Making more flexible ATISMART+ model for traffic simulations using a CAS

Traffic simulations usually require the search of a path to join two different points. Dijkstra’s algorithm [1] is one of the most commonly used for this task due to its easiness and quickness. In [2, 3] we developed an accelerated time simulation of car traffic in a smart city using Dijkstra’s algorithm to compute the paths. Dijkstra’s algorithm provides a shortest path between two different points but this is not a realistic situation for simulations. For example, in a car traffic situa- tion, the driver may not know the shortest path to follow. This ignorance can be produced, among others, because one of the following two facts: the driver may not know the exact length of the lanes, or, even knowing the exact length, the driver may not know how to find the shortest path. Even more, in many cases, a mixture of both facts occurs. A more realistic simulation should therefore consider these kind of facts. The algorithm used to compute the path from one point to another in a traffic simulation might consider the possibility of not using the shortest path. In this talk, we use a new probabilistic extension of Dijkstra’s algorithm which covers the above two situations. For this matter, two different modifications in Di- jkstra’s algorithm have been introduced: using non-exact length in lanes, and the choice of a non-shortest path between two different points. Both modifications are used in a non-deterministic way by means of using probability distributions (classi- cal distributions such as Normal or Poisson distributions or even "ad hoc" ones). A precise, fast, natural and elegant way of working with such probability distributions is the use of a CAS in order to deal with exact and explicit computations. As an example of use of this extension of Dijkstra’s algorithm, we will show the ATISMART+ model. This model provides more realistic accelerated time sim- ulations of car traffics in a smart city and was first introduced in [4] and extended in [5]. This model was developed combining J AVA for the GUI and M AXIMA for the mathematical core of the algorithm. The studies developed in the above mentioned works, dealt with Poisson, Ex- ponential, Uniform and Normal distributions. In this talk we will introduce, as a novelty, the possibility of using other continuous probability distributions such as: Lognormal, Weibul, Gamma, Beta, Chi-Square, Student’s t, Z, Pareto, Lo- gistic, Cauchy or Irwin-Hall, and other discrete distributions such as: Bernouille, Rademacher, Binomial, Geometric, Negative Binomial or Hypergeometric. Even 1 more, this new version allows to deal with any “ad-hoc” continuous, discrete or mixed user’s distributions. This fact improves the flexibility of ATISMART+ model.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Acoplamiento entre las comunidades planctónicas de un lago amazónico de aguas claras (lago Boa, Colombia)

Las comunidades planctónicas de un lago están relacionadas entre sí de diversas maneras. Para los lagos amazónicos colombianos poco es lo que se conoce sobre este acoplamiento. Se realizaron siete visitas al lago Boa (Caquetá Medio) desde mayo de 1999 a mayo de 2000, durante las cuales se tomaron muestras de bacterioplancton, fitoplancton, nanozooplancton (protozoos) y rotíferos y crustáceos (mesozooplancton) para conocer sus variaciones y sus relaciones numéricas a lo largo del ciclo hidrológico. Los promedios de abundancias de individuos por litro fluctuaron entre 4.1 · 109 a 1.4 · 1010 bacterias, 5.5 · 103 a 6.4 · 106 microalgas, 2.2 · 104 a 1.1 · 105 protozoos nanoplanctónicos y 8.1 a 240 organismos mesozooplanctónicos (rotíferos y crustáceos). Todas las comunidades tuvieron mayores abundancias en el periodo de aguas bajas, cuando el lago se desconectó del río Metá. El fitoplancton fue muy diverso y poco abundante; los grupos dominantes fueron las clorofitas, dinofitas y cianobacterias. El mesozooplancton fue escaso y estuvo compuesto principalmente por rotíferos. Dentro de los protozoos nanoplanctónicos predominaron los ciliados. Se halló una asociación estadística significativa entre las abundancias totales del fitoplancton y del bacterioplancton (p = 0.0001), lo cual sugiere algún grado de interdependencia de las dos comunidades. Durante los meses de inundación la fuerza física del pulso hidrológico parece causar que las comunidades funcionen con mayor autonomía, ya que en esta época el lago Boa se comporta como un verdadero sistema lótico.Planktonic communities of a lake are related in several forms. For Colombian Amazon lakes little is known about this coupling. Seven surveys in the Boa Lake (Middle Caquetá) were made between May of 1999 and May of 2000 to take samples of bacterioplankton, phytoplankton, nanozooplankton (protozoa) and rotifers and crustaceans (mesozooplankton), to study their variations and numerical relationships throughout the hydrological cycle. Average densities per liter were 4.1 · 109 a 1.4 · 1010 bacteria,5.5 · 103 a 6.4 · 106 phytoplankontes, 2.2 · 104 a 1.1 · 105 nanoplanktonic protozoa and 8.1 to 240 mesozooplanktontes (rotifers and crustaceans). All the communities had higher abundances in the low water period, when the lake was disconnected from the Met'a River. Phytoplankton was very diverse and scarce, but dominant groups were Chlorophyta, Dinophyta, and Cyanobacteria. Mesozooplankton was scarce and with low diversity, with rotifers as the most important group. Ciliates were predominant within nanoplanktonic protozoa. There was a significant statistical relationship between phytoplankton and bacterioplankton total densities (p = 0.0001), which suggesst some level of interdependence among these planktonic communities. During the flood months, the physical force of the hydrologic pulse seems to cause communities to become more autonomous, because at this time the Boa Lake acts more like a lotic system

