SERGHEI (SERGHEI-SWE) v1.0: a performance-portable high-performance parallel-computing shallow-water solver for hydrology and environmental hydraulics

The Simulation EnviRonment for Geomorphology, Hydrodynamics, and Ecohydrology in Integrated form (SERGHEI) is a multi-dimensional, multi-domain, and multi-physics model framework for environmental and landscape simulation, designed with an outlook towards Earth system modelling. At the core of SERGHEI's innovation is its performance-portable high-performance parallel-computing (HPC) implementation, built from scratch on the Kokkos portability layer, allowing SERGHEI to be deployed, in a performance-portable fashion, in graphics processing unit (GPU)-based heterogeneous systems. In this work, we explore combinations of MPI and Kokkos using OpenMP and CUDA backends. In this contribution, we introduce the SERGHEI model framework and present with detail its first operational module for solving shallow-water equations (SERGHEI-SWE) and its HPC implementation. This module is designed to be applicable to hydrological and environmental problems including flooding and runoff generation, with an outlook towards Earth system modelling. Its applicability is demonstrated by testing several well-known benchmarks and large-scale problems, for which SERGHEI-SWE achieves excellent results for the different types of shallow-water problems. Finally, SERGHEI-SWE scalability and performance portability is demonstrated and evaluated on several TOP500 HPC systems, with very good scaling in the range of over 20 000 CPUs and up to 256 state-of-the art GPUs

The detection of airborne transmission of tuberculosis from HIV-infected patients, using an in vivo air sampling model

Background. Nosocomial transmission of tuberculosis remains an important public health problem. We created an in vivo air sampling model to study airborne transmission of tuberculosis from patients coinfected with human immunodeficiency virus (HIV) and to evaluate environmental control measures. Methods. An animal facility was built above a mechanically ventilated HIV‐tuberculosis ward in Lima, Peru. A mean of 92 guinea pigs were continuously exposed to all ward exhaust air for 16 months. Animals had tuberculin skin tests performed at monthly intervals, and those with positive reactions were removed for autopsy and culture for tuberculosis. Results. Over 505 consecutive days, there were 118 ward admissions by 97 patients with pulmonary tuberculosis, with a median duration of hospitalization of 11 days. All patients were infected with HIV and constituted a heterogeneous group with both new and existing diagnoses of tuberculosis. There was a wide variation in monthly rates of guinea pigs developing positive tuberculin test results (0%–53%). Of 292 animals exposed to ward air, 159 developed positive tuberculin skin test results, of which 129 had laboratory confirmation of tuberculosis. The HIV‐positive patients with pulmonary tuberculosis produced a mean of 8.2 infectious quanta per hour, compared with 1.25 for HIV‐negative patients with tuberculosis in similar studies from the 1950s. The mean monthly patient infectiousness varied greatly, from production of 0–44 infectious quanta per hour, as did the theoretical risk for a health care worker to acquire tuberculosis by breathing ward air. Conclusions. HIV‐positive patients with tuberculosis varied greatly in their infectiousness, and some were highly infectious. Use of environmental control strategies for nosocomial tuberculosis is therefore a priority, especially in areas with a high prevalence of both tuberculosis and HIV infection

High paracellular nutrient absorption in intact bats is associated with high paracellular permeability in perfused intestinal segments

