Spatial clustering of molecular dynamics trajectories in protein unfolding simulations

Molecular dynamics simulations is a valuable tool to study protein unfolding in silico. Analyzing the relative spatial position of the residues during the simulation may indicate which residues are essential in determining the protein structure. We present a method, inspired by a popular data mining technique called Frequent Itemset Mining, that clusters sets of amino acid residues with a synchronized trajectory during the unfolding process. The proposed approach has several advantages over traditional hierarchical clustering.The authors acknowledge the support of the "Fundacao para a Ciencia e Tecnologia,Portugal, and the program FEDER, through grant PTDC/BIA-PRO/72838/2006 (to PJA and RMMB) and the Fellowships SFRH/BPD/42003/2007(to PGF) and SFRH/BD/16888/2004 (to CGS). We thank the Center for Computational Physics, Departamento de Fisica, Universidade de Coimbra, for the computer resources provided for the MD simulations

Mining approximate motifs in time series

The problem of discovering previously unknown frequent patterns in time series, also called motifs, has been recently introduced. A motif is a subseries pattern that appears a significant number of times. Results demonstrate that motifs may provide valuable insights about the data and have a wide range of applications in data mining tasks. The main motivation for this study was the need to mine time series data from protein folding/unfolding simulations. We propose an algorithm that extracts approximate motifs, i.e. motifs that capture portions of time series with a similar and eventually symmetric behaviour. Preliminary results on the analysis of protein unfolding data support this proposal as a valuable tool. Additional experiments demonstrate that the application of utility of our algorithm is not limited to this particular problem. Rather it can be an interesting tool to be applied in many real world problems.Fundação para a Ciência e a Tecnologia (FCT).Fundo Europeu de Desenvolvimento Regional (FEDER) - POCTI/BME/49583/2002; SFRH/BD/13462/2003; SFRH/BD/16888/2004

Chlorine determination in medicinal plants by potentiometry with ion-selective electrode after microwave-induced combustion

A method based on microwave-induced combustion (MIC) was applied for medicinal plants digestion allowing further chlorine determination by potentiometry using ion-selective electrode (ISE). Sample masses ranging from 500 to 1000 mg were evaluated for MIC digestion. Water and 10, 25, 50, and 100 mmol/L NH4OH were investigated as absorbing solutions. The accuracy of the proposed method was evaluated by using certified reference materials (CRMs), by recovery tests (500 µg/g), and also by comparison with the results obtained by inductively coupled plasma optical emission spectrometry (ICP-OES) after microwave-assisted alkaline extraction (MAE). Using water or NH4OH solutions (10 to 100 mmol/L), recoveries close to 100% and relative standard deviation lower than 5% were obtained. Results were in agreement with CRMs values (better than 95%) and also with those values obtained by using the MAE method. The main advantage of the proposed method was the complete combustion of high sample mass (1000 mg) resulting in low quantification limit (12.5 µg/g) and chlorine determination at low concentration by ISE. Another advantage of the proposed method was the high chlorine stability in digests (up to 30 days of storage) even using water as absorbing solution, which is in agreement with green analytical chemistry recommendations. Finally, the proposed MIC method was applied for commercial medicinal plants and the chlorine concentration was in the range of 59.4 ± 1.4 to 2038 ± 70 µg/g. The proposed MIC method was considered suitable for quality control for chlorine determination in medicinal plants

Redefinition of Heptapterus (Heptapteridae) and description of Heptapterus carmelitanorum, a new species from the upper Paraná River basin in Brazil

A new diagnosis and a new classification of Heptapterus are provided and a new species, H. carmelitanorum, is described. Heptapterus is diagnosed by the following character combination: adipose fin confluent with the caudal fin; non-bifurcate caudal fin; anal-fin insertion posterior to vertical through adipose-fin insertion; 10–23 anal-fin rays; anal fin not confluent with caudal fin; and extremely elongate body, with a head length of 16.1–24.9%SL. Species included in Heptapterus are H. borodini, H. carmelitanorum, H. carnatus, H. exilis, H. hollandi, H. mandimbusu, H. mbya, H. mustelinus, H. ornaticeps, and H. qenqo. Some of the character states diagnosing H. carmelitanorum among its congeners are the anal-fin insertion less than one eye diameter posterior to a vertical through the adipose-fin insertion (vs. more than one eye diameter in all congeners); the isognathous mouth (vs. slightly to moderately retrognathous, except H. borodini); and the keel formed by ventral procurrent caudal-fin rays shallow, far from reaching anal-fin base (vs. keel formed by ventral procurrent caudal-fin rays deep, continuing almost to the anal-fin base, except in H. borodini and H. hollandi).Fil: de Carvalho Deprá, Gabriel. Universidade Estadual de Maringá; BrasilFil: Aguilera, Gaston. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Fundación Miguel Lillo; ArgentinaFil: Faustino Fuster, Dario R.. Universidade Federal do Rio Grande do Sul; Brasil. Universidad Nacional Mayor de San Marcos; Perú. Universidad Nacional Autónoma de Huanta; PerúFil: Katz, Axel M.. Universidade Federal do Rio de Janeiro; BrasilFil: Azevedo Santos, Valter M.. Faculdade Eduvale de Avaré; Brasil. Universidade Federal do Pará; Brasil. Universidade Federal Do Tocantins; Brasi

