sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case studies illustrate that even with relatively few sMolBoxes, it is possible to express complex analytical tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods.acceptedVersio

Spin-orbit coupling and intrinsic spin mixing in quantum dots

Spin-orbit coupling effects are studied in quantum dots in InSb, a narrow-gap material. Competition between different Rashba and Dresselhaus terms is shown to produce wholesale changes in the spectrum. The large (and negative) $g$-factor and the Rashba field produce states where spin is no longer a good quantum number and intrinsic flips occur at moderate magnetic fields. For dots with two electrons, a singlet-triplet mixing occurs in the ground state, with observable signatures in intraband FIR absorption, and possible importance in quantum computation.Comment: REVTEX4 text with 3 figures (high resolution figs available by request). Submitted to PR

Ataxia de Friedreich: estudo clínico e molecular de 25 pacientes

INTRODUCTION: Friedreich's ataxia is a neurodegenerative disorder whose clinical diagnostic criteria for typical cases basically include: a) early age of onset (< 20 or 25 years), b) autosomal recessive inheritance, c) progressive ataxia of limbs and gait, and d) absence of lower limb tendon reflexes. METHODS: We studied the frequency and the size of expanded GAA and their influence on neurologic findings, age at onset, and disease progression in 25 Brazilian patients with clinical diagnosis of Friedreich's ataxia - 19 typical and 6 atypical - using a long-range PCR test. RESULTS: Abnormalities in cerebellar signs, in electrocardiography, and pes cavus occurred more frequently in typical cases; however, plantar response and speech were more frequently normal in this group when the both typical and atypical cases were compared. Homozygous GAA expansion repeats were detected in 17 cases (68%) - all typical cases. In 8 patients (32%) (6 atypical and 2 typical), no expansion was observed, ruling out the diagnosis of Friedreich's ataxia. In cases with GAA expansions, foot deformity, cardiac abnormalities, and some neurologic findings occurred more frequently; however, abnormalities in cranial nerves and in tomographic findings were detected less frequently than in patients without GAA expansions. DISCUSSION: Molecular analysis was imperative for the diagnosis of Friedreich's ataxia, not only for typical cases but also for atypical ones. There was no genotype-phenotype correlation. Diagnosis based only on clinical findings is limited; however, it aids in better screening for suspected cases that should be tested. Evaluation for vitamin E deficiency is recommended, especially in cases without GAA expansion.INTRODUÇÃO: A ataxia de Friedreich é uma doença neurodegenerativa e os critérios clínicos diagnósticos para os casos típicos incluem: a) idade de início precoce (< 20 ou 25 anos); b) herança autossômica recessiva; c) ataxia progressiva; e d) abolição dos reflexos tendinosos profundos. MÉTODOS: Estudou-se a freqüência e o tamanho das expansões GAA e a sua influência nos achados neurológicos, idade de início e progressão da doença, em 25 pacientes brasileiros com diagnóstico clínico de ataxia de Friedreich - 19 típicos e 6 atípicos, por PCR. RESULTADOS: Anormalidades sugestivas de comprometimento cerebelar, no ECG e a presença de pés cavos ocorreram com maior freqüência nos casos típicos; contudo, a resposta plantar e a fala mostraram-se mais freqüentemente normal neste grupo, quando comparados casos típicos e atípicos. A expansão GAA em homozigose foi detectada em 17 casos (68%) - todos típicos e, em 8 (32%) (6 atípicos e 2 típicos), não foi observada nenhuma expansão, excluindo-se o diagnóstico de ataxia de Friedreich. Deformidade de pés, anormalidades cardíacas e alguns achados neurológicos ocorreram mais freqüentemente, nos casos com expansão GAA, contudo, sinais de comprometimento dos pares cranianos e alterações dos achados tomográficos foram detectados menos frequentemente do que em pacientes sem expansão. DISCUSSÃO: A análise molecular é imprescindível para o diagnóstico de ataxia de Friedreich, não só para os casos típicos como também para os atípicos. Não há qualquer correlação entre o genótipo e o fenótipo. O diagnóstico baseado apenas nos achados clínicos é limitado, embora facilite a triagem para melhor selecionar os casos suspeitos que merecem ser testados. A dosagem sérica da vitamin E é recomendada , especialmente nos casos sem expansão GAA

