1,441 research outputs found
On the complexity of acyclic modules in automata networks
Modules were introduced as an extension of Boolean automata networks. They
have inputs which are used in the computation said modules perform, and can be
used to wire modules with each other. In the present paper we extend this new
formalism and study the specific case of acyclic modules. These modules prove
to be well described in their limit behavior by functions called output
functions. We provide other results that offer an upper bound on the number of
attractors in an acyclic module when wired recursively into an automata
network, alongside a diversity of complexity results around the difficulty of
deciding the existence of cycles depending on the number of inputs and the size
of said cycle.Comment: 21 page
Genome graphs detect human polymorphisms in active epigenomic state during influenza infection
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%–3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches
Implementation and Performance of the ATLAS Second Level Jet Trigger
ATLAS is one of the four major LHC experiments, designed to cover a wide range of physics topics. In order to cope with a rate of 40 MHz and 25 interactions per bunch crossing, the ATLAS trigger system is divided in three different levels. The first one (LVL1, hardware based) identifies signatures in 2 microseconds that are confirmed by the the following trigger levels (software based). The Second Level Trigger (LVL2) only looks at a region of the space around the LVL1 signature (called Region of Interest or ROI), confirming/rejecting the event in about 10 ms, while the Event Filter (Third Level Trigger, EF) has potential full event access and larger processing times, of the order of 1 s. The jet selection starts at the LVL1 with dedicated processors that search for high ET hadronic energy depositions. At the LVL2, the jet signatures are verified with the execution of a dedicated, fast jet reconstruction algorithm. Given the fact that the main jet's background are jets,the energy calibration at the LVL2 is one of the major dificulties of this trigger, allowing to distinguish low/high energy jets. The algorithm for the calibration has been chosen to be fast and robust, with a good performance. The other major dificulty is the execution time of the algorithm,dominated by the data unpacking time due to the large sizes of the jet ROI. In order to reduce the execution time, three possible granularities have been proposed and are being evaluated: cell based (standard), energy sums calculated at each Fron-End Board (FEB) and the use of the LVL1 Trigger Towers. The FEB and Trigger Tower granularities are also being used/evaluated for the reconstruction of the missing ET triggers at the Event Filter, given the short times available to process the full event. In this presentation, the design and implementation of the jet trigger of ATLAS will be discussed in detail, emphasasing the major dificulties of each selection step. The performance of the jet algorithm, including timing, eficiencies and rates will also be shown, with detailed comparisons of the different unpacking modes
Transposable elements are associated with the variable response to influenza infection
インフルエンザ重症度に関連する転移因子を特定: マルチオミクス解析で見えた「動く遺伝子」の新たな役割. 京都大学プレスリリース. 2023-05-11.A multiomics approach provides insights into flu severity. 京都大学プレスリリース. 2023-05-11.Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity
Is there scope for cost savings and efficiency gains in HIV services? A systematic review of the evidence from low- and middle-income countries.
OBJECTIVE: To synthesize the data available--on costs, efficiency and economies of scale and scope--for the six basic programmes of the UNAIDS Strategic Investment Framework, to inform those planning the scale-up of human immunodeficiency virus (HIV) services in low- and middle-income countries. METHODS: The relevant peer-reviewed and "grey" literature from low- and middle-income countries was systematically reviewed. Search and analysis followed Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. FINDINGS: Of the 82 empirical costing and efficiency studies identified, nine provided data on economies of scale. Scale explained much of the variation in the costs of several HIV services, particularly those of targeted HIV prevention for key populations and HIV testing and treatment. There is some evidence of economies of scope from integrating HIV counselling and testing services with several other services. Cost efficiency may also be improved by reducing input prices, task shifting and improving client adherence. CONCLUSION: HIV programmes need to optimize the scale of service provision to achieve efficiency. Interventions that may enhance the potential for economies of scale include intensifying demand-creation activities, reducing the costs for service users, expanding existing programmes rather than creating new structures, and reducing attrition of existing service users. Models for integrated service delivery--which is, potentially, more efficient than the implementation of stand-alone services--should be investigated further. Further experimental evidence is required to understand how to best achieve efficiency gains in HIV programmes and assess the cost-effectiveness of each service-delivery model
A guided tour of asynchronous cellular automata
Research on asynchronous cellular automata has received a great amount of
attention these last years and has turned to a thriving field. We survey the
recent research that has been carried out on this topic and present a wide
state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat
Early and Late Direct Costs in a Southern African Antiretroviral Treatment Programme: A Retrospective Cohort Analysis
Gary Maartens and colleagues describe the direct heath care costs and identify the drivers of cost over time in an HIV managed care program in Southern Africa
Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS
The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured
Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC
The uncertainty on the calorimeter energy response to jets of particles is
derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the
calorimeter response to single isolated charged hadrons is measured and
compared to the Monte Carlo simulation using proton-proton collisions at
centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009
and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter
response to specific types of particles (positively and negatively charged
pions, protons, and anti-protons) is measured and compared to the Monte Carlo
predictions. Finally, the jet energy scale uncertainty is determined by
propagating the response uncertainty for single charged and neutral particles
to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3%
for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table,
submitted to European Physical Journal
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