Dispersal syndromes are poorly associated with climatic niche differences in the Azorean seed plants

Aim: Environmental niche tracking is linked to the species ability to disperse. While well investigated on large spatial scales, dispersal constraints also influence small-scale processes and may explain the difference between the potential and the realized niche of species at small scales. Here we test whether niche size and niche fill differ systematically according to dispersal syndrome within isolated oceanic islands. We expect that species with higher dispersal abilities (anemochorous or endozoochorous) will have a higher niche fill, despite their environmental niche size. Location: Azores archipelago. Taxon: Native seed plants. Methods: We combined a georeferenced database of the species distribution within the archipelago (Azorean Biodiversity Portal/GBIF) with an expert-based dispersal syndrome categorization and a high-resolution climatic grid (CIELO model). Using four climatic variables (Annual Mean Temperature, Mean Diurnal Range, Annual Precipitation, Precipitation Seasonality), we calculated a four-dimensional hypervolume to estimate the niche size of each species. Niche fill was quantified as the suitable climatic space of the island that was occupied by the focal species. Results: We found a significant relationship between dispersal syndromes and niche size, and also between dispersal syndromes and niche fill. Such relationships presented no phylogenetic signal. Endozoochorous species display higher niche fill compared to epizoochorous and hydrochorous species, and larger niches than anemochorous and epizoochorous. Differences among the remaining groups are not significant for either niche size or for niche fill. Main conclusions: The ability of a species to track its niche at small scales is not tightly related to its dispersal syndrome, although endozoochorous species track their niche more efficiently than the rest of groups. Despite being intuitively appealing, dispersal syndrome classifications might not be the most appropriate tools for understanding dispersal processes at small scales.info:eu-repo/semantics/acceptedVersio

The metal-poor dwarf irregular galaxy candidate next to Mrk 1172

In this work we characterise the properties of the object SDSS J020536.84-081424.7, an extended nebular region with projected extension of $14 \times 14$ kpc$^{2}$ in the line of sight of the ETG Mrk 1172, using unprecedented spectroscopic data from MUSE. We perform a spatially resolved stellar population synthesis and estimate the stellar mass for both Mrk 1172 ($1 \times 10^{11} M_{\odot}$) and our object of study ($3 \times 10^{9} M_{\odot}$). While the stellar content of Mrk 1172 is dominated by an old ($\sim 10$ Gyr) stellar population, the extended nebular emission has its light dominated by young to intermediate age populations (from $\sim 100$ Myr to $\sim 1$ Gyr) and presents strong emission lines such as: H${\beta}$, [O III] ${\lambda}{\lambda}$4959,5007, H${\alpha}$, [N II] ${\lambda}{\lambda}$6549,6585 and [S II] ${\lambda}{\lambda}$6717,6732. Using these emission lines we find that it is metal-poor (with $Z \sim$ 1/3 $Z_{\odot}$, comparable to the LMC) and is actively forming stars ($0.70$ M$_{\odot}$ yr$^{-1}$), especially in a few bright clumpy knots that are readily visible in H${\alpha}$. The object has an ionised gas mass $\geq 3.8 \times 10^{5}$ M$_{\odot}$. Moreover, the motion of the gas is well described by a gas in circular orbit in the plane of a disk and is being affected by interaction with Mrk 1172. We conclude that SDSS J020536.84-081424.7 is most likely a dwarf irregular galaxy (dIGal)

Spatially resolved self-consistent spectral modelling of jellyfish galaxies from MUSE with FADO: trends with mass and stripping intensity