Comparison of selectivity of a family of chelating agents for trivalent (Al³⁺, Fe³⁺) and bivalent (Cu²⁺, Zn²⁺) metal ions

Chelation therapy is used for the treatment of metal intoxication in humans. Selectivity towards the target metal ion is one important characteristic of the chelating agent. In the frame of our research of chelating agents for iron and aluminium, we synthesized five new ligands (Figure 1), and studied their behavior toward the trivalent metal ions. L4, L5, L6 and L8 were found to be excellent ligands for the coordination of Fe3+ and Al3+. We are presenting here a study on the same ligands with the two essential bivalent metal ions, Zn2+ and Cu2+. The results of spectrophotometric, potentiometric, and NMR measurements performed to determine the equilibrium formation constants will be presented. The speciation of the complexes with the trivalent metal ions in presence of endogenous zinc and copper will be discussed

Brown howler monkey: alouatta guariba Humboldt, 1812

Alouatta guariba is endemic to the Atlantic Forest in eastern Brazil and northeast Argentina. In the south, its distribution is limited by the Camaquã river basin (Printes et al. 2001) and to the north by the Paraguaçu river in the state of Bahia (Gregorin 2006; Neves et al. 2018). The western boundary is marked by the limits of the Atlantic Forest. It occurs in the Brazilian states of Bahia, Espírito Santo, Rio de Janeiro, Minas Gerais, São Paulo, Paraná, Santa Catarina and Rio Grande do Sul (Mendes et al. 2008, Bicca-Marques et al. 2018). In Argentina the species is limited to the province of Misiones (Agostini et al. 2017).Fil: Buss, Gerson. Centro Nacional de Pesquisa e Conservação dos Primatas; BrasilFil: Oklander, Luciana Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Bicca Marques, Júlio César. Pontificia Universidad Catolica de Parana. Escola de Ciencias Da Vida.; BrasilFil: Hirano, Zelinda B.. Universidade Regional de Blumenau; BrasilFil: Chaves, Oscar M.. Pontificia Universidad Catolica de Parana. Escola de Ciencias Da Vida.; BrasilFil: Mendes, Sergio L.. Instituto Nacional da Mata Atlântica; BrasilFil: Neves, Leonardo G.. Universidade Estadual de Santa Cruz; BrasilFil: Melo, Fabiano R.. Universidade Federal de Viçosa.; BrasilFil: Rylands, Anthony B.. Wildlife Conservation Society; Estados UnidosFil: Jerusalinsky, Leandro. Centro Nacional de Pesquisa e Conservação dos Primatas Brasileiros; Brasi

Constraints on the structure and seasonal variations of Triton’s atmosphere from the 5 October 2017 stellar occultation and previous observations

J.M.O. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) and the European Social Fund (ESF) through the PhD grant SFRH/BD/131700/2017. The work leading to these results has received funding from the European Research Council under the European Community's H2020 2014-2021 ERC grant Agreement nffi 669416 "Lucky Star". We thank S. Para who supported some travels to observe the 5 October 2017 occultation. T.B. was supported for this research by an appointment to the National Aeronautics and Space Administration (NASA) Post-Doctoral Program at the Ames Research Center administered by Universities Space Research Association (USRA) through a contract with NASA. We acknowledge useful exchanges with Mark Gurwell on the ALMA CO observations. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium).Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. J.L.O., P.S.-S., N.M. and R.D. acknowledge financial support from the State Agency for Research of the Spanish MCIU through the "Center of Excellence Severo Ochoa" award to the Instituto de Astrofisica de Andalucia (SEV-2017-0709), they also acknowledge the financial support by the Spanish grant AYA-2017-84637-R and the Proyecto de Excelencia de la Junta de Andalucia J.A. 2012-FQM1776. The research leading to these results has received funding from the European Union's Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 687378, as part of the project "Small Bodies Near and Far" (SBNAF). P.S.-S. acknowledges financial support by the Spanish grant AYA-RTI2018-098657-J-I00 "LEO-SBNAF". The work was partially based on observations made at the Laboratorio Nacional de Astrofisica (LNA), Itajuba-MG, Brazil. The following authors acknowledge the respective CNPq grants: F.B.-R. 309578/2017-5; R.V.-M. 304544/2017-5, 401903/2016-8; J.I.B.C. 308150/2016-3 and 305917/2019-6; M.A. 427700/20183, 310683/2017-3, 473002/2013-2. This study was financed in part by the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior -Brasil (CAPES) -Finance Code 001 and the National Institute of Science and Technology of the e-Universe project (INCT do e-Universo, CNPq grant 465376/2014-2). G.B.R. acknowledges CAPES-FAPERJ/PAPDRJ grant E26/203.173/2016 and CAPES-PRINT/UNESP grant 88887.571156/2020-00, M.A. FAPERJ grant E26/111.488/2013 and A.R.G.Jr. FAPESP grant 2018/11239-8. B.E.M. thanks CNPq 150612/2020-6 and CAPES/Cofecub-394/2016-05 grants. Part of the photometric data used in this study were collected in the frame of the photometric observations with the robotic and remotely controlled telescope at the University of Athens Observatory (UOAO; Gazeas 2016). The 2.3 m Aristarchos telescope is operated on Helmos Observatory by the Institute for Astronomy, Astrophysics, Space Applications and Remote Sensing of the National Observatory of Athens. Observations with the 2.3 m Aristarchos telescope were carried out under OPTICON programme. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 730890. This material reflects only the authors views and the Commission is not liable for any use that may be made of the information contained therein. The 1. 2m Kryoneri telescope is operated by the Institute for Astronomy, Astrophysics, Space Applications and Remote Sensing of the National Observatory of Athens. The Astronomical Observatory of the Autonomous Region of the Aosta Valley (OAVdA) is managed by the Fondazione Clement Fillietroz-ONLUS, which is supported by the Regional Government of the Aosta Valley, the Town Municipality of Nus and the "Unite des Communes valdotaines Mont-Emilius". The 0.81 m Main Telescope at the OAVdA was upgraded thanks to a Shoemaker NEO Grant 2013 from The Planetary Society. D.C. and J.M.C. acknowledge funds from a 2017 'Research and Education' grant from Fondazione CRT-Cassa di Risparmio di Torino. P.M. acknowledges support from the Portuguese Fundacao para a Ciencia e a Tecnologia ref. PTDC/FISAST/29942/2017 through national funds and by FEDER through COMPETE 2020 (ref. POCI010145 FEDER007672). F.J. acknowledges Jean Luc Plouvier for his help. S.J.F. and C.A. would like to thank the UCL student support observers: Helen Dai, Elise Darragh-Ford, Ross Dobson, Max Hipperson, Edward Kerr-Dineen, Isaac Langley, Emese Meder, Roman Gerasimov, Javier Sanjuan, and Manasvee Saraf. We are grateful to the CAHA, OSN and La Hita Observatory staffs. This research is partially based on observations collected at Centro Astronomico HispanoAleman (CAHA) at Calar Alto, operated jointly by Junta de Andalucia and Consejo Superior de Investigaciones Cientificas (IAA-CSIC). This research was also partially based on observation carried out at the Observatorio de Sierra Nevada (OSN) operated by Instituto de Astrofisica de Andalucia (CSIC). This article is also based on observations made with the Liverpool Telescope operated on the island of La Palma by Liverpool John Moores University in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias with financial support from the UK Science and Technology Facilities Council. Partially based on observations made with the Tx40 and Excalibur telescopes at the Observatorio Astrofisico de Javalambre in Teruel, a Spanish Infraestructura Cientifico-Tecnica Singular (ICTS) owned, managed and operated by the Centro de Estudios de Fisica del Cosmos de Aragon (CEFCA). Tx40 and Excalibur are funded with the Fondos de Inversiones de Teruel (FITE). A.R.R. would like to thank Gustavo Roman for the mechanical adaptation of the camera to the telescope to allow for the observation to be recorded. R.H., J.F.R., S.P.H. and A.S.L. have been supported by the Spanish projects AYA2015-65041P and PID2019-109467GB-100 (MINECO/FEDER, UE) and Grupos Gobierno Vasco IT1366-19. Our great thanks to Omar Hila and their collaborators in Atlas Golf Marrakech Observatory for providing access to the T60cm telescope. TRAPPIST is a project funded by the Belgian Fonds (National) de la Recherche Scientifique (F.R.S.-FNRS) under grant PDR T.0120.21. TRAPPIST-North is a project funded by the University of Liege, and performed in collaboration with Cadi Ayyad University of Marrakesh. E.J. is a FNRS Senior Research Associate.Context. A stellar occultation by Neptune's main satellite, Triton, was observed on 5 October 2017 from Europe, North Africa, and the USA. We derived 90 light curves from this event, 42 of which yielded a central flash detection. Aims. We aimed at constraining Triton's atmospheric structure and the seasonal variations of its atmospheric pressure since the Voyager 2 epoch (1989). We also derived the shape of the lower atmosphere from central flash analysis. Methods. We used Abel inversions and direct ray-tracing code to provide the density, pressure, and temperature profiles in the altitude range similar to 8 km to similar to 190 km, corresponding to pressure levels from 9 mu bar down to a few nanobars. Results. (i) A pressure of 1.18 +/- 0.03 mu bar is found at a reference radius of 1400 km (47 km altitude). (ii) A new analysis of the Voyager 2 radio science occultation shows that this is consistent with an extrapolation of pressure down to the surface pressure obtained in 1989. (iii) A survey of occultations obtained between 1989 and 2017 suggests that an enhancement in surface pressure as reported during the 1990s might be real, but debatable, due to very few high S/N light curves and data accessible for reanalysis. The volatile transport model analysed supports a moderate increase in surface pressure, with a maximum value around 2005-2015 no higher than 23 mu bar. The pressures observed in 1995-1997 and 2017 appear mutually inconsistent with the volatile transport model presented here. (iv) The central flash structure does not show evidence of an atmospheric distortion. We find an upper limit of 0.0011 for the apparent oblateness of the atmosphere near the 8 km altitude.Portuguese Foundation for Science and Technology SFRH/BD/131700/2017European Social Fund (ESF) SFRH/BD/131700/2017European Research Council under the European Community's H2020 2014-2021 ERC grant 669416Spanish Government SEV-2017-0709 AYA-2017-84637-R AYA-RTI2018-098657-J-I00Junta de Andalucia 2012-FQM1776European Union's Horizon 2020 Research and Innovation Programme, as part of the project "Small Bodies Near and Far" (SBNAF) 687378Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ)Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF) 309578/2017-5 304544/2017-5 401903/2016-8 308150/2016-3 305917/2019-6 427700/2018-3 310683/2017-3 473002/2013-2Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) 001Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) 465376/2014-2 CAPES-FAPERJ/PAPDRJ grant E26/203.173/2016 CAPES-PRINT/UNESP grant 88887.571156/2020-00Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio De Janeiro (FAPERJ) E26/111.488/2013Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2018/11239-8Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) 150612/2020-6European Union's Horizon 2020 research and innovation programme 730890Regional Government of the Aosta ValleyTown Municipality of NusUnite des Communes valdotaines Mont-EmiliusPlanetary SocietyFondazione CRT-Cassa di Risparmio di TorinoPortuguese Foundation for Science and Technology PTDC/FISAST/29942/2017FEDER through COMPETE 2020 POCI010145 FEDER007672UK Research & Innovation (UKRI)Science & Technology Facilities Council (STFC)Fondos de Inversiones de Teruel (FITE)Spanish Government AYA2015-65041P PID2019-109467GB-100Grupos Gobierno Vasco IT1366-19Fonds de la Recherche Scientifique - FNRS PDR T.0120.21University of LiegeCAPES/Cofecub-394/2016-0

Comparative analysis between synthetic vitamin E and natural antioxidant sources from tomato, carrot and coriander in diets for market-sized dicentrarchus labrax

Synthetic vitamin E is commonly used in aquafeeds to prevent oxidative stress in fish and delay feed and flesh oxidation during storage, but consumers’ preferences tend towards natural antioxidant sources. The potential of vegetable antioxidants-rich coproducts, dried tomato (TO), carrot (CA) and coriander (CO) was compared to that of synthetic vitamin E included in diets at either a regular (CTRL; 100 mg kg−1) or reinforced dose (VITE; 500 mg kg−1). Natural antioxidants were added at 2% to the CTRL. Mixes were then extruded and dried, generating five experimental diets that were fed to European sea bass juveniles (114 g) over 12 weeks. Vitamin E and carotenoid content of extruded diets showed signs of degradation. The experimental diets had very limited effects on fish growth or body composition, immunomodulatory response, muscle and liver antioxidant potential, organoleptic properties or consumer acceptance. Altogether, experimental findings suggest that neither a heightened inclusion dose of 500 mg kg−1 of vitamin E, nor a 2% inclusion of natural antioxidants provided additional antioxidant protection, compared to fish fed diets including the regular dose of 100 mg kg−1 of vitamin E.info:eu-repo/semantics/publishedVersio

Evolutionary dynamics shape two passive defensive mechanisms in Neotropical snake radiations

We mapped the distribution of two defensive behaviors (balling and head hiding) of Neotropical snakes to evaluate its distribution in distinct phylogenetic groups. Balling behavior was observed in 58 out of the 167 examined species across seven families. Head hiding was observed in a total of 100 species across nine families. From the high prevalence of balling behavior in basal groups of snakes, such as Anomalepididae, Boidae, Leptotyphlopidae, Tropidophiidae, and Typhlopidae, and the low prevalence among species of recent diversification radiations, such as Elapidae and Viperidae, we suggest that this behavior evolved in basal groups and persisted in some derived taxa. Balling was not observed in association with other defensive strategies, while head hiding can occur in combination with caudal elevation, caudal vibration, and body flattening. Therefore, head hiding, in contrast to balling behavior, presents itself as putatively more flexible, as it should allow for an escalated degree of defensive displays

Association of LEC and tnpA Helicobacter pylori genes with gastric cancer in a Brazilian population

<p>Abstract</p> <p>Background</p> <p><it>H. pylori </it>seroprevalence in Brazilians varies and is dependent on socioeconomic status, sanitation conditions and ethnicity; furthermore, <it>H. pylori </it>is not always associated with the incidence of gastric cancer, suggesting the role of more virulent strains. The purpose of this study was to analyze the association of more virulent <it>H. pylori </it>strains with gastric cancer.</p> <p>Methods</p> <p>DNA was extracted from gastric biopsies of thirty-four cases of gastric cancer (11 intestinal-type, 23 diffuse-type), and thirty-four of patients with endoscopic gastritis. The presence of <it>cag</it>PAI genes (<it>cagA</it>, <it>cagA </it>promoter, <it>cagE</it>, <it>cagM</it>, <it>tnpB</it>, <it>tnpA</it>, <it>cagT </it>and the left end of the <it>cag</it>II (LEC)) and <it>babA </it>were analyzed by PCR.</p> <p>Results</p> <p>Comparison of <it>H. pylori </it>isolates from gastric cancer and gastritis patients showed significant associations of <it>tnpA </it>and LEC with gastric cancer (73.5% [OR, 6.66; 95% CI, 2.30-19.25] and 58.8% [OR, 10.71; 95% CI, 3.07-37.28] of cases, respectively). Other <it>cag</it>PAI genes were detected in both groups at similar frequencies.</p> <p>Conclusions</p> <p><it>tnpA </it>and LEC of <it>H. pylori cag</it>PAI were associated with gastric cancer; nonetheless, these results were restricted within this group of patients and further studies are needed to confirm these results in a larger sample and determine their role in gastric carcinogenesis.</p