BSM Physics: What the Higgs Can Tell Us

This discovery of the Higgs boson last year has created new possibilities for testing candidate theories for explaining physics beyond the Standard Model. Here we explain the ways in which new physics can leave its marks in the experimental Higgs data, and how we can use the data to constrain and compare different models. In this proceedings paper we use two models, Minimal Universal Extra Dimensions and the 4D Composite Higgs model, as examples to demonstrate the technique.Comment: V2 corrected typo in author name. Submitted to the proceedings of the 41st ITEP Winter School, Mosco

Scheduling Dynamic Parallelism On Accelerators

Resource management on accelerator based systems is complicated by the disjoint nature of the main CPU and accelerator, which involves separate memory hierarhcies, different degrees of parallelism, and relatively high cost of communicating between them. For applications with irregular parallelism, where work is dynamically created based on other computations, the accelerators may both consume and produce work. To maintain load balance, the accelerators hand work back to the CPU to be scheduled. In this paper we consider multiple approaches for such scheduling problems and use the Cell BE system to demonstrate the different schedulers and the trade-offs between them. Our evaluation is done with both microbenchmarks and two bioinformatics applications (PBPI and RAxML). Our baseline approach uses a standard Linux scheduler on the CPU, possibly with more than one process per CPU. We then consider the addition of cooperative scheduling to the Linux kernel and a user-level work-stealing approach. The two cooperative approaches are able to decrease SPE idle time, by 30 % and 70%, respectively, relative to the baseline scheduler. In both cases we believe the changes required to application level codes, e.g., a program written with MPI processes that use accelerator based compute nodes, is reasonable, although the kernel level approach provides more generality and ease of implementation, but often less performance than work stealing approach

Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples

Rapid antimicrobial susceptibility testing (AST) is urgently needed for informing treatment decisions and preventing the spread of antimicrobial resistance resulting from the misuse and overuse of antibiotics. To date, no phenotypic AST exists that can be performed within a single patient visit (30 min) directly from clinical samples. We show that AST results can be obtained by using digital nucleic acid quantification to measure the phenotypic response of Escherichia coli present within clinical urine samples exposed to an antibiotic for 15 min. We performed this rapid AST using our ultrafast (~7 min) digital real-time loop-mediated isothermal amplification (dLAMP) assay [area under the curve (AUC), 0.96] and compared the results to a commercial (~2 hours) digital polymerase chain reaction assay (AUC, 0.98). The rapid dLAMP assay can be used with SlipChip microfluidic devices to determine the phenotypic antibiotic susceptibility of E. coli directly from clinical urine samples in less than 30 min. With further development for additional pathogens, antibiotics, and sample types, rapid digital AST (dAST) could enable rapid clinical decision-making, improve management of infectious diseases, and facilitate antimicrobial stewardship

Relating the metatranscriptome and metagenome of the human gut

Although the composition of the human microbiome is now wellstudied, the microbiota’s \u3e8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. Within-subject microbial species, gene, and transcript abundances were highly concordant across sampling methods, with only a small fraction of transcripts (\u3c5%) displaying between-method variation. Next, we investigated relationships between the oral and gut microbial communities, identifying a subset of abundant oral microbes that routinely survive transit to the gut, but with minimal transcriptional activity there. Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substantial fraction (41%) of microbial transcripts were not differentially regulated relative to their genomic abundances. Of the remainder, consistently underexpressed pathways included sporulation and amino acid biosynthesis, whereas up-regulated pathways included ribosome biogenesis and methanogenesis. Across subjects, metatranscriptional profiles were significantly more individualized than DNA-level functional profiles, but less variable than microbial composition, indicative of subject-specific whole-community regulation. The results thus detail relationships between community genomic potential and gene expression in the gut, and establish the feasibility of metatranscriptomic investigations in subject-collected and shipped samples

New Constraints on Cosmic Reionization from the 2012 Hubble Ultra Deep Field Campaign

