HEPfit is a flexible open-source tool which, given the Standard Model or any of its extensions, allows to (i) fit the model parameters to a given set of experimental observables; (ii) obtain ...predictions for observables. HEPfit can be used either in Monte Carlo mode, to perform a Bayesian Markov Chain Monte Carlo analysis of a given model, or as a library, to obtain predictions of observables for a given point in the parameter space of the model, allowing HEPfit to be used in any statistical framework. In the present version, around a thousand observables have been implemented in the Standard Model and in several new physics scenarios. In this paper, we describe the general structure of the code as well as models and observables implemented in the current release.
Visceral leishmaniasis (VL) caused by Leishmania infantum became a disease of urban areas in Brazil in the last 30 years and there has been an increase in asymptomatic L. infantum infection with ...these areas.
A retrospective study of human VL was performed in the state of Rio Grande do Norte, Brazil, for the period of 1990-2014. The data were divided into five-time periods. For all VL cases, data on sex, age, nutritional status and childhood vaccination were collected. Geographic information system tools and statistical models were used to analyze the dispersion of human VL. The mean annual incidence of VL was 4.6 cases/100,000 inhabitants, with total 3,252 cases reported. The lethality rate was 6.4%. Over time the annual incidence of VL decreased in the 0-4 years (p<0.0001) and 5-9 (p <0.0001) age groups, but increased in ages 20-39 (p<0.001) and >40 years (p<0.0001). VL occurred more often in males (β2 = 2.5; p<0.0001). The decreased incidence of VL in children was associated with improved nutritional status and childhood immunizations including measles, poliomyelitis, BCG, and hepatitis B. Human VL correlated temporally and geographically with canine L. infantum infection (p = 0.002, R2 = 0.438), with rainfall and with Lutzomyia longipalpis density (r = 0.762). Overall, the incidence of VL decreased, while VL-AIDS increased, especially between 2010-2014. VL was more frequently found in areas that lacked urban infrastructure, detected by lack of garbage collection and sewers, whereas HIV infection was associated with higher levels of schooling and evidence of higher socioeconomic status.
The demographics of VL in northeastern Brazil have changed. Disease incidence has decreased in children and increased in adults. They were associated with improvements in nutrition, socioeconomic status and immunization rates. Concurrent VL-AIDS poses a serious challenge for the future.
Ionic liquids (ILs) are a novel class of solvents with interesting physicochemical properties. Many different applications have been reported for ILs as alternatives to organic solvents in chemical ...and bioprocesses. Despite the argued advantage of having low vapor pressure, even the most hydrophobic ILs show some degree of solubility in water, allowing their dispersion into aquatic systems and raising concerns on its pollutant potential. Moreover, nowadays most widespread notion concerning the ILs toxicity is that there is a direct relationship with their hydrophobicity/lipophilicity. This work aims at enlarging the currently limited knowledge on ILs toxicity by addressing negative impacts in aquatic ecosystems and investigating the possibility of designing hydrophobic ILs of low ecotoxicity, by the manipulation of their chemical structures. The impact of aromaticity on the toxicity of different cations (pyridinium, piperidinium, pyrrolidinium and imidazolium) and hydrophobic anions (bis(trifluoromethylsulfonyl)imide NTf
2
and hexafluorophosphate PF
6
) was analysed. Concomitantly, several imidazolium-based ILs of the type C
n
C
m
C
j
imNTf
2
were also studied to evaluate the effects of the position of the alkyl chain on the ILs’ toxicity. For that purpose, standard assays were performed using organisms of different trophic levels,
Vibrio fischeri
,
Pseudokirchneriella subcapitata
and
Daphnia magna
, allowing to evaluate the consistency of the structure–activity relationships across different biological targets. The results here reported suggest the possibility of designing ILs with an enhanced hydrophobic character and lower toxicity, by elimination of their aromatic nature.
Computed tomography perfusion (CTP) is widely used in the evaluation of acute ischemic stroke patients for endovascular thrombectomy (EVT). The stability of CTP core estimation is suboptimal and ...varies between software packages. We aimed to quantify the volumetric and spatial agreement between the CTP ischemic core and follow-up infarct for four ischemic core estimation approaches using syngo.via.
