A native tensor-vector multiplication algorithm for high performance computing

Tensor computations are important mathematical operations for applications that rely on multidimensional data. The tensor-vector multiplication (TVM) is the most memory-bound tensor contraction in this class of operations. This paper proposes an open-source TVM algorithm which is much simpler and efficient than previous approaches, making it suitable for integration in the most popular BLAS libraries available today. Our algorithm has been written from scratch and features unit-stride memory accesses, cache awareness, mode obliviousness, full vectorization and multi-threading as well as NUMA awareness for non-hierarchically stored dense tensors. Numerical experiments are carried out on tensors up to order 10 and various compilers and hardware architectures equipped with traditional DDR and high bandwidth memory (HBM). For large tensors the average performance of the TVM ranges between 62% and 76% of the theoretical bandwidth for NUMA systems with DDR memory and remains independent of the contraction mode. On NUMA systems with HBM the TVM exhibits some mode dependency but manages to reach performance figures close to peak values. Finally, the higher-order power method is benchmarked with the proposed TVM kernel and delivers on average between 58% and 69% of the theoretical bandwidth for large tensors.This work was supported in part by MCIN/AEI and ESF under Grant RYC2019-027592-I, and in part by the HPC Technology Innovation Lab, a Barcelona Supercomputing Center and Huawei research cooperation agreement (2020).Peer ReviewedPostprint (author's final draft

The acid crater lake of Taal Volcano, Philippines: hydrogeochemical and hydroacoustic data related to the 2010–11 volcanic unrest

Studies of the water chemistry of Taal crater lake and echo-sounding surveys have provided new insights into its chemical and physical dynamics. During the volcano-seismic unrest of April 2010–June 2011, the waters of Taal crater lake showed changes in chemical composition and increases in CO2 emissions associated with the seismic unrest. The chemical and isotopic data show that the lake water has contributions from both seawater and meteoric water and receives injections of deep hydrothermal water and gases during periods of intense volcano-seismic unrest. These inflationary periods may lead to faulting of the impermeable cap rock that usually seals the deeper Taal hydrothermal reservoir in response to degassing and convective movements in the underlying Taal magma chamber.Instituto Volcanológico de Canarias, EspañaEnvironmental Research Division, Instituto Tecnológico y de Energías Renovables, EspañaAgencia Insular de Energía de Tenerife, EspañaÁrea de Geología Marina, Instituto Geológico y Minero de España, EspañaInstitute of Agriculture and Environment, Massey University, AustraliaPhilippine Institute of Volcanology and Seismology, FilipinasGeochemical Research Center, The University of Tokyo, JapónEarth & Environmental Sciences, Wesleyan University, Estados UnidosPeer reviewe

The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

[Background] Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci.[Results] In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature. We detected four genomic regions involved in the adaptation at low temperature, three of them located in the subtelomeric regions (chromosomes XIII, XV and XVI) and one in the chromosome XIV. The QTL analysis revealed that subtelomeric regions play a key role in defining individual variation, which emphasizes the importance of these regions’ adaptive nature.[Conclusions] The reciprocal hemizygosity analysis (RHA), run to validate the genes involved in low-temperature fermentation, showed that genetic variation in mitochondrial proteins, maintenance of correct asymmetry and distribution of phospholipid in the plasma membrane are key determinants of low-temperature adaptation.This work has been financially supported from the Spanish Government through MINECO and FEDER funds (AGL2013-47300-C3-3-R and PCIN-2015-143 grants) and from Generalitat Valenciana through PROMETEOII/2014/042 grant, awarded to JMG. This study has been carried out in the context of the European Project ERA-IB “YeastTempTation” EGR thanks the Spanish government for an FPI grant BES-2011-044498 and MM also thanks the Generalitat Valenciana for a VALi+d ACIF/2015/194 grant. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe

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 Intellectual Structure of Social and Sustainable Public Procurement Research: A Co-Citation Analysis