Understanding cosmic reionization requires the identification and characterization of early sources of hydrogen-ionizing photons. The 2012 Hubble Ultra Deep Field (UDF12) campaign has acquired the deepest infrared images with the Wide Field Camera 3 aboard Hubble Space Telescope and, for the first time, systematically explored the galaxy population deep into the era when cosmic microwave background (CMB) data indicates reionization was underway. The UDF12 campaign thus provides the best constraints to date on the abundance, luminosity distribution, and spectral properties of early star-forming galaxies. We synthesize the new UDF12 results with the most recent constraints from CMB observations to infer redshift-dependent ultraviolet (UV) luminosity densities, reionization histories, and electron scattering optical depth evolution consistent with the available data. Under reasonable assumptions about the escape fraction of hydrogen ionizing photons and the intergalactic medium clumping factor, we find that to fully reionize the universe by redshift z~6 the population of star-forming galaxies at redshifts z~7-9 likely must extend in luminosity below the UDF12 limits to absolute UV magnitudes of M_UV\sim -13 or fainter. Moreover, low levels of star formation extending to redshifts z~15-25, as suggested by the normal UV colors of z\simeq7-8 galaxies and the smooth decline in abundance with redshift observed by UDF12 to z\simeq10, are additionally likely required to reproduce the optical depth to electron scattering inferred from CMB observations.Comment: Version accepted by ApJ (originally submitted Jan 5, 2013). The UDF12 website can be found at http://udf12.arizona.ed

Genetics of stroke in a UK African ancestry case-control study: South London Ethnicity and Stroke Study.

OBJECTIVE: Despite epidemiologic data showing an increased stroke incidence in African ancestry populations, genetic studies in this group have so far been limited, and there has been little characterization of the genetic contribution to stroke liability in this population, particularly for stroke subtypes. METHODS: We evaluated the evidence that genetic factors contribute to stroke and stroke subtypes in a population of 917 African and African Caribbean stroke cases and 868 matched controls from London, United Kingdom. We (1) estimated the heritability of stroke in this population using genomic-relatedness matrix-restricted maximum likelihood approaches, (2) assessed loci associated with stroke in Europeans in our population, and (3) evaluated the influence of genetic factors underlying cardiovascular risk factors on stroke using polygenic risk scoring. RESULTS: Our results indicate a substantial genetic contribution to stroke risk in African ancestry populations (h2 = 0.35 [SE = 0.19], p = 0.043). Polygenic risk scores indicate that cardiovascular risk scores contribute to the genetic liability (odds ratio [OR] 1.09 [95% confidence interval (CI) 1.01-1.17], p = 0.029) and point to a strong influence of type 2 diabetes in large vessel stroke (OR 1.62 [95% CI 1.19-2.22], p = 0.0024). Single nucleotide polymorphisms associated with ischemic stroke in Europeans shared direction of effect in SLESS (p = 0.031), suggesting that disease mechanisms are shared across ancestries. CONCLUSIONS: Stroke in African ancestry populations is highly heritable and influenced by genetic determinants underlying cardiovascular risk factors. In addition, stroke loci identified in Europeans share direction of effect in African populations. Future genome-wide association studies must focus on incorporating African ancestry individuals

A Characterization of the Shallow-Water Coral Reefs and Associated Habitats of Puerto Rico

We mapped bottom types and shelf zones of 1600 km2 or about one fourth of Puerto Rico’s insular shelf from the shoreline to the shelf edge. Overall map accuracy for these bottom types is estimated as 93.6% correct. Maps were produced through visual interpretation of benthic features using orthorectified aerial photographs within a Geographic Information System with customizable software. The maps are one component of an integrated mapping and monitoring program underway by NOAA and its partners in the US Coral Reef Task Force to assess all US reef ecosystems. Maps are currently being used to enhance coastal research and management activities in Puerto Rico such as fisheries assessments and designation of important fish habitats