Updates on the Low-Level Abstraction of Memory Access

Choosing the best memory layout for each hardware architecture is increasingly important as more and more programs become memory bound. For portable codes that run across heterogeneous hardware architectures, the choice of the memory layout for data structures is ideally decoupled from the rest of a program. The low-level abstraction of memory access (LLAMA) is a C++ library that provides a zero-runtime-overhead abstraction layer, underneath which memory mappings can be freely exchanged to customize data layouts, memory access and access instrumentation, focusing on multidimensional arrays of nested, structured data. After its scientific debut, several improvements and extensions have been added to LLAMA. This includes compile-time array extents for zero-memory-overhead views, support for computations during memory access, new mappings for bit-packing, switching types, byte-splitting, memory access instrumentation, and explicit SIMD support. This contribution provides an overview of recent developments in the LLAMA library

Challenges and opportunities integrating LLAMA into AdePT

Particle transport simulations are a cornerstone of high-energy physics (HEP), constituting a substantial part of the computing workload performed in HEP. To boost the simulation throughput and energy efficiency, GPUs as accelerators have been explored in recent years, further driven by the increasing use of GPUs on HPCs. The Accelerated demonstrator of electromagnetic Particle Transport (AdePT) is an advanced prototype for offloading the simulation of electromagnetic showers in Geant4 to GPUs, and still undergoes continuous development and optimization. Improving memory layout and data access is vital to use modern, massively parallel GPU hardware efficiently, contributing to the challenge of migrating traditional CPU based data structures to GPUs in AdePT. The low-level abstraction of memory access (LLAMA) is a C++ library that provides a zero-runtime-overhead data structure abstraction layer, focusing on multidimensional arrays of nested, structured data. It provides a framework for defining and switching custom memory mappings at compile time to define data layouts and instrument data access, making LLAMA an ideal tool to tackle the memory-related optimization challenges in AdePT. Our contribution shares insights gained with LLAMA when instrumenting data access inside AdePT, complementing traditional GPU profiler outputs. We demonstrate traces of read/write counts to data structure elements as well as memory heatmaps. The acquired knowledge allowed for subsequent data layout optimizations

QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure

QSCOP is a quantitative structural classification of proteins which distinguishes itself from other classifications by two essential properties: (i) QSCOP is concurrent with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and (ii) QSCOP covers the widely used SCOP classification with layers of quantitative structural information. The QSCOP-BLAST web server presented here combines the BLAST sequence search engine with QSCOP to retrieve, for a given query sequence, all structural information currently available. The resulting search engine is reliable in terms of the quality of results obtained, and it is efficient in that results are displayed instantaneously. The hierarchical organization of QSCOP is used to control the redundancy and diversity of the retrieved hits with the benefit that the often cumbersome and difficult interpretation of search results is an intuitive and straightforward exercise. We demonstrate the use of QSCOP-BLAST by example. The server is accessible at http://qscop-blast.services.came.sbg.ac.at

Do You Plead Connected? - Understanding How Lawyers Deal With Constant Connectivity

Being available and responsive has become an imperative to accomplish the complex work of knowledge workers and to adequately satisfy today’s business needs. As a consequence, individuals are required to adopt strategies to cope with increasing connectivity levels. We conducted a Q methodological study among 34 lawyers from Switzerland and Austria to examine the adoption of different strategies for dealing with constant connectivity. Our findings reveal four ICT user types, whereof three types successfully deploy a coping strategy while one type fails. We observe that specific determinants such as the work environment, the hierarchical position, the perceived autonomy as well as personality traits have substantial influence on the adoption of a coping strategy

Can we learn where people go?

In most agent-based simulators, pedestrians navigate from origins to destinations. Consequently, destinations are essential input parameters to the simulation. While many other relevant parameters as positions, speeds and densities can be obtained from sensors, like cameras, destinations cannot be observed directly. Our research question is: Can we obtain this information from video data using machine learning methods? We use density heatmaps, which indicate the pedestrian density within a given camera cutout, as input to predict the destination distributions. For our proof of concept, we train a Random Forest predictor on an exemplary data set generated with the Vadere microscopic simulator. The scenario is a crossroad where pedestrians can head left, straight or right. In addition, we gain first insights on suitable placement of the camera. The results motivate an in-depth analysis of the methodology

Molecular characterization of the feline T-cell receptor γ alternate reading frame protein (TARP) ortholog

T-cell receptor γ alternate reading frame protein (TARP) is expressed by human prostate epithelial, prostate cancer, and mammary cancer cells, but is not found in normal mammary tissue. To date, this protein has only been described in humans. Additionally, no animal model has been established to investigate the potential merits of TARP as tumor marker or a target for adoptive tumor immunotherapy. In this study conducted to characterize feline T-cell receptor γ sequences, constructs very similar to human TARP transcripts were obtained by RACE from the spleen and prostate gland of cats. Transcription of TARP in normal, hyperplastic, and neoplastic feline mammary tissues was evaluated by conventional RT-PCR. In felines similarly to the situation reported in humans, a C-region encoding two open reading frames is spliced to a J-region gene. In contrast to humans, the feline J-region gene was found to be a pseudogene containing a deletion within its recombination signal sequence. Our findings demonstrated that the feline TARP ortholog is transcribed in the prostate gland and mammary tumors but not normal mammary tissues as is the case with human TARP

The pangenome of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV)

The alphabaculovirusAnticarsia gemmatalismultiple nucleopolyhedrovirus (AgMNPV) is the world’s most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations ofAnticarsia gemmatalis(Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The genebro-athat might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a uniquernf12-likegene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general

ROOT for the HL-LHC: data format

This document discusses the state, roadmap, and risks of the foundational components of ROOT with respect to the experiments at the HL-LHC (Run 4 and beyond). As foundational components, the document considers in particular the ROOT input/output (I/O) subsystem. The current HEP I/O is based on the TFile container file format and the TTree binary event data format. The work going into the new RNTuple event data format aims at superseding TTree, to make RNTuple the production ROOT event data I/O that meets the requirements of Run 4 and beyond

Preclinical Assessment of Bacteriophage Therapy against Experimental Acinetobacter baumannii Lung Infection

Respiratory infections caused by multidrug-resistant Acinetobacter baumannii are difficult to treat and associated with high mortality among critically ill hospitalized patients. Bacteriophages (phages) eliminate pathogens with high host specificity and efficacy. However, the lack of appropriate preclinical experimental models hampers the progress of clinical development of phages as therapeutic agents. Therefore, we tested the efficacy of a purified lytic phage, vB_AbaM_Acibel004, against multidrug-resistant A. baumannii clinical isolate RUH 2037 infection in immunocompetent mice and a human lung tissue model. Sham- and A. baumannii-infected mice received a single-dose of phage or buffer via intratracheal aerosolization. Group-specific differences in bacterial burden, immune and clinical responses were compared. Phage-treated mice not only recovered faster from infection-associated hypothermia but also had lower pulmonary bacterial burden, lower lung permeability, and cytokine release. Histopathological examination revealed less inflammation with unaffected inflammatory cellular recruitment. No phage-specific adverse events were noted. Additionally, the bactericidal effect of the purified phage on A. baumannii was confirmed after single-dose treatment in an ex vivo human lung infection model. Taken together, our data suggest that the investigated phage has significant potential to treat multidrug-resistant A. baumannii infections and further support the development of appropriate methods for preclinical evaluation of antibacterial efficacy of phages