This article belongs to the Special Issue Encouraging Social and Environmental Sustainability through Public Procurement.Public procurement has recently taken into account social and sustainable factors, increasing academic literature in this field. The aim of this paper is to map the intellectual structure of social and sustainable public procurement research by means of delimiting the scientific domain’s research traditions, its disciplinary composition, and influential research topics. Given that there is a literature gap in bibliometric studies applied to this field, we conducted a co-citation analysis to identify the intellectual structure of this area of knowledge. Co-citation analyses identify networks of interconnections and, consequently, detect the most (and the least) active research areas, being a good complement to traditional literature reviews. This article contributes to science development because it is the first paper to carry out a bibliometric analysis in the field of social and sustainable public procurement, as well as the first one to conduct a co-citation analysis among public procurement research. Consequently, it is also the first article to detect which papers have become burst in this research field. The results show twelve different clusters of publications that were cited by researchers who wrote papers on social and sustainable public procurement. In other words, the sources of knowledge that scholars used as references are analysed, identifying papers that can be considered turning points, as well as those that became specially cited over a discrete period of time. Six different research trends were identified over the last decade in regard to social and sustainable public procurement research. The conclusions highlight the relevance of the findings, especially because they provide guidance to researchers when conducting literature reviews, given that the most significant journals and papers are identified.We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI), Universidad Rey Juan Carlos and Escuela de Turismo y Dirección Hotelera (EUTDH), Universidad Autónoma de Barcelona.Peer reviewe

Taxane-induced attenuation of the CXCR2/BCL-2 axis aensitizes prostate cancer to platinum-based treatment

Background: Taxanes are the most active chemotherapy agents in metastatic castration-resistant prostate cancer (mCRPC) patients; yet, resistance occurs almost invariably, representing an important clinical challenge. Taxane-platinum combinations have shown clinical benefit in a subset of patients, but the mechanistic basis and biomarkers remain elusive. Objective: To identify mechanisms and response indicators for the antitumor efficacy of taxane-platinum combinations in mCRPC. Design, setting, and participants: Transcriptomic data from a publicly available mCRPC dataset of taxane-exposed and taxane-naïve patients were analyzed to identify response indicators and emerging vulnerabilities. Functional and preclinical validation was performed in taxane-resistant mCRPC cell lines and genetically engineered mouse models (GEMMs). Intervention: Metastatic CRPC cells were treated with docetaxel, cisplatin, carboplatin, the CXCR2 antagonist SB265610, and the BCL-2 inhibitor venetoclax. Gain and loss of function in culture of CXCR2 and BCL-2 were achieved by overexpression or siRNA silencing. Preclinical assays in GEMM mice tested the antitumor efficacy of taxane-platinum combinations. Outcome measurements and statistical analysis: Proliferation, apoptosis, and colony assays measured drug activity in vitro. Preclinical endpoints in mice included growth, survival, and histopathology. Changes in CXCR2, BCL-2, and chemokines were analyzed by reverse transcriptase quantitative polymerase chain reaction and Western blot. Human expression data were analyzed using Gene Set Enrichment Analysis, hierarchical clustering, and correlation studies. GraphPad Prism software and R-studio were used for statistical and data analyses. Results and limitations: Transcriptomic data from taxane-exposed human mCRPC tumors correlate with a marked negative enrichment of apoptosis and inflammatory response pathways accompanied by a marked downregulation of CXCR2 and BCL-2. Mechanistically, we show that docetaxel inhibits CXCR2 and that BCL-2 downregulation occurs as a downstream effect. Further, we demonstrated in experimental models that the sensitivity to cisplatin is dependent on CXCR2 and BCL-2, and that targeting them sensitizes prostate cancer (PC) cells to cisplatin. In vivo taxane-platinum combinations are highly synergistic, and previous exposure to taxanes sensitizes mCRPC tumors to second-line cisplatin treatment. Conclusions: The hitherto unappreciated attenuation of the CXCR2/BCL-2 axis in taxane-treated mCRPC patients is an acquired vulnerability with potential predictive activity for platinum-based treatments. Patient summary: A subset of patients with aggressive and therapy-resistant prostate cancer benefits from taxane-platinum combination chemotherapy; however, we lack the mechanistic understanding of how that synergistic effect occurs. Here, using patient data and preclinical models, we found that taxanes reduce cancer cell escape mechanisms to chemotherapy-induced cell death, hence making these cells more vulnerable to additional platinum treatment.This work was supported by funding from the “Badalona Foundation Against Cancer” grant (Albert Font) and from Instituto de Salut Carlos III (PI16/01070 and CP15/00090; Alvaro Aytes), the European Association of Urology Research Foundation (EAURF/407003/XH; Alvaro Aytes),Fundacion BBVA (Alvaro Aytes), Department of Defense Award (W81XWH-18-1-0193; Alvaro Aytes), the CERCA Program/Generalitat de Catalunya (Alvaro Aytes), and FEDER funds/European Regional Development Fund (ERDF)—a way to Build Europe (Alvaro Aytes