Resolving the fine structure in the energy landscapes of repeat proteins

Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.M.N.S. was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; Grant 130147/2020-6). This research was supported by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-2019745). A.B.O. acknowledges the Robert A. Welch Postdoctoral Fellow program. P.G.W. is also supported by the D.R. Bullard-Welch Chair at Rice University (Grant C-0016). V.B.P.L. was supported by CNPq (Grant 310017/2020-3) and FAPESP (Grants 2019/22540-3 and 2018/18668-1). D.U.F. is a CONICET researcher and is supported by Grant PICT2016/1467, UBACYT, and NASA Astrobiology Institute-Enigma (Grant 80NSSC18M0093).Peer ReviewedPostprint (published version

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Aligning the CMS Muon Chambers with the Muon Alignment System during an Extended Cosmic Ray Run

Peer reviewe

Measurement of the Top Pair Production Cross Section in the Dilepton Decay Channel in ppbar Collisions at sqrt s = 1.96 TeV

Submitted to Phys. Rev. DA measurement of the \ttbar production cross section in \ppbar collisions at $\sqrt{{\rm s}}$ = 1.96 TeV using events with two leptons, missing transverse energy, and jets is reported. The data were collected with the CDF II Detector. The result in a data sample corresponding to an integrated luminosity 2.8 fb$^{-1}$ is: \sigma_{\ttbar} = 6.27 $\pm$ 0.73(stat) $\pm$ 0.63(syst) $\pm$ 0.39(lum) pb. for an assumed top mass of 175 GeV/$c^{2}$.A measurement of the tt̅ production cross section in pp̅ collisions at √s=1.96  TeV using events with two leptons, missing transverse energy, and jets is reported. The data were collected with the CDF II detector. The result in a data sample corresponding to an integrated luminosity 2.8  fb-1 is σtt̅ =6.27±0.73(stat)±0.63(syst)±0.39(lum)  pb. for an assumed top mass of 175  GeV/c2.Peer reviewe

Ação inseticida do extrato de Derris amazonica Killip para Cerotoma arcuatus Olivier (Coleoptera: Chrysomelidae

A abundância e o potencial inseticida de Derris amazonica e a necessidade de controle de Cerotoma arcuatus Olivier (Coleoptera: Chrysomelidae) na cultura do feijão-caupi (Vigna unguiculata L. Walp) estimularam a realização desta pesquisa, que objetivou avaliar a ação inseticida do extrato de D. amazonica a adultos de C. arcuatus em condições de laboratório. Os bioensaios testaram as vias de intoxicação por ingestão de folhas contaminadas, contato com superfície contaminada e aplicação tópica, com delineamento experimental inteiramente casualizado, com quatro repetições. Os valores de mortalidade e consumo foliar dos insetos foram submetidos à análise de regressão, sendo utilizada a análise de Probit para determinação das CL50, da DL50 e dos TL50. O extrato de D. amazonica, contendo 3,7% de rotenona, foi tóxico para adultos de C. arcuatus via ingestão de folhas contaminadas (CL50=15,14 µL do extrato.mL-1 de água), superfície contaminada (CL50=0,45 µL do extrato.cm-2) e aplicação tópica (DL50=1,44 µL do extrato.g-1 do inseto). Mortalidades de adultos de C. arcuatus superiores a 80% e os menores tempos letais médios foram obtidos na concentração de 5% (v v-1) do extrato em todos os bioensaios. O consumo foliar de adultos de C. arcuatus foi inversamente proporcional a concentração do extrato quando expostos por via de ingestão foliar ou aplicação tópica, sendo inclusive observada inibição da alimentação dos indivíduos. O extrato de D. amazonica é tóxico para C. arcuatus e inibe a alimentação dos insetos a partir da concentração de 1% (v v-1).The abundance and insecticidal potential of Derris amazonica in addition to need of controlling Cerotoma arcuatus for bean crop stimulated this research. The objective of this work was to evaluate insecticide action of the extract of D. amazonica to adults of C. arcuatus in laboratory conditions. The bioassays were carried out using three distend methodologies: leaf intake, contact in treated surface (filter paper) and topical application. A completed randomized experimental design was used with four replications. Mortality values and leaf consumption of the insects were subjected to regression analyses, being the Probit analyses used to determine of the i.e., LC50, LT50 and LD50. The extract of D. amazonica containing 3.7% of rotenone was toxic to adults C. arcuatus when exposed to treated leaves (LC50 = 15.14 µl.mL-1), treated surface (LC50 = 0.45 µl.cm-2) and subjected to topical exposure (LD50 = 1.44 µl.g-1). In all bioassays the adults mortality was higher than 80% with lower median lethal times obtained with 5% (v.v-1) concentrations of the extract. Leaf consumption by adults C. arcuatus was inversely proportional to the concentration of the extract when exposed by leaf intake or topical application, also being observed inhibition of feeding individuals. The extract of D. amazonica is toxic to C. arcuatus and inhibits the feeding of insects from the concentration of 1% (v v-1)

Catálogo Taxonômico da Fauna do Brasil: setting the baseline knowledge on the animal diversity in Brazil

The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classifications. In this context, the Brazilian megadiverse fauna is no exception, and the Catálogo Taxonômico da Fauna do Brasil (CTFB) (http://fauna.jbrj.gov.br/), made public in 2015, represents a database on biodiversity anchored on a list of valid and expertly recognized scientific names of animals in Brazil. The CTFB is updated in near real time by a team of more than 800 specialists. By January 1, 2024, the CTFB compiled 133,691 nominal species, with 125,138 that were considered valid. Most of the valid species were arthropods (82.3%, with more than 102,000 species) and chordates (7.69%, with over 11,000 species). These taxa were followed by a cluster composed of Mollusca (3,567 species), Platyhelminthes (2,292 species), Annelida (1,833 species), and Nematoda (1,447 species). All remaining groups had less than 1,000 species reported in Brazil, with Cnidaria (831 species), Porifera (628 species), Rotifera (606 species), and Bryozoa (520 species) representing those with more than 500 species. Analysis of the CTFB database can facilitate and direct efforts towards the discovery of new species in Brazil, but it is also fundamental in providing the best available list of valid nominal species to users, including those in science, health, conservation efforts, and any initiative involving animals. The importance of the CTFB is evidenced by the elevated number of citations in the scientific literature in diverse areas of biology, law, anthropology, education, forensic science, and veterinary science, among others

In-line monitoring of the coffee roasting process with near infrared spectroscopy: Measurement of sucrose and colour

In this work, a real-time and in-situ analytical tool based on near infrared spectroscopy is proposed to predict two of the most relevant coffee parameters during the roasting process, sucrose and colour. The methodology was developed taking in consideration different coffee varieties (Arabica and Robusta), coffee origins (Brazil, East-Timor, India and Uganda) and roasting process procedures (slow and fast). All near infrared spectroscopy-based calibrations were developed resorting to partial least squares regression. The results proved the suitability of this methodology as demonstrated by rangeerror- ratio and coefficient of determination higher than 10 and 0.85 respectively, for all modelled parameters. The relationship between sucrose and colour development during the roasting process is further discussed, in light of designing in real-time coffee products with similar visual appearance and distinct organoleptic profile