Influence of sex on the timing of coronary angiography and the prescription of antiplatelet therapy in patients with nonST-segment elevation myocardial infarction. / Impacto del sexo en los tiempos de cateterismo y en el uso de pretratamiento antiagregante plaquetario en pacientes con síndrome coronario agudo sin elevación del segmento ST (SCASEST).

OBJECTIVES: To assess differences in the clinical management of nonST-segment elevation myocardial infarction (NSTEMI), including in-hospital events, according to biological sex. MATERIAL AND METHODS: Prospective observational multicenter study of patients diagnosed with NSTEMI and atherosclerosis who underwent coronary angiography. RESULTS: We enrolled 1020 patients in April and May 2022; 240 (23.5%) were women. Women were older than men on average (72.6 vs 66.5 years, P .001), and more women were frail (17.1% vs 5.6%, P .001). No difference was observed in pretreatment with any P2Y12 inhibitor (prescribed in 68.8% of women vs 70.2% of men, P = .67); however, more women than men were prescribed clopidogrel (56% vs 44%, P = .009). Women prescribed clopidogrel were more often under the age of 75 years and not frail. Coronary angiography was performed within 24 hours less corooften in women (29.8% vs 36.9%, P = .03) even when high risk was recognized. Frailty was independently associated with deferring coronary angiography in the adjusted analysis; biological sex by itself was not related. The frequency and type of revascularization were the same in both sexes, and there were no differences in in-hospital cardiovascular events. CONCLUSION: Women were more often prescribed less potent antithrombotic therapy than men. Frailty, but not sex, correlated independently with deferral of coronary angiography. However, we detected no differences in the frequency of coronary revascularization or in-hospital events according to sex.

OBJETIVO: Evaluar las diferencias en el manejo clínico y eventos intrahospitalarios en una cohorte de pacientes con síndrome coronario agudo sin elevación del segmento ST (SCASEST) en función del sexo. METODO: Estudio observacional, prospectivo y multicéntrico que incluyó pacientes consecutivos con diagnóstico de SCASEST sometidos a coronariografía con enfermedad ateroesclerótica responsable. RESULTADOS: Entre abril y mayo de 2022 se incluyeron 1.020 pacientes; de ellos, 240 eran mujeres (23,5%). En comparación con los hombres, las mujeres fueron mayores (72,6 años vs 66,5 años; p 0,001) y más frágiles (17,1% vs 5,6%; p 0,001). No hubo diferencias en el pretratamiento con un inhibidor del receptor P2Y12 (68,8% vs 70,2%, p = 0,67), aunque las mujeres recibieron más pretratamiento con clopidogrel (56% vs 44%, p = 0,009), principalmente aquellas de edad 75 años y sin fragilidad. En las mujeres se realizaron menos coronariografías precoces (# 24 h) (29,8% vs 36,9%; p = 0,03) a pesar de presentar la misma indicación (criterios de alto riesgo). En el análisis ajustado, la fragilidad, pero no el sexo, se asoció de forma independiente con la realización de una coronariografía diferida. La tasa y el tipo de revascularización fue igual en ambos sexos, y no hubo diferencias en los eventos cardiovasculares intrahospitalarios. CONCLUSIONES: Las mujeres recibieron con mayor frecuencia un tratamiento antitrombótico menos potente. La fragilidad y no el sexo se asoció con la realización de coronariografía diferida. Sin embargo, no hubo diferencias en la tasa de revascularización coronaria ni en los eventos intrahospitalarios en función del sexo.