We included successfully reperfused, EVT-treated patients with baseline CTP and 24h follow-up diffusion weighted magnetic resonance imaging (DWI) (November 2017-September 2020). Data were processed with syngo.via VB40 using four core estimation approaches based on: cerebral blood volume (CBV)<1.2mL/100mL with and without smoothing filter, relative cerebral blood flow (rCBF)<30%, and rCBF<20%. The follow-up infarct was segmented on DWI.
In 59 patients, median estimated CTP core volumes for four core estimation approaches ranged from 12-39 mL. Median 24h follow-up DWI infarct volume was 11 mL. The intraclass correlation coefficient (ICC) showed moderate-good volumetric agreement for all approaches (range 0.61-0.76). Median Dice was low for all approaches (range 0.16-0.21). CTP core overestimation >10mL occurred least frequent (14/59 24% patients) using the CBV-based core estimation approach with smoothing filter.
In successfully reperfused patients who underwent EVT, syngo.via CTP ischemic core estimation showed moderate volumetric and spatial agreement with the follow-up infarct on DWI. In patients with complete reperfusion after EVT, the volumetric agreement was excellent. A CTP core estimation approach based on CBV<1.2 mL/100mL with smoothing filter least often overestimated the follow-up infarct volume and is therefore preferred for clinical decision making using syngo.via.
The outbreak of COVID-19 in 2020 has led to a surge in the interest in the mathematical modeling of infectious diseases. Disease transmission may be modeled as compartmental models, in which the ...population under study is divided into compartments and has assumptions about the nature and time rate of transfer from one compartment to another. Usually, they are composed of a system of ordinary differential equations in time. A class of such models considers the Susceptible, Exposed, Infected, Recovered, and Deceased populations, the SEIRD model. However, these models do not always account for the movement of individuals from one region to another. In this work, we extend the formulation of SEIRD compartmental models to diffusion–reaction systems of partial differential equations to capture the continuous spatio-temporal dynamics of COVID-19. Since the virus spread is not only through diffusion, we introduce a source term to the equation system, representing exposed people who return from travel. We also add the possibility of anisotropic non-homogeneous diffusion. We implement the whole model in libMesh, an open finite element library that provides a framework for multiphysics, considering adaptive mesh refinement and coarsening. Therefore, the model can represent several spatial scales, adapting the resolution to the disease dynamics. We verify our model with standard SEIRD models and show several examples highlighting the present model’s new capabilities.
This study was carried out to evaluate the performance of Brazilian Somalis sheep to natural infections by gastrointestinal nematodes. During 98 days, 75 weaned sheep, initially 3–4 months old, were ...kept on the same pasture and evaluated. Fecal and blood samples were collected for parasitological and hematological exams. After this period, the eight most resistant and the eight most susceptible animals were selected based on their individual averages of nematode fecal egg counts and were slaughtered for worm burden determination and nematodes identification. Abomasum and abomasum lymph nodes were also recovered for gene expression analysis. The animals selected as resistant had lower fecal egg counts during experimental period and smaller worm burdens than the susceptible ones (P < 0.05). The genus Haemonchus, followed by Trischostrongylus and Oesophagostomum, were identified in composite cultures. Haemonchus contortus was the specie identified in the abomasum. Packed cell volume and total plasma protein means were higher in the resistant group (27.2 % and 6.1 g/dL) than in the susceptible one (22.5 % and 5.3 g/dL), respectively. Regarding cytokine gene expression, IL-4 (P < 0.05) was up-regulated in the abomasum of resistant animals and TNF-α (P < 0.03) and IFN-γ (P < 0.03) in susceptible ones. In abomasum lymph nodes, IL-4 (P < 0.04) and IL-13 (P < 0.05) were up-regulated in the resistant animals and IFN-γ in the susceptible one (P < 0.01). This work provides further evidence that, within a given animal breed, individuals have different responses when infected by gastrointestinal nematodes. Resistant animals who responded more quickly and efficiently to these infections activated a TH2-type response.
In this paper we calculate the variation of the estimated vaccine efficacy (VE) due to the time-dependent force of infection resulting from the difference between the moment the Clinical Trial (CT) ...begins and the peak in the outbreak intensity. Using a simple mathematical model we tested the hypothesis that the time difference between the moment the CT begins and the peak in the outbreak intensity determines substantially different values for VE. We exemplify the method with the case of the VE efficacy estimation for one of the vaccines against the new coronavirus SARS-CoV-2.
The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the ...database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.
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