Water-soluble nutrients are absorbed by the small intestine via transcellular and paracellular mechanisms. Based on a few previous studies, the capacity for paracellular nutrient absorption seems greater in flying mammals than in nonflying mammals, but there has been little investigation of the mechanisms driving this difference. Therefore, we studied three species each of bats (Artibeus lituratus, Sturnira lilium and Carollia perspicillata) and nonflying mammals (Akodon montensis, Mus musculus and Rattus norvegicus). Using standard pharmacokinetic techniques in intact animals, we confirmed the greater paracellular nutrient absorption in the fliers, comparing one species in each group. Then we conducted in situ intestinal perfusions on individuals of all species. In both approaches, we measured the absorption of 3OMD-glucose, a nonmetabolizable glucose analog absorbed both paracellularly and transcellularly, as well as l-arabinose, which has no mediated transport. Fractional absorption of l-arabinose was three times higher in the bat (S. lilium: 1.2±0.24) than in the rodent (A. montensis: 0.35±0.04), whereas fractional absorption of 3OMD-glucose was complete in both species (1.46±0.4 and 0.97±0.12, respectively). In agreement, bats exhibited two to 12 times higher l-arabinose clearance per square centimeter nominal surface area than rodents in intestinal perfusions. Using l-arabinose, we estimated that the contribution of the paracellular pathway to total glucose absorption was higher in all three bats (109–137%) than in the rodents (13–39%). These findings contribute to an emerging picture that reliance on the paracellular pathway for nutrient absorption is much greater in bats relative to nonflying mammals and that this difference is driven by differences in intestinal permeability to nutrient-sized molecules.Fil: Brun, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Price, Edwin R.. University Of Wisconsin; Estados UnidosFil: Gontero Fourcade, Manuel Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Fernández Marinone, Guido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentina. Universidad Nacional de San Luis. Facultad de Quimica, Bioquimica y Farmacia. Departamento de Bioquímica y Ciencias Biológicas; ArgentinaFil: Cruz Neto, Ariovaldo P.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Caviedes Vidal, Enrique Juan Raul. Universidad Nacional de San Luis. Facultad de Quimica, Bioquimica y Farmacia. Departamento de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Karasov, William H.. University of Wisconsin; Estados Unido

Hospital control and multidrug-resistant pulmonary tuberculosis in female patients, Lima, Peru.

We examined the prevalence of tuberculosis (TB), rate of multidrug-resistant (MDR) TB, and characteristics of TB on a female general medicine ward in Peru. Of 250 patients, 40 (16%) were positive by sputum culture and 27 (11%) by smear, and 8 (3%) had MDRTB. Thirteen (33%) of 40 culture-positive patients had not been suspected of having TB on admission. Six (46%) of 13 patients whose TB was unsuspected on admission had MDRTB, compared with 2 (7%) of 27 suspected cases (p = 0.009). Five (63%) of 8 MDRTB patients were smear positive and therefore highly infective. In developing countries, hospital control, a simple method of reducing the spread of MDRTB, is neglected

Early and efficient detection of Mycobacterium tuberculosis in sputum by microscopic observation of broth cultures.

Early, efficient and inexpensive methods for the detection of pulmonary tuberculosis are urgently needed for effective patient management as well as to interrupt transmission. These methods to detect M. tuberculosis in a timely and affordable way are not yet widely available in resource-limited settings. In a developing-country setting, we prospectively evaluated two methods for culturing and detecting M. tuberculosis in sputum. Sputum samples were cultured in liquid assay (micro broth culture) in microplate wells and growth was detected by microscopic observation, or in Löwenstein-Jensen (LJ) solid media where growth was detected by visual inspection for colonies. Sputum samples were collected from 321 tuberculosis (TB) suspects attending Bugando Medical Centre, in Mwanza, Tanzania, and were cultured in parallel. Pulmonary tuberculosis cases were diagnosed using the American Thoracic Society diagnostic standards. There were a total of 200 (62.3%) pulmonary tuberculosis cases. Liquid assay with microscopic detection detected a significantly higher proportion of cases than LJ solid culture: 89.0% (95% confidence interval [CI], 84.7% to 93.3%) versus 77.0% (95% CI, 71.2% to 82.8%) (p = 0.0007). The median turn around time to diagnose tuberculosis was significantly shorter for micro broth culture than for the LJ solid culture, 9 days (interquartile range [IQR] 7-13), versus 21 days (IQR 14-28) (p<0.0001). The cost for micro broth culture (labor inclusive) in our study was US $4.56 per sample, versus US$11.35 per sample for the LJ solid culture. The liquid assay (micro broth culture) is an early, feasible, and inexpensive method for detection of pulmonary tuberculosis in resource limited settings