Tiempos de cateterismo y uso de pretratamiento antiagregante plaquetario en pacientes con SCASEST en España / Timing of coronary angiography and use of antiplatelet pretreatment in patients with NSTEACS in Spain

Introducción y objetivos El momento óptimo para un cateterismo en el síndrome coronario agudo sin elevación del segmento ST (SCASEST) y la necesidad de pretratamiento son motivo de controversia. El objetivo principal del registro IMPACT-TIMING-GO es conocer el porcentaje de pacientes examinados con una coronariografía precoz (0-24 h) y que no recibieron doble antiagregación plaquetaria antes del cateterismo (estrategia sin pretratamiento) en España. Métodos Estudio observacional, prospectivo y multicéntrico, que incluyó a pacientes consecutivos con diagnóstico de SCASEST sometidos a cateterismo en los que se evidenció enfermedad coronaria ateroesclerótica causal. Resultados Entre abril y mayo de 2022 se incluyó a 1.021 pacientes (media de edad, 67±12 años; el 23,6% mujeres). El 86,8% de los pacientes cumplían criterios de alto riesgo (elevación de troponina, cambios electrocardiográficos o puntuación GRACE>140); sin embargo, únicamente el 37,8% se sometió a una estrategia invasiva precoz, y el 30,3% no recibió pretratamiento. Globalmente, solo el 13,6% de los pacientes se sometieron a una estrategia invasiva precoz sin un segundo antiagregante plaquetario, y la estrategia diferida con pretratamiento fue la más utilizada (46%). Durante el ingreso, 9 pacientes (0,9%) fallecieron y 34 (3,3%) presentaron una hemorragia grave. Conclusiones En España, solo el 13,6% de los pacientes con SCASEST sometidos a cateterismo reciben una estrategia invasiva precoz sin pretratamiento. La incidencia de eventos cardiovasculares y hemorragias graves en el ingreso es baja. (AU)

Introduction and objectives The optimal timing of coronary angiography in patients admitted with non–ST-segment elevation acute coronary syndrome (NSTEACS) as well as the need for pretreatment are controversial. The main objective of the IMPACT-TIMING-GO registry was to assess the proportion of patients undergoing an early invasive strategy (0-24hours) without dual antiplatelet therapy (no pretreatment strategy) in Spain. Methods This observational, prospective, and multicenter study included consecutive patients with NSTEACS who underwent coronary angiography that identified a culprit lesion. Results Between April and May 2022, we included 1021 patients diagnosed with NSTEACS, with a mean age of 67±12 years (23.6% women). A total of 87% of the patients were deemed at high risk (elevated troponin; electrocardiogram changes; GRACE score>140) but only 37.8% underwent an early invasive strategy, and 30.3% did not receive pretreatment. Overall, 13.6% of the patients underwent an early invasive strategy without pretreatment, while the most frequent strategy was a deferred angiography under antiplatelet pretreatment (46%). During admission, 9 patients (0.9%) died, while major bleeding occurred in 34 (3.3%). Conclusions In Spain, only 13.6% of patients with NSTEACS undergoing coronary angiography received an early invasive strategy without pretreatment. The incidence of cardiovascular and severe bleeding events during admission was low. (AU)

Timing of coronary angiography and use of antiplatelet pretreatment in patients with NSTEACS in Spain.

INTRODUCTION AND OBJECTIVES: The optimal timing of coronary angiography in patients admitted with non-ST-segment elevation acute coronary syndrome (NSTEACS) as well as the need for pretreatment are controversial. The main objective of the IMPACT-TIMING-GO registry was to assess the proportion of patients undergoing an early invasive strategy (0-24hours) without dual antiplatelet therapy (no pretreatment strategy) in Spain. METHODS: This observational, prospective, and multicenter study included consecutive patients with NSTEACS who underwent coronary angiography that identified a culprit lesion. RESULTS: Between April and May 2022, we included 1021 patients diagnosed with NSTEACS, with a mean age of 67±12 years (23.6% women). A total of 87% of the patients were deemed at high risk (elevated troponin; electrocardiogram changes; GRACE score>140) but only 37.8% underwent an early invasive strategy, and 30.3% did not receive pretreatment. Overall, 13.6% of the patients underwent an early invasive strategy without pretreatment, while the most frequent strategy was a deferred angiography under antiplatelet pretreatment (46%). During admission, 9 patients (0.9%) died, while major bleeding occurred in 34 (3.3%). CONCLUSIONS: In Spain, only 13.6% of patients with NSTEACS undergoing coronary angiography received an early invasive strategy without pretreatment. The incidence of cardiovascular and severe bleeding events during admission was low.

Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29.

The genome-organizing protein p6 of Bacillus subtilis bacteriophage φ29 plays an essential role in viral development by activating the initiation of DNA replication and participating in the early-to-late transcriptional switch. These activities require the formation of a nucleoprotein complex in which the DNA adopts a right-handed superhelix wrapping around a multimeric p6 scaffold, restraining positive supercoiling and compacting the viral genome. Due to the absence of homologous structures, prior attempts to unveil p6's structural architecture failed. Here, we employed AlphaFold2 to engineer rational p6 constructs yielding crystals for three-dimensional structure determination. Our findings reveal a novel fold adopted by p6 that sheds light on its self-association mechanism and its interaction with DNA. By means of protein-DNA docking and molecular dynamic simulations, we have generated a comprehensive structural model for the nucleoprotein complex that consistently aligns with its established biochemical and thermodynamic parameters. Besides, through analytical ultracentrifugation, we have confirmed the hydrodynamic properties of the nucleocomplex, further validating in solution our proposed model. Importantly, the disclosed structure not only provides a highly accurate explanation for previously experimental data accumulated over decades, but also enhances our holistic understanding of the structural and functional attributes of protein p6 during φ29 infection.

A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers.

The muscle spindle is an essential proprioceptor, significantly involved in sensing limb position and movement. Although biological spindle models exist for years, the gold-standard for motor control in biomechanics are still sensors built of homogenized spindle output models due to their simpler combination with neuro-musculoskeletal models. Aiming to improve biomechanical simulations, this work establishes a more physiological model of the muscle spindle, aligned to the advantage of easy integration into large-scale musculoskeletal models. We implemented four variations of a spindle model in Matlab/Simulink®: the Mileusnic et al. (2006) model, Mileusnic model without mass, our enhanced Hill-type model, and our enhanced Hill-type model with parallel damping element (PDE). Different stretches in the intrafusal fibers were simulated in all model variations following the spindle afferent recorded in previous experiments in feline soleus muscle. Additionally, the enhanced Hill-type models had their parameters extensively optimized to match the experimental conditions, and the resulting model was validated against data from rats' triceps surae muscle. As result, the Mileusnic models present a better overall performance generating the afferent firings compared to the common data evaluated. However, the enhanced Hill-type model with PDE exhibits a more stable performance than the original Mileusnic model, at the same time that presents a well-tuned Hill-type model as muscle spindle fibers, and also accounts for real sarcomere force-length and force-velocity aspects. Finally, our activation dynamics is similar to the one applied to Hill-type model for extrafusal fibers, making our proposed model more easily integrated in multi-body simulations.

Predicting protein stability changes upon mutation using a simple orientational potential.

MOTIVATION: Structure-based stability prediction upon mutation is crucial for protein engineering and design, and for understanding genetic diseases or drug resistance events. For this task, we adopted a simple residue-based orientational potential that considers only three backbone atoms, previously applied in protein modeling. Its application to stability prediction only requires parametrizing 12 amino acid-dependent weights using cross-validation strategies on a curated dataset in which we tried to reduce the mutations that belong to protein-protein or protein-ligand interfaces, extreme conditions and the alanine over-representation. RESULTS: Our method, called KORPM, accurately predicts mutational effects on an independent benchmark dataset, whether the wild-type or mutated structure is used as starting point. Compared with state-of-the-art methods on this balanced dataset, our approach obtained the lowest root mean square error (RMSE) and the highest correlation between predicted and experimental ΔΔG measures, as well as better receiver operating characteristics and precision-recall curves. Our method is almost anti-symmetric by construction, and it performs thus similarly for the direct and reverse mutations with the corresponding wild-type and mutated structures. Despite the strong limitations of the available experimental mutation data in terms of size, variability, and heterogeneity, we show competitive results with a simple sum of energy terms, which is more efficient and less prone to overfitting. AVAILABILITY AND IMPLEMENTATION: https://github.com/chaconlab/korpm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Non-Sterile to Sterile Compounding: An Unconventional Response During the COVID-19 Pandemic.

The drug supply chain has suffered many interruptions over the past decade. The COVID-19 pandemic exacerbated an already fragile infrastructure for supplying critical medications to hospitals and health-systems. The purpose of this paper is to provide insight to the history, thought-processes, and response to critical medication shortages during the COVID-19 pandemic, with a focus on hydromorphone infusions and the action steps taken to engage in non-sterile to sterile (NSTS) compounding. Over a period of 6 weeks, we compounded 1,613 NSTS hydromorphone infusion bags. All lots were cleared for sterility, particulate, potency, and endotoxin testing by an outside FDA registered laboratory. We did not have any safety reports filed specific to the NSTS compounded hydromorphone infusion bags. Over a period of 15 weeks, 715 infusions were consumed. The drug supply chain suffers frequent interruptions and critical shortages, particularly in times of a natural disaster or a global pandemic. Non-sterile to sterile compounding is often associated with risks of inaccuracies, impurities, and contamination. There are instances in which non-sterile to sterile compounding is appropriate and should be considered in times of drug shortages to support the care of hospitalized patients.

Local Normal Mode Analysis for Fast Loop Conformational Sampling.

We propose and validate a novel method to efficiently explore local protein loop conformations based on a new formalism for constrained normal mode analysis (NMA) in internal coordinates. The manifold of possible loop configurations imposed by the position and orientation of the fixed loop ends is reduced to an orthogonal set of motions (or modes) encoding concerted rotations of all the backbone dihedral angles. We validate the sampling power on a set of protein loops with highly variable experimental structures and demonstrate that our approach can efficiently explore the conformational space of closed loops. We also show an acceptable resemblance of the ensembles around equilibrium conformations generated by long molecular simulations and constrained NMA on a set of exposed and diverse loops. In comparison with other methods, the main advantage is the lack of restrictions on the number of dihedrals that can be altered simultaneously. Furthermore, the method is computationally efficient since it only requires the diagonalization of a tiny matrix, and the modes of motions are energetically contextualized by the elastic network model, which includes both the loop and the neighboring residues.

Prevalencia de infección por SARS-CoV-2 durante la primera oleada de la pandemia entre personal sanitario y no sanitario del Hospital General de Segovia, Castilla y León / Prevalence of SARS-CoV-2 infection during the first wave of the pandemic among health and non-health personnel of the General Hospital of Segovia, Castilla y León

Introducción. Los trabajadores sanitarios y no sanitarios(TSyNS) de un hospital están más expuestos al contagio porSARS-CoV-2 que la población general. Estudiamos la prevalencia de esta infección en los trabajadores del hospital de Segovia tras la primera ola.Material y métodos. Estudio monocéntrico, observacional, transversal, realizado entre el 29 de abril y el 14 de mayode 2020. Se diagnosticó la infección mediante test de inmunocromatografía capilar para anticuerpos IgG y/o IgM, o PCR. Seestudiaron variables laborales, de salud, y de exposición.Resultados. Participaron en el estudio 1.335 TSyNS de untotal 1.667 (80,1%), un 79,3% mujeres, con una edad media de47,3 años, y de 47,1 para los hombres. La prevalencia de infectados fue del 21,95%, el 24,7% asintomáticos. La edad presentó una OR significativa de 1,02/año. La exposición extralaboralaumentó la prevalencia un 16,8%. El uso continuado del Equipo de Protección Individual (EPI) y la administración de nebulizaciones presentaron una OR de 0,54 y 0,46 respectivamente.Los síntomas asociados a mayor prevalencia fueron anosmia(OR 9,31), ageusia (OR 3,05), y fiebre (OR 1,94). Hasta la fecha,el 75% de los TSyTNS infectados lo hicieron en la primera ola.Conclusiones. La prevalencia es mayor entre los TSyNSque en la población general. La edad se asocia a una mayorprevalencia de infección. Casi un 25% de los infectados fueasintomático. El uso de EPI de forma continuada se asoció amenor prevalencia. Los síntomas con mayor asociación fueronfiebre, anosmia, y ageusia. (AU)

Introduction. Health and non-health workers (H&NH-W)in a hospital are more exposed to SARS-CoV-2 infection thanthe general population. We studied the prevalence of this infection in these workers of Segovia´s Hospital after the firstepidemic wave.Material and methods. Monocentric, observational,cross-sectional study, carried out between April 29 and May14, 2020. The infection was diagnosed by capillary immunochromatography test for IgG and / or IgM antibodies, or PCR.Work, health, and exposure variables were studied.Results. A total of 1,335 H&NH-W participated in thestudy out of a total of 1,667 (80.1%), 79.3% women, with amean age of 47.3 years, and 47.1 for men. The prevalence ofinfected was 21.95%, 24.7% asymptomatic. Age presented asignificant OR of 1.02/year. Exposure outside of work increasedthe prevalence by 16.8%. The continued use of Personal Protective Equipment (PPE) and the administration of nebulizations presented an OR of 0.54 and 0.46 respectively. The symptoms associated with the highest prevalence were anosmia(OR 9.31), ageusia (OR 3.05), and fever (OR 1.94). Today, about75% of H&NH-W were infected in the first wave.Conclusions. The prevalence is higher among healthcareworkers than the population they serve. Age is associated witha higher prevalence of infection. Almost a quarter of thoseinfected were asymptomatic. The continuous use of PPE wasassociated with a lower prevalence, for that the administrationof nebulisations could be safe. The symptoms with the greatestassociation were fever, anosmia, and ageusia (AU)

Platelet VPS16B is dependent on VPS33B expression, as determined in two siblings with arthrogryposis, renal dysfunction, and cholestasis syndrome.

BACKGROUND: Platelet α-granule biogenesis in precursor megakaryocytes is critically dependent on VPS33B and VPS16B, as demonstrated by the platelet α-granule deficiency seen in the rare multisystem disorder arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome associated with biallelic pathogenic variants in VPS33B and VIPAS39 (encoding VPS16B). VPS33B and VPS16B are ubiquitously expressed proteins that are known to interact and play key roles in protein sorting and trafficking between subcellular locations. However, there remain significant gaps in our knowledge of the nature of these interactions in primary cells from patients with ARC syndrome. OBJECTIVES: To use primary cells from patients with ARC syndrome to better understand the interactions and roles of VPS33B and VPS16B in platelets and precursor megakaryocytes. PATIENTS/METHODS: The proband and his male sibling were clinically suspected to have ARC syndrome. Confirmatory genetic testing and platelet phenotyping, including electron microscopy and protein expression analysis, was performed with consent in a research setting. RESULTS: We describe the first case of ARC syndrome identified in Costa Rica, associated with a novel homozygous nonsense VPS33B variant that is linked with loss of expression of both VPS33B and VPS16B in platelets. CONCLUSION: These results indicate that stable expression of VPS16B in platelets, their precursor megakaryocytes, and other cells is dependent on VPS33B. We suggest that systematic evaluation of primary cells from patients with a range of VPS33B and VIPAS39 variants would help to elucidate the interactions and functions of these proteins.

Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation.

Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of dopamine (DA) and other catecholamines, and its dysfunction leads to DA deficiency and parkinsonisms. Inhibition by catecholamines and reactivation by S40 phosphorylation are key regulatory mechanisms of TH activity and conformational stability. We used Cryo-EM to determine the structures of full-length human TH without and with DA, and the structure of S40 phosphorylated TH, complemented with biophysical and biochemical characterizations and molecular dynamics simulations. TH presents a tetrameric structure with dimerized regulatory domains that are separated 15 Å from the catalytic domains. Upon DA binding, a 20-residue α-helix in the flexible N-terminal tail of the regulatory domain is fixed in the active site, blocking it, while S40-phosphorylation forces its egress. The structures reveal the molecular basis of the inhibitory and stabilizing effects of DA and its counteraction by S40-phosphorylation, key regulatory mechanisms for homeostasis of DA and TH.

Current approaches to flexible loop modeling.

Loops are key components of protein structures, involved in many biological functions. Due to their conformational variability, the structural investigation of loops is a difficult topic, requiring a combination of experimental and computational methods. This paper provides a brief overview of current computational approaches to flexible loop modeling, and presents the main ingredients of the most standard protocols. Despite great progress in recent years, accurately modeling the conformational variability of long flexible loops remains a challenging problem. Future advances in this field will likely come from a tight coupling of experimental and computational techniques, which would enable a better understanding of the relationships between loop sequence, structural flexibility, and functional roles. In fine, accurate loop modeling will open the road to loop design problems of interest for applications in biomedicine and biotechnology.

InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.

The InterEvDock3 protein docking server exploits the constraints of evolution by multiple means to generate structural models of protein assemblies. The server takes as input either several sequences or 3D structures of proteins known to interact. It returns a set of 10 consensus candidate complexes, together with interface predictions to guide further experimental validation interactively. Three key novelties were implemented in InterEvDock3 to help obtain more reliable models: users can (i) generate template-based structural models of assemblies using close and remote homologs of known 3D structure, detected through an automated search protocol, (ii) select the assembly models most consistent with contact maps from external methods that implement covariation-based contact prediction with or without deep learning and (iii) exploit a novel coevolution-based scoring scheme at atomic level, which leads to significantly higher free docking success rates. The performance of the server was validated on two large free docking benchmark databases, containing respectively 230 unbound targets (Weng dataset) and 812 models of unbound targets (PPI4DOCK dataset). Its effectiveness has also been proven on a number of challenging examples. The InterEvDock3 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock3/.

Atomic-level evolutionary information improves protein-protein interface scoring.

MOTIVATION: The crucial role of protein interactions and the difficulty in characterizing them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous incorporation of conservation and coevolution information has shown promise for improving protein-protein scoring. Here, we present a novel strategy to integrate atomic-level evolutionary information into different types of scoring functions to improve their docking discrimination. RESULTS: We applied this general strategy to our residue-level statistical potential from InterEvScore and to two atomic-level scores, SOAP-PP and Rosetta interface score (ISC). Including evolutionary information from as few as 10 homologous sequences improves the top 10 success rates of individual atomic-level scores SOAP-PP and Rosetta ISC by 6 and 13.5 percentage points, respectively, on a large benchmark of 752 docking cases. The best individual homology-enriched score reaches a top 10 success rate of 34.4%. A consensus approach based on the complementarity between different homology-enriched scores further increases the top 10 success rate to 40%. AVAILABILITY AND IMPLEMENTATION: All data used for benchmarking and scoring results, as well as a Singularity container of the pipeline, are available at http://biodev.cea.fr/interevol/interevdata/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions.

MOTIVATION: Despite the progress made in studying protein-ligand interactions and the widespread application of docking and affinity prediction tools, improving their precision and efficiency still remains a challenge. Computational approaches based on the scoring of docking conformations with statistical potentials constitute a popular alternative to more accurate but costly physics-based thermodynamic sampling methods. In this context, a minimalist and fast sidechain-free knowledge-based potential with a high docking and screening power can be very useful when screening a big number of putative docking conformations. RESULTS: Here, we present a novel coarse-grained potential defined by a 3D joint probability distribution function that only depends on the pairwise orientation and position between protein backbone and ligand atoms. Despite its extreme simplicity, our approach yields very competitive results with the state-of-the-art scoring functions, especially in docking and screening tasks. For example, we observed a twofold improvement in the median 5% enrichment factor on the DUD-E benchmark compared to Autodock Vina results. Moreover, our results prove that a coarse sidechain-free potential is sufficient for a very successful docking pose prediction. AVAILABILITYAND IMPLEMENTATION: The standalone version of KORP-PL with the corresponding tests and benchmarks are available at https://team.inria.fr/nano-d/korp-pl/ and https://chaconlab.org/modeling/korp-pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.

