An Efficient Ant Colony Optimization Framework for HPC Environments

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Combinatorial optimization problems arise in many disciplines, both in the basic sciences and in applied fields such as engineering and economics. One of the most popular combinatorial optimization methods is the Ant Colony Optimization (ACO) metaheuristic. Its parallel nature makes it especially attractive for implementation and execution in High Performance Computing (HPC) environments. Here we present a novel parallel ACO strategy making use of efficient asynchronous decentralized cooperative mechanisms. This strategy seeks to fulfill two objectives: (i) acceleration of the computations by performing the ants’ solution construction in parallel; (ii) convergence improvement through the stimulation of the diversification in the search and the cooperation between different colonies. The two main features of the proposal, decentralization and desynchronization, enable a more effective and efficient response in environments where resources are highly coupled. Examples of such infrastructures include both traditional HPC clusters, and also new distributed environments, such as cloud infrastructures, or even local computer networks. The proposal has been evaluated using the popular Traveling Salesman Problem (TSP), as a well-known NP-hard problem widely used in the literature to test combinatorial optimization methods. An exhaustive evaluation has been carried out using three medium and large size instances from the TSPLIB library, and the experiments show encouraging results with superlinear speedups compared to the sequential algorithm (e.g. speedups of 18 with 16 cores), and a very good scalability (experiments were performed with up to 384 cores improving execution time even at that scale).This work was supported by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by Xunta de Galicia and FEDER funds of the EU (Centro de Investigación de Galicia accreditation 2019–2022, ref. ED431G 2019/01; Consolidation Program of Competitive Reference Groups, ref. ED431C 2021/30). JRB acknowledges funding from the Ministry of Science and Innovation of Spain MCIN / AEI / 10.13039/501100011033 through grant PID2020-117271RB-C22 (BIODYNAMICS), and from MCIN / AEI / 10.13039/501100011033 and “ERDF A way of making Europe” through grant DPI2017-82896-C2-2-R (SYNBIOCONTROL). Authors also acknowledge the Galician Supercomputing Center (CESGA) for the access to its facilities. Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C 2021/3

Characterization of High-Risk HPV/EBV Co-Presence in Pre-Malignant Cervical Lesions and Squamous Cell Carcinomas

High-risk human papillomaviruses (HR-HPVs) are the etiological agents of cervical cancer. However, a low proportion of HR-HPV-infected women finally develop this cancer, which suggests the involvement of additional cofactors. Epstein–Barr virus (EBV) has been detected in cervical squamous cell carcinomas (SCCs) as well as in low-(LSIL) and high-grade (HSIL) squamous in-traepithelial lesions, although its role is unknown. In this study, we characterized HR-HPV/EBV co-presence and viral gene expression in LSIL (n = 22), HSIL (n = 52), and SCC (n = 19) from Chilean women. Additionally, phenotypic changes were evaluated in cervical cancer cells ectopically expressing BamHI-A Rightward Frame 1 (BARF1). BARF1 is a lytic gene also expressed in EBV-positive epithelial tumors during the EBV latency program. HPV was detected in 6/22 (27.3%) LSIL, 38/52 (73.1%) HSIL, and 15/19 (78.9%) SCC cases (p < 0.001). On the other hand, EBV was detected in 16/22 (72.7%) LSIL, 27/52 (51.9%) HSIL, and 13/19 (68.4%) SCC cases (p = 0.177). HR-HPV/EBV co-presence was detected in 3/22 (13.6%) LSIL, 17/52 (32.7%) HSIL, and 11/19 (57.9%) SCC cases (p = 0.020). Additionally, BARF1 transcripts were detected in 37/55 (67.3%) of EBV positive cases and in 19/30 (63.3%) of HR-HPV/EBV positive cases. Increased proliferation, migration, and epithelial-mesenchymal transition (EMT) was observed in cervical cancer cells expressing BARF1. Thus, both EBV and BARF1 transcripts are detected in low-and high-grade cervical lesions as well as in cervical carcinomas. In addition, BARF1 can modulate the tumor behavior in cervical cancer cells, suggesting a role in increasing tumor aggressiveness.Fil: Blanco, Rancés. Universidad de Chile. Facultad de Medicina. Institutos de Ciencias Biomedicas.; ChileFil: Carrillo-Beltrán, Diego. Universidad de Tarapaca. Instituto de Alta Investigacion.; ChileFil: Muñoz, Juan P.. Universidad de Tarapaca. Instituto de Alta Investigacion.; ChileFil: Osorio, Julio C.. Universidad de Chile; ChileFil: Tapia, Julio C.. Universidad de Chile. Facultad de Medicina. Institutos de Ciencias Biomedicas.; ChileFil: Burzio, Verónica A.. Universidad Andrés Bello; ChileFil: Gallegos, Iván. Universidad de Santiago de Chile. Hospital Clinico San Borja Arriaran; ChileFil: Calaf, Gloria M.. Universidad de Tarapaca. Instituto de Alta Investigacion.; ChileFil: Chabay, Paola Andrea. Gobierno de la Ciudad de Buenos Aires. Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas; ArgentinaFil: Aguayo, Francisco. Universidad de Chile. Facultad de Medicina. Institutos de Ciencias Biomedicas.; Chil

Influence of granulation process parameters on food tablet properties formulated using natural powders (Opuntia ficus and Chlorella spp.)

