Piecewise smooth chebfuns

Algorithms are described that make it possible to manipulate piecewise-smooth functions on real intervals numerically with close to machine precision. Breakpoints are introduced in some such calculations at points determined by numerical rootfinding, and in others by recursive subdivision or automatic edge detection. Functions are represented on each smooth subinterval by Chebyshev series or interpolants. The algorithms are implemented in object-oriented MATLAB in an extension of the chebfun system, which was previously limited to smooth functions on [-1, 1]

Evolution of within-host variants of the hepatitis C virus

Introduction: Comprehensive investigation of the within-host evolution of hepatitis C virus (HCV) variants has been difficult without high coverage deep sequencing data and bioinformatics tools to characterise these variants. With the advent of high throughput, long-read sequencing platforms such as Oxford Nanopore Technology (ONT), capturing within-host evolution of HCV using full genome sequences has become feasible. This study aimed to provide the proof of concept that within-host evolutionary analysis of HCV using near-full-length genomes, is achievable. Methods: Five treatment naïve subjects with chronic HCV infection were sampled longitudinally from 6 months to 5 years post-infection, with 3–5 sampling timepoints per subject. Near full-length sequences generated using the ONT platform encompassing within-host HCV variants were analysed using an in-house bioinformatic tool. A 200-sequence proxy alignment of the viral variants was made for each subject and timepoint, proportionately representing the observed within-host variants. This alignment was then used in a Bayesian evolutionary analysis using BEAST software suite (v1.8). Results: The estimated within-host substitution rates ranged between 0.89 and 6.19 × 10−5 substitutions/site/day. At most timepoints, observed viral lineages were closely related to those from the immediately preceding timepoint, and genetic diversity bottlenecks were observed at intervals in both the acute and chronic phases of infection. The highest within-host mutation rates were observed in the Envelope-P7 and NS5 regions while the Core region was the most conserved. Conclusion: This study demonstrates the feasibility of studying within-host evolution of near-full-length HCV genomes, using long-read sequencing platforms. When considered in conjunction with meta-data such as the host immune response, these methods may offer high resolution insights into immune escape (in vivo or in vitro) to inform vaccine design and to predict spontaneous clearance

Emprendimientos turísticos locales y su impacto en el desarrollo socioeconómico del distrito de Valera provincia de Bongará región Amazonas 2020

Los emprendimientos turísticos están relacionados a cualquier iniciativa de empezar un negocio dentro del sector turismo, como es el caso de los negocios que han iniciado a raíz del turismo en el distrito de Valera generando muchos cambios en las actividades económicas del lugar; por ello la tesis cuyo título es Emprendimientos turísticos locales y su impacto en el desarrollo socioeconómico del distrito de Valera; parte del objetivo general de determinar los impactos de los emprendimientos turísticos. La metodología utilizada en la investigación fueron los métodos inductivo, deductivo, descriptivo y analítico y para el recojo de información se tuvo en cuenta a la población local, las técnicas de estudio fueron las encuestas y la observación con sus respectivos instrumentos. Dentro de los principales resultados se tiene: La identificación de los emprendimientos turísticos locales del distrito de Valera, los impactos indirectos de los emprendimientos turísticos locales, los impactos directos de los emprendimientos turísticos locales de Valera y las estrategias para maximizar los impactos positivos y mitigar los impactos socioeconómicos negativos del Distrito de Valera provincia de Bongará. Como conclusión de la investigación se tiene que los emprendimientos turísticos locales han generado impactos socioeconómicos positivos en el distrito y que estos a su vez son directos e indirectos

When chefs adopt a school? An evaluation of a cooking intervention in English primary schools