Single Center Experience with Robot Technologies for Sterile Compounding: A Retrospective Review.

The compounding of sterile medication admixtures is a labor-intensive process and subject to potential human error. The addition of robotic devices and workflow technology may mitigate some of the challenges of compounding sterile product admixtures, especially for those associated with antineoplastic and hazardous medications. This article discusses the single-center experiences from October 2009 through August 2017 with various sterile compounding robotic technologies. The robotic devices included Intellifill  i.v., Cytocare, i.v.Station, i.v.Station ONCO, and i.v.Soft Assist. The objective of this analysis was to describe the experience with robotic technology and workflow devices in compounding sterile medication admixtures. The number of prepared doses for each device was tracked, and each device had a tool to validate the dose accuracy via specific gravity measurement. Nonhazardous preparations with a dose variation of > (+/- 10%) were considered failures. For hazardous medications, variation of > (+/- 5%) was considered a failure. Doses that were prepared manually were also analyzed. The Intellifill i.v. robot was used to compound more than 1,000,000 admixtures (75% of all compounded  products). The i.v.Station, Cytocare, i.v.Station  ONCO, and i.v.Soft Assist robots compounded 14%, 7%,  3%, and 0.7% of the total chemotherapy doses required. Identified barriers to optimal performance included device (hardware) and software failures as well as shortages with specific fluid and drug containers. The qualitative analysis was done for 36 drugs that were prepared using i.v.Station and i.v.Station ONCO. The passing rate was estimated to be 95%. Barriers to use the device included lack of the appropriate medication container, diluent supplies issues, and software failure. Robotic devices and workflow technology for compounding sterile medication admixtures were unable to produce all routine parenteral doses required daily.

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.

KORP: knowledge-based 6D potential for fast protein and loop modeling.

MOTIVATION: Knowledge-based statistical potentials constitute a simpler and easier alternative to physics-based potentials in many applications, including folding, docking and protein modeling. Here, to improve the effectiveness of the current approximations, we attempt to capture the six-dimensional nature of residue-residue interactions from known protein structures using a simple backbone-based representation. RESULTS: We have developed KORP, a knowledge-based pairwise potential for proteins that depends on the relative position and orientation between residues. Using a minimalist representation of only three backbone atoms per residue, KORP utilizes a six-dimensional joint probability distribution to outperform state-of-the-art statistical potentials for native structure recognition and best model selection in recent critical assessment of protein structure prediction and loop-modeling benchmarks. Compared with the existing methods, our side-chain independent potential has a lower complexity and better efficiency. The superior accuracy and robustness of KORP represent a promising advance for protein modeling and refinement applications that require a fast but highly discriminative energy function. AVAILABILITY AND IMPLEMENTATION: http://chaconlab.org/modeling/korp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion.

Robust innate immune detection of rapidly evolving pathogens is critical for host defense. Nucleotide-binding domain leucine-rich repeat (NLR) proteins function as cytosolic innate immune sensors in plants and animals. However, the structural basis for ligand-induced NLR activation has so far remained unknown. NAIP5 (NLR family, apoptosis inhibitory protein 5) binds the bacterial protein flagellin and assembles with NLRC4 to form a multiprotein complex called an inflammasome. Here we report the cryo-electron microscopy structure of the assembled ~1.4-megadalton flagellin-NAIP5-NLRC4 inflammasome, revealing how a ligand activates an NLR. Six distinct NAIP5 domains contact multiple conserved regions of flagellin, prying NAIP5 into an open and active conformation. We show that innate immune recognition of multiple ligand surfaces is a generalizable strategy that limits pathogen evolution and immune escape.