Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

We describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13 Submissions were made by three free-modelling methods which combine the predictions of three neural networks. All three systems were guided by predictions of distances between pairs of residues produced by a neural network. Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. The third system shows that simple gradient descent on a properly constructed potential is able to perform on-par with more expensive traditional search techniques and without requiring domain segmentation. In the CASP13 free-modelling assessors' ranking by summed z-scores, this system scored highest with 68.3 vs 48.2 for the next closest group. (An average GDT_TS of 61.4.) The system produced high-accuracy structures (with GDT_TS scores of 70 or higher) for 11 out of 43 free-modelling domains. Despite not explicitly using template information, the results in the template category were comparable to the best performing template-based methods

Improved protein structure prediction using potentials from deep learning

Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence1. This problem is of fundamental importance as the structure of a protein largely determines its function2; however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures3. Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction5 (CASP13)—a blind assessment of the state of the field—AlphaFold created high-accuracy structures (with template modelling (TM) scores6 of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined7

Anticoagulant therapy for splanchnic vein thrombosis: an individual patient data meta-analysis

Robust evidence on the optimal management of splanchnic vein thrombosis (SVT) is lacking. We conducted an individual-patient meta-analysis to evaluate the effectiveness and safety of anticoagulation for SVT. Medline, Embase, and clincaltrials.gov were searched up to June 2021 for prospective cohorts or randomized clinical trials including patients with SVT. Data from individual datasets were merged, and any discrepancy with published data was resolved by contacting study authors. Three studies of a total of 1635 patients were included. Eighty-five percent of patients received anticoagulation for a median duration of 316 days (range, 1-730 days). Overall, incidence rates for recurrent venous thromboembolism (VTE), major bleeding, and mortality were 5.3 per 100 patient-years (p-y; 95% confidence interval [CI], 5.1-5.5), 4.4 per 100 p-y (95% CI, 4.2-4.6), and 13.0 per 100 p-y (95% CI, 12.4-13.6), respectively. The incidence rates of all outcomes were lower during anticoagulation and higher after treatment discontinuation or when anticoagulation was not administered. In multivariable analysis, anticoagulant treatment appeared to be associated with a lower risk of recurrent VTE (hazard ratio [HR], 0.42; 95% CI, 0.27-0.64), major bleeding (HR, 0.47; 95% CI, 0.30-0.74), and mortality (HR, 0.23; 95% CI, 0.17-0.31). Results were consistent in patients with cirrhosis, solid cancers, myeloproliferative neoplasms, unprovoked SVT, and SVT associated with transient or persistent nonmalignant risk factors. In patients with SVT, the risk of recurrent VTE and major bleeding is substantial. Anticoagulant treatment is associated with reduced risk of both outcomes. © 2022 by The American Society of Hematology

Mercury's Interior Structure Constrained by Density and P-Wave Velocity Measurements of Liquid Fe-Si-C Alloys

peer reviewe

The quijote simulations

The Quijote simulations are a set of 44,100 full N-body simulations spanning more than 7000 cosmological models in the hyperplane. At a single redshift, the simulations contain more than 8.5 trillion particles over a combined volume of 44,100 each simulation follows the evolution of 2563, 5123, or 10243 particles in a box of 1 h -1 Gpc length. Billions of dark matter halos and cosmic voids have been identified in the simulations, whose runs required more than 35 million core hours. The Quijote simulations have been designed for two main purposes: (1) to quantify the information content on cosmological observables and (2) to provide enough data to train machine-learning algorithms. In this paper, we describe the simulations and show a few of their applications. We also release the petabyte of data generated, comprising hundreds of thousands of simulation snapshots at multiple redshifts; halo and void catalogs; and millions of summary statistics, such as power spectra, bispectra, correlation functions, marked power spectra, and estimated probability density functions

Symptom-related screening programme for early detection of chronic thromboembolic pulmonary hypertension after acute pulmonary embolism: the SYSPPE study

Background Chronic thromboembolic pulmonary hypertension (CTEPH) is the most severe long-term complication of acute pulmonary embolism (PE). We aimed to evaluate the impact of a symptom screening programme to detect CTEPH in PE survivors.Methods This was a multicentre cohort study of patients diagnosed with acute symptomatic PE between January 2017 and December 2018 in 16 centres in Spain. Patients were contacted by phone 2 years after the index PE diagnosis. Those with dyspnoea corresponding to a New York Heart Association (NYHA)/WHO scale≥II, visited the outpatient clinic for echocardiography and further diagnostic tests including right heart catheterisation (RHC). The primary outcome was the new diagnosis of CTEPH confirmed by RHC.Results Out of 1077 patients with acute PE, 646 were included in the symptom screening. At 2 years, 21.8% (n=141) reported dyspnoea NYHA/WHO scale≥II. Before symptom screening protocol, five patients were diagnosed with CTEPH following routine care. In patients with NYHA/WHO scale≥II, after symptom screening protocol, the echocardiographic probability of pulmonary hypertension (PH) was low, intermediate and high in 76.6% (n=95), 21.8% (n=27) and 1.6% (n=2), respectively. After performing additional diagnostic test in the latter 2 groups, 12 additional CTEPH cases were confirmed.Conclusions The implementation of this simple strategy based on symptom evaluation by phone diagnosed more than doubled the number of CTEPH cases. Dedicated follow-up algorithms for PE survivors help diagnosing CTEPH earlier.Thrombosis and Hemostasi

Bioreguladores y la calidad de la planta de pascua

Paclobutrazol at 0, 12.5, 25 and 37.5 mg/L and uniconazole at 0, 5, 10 and 15 mg/L were applied both as a foliar spray and as a soil drench to 'Eckespoint Freedom Red' and 'Gross Supjibi Red' poinsettia plants. In both poinsettia cultivars plant size was effectively reduced by paclobutrazol and uniconazole as soil drenches at all concentrations. Applying paclobutrazol (12.5 mg/L) or uniconazole (5 mg/L) as a soil drench reduced poinsettia plant size for a longer period of time than applying either as foliar spray. Growth regulators applied as a soil drench also reduced the bract diameter of both cultivars. The use of growth regulators such as paclobutrazol and uniconazole on poinsettia production can improve plant quality (size) in Puerto Rico.Se aplicó paclobutrazol a 0, 12.5, 25 y 37.5 mg/L y uniconazole a 0, 5, 10 y 15 mg/L a las plantas de pascua 'Eckespoint Freedom Red' y 'Gross Supjibi Red', mediante aspersiones al follaje o empapando el suelo. En ambos cultivares el tamaño de las plantas de pascua se redujo significativamente cuando el suelo se empapó con cualesquiera de las tres concentraciones de paclobutrazol o uniconazole. Cuando se empapó el suelo con paclobutrazol (12.5 mg/L) o uniconazole (5 mg/L) se redujo el tamaño de la planta de pascua por un período más prolongado que cuando se asperjó el follaje. Los reguladores de crecimiento aplicados empapando el suelo causaron una reducción en el diámetro de las bracteas de ambos cultivares. El uso de reguladores de crecimiento como paclobutrazol y uniconazole en la planta de pascua puede mejorar la calidad (tamaño) de éstas en Puerto Rico

G-Tunnel Pressurized Slot-Testing Preparations; Yucca Mountain Site Characterization Project

Designers and analysts of radioactive waste repositories must be able to predict the mechanical behavior of the host rock. Sandia National laboratories elected to conduct a development program on pressurized slot testing and featured (1) development of an improved method to cut slots using a chain saw with diamond-tipped cutters, (2) measurements useful for determining in situ stresses normal to slots, (3) measurements applicable for determining the in situ modulus of deformation parallel to a drift surface, and (4) evaluations of the potentials of pressurized slot strength testing. This report describes the preparations leading to the measurements and evaluations