Intestinal Immunomodulation and Shifts on the Gut Microbiota of BALB/c Mice Promoted by Two Bifidobacterium and Lactobacillus Strains Isolated from Human Samples

Bifidobacterium animalis subsp. lactis IPLA 20020 and Lactobacillus gasseri IPLA 20212, two strains isolated from human samples, were evaluated for safety and influence over the intestinal microbiota and cytokine production by the intestinal tissue of adult BALB/c mice. Mice were divided into four groups receiving during 8 days PBS or a suspension of each strain, prepared fresh or lyophilized (bifidobacteria), at an amount of 4x108 viable cells/day. This dose could be comparable to the probiotic intake of a human adult who consumed about 100-200 mL of functional fermented milk per day, considering the usual level of probiotics in commercial products. No microbial translocation to liver or alterations in food intake, weight, and behavior were observed in treated mice. Intestinal content of secretory immunoglobulin A (s-IgA) was not affected, discarding any adverse effect on the mucosa-associated immunity. The profile of intestinal proinflammatory/regulatory cytokines after intervention evidenced that the microbial strain administered and its cellular state (fresh or lyophilized) as well as the host tissue analyzed (small or large intestine) influenced the immune response and suggests a moderate shift towards a T helper 1 profile (Th1) in the large intestine after the administration of both strains. Changes on relative levels of some intestinal microbial groups were evidenced after intervention. It is noteworthy that butyrate was positively associated with a balanced pro-Th1 immune response. Therefore, B. animalis subsp. lactis IPLA20020 and L. gasseri IPLA 20212 could be considered potential probiotic candidates to be included in functional foods for balancing the intestinal immune response.Fil: Nogacka, Alicja M.. Instituto de Investigación Sanitaria del Principado de Asturias; España. Consejo Superior de Investigaciones Científicas. Instituto Superior de Productos Lácteos de Asturias; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Lactología Industrial. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Instituto de Lactología Industrial; ArgentinaFil: Oddi, Sofia Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Lactología Industrial. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Instituto de Lactología Industrial; ArgentinaFil: Salazar, Nuria. Instituto de Investigación Sanitaria del Principado de Asturias; España. Consejo Superior de Investigaciones Científicas. Instituto Superior de Productos Lácteos de Asturias; EspañaFil: Reinheimer, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Lactología Industrial. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Instituto de Lactología Industrial; ArgentinaFil: Gueimonde, Miguel. Instituto de Investigación Sanitaria del Principado de Asturias; España. Consejo Superior de Investigaciones Científicas. Instituto Superior de Productos Lácteos de Asturias; EspañaFil: Vinderola, Celso Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Lactología Industrial. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Instituto de Lactología Industrial; ArgentinaFil: De Los Reyes Gavilán, Clara G.. Consejo Superior de Investigaciones Científicas. Instituto Superior de Productos Lácteos de Asturias; España. Instituto de Investigación Sanitaria del Principado de Asturias; Españ

