36 research outputs found
The Transactional Conflict Problem
The transactional conflict problem arises in transactional systems whenever
two or more concurrent transactions clash on a data item.
While the standard solution to such conflicts is to immediately abort one of
the transactions, some practical systems consider the alternative of delaying
conflict resolution for a short interval, which may allow one of the
transactions to commit. The challenge in the transactional conflict problem is
to choose the optimal length of this delay interval so as to minimize the
overall running time penalty for the conflicting transactions. In this paper,
we propose a family of optimal online algorithms for the transactional conflict
problem.
Specifically, we consider variants of this problem which arise in different
implementations of transactional systems, namely "requestor wins" and
"requestor aborts" implementations: in the former, the recipient of a coherence
request is aborted, whereas in the latter, it is the requestor which has to
abort. Both strategies are implemented by real systems.
We show that the requestor aborts case can be reduced to a classic instance
of the ski rental problem, while the requestor wins case leads to a new version
of this classical problem, for which we derive optimal deterministic and
randomized algorithms.
Moreover, we prove that, under a simplified adversarial model, our algorithms
are constant-competitive with the offline optimum in terms of throughput.
We validate our algorithmic results empirically through a hardware simulation
of hardware transactional memory (HTM), showing that our algorithms can lead to
non-trivial performance improvements for classic concurrent data structures
Preparation and structural properties of thin films and multilayers of the Heusler compounds Cu2MnAl, Co2MnSn, Co2MnSi and Co2MnGe
We report on the preparation of thin films and multilayers of the
intermetallic Heusler compound CuMnAl, Co2MnSn, Co2MnSi and Co2MnGe by
rf-sputtering on MgO and Al2O3 substrates. Cu2MnAl can be grown epitaxially
with (100)-orientation on MgO (100) and in (110)-orientation on Al2O3 a-plane.
The Co based Heusler alloys need metallic seedlayers to induce high quality
textured growth. We also have prepared multilayers with smooth interfaces by
combining the Heusler compounds with Au and V. An analysis of the ferromagnetic
saturation magnetization of the films indicates that the Cu2MnAl-compound tends
to grow in the disordered B2-type structure whereas the Co-based Heusler alloy
thin films grow in the ordered L21 structure. All multilayers with thin layers
of the Heusler compounds exhibit a definitely reduced ferromagnetic
magnetization indicating substantial disorder and intermixing at the
interfaces.Comment: 21 pages, 8 figure
Half-metallicity and Slater-Pauling behavior in the ferromagnetic Heusler alloys
Introductory chapter for the book "Halfmetallic Alloys - Fundamentals and
Applications" to be published in the series Springer Lecture Notes on Physics,
P. H. Dederichs and I. Galanakis (eds). It contains a review of the theoretical
work on the half-metallic Heusler alloys.Comment: Introductory chapter for the book "Halfmetallic Alloys - Fundamentals
and Applications" to be published in the series Springer Lecture Notes on
Physics, P. H. Dederichs and I. Galanakis (eds
Slater-Pauling Behavior of the Half-Ferromagnetic Full-Heusler Alloys
Using the full-potential screened Korringa-Kohn-Rostoker method we study the
full-Heusler alloys based on Co, Fe, Rh and Ru. We show that many of these
compounds show a half-metallic behavior, however in contrast to the
half-Heusler alloys the energy gap in the minority band is extremely small.
These full-Heusler compounds show a Slater-Pauling behavior and the total
spin-magnetic moment per unit cell (M_t) scales with the total number of
valence electrons (Z_t) following the rule: M_t=Z_t-24. We explain why the
spin-down band contains exactly 12 electrons using arguments based on the group
theory and show that this rule holds also for compounds with less than 24
valence electrons. Finally we discuss the deviations from this rule and the
differences compared to the half-Heusler alloys.Comment: 10 pages, 8 figures, revised figure 3, new text adde
Exposure to the Amino Acids Histidine, Lysine, and Threonine Reduces mTOR Activity and Affects Neurodevelopment in a Human Cerebral Organoid Model
Evidence of the impact of nutrition on human brain development is compelling. Previous in vitro and in vivo results show that three specific amino acids, histidine, lysine, and threonine, synergistically inhibit mTOR activity and behavior. Therefore, the prenatal availability of these amino acids could be important for human neurodevelopment. However, methods to study the underlying mechanisms in a human model of neurodevelopment are limited. Here, we pioneer the use of human cerebral organoids to investigate the impact of amino acid supplementation on neurodevelopment. In this study, cerebral organoids were exposed to 10 mM and 50 mM of the amino acids threonine, histidine, and lysine. The impact was determined by measuring mTOR activity using Western blots, general cerebral organoid size, and gene expression by RNA sequencing. Exposure to threonine, histidine, and lysine led to decreased mTOR activity and markedly reduced organoid size, supporting findings in rodent studies. RNA sequencing identified comprehensive changes in gene expression, with enrichment in genes related to specific biological processes (among which are mTOR signaling and immune function) and to specific cell types, including proliferative precursor cells, microglia, and astrocytes. Altogether, cerebral organoids are responsive to nutritional exposure by increasing specific amino acid concentrations and reflect findings from previous rodent studies. Threonine, histidine, and lysine exposure impacts the early development of human cerebral organoids, illustrated by the inhibition of mTOR activity, reduced size, and altered gene expression
Pan-cancer analysis of whole genomes
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe
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Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts
The transactional conflict problem
The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely "requestor wins'' and "requestor aborts'' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constant-competitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to non-trivial performance improvements for classic concurrent data structures