This article sets out the findings from research on the impact of a, UK based, chefs in schools teaching programme on food, health, nutrition and cookery. Professional chefs link with local schools, where they deliver up to three sessions to one class over a year. The research measured the impact of a standardised intervention package and changes in food preparation and consumption as well as measuring cooking confidence. The target group was 9–11 year olds in four schools. The main data collection method was a questionnaire delivered 2 weeks before the intervention and 2 weeks afterwards. There was a group of four matched control schools. Those taking part in the intervention were enthused and engaged by the sessions and the impact measures indicated an intention to change. There were gains in skills and confidence to prepare and ask for the ingredients to be purchased for use in the home. Following the session with the chef, the average reported cooking confidence score increased from 3.09 to 3.35 (by 0.26 points) in the intervention group – a statistically significant improvement. In the control group this change was not statistically significant. Children’s average reported vegetable consumption increased after the session with the chef, with the consumption score increasing from 2.24 to 2.46 points (0.22 points) again, a statistically significant increase with no significant changes in the control group. The research highlights the need to incorporate evaluation into school cooking initiatives as the findings can provide valuable information necessary to fine-tune interventions and to ensure consistency of the healthy eating messages

Neutron Autoradiography Combined With UV-C Sensitization: Toward the Intracellular Localization of Boron

Our group has reported the imprint formation of biological material on polycarbonate nuclear track detectors by UV-C exposure, which is used as an approach to simultaneously visualize cell imprints and nuclear tracks coming from the boron neutron capture reaction. Considering that the cell nucleus has a higher UV-C absorption than the cytoplasm and that hematoxylin preferentially stains the nucleus, we proposed to enhance the contrast between these two main cell structures by hematoxylin staining before UV-C sensitization. In this study, several experiments were performed in order to optimize UV-C exposure parameters and chemical etching conditions for cell imprint formation using the SK-BR-3 breast cancer cell line. The proposed method improves significantly the resolution of the cell imprints. It allows clear differentiation of the nucleus from the rest of the cell, together with nuclear tracks pits. Moreover, it reduces considerably the UV-C exposure time, an important experimental issue. The proposed methodology can be applied to study the boron distribution independently from the chosen cell line and/or boron compounds.Fil: Gadan, Mario Alberto. Comisión Nacional de Energía Atómica; ArgentinaFil: Lloyd, Rodrigo. Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica; Argentina. Comisión Nacional de Energía Atómica; ArgentinaFil: Saint Martin, María Laura Gisela. Comisión Nacional de Energía Atómica; ArgentinaFil: Olivera, María S.. Comisión Nacional de Energía Atómica; ArgentinaFil: Policastro, Lucia Laura. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnologia. Unidad Ejecutora Instituto de Nanociencia y Nanotecnologia - Nodo Constituyentes | Comision Nacional de Energia Atomica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnologia. Unidad Ejecutora Instituto de Nanociencia y Nanotecnologia - Nodo Constituyentes.; ArgentinaFil: Portu, Agustina Mariana. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Effect of prior Zika and dengue virus exposure on the severity of a subsequent dengue infection in adults

Given the structural similarity between Zika and dengue viruses, prior infection from one virus is hypothesized to modulate the severity of a subsequent infection from the other virus. A previous paediatric cohort study observed that a prior Zika infection may increase the risk of a subsequent symptomatic or severe dengue infection. The Colombo Dengue study is a prospective hospital-based cohort study in Sri Lanka that recruits symptomatic adult dengue patients within the first three days of fever. Anti-Dengue Envelope and anti-Zika NS1 IgG antibodies were tested by ELISA (Euroimmun, Lubeck, Germany) in all recruited patients. Associations between pre-morbid seroprevalence for either or both infections and adverse clinical outcomes of the current dengue infection were explored. A total of 507 dengue infected patients were assessed of whom 342 (68%) and 132 (26%) patients had anti-dengue IgG and anti-Zika IgG respectively. People with combined prior dengue and zika exposure as well as prior dengue exposure alone, were at increased risk of plasma leakage, compensated and uncompensated shock, and severe dengue (p < 0·05), compared to people without prior exposure to either infection. The effect of prior Zika exposure alone could not be established due to the small the number of primary dengue infections with prior Zika exposure

Testing accuracy in 2D and 3D geometric morphometric methods for cut mark identification and classification

