Phylogenomics and the dynamic genome evolution of the genus Streptococcus

The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group

Comparison of Airborne and Ground-Based Function Allocation Concepts for NextGen Using Human-In-The-Loop Simulations

This paper presents an air/ground functional allocation experiment conducted by the National Aeronautics and Space Administration (NASA) using two human-in-the-Loop simulations to compare airborne and ground-based approaches to NextGen separation assurance. The approaches under investigation are two trajectory-based four-dimensional (4D) concepts; one referred to as "airborne trajectory management with self-separation" (airborne) the other as "ground-based automated separation assurance" (ground-based). In coordinated simulations at NASA's Ames and Langley Research Centers, the primary operational participants -controllers for the ground-based concept and pilots for the airborne concept - manage the same traffic scenario using the two different 4D concepts. The common scenarios are anchored in traffic problems that require a significant increase in airspace capacity - on average, double, and in some local areas, close to 250% over current day levels - in order to enable aircraft to safely and efficiently traverse the test airspace. The simulations vary common independent variables such as traffic density, sequencing and scheduling constraints, and timing of trajectory change events. A set of common metrics is collected to enable a direct comparison of relevant results. The simulations will be conducted in spring 2010. If accepted, this paper will be the first publication of the experimental approach and early results. An initial comparison of safety and efficiency as well as operator acceptability under the two concepts is expected

Comparison of Ground-Based and Airborne Function Allocation Concepts for NextGen Using Human-In-The-Loop Simulations

Investigation of function allocation for the Next Generation Air Transportation System is being conducted by the National Aeronautics and Space Administration (NASA). To provide insight on comparability of different function allocations for separation assurance, two human-in-the-loop simulation experiments were conducted on homogeneous airborne and ground-based approaches to four-dimensional trajectory-based operations, one referred to as ground-based automated separation assurance (groundbased) and the other as airborne trajectory management with self-separation (airborne). In the coordinated simulations at NASA s Ames and Langley Research Centers, controllers for the ground-based concept at Ames and pilots for the airborne concept at Langley managed the same traffic scenarios using the two different concepts. The common scenarios represented a significant increase in airspace demand over current operations. Using common independent variables, the simulations varied traffic density, scheduling constraints, and the timing of trajectory change events. Common metrics were collected to enable a comparison of relevant results. Where comparisons were possible, no substantial differences in performance or operator acceptability were observed. Mean schedule conformance and flight path deviation were considered adequate for both approaches. Conflict detection warning times and resolution times were mostly adequate, but certain conflict situations were detected too late to be resolved in a timely manner. This led to some situations in which safety was compromised and/or workload was rated as being unacceptable in both experiments. Operators acknowledged these issues in their responses and ratings but gave generally positive assessments of the respective concept and operations they experienced. Future studies will evaluate technical improvements and procedural enhancements to achieve the required level of safety and acceptability and will investigate the integration of airborne and ground-based capabilities within the same airspace to leverage the benefits of each concept

High-resolution μCT of a mouse embryo using a compact laser-driven X-ray betatron source

High-resolution microcomputed tomography with benchtop X-ray sources requires long scan times because of the heat load limitation on the anode. We present an alternative, high-brightness plasma-based X-ray source that does not suffer from this restriction. A demonstration of tomography of a centimeter-scale complex organism achieves equivalent quality to a commercial scanner. We will soon be able to record such scans in minutes, rather than the hours required by conventional X-ray tubes

Reflections from the Workshop on AI-Assisted Decision Making for Conservation

In this white paper, we synthesize key points made during presentations and discussions from the AI-Assisted Decision Making for Conservation workshop, hosted by the Center for Research on Computation and Society at Harvard University on October 20-21, 2022. We identify key open research questions in resource allocation, planning, and interventions for biodiversity conservation, highlighting conservation challenges that not only require AI solutions, but also require novel methodological advances. In addition to providing a summary of the workshop talks and discussions, we hope this document serves as a call-to-action to orient the expansion of algorithmic decision-making approaches to prioritize real-world conservation challenges, through collaborative efforts of ecologists, conservation decision-makers, and AI researchers.Comment: Co-authored by participants from the October 2022 workshop: https://crcs.seas.harvard.edu/conservation-worksho

Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity

Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes were evaluated by mining GWAS datasets. eQTL analysis identified 1,971 and 2,078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2, were identified in both tissues. 62.1% of top cis-eSNPs were within ±50kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes, (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically-regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde