Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

The description of nonequilibrium processes in nano-sized objects, where the typical energies involved are a few times, is increasingly becoming central to disciplines as diverse as condensed-matter physics, materials science, and biophysics. Major recent developments towards a unified treatment of arbitrarily large fluctuations in small systems are described by fluctuation theorems that relate the probabilities of a system absorbing from or releasing to the bath a given amount of energy in a nonequilibrium process. Here we experimentally verify the Crooks Fluctuation Theorem (CFT) under weak and strong nonequilibrium conditions by using optical tweezers to measure the irreversible mechanical work during the unfolding and refolding of a small RNA hairpin and an RNA three-helix junction. We also show that the CFT provides a powerful way to obtain folding free energies in biomolecules by determining the crossing between the unfolding and refolding irreversible work distributions. The method makes it possible to obtain folding free energies in nonequilibrium processes that dissipate up to of the average total work exerted, thereby paving the way for reconstructing free energy landscapes along reaction coordinates in nonequilibrium single-molecule experiments.Comment: PDF file, 19 pages. Supplementary information available online at www.nature.co

A stem spacing‐based non‐dimensional model for predicting longitudinal dispersion in low‐density emergent vegetation

Predicting how pollutants disperse in vegetation is necessary to protect natural watercourses. This can be done using the one-dimensional advection dispersion equation, which requires estimates of longitudinal dispersion coefficients in vegetation. Dye tracing was used to obtain longitudinal dispersion coefficients in emergent artificial vegetation of different densities and stem diameters. Based on these results, a simple non-dimensional model, depending on velocity and stem spacing, was developed to predict the longitudinal dispersion coefficient in uniform emergent vegetation at low densities (solid volume fractions < 0.1). Predictions of the longitudinal dispersion coefficient from this simple model were compared with predictions from a more complex expression for a range of experimental data, including real vegetation. The simple model was found to predict correct order of magnitude dispersion coefficients and to perform as well as the more complex expression. The simple model requires fewer parameters and provides a robust engineering approximation

A new calibration method for charm jet identification validated with proton-proton collision events at √s = 13 TeV

ArXiv ePrint: 2111.03027Copyright © 2022 CERN for the benefit of the CMS collaboration. Many measurements at the LHC require efficient identification of heavy-flavour jets, i.e. jets originating from bottom (b) or charm (c) quarks. An overview of the algorithms used to identify c jets is described and a novel method to calibrate them is presented. This new method adjusts the entire distributions of the outputs obtained when the algorithms are applied to jets of different flavours. It is based on an iterative approach exploiting three distinct control regions that are enriched with either b jets, c jets, or light-flavour and gluon jets. Results are presented in the form of correction factors evaluated using proton-proton collision data with an integrated luminosity of 41.5 fb-1 at  √s = 13 TeV, collected by the CMS experiment in 2017. The closure of the method is tested by applying the measured correction factors on simulated data sets and checking the agreement between the adjusted simulation and collision data. Furthermore, a validation is performed by testing the method on pseudodata, which emulate various mismodelling conditions. The calibrated results enable the use of the full distributions of heavy-flavour identification algorithm outputs, e.g. as inputs to machine-learning models. Thus, they are expected to increase the sensitivity of future physics analyses.SCOAP

Aspectos epidemiológicos e clínicos dos acidentes ofídicos ocorridos nos municípios do Estado do Amazonas Epidemiological and clinical aspects of snake accidentes in the municipalities of the State of Amazonas, Brazil

No Amazonas, o acidente ofídico é um problema de saúde pública pouco conhecido. Por este motivo, foi realizado um estudo descritivo dos acidentes ofídicos atendidos nas Unidades de Saúde de 34 municípios, um distrito e dois pelotões de fronteira do Estado do Amazonas. As características mais comuns encontradas dentre os pacientes foram: agricultor (50,4%), do sexo masculino (81,3%), em idade produtiva (72,1%), picado no membro inferior (88,5%), por jararaca (48,6%) ou surucucu (46,8%), na zona rural de seu município (70,2%) e que só recebeu atendimento médico em tempo superior a seis horas, após acidente (57,3%). As manifestações locais mais freqüentes foram: edema (76,9%), dor (68,7%), eritema (10,2%) e hemorragia (9,3%). Hemorragia (18,8%) foi a manifestação sistêmica mais freqüente. O antiveneno foi administrado em apenas 65,9% dos pacientes. A via mais utilizada foi a endovenosa (52,3%), sendo relevante o uso de vias não mais recomendadas (47,7%). O antiveneno administrado, na maioria dos pacientes, foi o antibotrópico (66,7%). As complicações mais freqüentes foram abcesso (13,7%), necrose (12,3%), infecção secundária (8,3%), insuficiência renal (2,5%) e gangrena (2,5%). Os procedimentos médicos mais usados para o tratamento das complicações foram: drenagem (52,6%), debridamento (28,9%), amputação (10,5%), limpeza cirúrgica (5,3%) e diálise peritoneal (2,6%). A letalidade foi de 1%.<br>In the State of Amazonas, accidents with snakes are a public health problem. For this reasons, the objective of this work was to carry out a descriptive study of the snake accidents attended in the health units of 34 municipalities, one district and two border platoons in the State of Amazonas. The characteristics most commonly observed among those involved in snake accidents were: farmers (50.4%), male (81.3%), belonging to the working age-group (72.1%), bitten on an upper limb (88.5%) by a "jararaca" (48.6%) or a "surucucu" (46.8%) in the rural part of the municipality (70.2%). The local signs and symptoms most frequently observed in those who received medical care more than 6 hours after the accident (57.3%) were edema (76.9%), pain (68.7%), erithema (10.2%) and hemorrhage (9.3%). The systemic manifestation most frequently observed was hemorrhage (18.8%). Serotherapy was administered in only 65.9% of patients, the intravenous route being the route most commonly used to administer the antivenin (52.3%), while other non- recommended routes were widely used. In the majority of patients the antivenin given was antibotropic. The most frequent complications were: abscess 13.7%, necrosis 12.3%, secondary infection 8.3%, renal insufficiency 2.5% and gangrene 2.5%. The medical procedures most used in the treatment of these complications were drainage 52.6%, debridement 28.9%, amputation 10.5%, surgical cleaning 5.3% and peritoneal dialysis 2.6%. The fatality rate was 1%