Inside the adaptation process of Lactobacillus delbrueckii subsp. lactis to bile

Progressive adaptation to bile might render some lactobacilli able to withstand physiological bile salt concentrations. In this work, the adaptation to bile was evaluated on previously isolated dairy strains of Lactobacillus delbrueckii subsp. lactis 200 and L. delbrueckii subsp. lactis 200+, a strain derived thereof with stable bile-resistant phenotype. The adaptation to bile was obtained by comparing cytosolic proteomes of both strains grown in the presence or absence of bile. Proteomics were complemented with physiological studies on both strains focusing on glycolytic end-products, the ability to adhere to the human intestinal epithelial cell line HT29-MTX and survival to simulated gastrointestinal conditions. Protein pattern comparison of strains grown with and without bile allowed us to identify 9 different proteins whose production was regulated by bile in both strains, and 17 proteins that showed differences in their levels between the parental and the bile-resistant derivative. These included general stress response chaperones, proteins involved in transcription and translation, in peptidoglycan/exopolysaccharide biosynthesis, in the lipid and nucleotide metabolism and several glycolytic and pyruvate catabolism enzymes. Differences in the level of metabolic end-products of the sugar catabolism were found between the strains 200 and 200+. A decrease in the adhesion of both strains to the intestinal cell line was detected in the presence of bile. In simulated gastric and intestinal juices, a protective effect was exerted by milk improving the survival of both microorganisms. These results indicate that bile tolerance in L. delbrueckii subsp. lactis involves several mechanisms responding to the deleterious impact of bile salts on bacterial physiology. © 2010 Elsevier B.V.This work was supported by the following funds in Argentina: Programación CAI+D 2006 37-203 (Universidad Nacional del Litoral, Santa Fe, Argentina), Project PICT 2004 No. 09 20358 and PICT Jóvenes 2005 No. 32118 from the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), and Project PIP 5321 from CONICET. The following Spanish funds are acknowledged: projects AGL2006-03336 and AGL2007-62736 from the Ministry of Science and Innovation. Patricia Burns received a 6-month grant from the Agencia Española de Cooperación Internacional for a research stay at IPLA (CSIC). Lorena Ruiz and Borja Sánchez were the recipients of a predoctoral I3P fellowship from CSIC and a postdoctoral Juan de la Cierva contract from the Spanish Ministry of Science and Innovation, respectively. Spanish and Argentinian groups shared a joint collaboration project CSIC–CONICET (reference 2005AR0047).Peer Reviewe

New Perspectives for UAV-Based Modelling the Roman Gold Mining Infrastructure in NW Spain

This contribution discusses the potential of UAV-assisted (unmanned aerial vehicles) photogrammetry for the study and preservation of mining heritage sites using the example of Roman gold mining infrastructure in northwestern Spain. The study area represents the largest gold area in Roman times and comprises 7 mining elements of interest that characterize the most representative examples of such ancient works. UAV technology provides a non-invasive procedure valuable for the acquisition of digital information in remote, difficult to access areas or under the risk of destruction. The proposed approach is a cost-effective, robust and rapid method for image processing in remote areas were no traditional surveying technologies are available. It is based on a combination of data provided by aerial orthoimage and LiDAR (Light Detection and Ranging) to improve the accuracy of UAV derived data. The results provide high-resolution orthomosaic, DEMs and 3D textured models that aim for the documentation of ancient mining scenarios, providing high-resolution digital information that improves the identification, description and interpretation of mining elements such as the hydraulic infrastructure, the presence of open-cast mines which exemplifies the different exploitation methods, and settlements. However, beyond the scientific and technical information provided by the data, the 3D documentation of ancient mining scenarios is a powerful tool for an effective and wider public diffusion ensuring the visualization, preservation and awareness over the importance and conservation of world mining heritage sites