The analysis of bone surface modifications (BSMs) is a prominent part of paleoanthropological studies, namely taphonomic research. Behavioral interpretations of the fossil record hinge strongly upon correct assessment of BSMs. With the significant impact of microscopic analysis to the study of BSMs, multiple authors have discussed the reliability of these technological improvements for gaining resolution in BSM discrimination. While a certain optimism is present, some important questions are ignored and others overemphasized without appropriate empirical support. This specifically affects the study of cut marks. A diversity of geometric morphometric approaches applied to the study of cut marks have resulted in the coexistence (and competition) of different 2D and 3D methods. The present work builds upon the foundation of experiments presented by Maté-González et al. (2015), Courtenay et al. (2017) and Otárola-Castillo et al. (2018) to contrast for the first time 2D and 3D methods in their resolution of cut mark interpretation and classification. The results presented here show that both approaches are equally valid and that the use of sophisticated 3D methods do not contribute to an improvement in accuracy

An Evaluation of Landmark-Based Methods to Explore Tooth Score Morphology: A Case Study on Felids and Hyenids

Taphonomic studies aim to identify the modifying agents that intervene in bone assemblages found at archaeopaleontological sites. Carnivores may modify, accumulate, or scavenge skeletal parts inflicting tooth marks, including scores, on the cortical surface. Several works have studied tooth score morphology to discern which carnivore group modified the bone assemblages, achieving different results. In the present study, different methods based on the use of landmarks and semilandmarks have been tested to describe and analyze the score profile cross-sections of spotted and brown hyenas, leopards, and lions. According to our results, the already published seven-landmark method is useful in order to differentiate between carnivore species from different families (e.g., felids and hyenids). Meanwhile, felid species (e.g., leopards and lions) cannot be consistently distinguished using any of the methods tested here. In contrast, hyenid species can be morphologically differentiated. On the other hand, the use of semilandmarks does not generally improve morphological characterization and distinction, but low numbers of landmarks and the inclusion of the score’s deepest point might provide the best results when semi-automatic semilandmark models are preferred to avoid sampling biases.The grant IJC2020-043576-I funded by MCIN/AEI/10.13039/501100011033 and the “European Union NextGenerationEU/PRTR” has been awarded to M.C.A. The grant RYC2021-034813-I funded by MCIN/AEI/10.13039/501100011033 and the European Union “NextGenerationEU”/PRTR has been awarded to M.Á.M.-G. During the development of the present work, J.A. was funded by the Euskal Herriko Unibertsitatea [ESPDOC21/05]. L.A.C. is funded by the Spanish Ministry of Science, Innovation and Universities by an FPI Predoctoral grant PRE2019-089411 associated with project RTI2018-099850-B-I0

Asmparts: assembly of biological model parts

We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation in part characterisation by considering a model of each part. We have used model parts in SBML to design transcriptional networks. Our software is open source, it works in linux and windows platforms, and it could be used to automatically produce models in a server. Our tool not only facilitates model design, but it will also help to promote the establishment of a registry of model parts

An Evaluation of Landmark-Based Methods to Explore Tooth Score Morphology: A Case Study on Felids and Hyenids

Taphonomic studies aim to identify the modifying agents that intervene in bone assemblages found at archaeopaleontological sites. Carnivores may modify, accumulate, or scavenge skeletal parts inflicting tooth marks, including scores, on the cortical surface. Several works have studied tooth score morphology to discern which carnivore group modified the bone assemblages, achieving different results. In the present study, different methods based on the use of landmarks and semilandmarks have been tested to describe and analyze the score profile cross-sections of spotted and brown hyenas, leopards, and lions. According to our results, the already published seven-landmark method is useful in order to differentiate between carnivore species from different families (e.g., felids and hyenids). Meanwhile, felid species (e.g., leopards and lions) cannot be consistently distinguished using any of the methods tested here. In contrast, hyenid species can be morphologically differentiated. On the other hand, the use of semilandmarks does not generally improve morphological characterization and distinction, but low numbers of landmarks and the inclusion of the score’s deepest point might provide the best results when semi-automatic semilandmark models are preferred to avoid sampling biases