Conclusions and Relevance: Behavioral variant FTD shows variable progression over time. Clinicians can use a detailed neurologic and cognitive assessment to identify key predictive features of progression when faced with possible BVFTD, whereas a diagnosis of probable BVFTD is accurate in a clinical setting

Clinical Best Practice Advice for Hepatology and Liver Transplant Providers During the COVID‐19 Pandemic: AASLD Expert Panel Consensus Statement

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156235/2/hep31281.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156235/1/hep31281_am.pd

Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome

BackgroundAlthough the reference human genome sequence was declared finished in 2003, some regions of the genome remain incomplete due to their complex architecture. One such region, 1q21.1-q21.2, is of increasing interest due to its relevance to human disease and evolution. Elucidation of the exact variants behind these associations has been hampered by the repetitive nature of the region and its incomplete assembly. This region also contains 238 of the 270 human DUF1220 protein domains, which are implicated in human brain evolution and neurodevelopment. Additionally, examinations of this protein domain have been challenging due to the incomplete 1q21 build. To address these problems, a single-haplotype hydatidiform mole BAC library (CHORI-17) was used to produce the first complete sequence of the 1q21.1-q21.2 region.ResultsWe found and addressed several inaccuracies in the GRCh37sequence of the 1q21 region on large and small scales, including genomic rearrangements and inversions, and incorrect gene copy number estimates and assemblies. The DUF1220-encoding NBPF genes required the most corrections, with 3 genes removed, 2 genes reassigned to the 1p11.2 region, 8 genes requiring assembly corrections for DUF1220 domains (~91 DUF1220 domains were misassigned), and multiple instances of nucleotide changes that reassigned the domain to a different DUF1220 subtype. These corrections resulted in an overall increase in DUF1220 copy number, yielding a haploid total of 289 copies. Approximately 20 of these new DUF1220 copies were the result of a segmental duplication from 1q21.2 to 1p11.2 that included two NBPF genes. Interestingly, this duplication may have been the catalyst for the evolutionarily important human lineage-specific chromosome 1 pericentric inversion.ConclusionsThrough the hydatidiform mole genome sequencing effort, the 1q21.1-q21.2 region is complete and misassemblies involving inter- and intra-region duplications have been resolved. The availability of this single haploid sequence path will aid in the investigation of many genetic diseases linked to 1q21, including several associated with DUF1220 copy number variations. Finally, the corrected sequence identified a recent segmental duplication that added 20 additional DUF1220 copies to the human genome, and may have facilitated the chromosome 1 pericentric inversion that is among the most notable human-specific genomic landmarks

TEV gamma ray emission from the active galactic nucleus Markarian 421

TeV energy gamma ray emission from the blazar Markarian 421 was detected with the Whipple 10 meter imaging Cherenkov telescope initially during the observation period March‐June 1992 at an average photon flux of 1.5×10−11 cm2 s−1. The photon spectrum in the TeV range lies on the extrapolation of the data points observed by EGRET during viewing phase I and indicates that the emission follows an unchanged power law between 100 MeV and 10 TeV with no significant intergalactic absorption. More recent observations from the spring of 1993 confirm the 1992 measurements. Here we give an update on the status of the observations, the analysis for time variability, and the results from the analysis to determine the spectral index for Markarian 421 at TeV energies.The search for TeV emission from other extragalactic sources detected by the EGRET instrument on the Compton Gamma Ray Observatory at GeV energies have so far been negative.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87648/2/597_1.pd

Observations of the Crab nebula at TeV energies

The results of four years of observation of the Crab Nebula at TeV energies by the Whipple group are discussed and the status of the Crab Nebula as a standard candle for TeV astronomy is reviewed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87647/2/270_1.pd

Searches for bursts of TEV gamma rays on time‐scales of seconds

The Whipple Observatory gamma‐ray telescope has a high sensitivity to sources of gamma rays in the 0.4 to 4 TeV energy range. Although this sensitivity is used primarily to search for discrete sources of gamma‐rays the instrument also has sensitivity to gamma‐ray bursts on time‐scales from milliseconds to seconds. The field of view is limited but the source location capability is good. Such bursts could radiate with peak luminosity at TeV energies and could originate from(a) primordial black holes or (b) cosmic strings; they could also be the high energy counterparts of BATSE‐type bursts and hence of unknown origin. The search of the Whipple data‐base for statistically unlikely consecutive events on time‐scales of second will be described and compared with the theoretical predictions. © 1994 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87630/2/470_1.pd

Plasma Dynamics

Contains reports on six research projects.National Science Foundation (Grant ENG79-07047)U.S. Air Force - Office of Scientific Research (Grant AFOSR77-3143D)U.S. Air Force - Office of Scientific Research (Contract AFOSR82-0063)U.S. Department of Energy (Contract DE-ACO2-78-ET-51013)U.S. Department of Energy (Contract DE-AC02-78ET-53073.A002

Cerebellar Integrity in the Amyotrophic Lateral Sclerosis - Frontotemporal Dementia Continuum

Amyotrophic lateral sclerosis (ALS) and behavioural variant frontotemporal dementia (bvFTD) are multisystem neurodegenerative disorders that manifest overlapping cognitive, neuropsychiatric and motor features. The cerebellum has long been known to be crucial for intact motor function although emerging evidence over the past decade has attributed cognitive and neuropsychiatric processes to this structure. The current study set out i) to establish the integrity of cerebellar subregions in the amyotrophic lateral sclerosis-behavioural variant frontotemporal dementia spectrum (ALS-bvFTD) and ii) determine whether specific cerebellar atrophy regions are associated with cognitive, neuropsychiatric and motor symptoms in the patients. Seventy-eight patients diagnosed with ALS, ALS-bvFTD, behavioural variant frontotemporal dementia (bvFTD), most without C9ORF72 gene abnormalities, and healthy controls were investigated. Participants underwent cognitive, neuropsychiatric and functional evaluation as well as structural imaging using voxel-based morphometry (VBM) to examine the grey matter subregions of the cerebellar lobules, vermis and crus. VBM analyses revealed: i) significant grey matter atrophy in the cerebellum across the whole ALS-bvFTD continuum; ii) atrophy predominantly of the superior cerebellum and crus in bvFTD patients, atrophy of the inferior cerebellum and vermis in ALS patients, while ALS-bvFTD patients had both patterns of atrophy. Post-hoc covariance analyses revealed that cognitive and neuropsychiatric symptoms were particularly associated with atrophy of the crus and superior lobule, while motor symptoms were more associated with atrophy of the inferior lobules. Taken together, these findings indicate an important role of the cerebellum in the ALS-bvFTD disease spectrum, with all three clinical phenotypes demonstrating specific patterns of subregional atrophy that associated with different symptomology