In this research two natural health supplements, cactus flour (Opuntia ficus) and microalgae biomass (Chlorella spp.) have been examined as novel ingredients to formulate health supplement tablets. The physical and mechanical properties of the pure powders were quantified, and their ability to be tableted directly without additional processing was investigated. High-shear wet granulation (HSWG) was explored to improve the flowability and compression characteristics of the powders. Using an L9 Taguchi experimental design, the effect of critical process parameters of HSWG was examined on quality attributes of tablets. Tablets were successfully formulated without the addition of excipients following wet granulation. Consistent and acceptable quality tablets were produced based on the optimal processing conditions determined by L9 Taguchi design. The tablet tensile strength achieved was 0.91 ± 0.05 MPa with a disintegration time < 30 min and a friability value of 0.05 ± 0.02%. The tablets obtained in the present study are comparable with commercial available natural supplement tablets in terms of disintegration time, friability and tensile strength. The research provided a basis for the potential use of Cactus (Opuntia spp.) and microalgae (Chlorella sp.) powders as novel ingredients for the development of dietary supplements tablets, and to be used as excipients for the production of pharmaceutical tablets

In Vitro and In Vivo Efficacy of Ether Lipid Edelfosine against Leishmania spp. and SbV-Resistant Parasites

Leishmaniasis represents a major international health problem, has a high morbidity and mortality rate, and is classified as an emerging and uncontrolled disease by the World Health Organization. The migration of population from endemic to nonendemic areas, and tourist activities in endemic regions are spreading the disease to new areas. Unfortunately, treatment of leishmaniasis is far from satisfactory, with only a few drugs available that show significant side-effects. Here, we show in vitro and in vivo evidence for the antileishmanial activity of the ether phospholipid edelfosine, being effective against a wide number of Leishmania spp. causing cutaneous, mucocutaneous and visceral leishmaniasis. Our experimental mouse and hamster models demonstrated not only a significant antileishmanial activity of edelfosine oral administration against different wild-type Leishmania spp., but also against parasites resistant to pentavalent antimonials, which constitute the first line of treatment worldwide. In addition, edelfosine exerted a higher antileishmanial activity and a lower proneness to generate drug resistance than miltefosine, the first drug against leishmaniasis that can be administered orally. These data, together with our previous findings, showing an anti-inflammatory action and a very low toxicity profile, suggest that edelfosine is a promising orally administered drug for leishmaniasis, thus warranting clinical evaluation

Temperature-Related Mortality Impacts Under and Beyond Paris Agreement Climate Change Scenarios

The Paris Agreement binds all nations to undertake ambitious efforts to combat climate change, with the commitment to Bhold warming well below 2 °C in global mean temperature (GMT), relative to pre-industrial levels, and to pursue efforts to limit warming to 1.5 °C^. The 1.5 °C limit constitutes an ambitious goal for which greater evidence on its benefits for health would help guide policy and potentially increase the motivation for action. Here we contribute to this gap with an assessment on the potential health benefits, in terms of reductions in temperature-related mortality, derived from the compliance to the agreed temperature targets, compared to more extreme warming scenarios. We performed a multi-region analysis in 451 locations in 23 countries with different climate zones, and evaluated changes in heat and coldrelated mortality under scenarios consistent with the Paris Agreement targets (1.5 and 2 °C) and more extreme GMT increases (3 and 4 °C), and under the assumption of no changes in demographic distribution and vulnerability. Our results suggest that limiting warming below 2 °C could prevent large increases in temperature-related mortality in most regions worldwide. The comparison between 1.5 and 2 °C is more complex and characterized by higher uncertainty, with geographical differences that indicate potential benefits limited to areas located in warmer climates, where direct climate change impacts will be more discernible

Temperature-Related Mortality Impacts Under and Beyond Paris Agreement Climate Change Scenarios

The Paris Agreement binds all nations to undertake ambitious efforts to combat climate change, with the commitment to Bhold warming well below 2 °C in global mean temperature (GMT), relative to pre-industrial levels, and to pursue efforts to limit warming to 1.5 °C^. The 1.5 °C limit constitutes an ambitious goal for which greater evidence on its benefits for health would help guide policy and potentially increase the motivation for action. Here we contribute to this gap with an assessment on the potential health benefits, in terms of reductions in temperature-related mortality, derived from the compliance to the agreed temperature targets, compared to more extreme warming scenarios. We performed a multi-region analysis in 451 locations in 23 countries with different climate zones, and evaluated changes in heat and coldrelated mortality under scenarios consistent with the Paris Agreement targets (1.5 and 2 °C) and more extreme GMT increases (3 and 4 °C), and under the assumption of no changes in demographic distribution and vulnerability. Our results suggest that limiting warming below 2 °C could prevent large increases in temperature-related mortality in most regions worldwide. The comparison between 1.5 and 2 °C is more complex and characterized by higher uncertainty, with geographical differences that indicate potential benefits limited to areas located in warmer climates, where direct climate change impacts will be more discernible

Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood appr

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic

Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations.

The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) has assembled data on 18,435 families with BRCA1 mutations and 11,351 families with BRCA2 mutations ascertained from 69 centers in 49 countries on six continents. This study comprehensively describes the characteristics of the 1,650 unique BRCA1 and 1,731 unique BRCA2 deleterious (disease-associated) mutations identified in the CIMBA database. We observed substantial variation in mutation type and frequency by geographical region and race/ethnicity. In addition to known founder mutations, mutations of relatively high frequency were identified in specific racial/ethnic or geographic groups that may reflect founder mutations and which could be used in targeted (panel) first pass genotyping for specific populations. Knowledge of the population-specific mutational spectrum in BRCA1 and BRCA2 could inform efficient strategies for genetic testing and may justify a more broad-based oncogenetic testing in some populations

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research