GENERALIZED URTICARIA AS A VASCULITIC MANIFESTATION IN A PATIENT WITH SARS-CoV-2 INFECTION: A CASE REPORT IN COLOMBIA

Skin manifestations have been reported in up to 20% of cases of SARS-CoV-2 infection, including morbilliform rash (22%), pernio-like acral lesions (18%), urticaria (16%), and macular erythema (13%). It is believed that in the case of SARS-CoV-2 infection, the mechanism involved is an inflammatory response that generates immune dysregulation, vascular congestion, vasculitis, vascular thrombosis, or neoangiogenesis. This case study, present the case of a patient with no previous history of urticarial reactions, autoimmune diseases, or exposure to medications who develops generalized urticaria lasting more than 24 hours and who was diagnosed with SARS-CoV-2 infection by RT-PCR with a nasopharyngeal swab. We suggest in this patient vasculitic urticaria as a manifestation of SARS-CoV-2 infection

Phytoplankton chlorophyte structure as related to ENSO events in a saline lowland river (Salado River, Buenos Aires, Argentina)

We analyzed the phytoplankton present in the lower sector of the Salado River (Buenos Aires, Argentina) for 10 years (1995–2005) and detected significant changes occurring in chlorophyte abundance and species richness during La Niña event (1998–1999), which period was analyzed throughout the entire basin (main stream and tributaries). We compared the physicochemical and biologic variables between two El Niño–La Niña–Southern Oscillation (ENSO) periods – El Niño (March 1997–January 1998) and La Niña (May 1998–May 1999) – to identify possible indicators of a relationship between climatic anomalies and chlorophyte performance. Chlorophyte density increased during the La Niña. Under normal or extreme hydrologic conditions, mobile (Chlamydomonas spp.) and nonmobile (Monoraphidium spp.) chlorophytes codominated. These species belonged to Reynolds's functional groups X1 and X2, those typical of nutrient-enriched environments. Comparative analyses between El Niño and La Niña periods indicated significant differences in physicochemical (K+, dissolved polyphenols, particulate reactive phosphorus, alkalinity, pH) and biologic (species diversity and richness, phytoplankton and chlorophyte total densities) variables between the two periods at all basin sites. During the La Niña condition, species richness was greater owing to interconnected shallow lakes and drainage-channel inputs, while the Shannon diversity index was lower because of the high abundance values of Monoraphidium minutum. A detailed analysis of the chlorophytes in the entire basin, indicated that changes in density and species dominance occurred on a regional scale although diverse chlorophyte assemblages were identified in the different sectors of the Salado River basin. After La Niña event, the entire basin had the potential to revert to the previous density values, showing the resilience to global environmental changes and the ability to reestablish the general conditions of stability.Fil: Solari, Lía Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Gabellone, Nestor Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Claps, Maria Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Casco, Maria Adela. Universidad Nacional de la Plata. Facultad de Ciencias Naturales y Museo. Division Ficologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Quaini, Karina Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Neschuk, Nancy Carolina. Dirección Provincial de Saneamiento y Obras Hidráulicas del Ministerio de Infraestructura, Vivienda y Servicios Públicos de la Provincia de Buenos Aires; Argentin

A study on the impact of AL-FEC techniques on TV over IP Quality of Experience

In this contribution, an evaluation of the effectiveness of Application Layer-Forward Error Correction (AL-FEC) scheme in video communications over unreliable channels is presented. In literature, several AL-FEC techniques for reducing the effect of noisy transmission on multimedia communication have been adopted. Recently, their use has been proposed for inclusion in TV over IP broadcasting international standards. The objective of the analysis performed in this paper is to verify the effectiveness of AL-FEC techniques in terms of perceived Quality of Service (QoS) and more in general of Quality of Experience (QoE), and to evaluate the trade-off between AL-FEC redundancy and video quality degradation for a given packet loss ratio. To this goal, several channel error models are investigated (random i.i.d. losses, burst losses, and network congestions) on test sequences encoded at 2 and 4 Mbps. The perceived quality is evaluated by means of three quality metrics: the full-reference objective quality metric NTIA-VQM combined with the ITU-T Rec. G.1070, the full-reference DMOS-KPN metric, and the pixel-wise error comparison performed by using the PSNR distortion measure. A post-processing synchronization between the original and the reconstructed stream has also been designed for improving the fidelity of the performed quality measures. The experimental results show the effectiveness and the limits of the Application Layer protection schemes. © 2011 Battisti et al; licensee Springer