We present a spatially resolved stellar population analysis of 61 jellyfish galaxies and 47 control galaxies observed with ESO/MUSE attempting to understand the general trends of the stellar populations as a function of the stripping intensity and mass. This is the public sample from the GASP programme, with $0.01 < z < 0.15$ and $8.9 <\log(M_{\star}/M_{\odot}) < 12.0$. We apply the spectral population synthesis code FADO to fit self-consistently both the stellar and nebular contributions to the spectra of the sources. We present 2D morphological maps for mean stellar ages, metallicities, gas-phase oxygen abundances, and star formation rates for the galaxies with Integrated Nested Laplace Approximation ({\sc inla}), which is efficient in reconstructing spatial data of extended sources. We find that ``extreme stripping'' and ``stripping'' galaxies are typically younger than the other types. Regarding stellar and nebular metallicities, the ``stripping'' and ``control passive'' galaxies are the most metal-poor. Based on the phase space for jellyfish cluster members we find trends in ages, metallicities, and abundances with different regions of the diagram. We also compute radial profiles for the same quantities. We find that both the stripping and the stellar masses seem to influence the profiles, and we see differences between various groups and distinct mass bins. The radial profiles for different mass bins present relations already shown in the literature for undisturbed galaxies, i.e., profiles of ages and metallicities tend to increase with mass. However, beyond $\sim0.75$ effective radius, the ages of the most massive galaxies become similar to or lower than the ages of the lower mass ones.Comment: Accepted by MNRAS. 71 pages (13 of main text and 58 of supplementay material). 123 figure

Social and moral psychology of COVID-19 across 69 countries

The COVID-19 pandemic has affected all domains of human life, including the economic and social fabric of societies. One of the central strategies for managing public health throughout the pandemic has been through persuasive messaging and collective behaviour change. To help scholars better understand the social and moral psychology behind public health behaviour, we present a dataset comprising of 51,404 individuals from 69 countries. This dataset was collected for the International Collaboration on Social & Moral Psychology of COVID-19 project (ICSMP COVID-19). This social science survey invited participants around the world to complete a series of moral and psychological measures and public health attitudes about COVID-19 during an early phase of the COVID-19 pandemic (between April and June 2020). The survey included seven broad categories of questions: COVID-19 beliefs and compliance behaviours; identity and social attitudes; ideology; health and well-being; moral beliefs and motivation; personality traits; and demographic variables. We report both raw and cleaned data, along with all survey materials, data visualisations, and psychometric evaluations of key variables

Migration routes and non-breeding areas of Common Terns (Sterna hirundo) from the Azores

We describe the migration routes and non-breeding areas of Common Terns (Sterna hirundo) from the Azores Archipelago, based on ringing (banding) recoveries and tracking of three birds using geolocators. Over 20 years, there have been 55 transatlantic recoveries of Common Terns from the Azores population: six from Argentina and 49 from Brazil. The three tracked birds migrated south in different months (August, September, November), but the northern migration was more synchronous, with all leaving in April. The birds were tracked to three areas of the South American coast: the male spent November–April on the northern Brazilian coast (13°N–2°S), whereas the two females first spent some time off central-eastern Brazil (4–16°S; one for 1 week, the other for 3 months) and then moved south to the coast of south-eastern Brazil, Uruguay and northern Argentina (24–39°S). Although caution is needed given the small sample size and errors associated with geolocation, the three tracked terns potentially travelled a total of ~23 200 km to and returning from their non-breeding areas, representing an average movement of ~500 km day–1. With the exception of Belém, in northern Brazil, and Lagoa do Peixe, in southern Brazil, the coastal areas used by the tracked birds were also those with concentrations of ringing recoveries, confirming their importance as non-breeding areas for birds from the Azores

Impact of cardiology referral: clinical outcomes and factors associated with physicians' adherence to recommendations

OBJECTIVES: Cardiology referral is common for patients admitted for non-cardiac diseases. Recommendations from cardiologists may involve complex and aggressive treatments that could be ignored or denied by other physicians. The purpose of this study was to compare the outcomes of patients who were given recommendations during cardiology referrals and to examine the clinical outcomes of patients who did not follow the recommendations. METHODS: We enrolled 589 consecutive patients who received in-hospital cardiology consultations. Data on recommendations, implementation of suggestions and outcomes were collected. RESULTS: Regarding adherence of the referring service to the recommendations, 77% of patients were classified in the adherence group and 23% were classified in the non-adherence group. Membership in the non-adherence group (