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.This work is supported by the project PID2019-103900GB-I00 funded by MCIN/AEI /10.13039/501100011033 and Programa Operativo FEDER Andalucía 2014–2020 (US-1380953) to L.M.E. Work by L.M.E. and J.A.A.-S.R. has been funded by the Junta de Andalucía (Consejerı´a de economı´a, conocimiento, empresas y Universidad) grant PY18-631 co-funded by FEDER funds. A.T. has been funded by a ‘‘Contrato predoctoral PIF’’ from Universidad de Sevilla. C.G.-V. has been funded by a ‘‘Contrato predoctoral para la formacio´ n de doctores’’ BES-2017-082306. G.B. was supported by a Comunidad de Madrid contract (CAM) and by an FPI grant from MINECO (BES-2022-077789). F.M.-B. was supported by MICINN (PID2020-120367GB-I00) and Fundacio´ n Ramo´ n Areces (CIVP18A3904). P.G.-G. has been funded by Margarita Salas Fellowship – NextGenerationEU. C.H.F.-E. has been funded by Marı´a Zambrano Fellowship – NextGenerationEU. I.A.-C. would like to acknowledge that his work has been partially supported by the University of the Basque Country UPV/EHU grant GIU19/027 and by grant PID2021-126701OB-I00, funded by MCIN/AEI/10.13039/501100011033 and by ‘‘ERDF A way of making Europe." L.M.E. also wants to thank PIE-202120E047 – Conexiones-Life network for networking and input

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.Ministerio de Ciencia e Innovación PID2019-103900GB-I00, PID2020-120367GB-I00, PID2021-126701OB-I00Junta de Andalucía US-1380953, PY18-631Ministerio de Economía y Competitividad BES-2022-07778

A cluster-randomized trial of hydroxychloroquine for prevention of Covid-19

Background: current strategies for preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited to nonpharmacologic interventions. Hydroxychloroquine has been proposed as a postexposure therapy to prevent coronavirus disease 2019 (Covid-19), but definitive evidence is lacking. Methods: we conducted an open-label, cluster-randomized trial involving asymptomatic contacts of patients with polymerase-chain-reaction (PCR)-confirmed Covid-19 in Catalonia, Spain. We randomly assigned clusters of contacts to the hydroxychloroquine group (which received the drug at a dose of 800 mg once, followed by 400 mg daily for 6 days) or to the usual-care group (which received no specific therapy). The primary outcome was PCR-confirmed, symptomatic Covid-19 within 14 days. The secondary outcome was SARS-CoV-2 infection, defined by symptoms compatible with Covid-19 or a positive PCR test regardless of symptoms. Adverse events were assessed for up to 28 days. Results: the analysis included 2314 healthy contacts of 672 index case patients with Covid-19 who were identified between March 17 and April 28, 2020. A total of 1116 contacts were randomly assigned to receive hydroxychloroquine and 1198 to receive usual care. Results were similar in the hydroxychloroquine and usual-care groups with respect to the incidence of PCR-confirmed, symptomatic Covid-19 (5.7% and 6.2%, respectively; risk ratio, 0.86 [95% confidence interval, 0.52 to 1.42]). In addition, hydroxychloroquine was not associated with a lower incidence of SARS-CoV-2 transmission than usual care (18.7% and 17.8%, respectively). The incidence of adverse events was higher in the hydroxychloroquine group than in the usual-care group (56.1% vs. 5.9%), but no treatment-related serious adverse events were reported. Conclusions: postexposure therapy with hydroxychloroquine did not prevent SARS-CoV-2 infection or symptomatic Covid-19 in healthy persons exposed to a PCR-positive case patient. (Funded by the crowdfunding campaign YoMeCorono and others; BCN-PEP-CoV2 ClinicalTrials.gov number, NCT04304053.)

Supplemental information CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

Document S1. Figures S1–S6 Table S1. Extracted features from 353 curated cysts (104 cysts at 4 days, 103 cysts at 7 days, 116 cysts at 10 days), related to Figure 2 Table S2. Hyperparameter search space for our proposed 3D ResU-Net, related to Figure 1 Table S3. Performance evaluation of our pipeline (CartoCell) on images of different epithelial tissues and comparison with other state-of-the-art segmentation methods, using the evaluation metrics described in STAR Methods, related to Figure 1 Table S4. Relative error between features extracted using automatically segmented cysts and manually curated cysts (STAR Methods), related to Figure 1 Table S5. Cyst morphology and scutoid location statistics, related to Figure 2 Table S6. Comparison of morphology and packing features of normoxic and hypoxic MDCK cysts, related to Figure 2 Table S7. Classification of the developmental stages of Drosophila egg chambers employed, related to Figure 3 Document S2. Article plus supplemental informationPeer reviewe