Decoding functional proteome information in model organisms using protein language models.

Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.

Single-dose high-dose-rate brachytherapy versus two and three fractions for locally advanced prostate cancer.

BACKGROUND: Single-dose high-dose-rate brachytherapy (SD-HDR-BT) was compared to two or three fraction HDR BT in intermediate and high-risk localized prostate cancer with median follow-up of 10 years. MATERIALS AND METHODS: 293 patients received 1 × 19Gy or 1 × 20Gy (Group A = 49), 2 × 13Gy (Group B = 138), or 3 × 10.5 Gy (Group C = 106) HDR BT. The primary endpoint was biochemical relapse-free interval (bRFI). Late genitourinary (GU) and gastrointestinal (GI) morbidity used RTOG scales and the International Prostate Symptom Score (IPSS). Freedom from biochemical relapse (bRFI), overall survival (OS) and GU, GI and IPSS morbidity were calculated using Kaplan-Meier (K-M) method and log-rank test. Univariate and multivariate hazard ratios (HR) were obtained using Cox's proportional hazard. RESULTS: At 10 years, K-M estimates of bRFI were 64 % (Group A), 72 % (Group B), and 76 % (Group C) (p = 0.2). No statistically significant difference was seen in OS. In multivariate analysis risk-category and ADT administration, but not dose, were significant predictors of relapse (p = 0.0003 and 0.03, respectively). At ten years, GU grade 3 events were 8 % (A), 2 % (B) and 13 % (C); (p = 0.01). IPSS ≥ 20 was 31 % (A), 20 % (B) and 23 % (C); (p = 0.6) and grade 3 GI was 0 % in groups A and B and 2 % in C; (p = 0.3). No GU or GI grade-4 events were observed. Pre-treatment IPSS was a highly significant predictor of failure in multivariate analysis. CONCLUSIONS: Long-term outcome data show reduced but not statistically significant difference in PSA control, and no difference in overall survival, between SD-HDR-BT and 2 or 3 fractions of HDR-BT.

Structure and rheology of the polysaccharides from Schizymenia dubyi: Isolation of an unusual glucurono-carrageenan.

The system of polysaccharides from Schizymenia dubyi (Nemastomatales) was investigated. It contains a mixture of hybrid dl galactans (SH-S) and carrageenan-like polysaccharides, which were separated by means of precipitation with KCl at high concentrations. The structural features of the carrageenan-like fraction (SH-I) were investigated by methylation analysis, desulfation, uronic acid reduction, and NMR spectroscopy. It was concluded that the structure has the typical alternance α-(1 â†’ 3), ß-(1 â†’ 4) of d-galactose units, with most of the 3-linked units sulfated in O-2 (and some in O-4), and most of the 4-linked units sulfated in O-3, and substituted in O-2 by single stubs of ß-d-glucuronic acid (partly sulfated in each of the three available positions). This substituent has been only seldom found in red seaweed galactans. Rheological studies of 5 % and 10 % w/v SH, SH-S and SH-I aqueous systems, either without ions, or in KCl or CaCl2 solution gave thickening behaviors. Their random coil conformations justify the pseudoplastic behavior observed in the viscosity versus shear rate curves. As SH-S and SH-I are both contained in SH, an interpenetrating network could form in SH between the glucurono-carrageenan and the agaran, as inferred from the mechanical spectra recorded in water, especially with potassium ion.

Case-based explanation of standard work tools for selective dorsal rhizotomy for cerebral palsy.

OBJECTIVE: Spasticity is a challenging feature of cerebral palsy (CP) that may be managed with selective dorsal rhizotomy (SDR). Although standard work tools (SWTs) have recently been utilized to inform a standard of care for neurosurgical procedures, no SWTs for SDR have been previously described. The authors present the multidisciplinary approach SWTs for SDR used at their institutions to promote consistency in the field and minimize complication rates. METHODS: A multidisciplinary approach was used to define all steps in the SDR pathway. Preoperative, intraoperative, and postoperative workflows were synthesized, with specific efforts to improve mobility through inpatient rehabilitation and minimize infection. RESULTS: The SWTs have been implemented at two institutions for 7 years. An illustrative case of a patient aged 3 years 10 months with a history of premature birth at 29 weeks, spastic-diplegic CP, right-sided periventricular leukomalacia, and developmental delay who underwent L2-S1 SDR is presented. CONCLUSIONS: The authors detail SWTs for SDR developed by a multidisciplinary team with specific steps at all points in the patient pathway. The illustrative case emphasizes that SWTs may help ensure the safety of SDR while maximizing its long-term efficacy for individuals with CP.

Amidation of arabinoglucuronoxylans to modulate their flow behavior.

Arabinoglucuronoxylans obtained from the exudate of Cercidium praecox (Brea gum) were subjected to an amidation reaction to modulate their flow behavior to obtain a product with similar behavior to gum Arabic. The amidation reaction of the uronic acids present in this exudate was studied using the 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and N-hydroxysuccinimide (NHS) system with the aim of maximizing product yield and minimizing by-product. An analysis of the significant factors involved in the reaction was carried out and a response surface methodology was conducted to optimize the stoichiometry of the reagents used. It was possible to obtain models for predicting the degree of amidation (DA) of arabinoglucuronoxylans and the formation of by-products. The formation of a secondary product derived from the amino acid ß-alanine which has not been reported previously in the reaction with polysaccharides, was described. The flow behavior of an amidated product (DA = 52 %) was determined, showing a pseudoplastic behavior and a decreased Newtonian viscosity (η0 = 36.2 Pa s) at the lowest shear rate range with respect to native product solution (η0 = 115 Pa s). Amidated arabinoglucuronoxylans had a flow behavior more similar to that of gum Arabic.

Mexican consensus on cow's milk protein allergy.

BACKGROUND: The aim of this study is to present the current views of a diverse group of experts on the diagnosis and treatment of Cow's Milk Protein Allergy (CMPA) in children under 2 years of age in Mexico. MATERIAL AND METHODS: The study, led by a scientific committee of five experts in CMPA, was divided into six phases, including a modified Delphi process. A total of 20 panelists, all of whom were pediatric specialists, participated in administering a comprehensive 38-item questionnaire. The questionnaire was divided into two blocks: Diagnosis and Treatment (20 items each). RESULTS: Consensus was reached on all the proposed items, with an agreement rate of over 70% for each of them. As a result, a diagnostic and treatment algorithm was developed that emphasized the reduction of unnecessary diagnostic studies and encouraged breastfeeding whenever possible. In cases where breast milk is not available, appropriate use of hypoallergenic formulas was recommended. In addition, recommendations on treatment duration and gradual reintroduction of cow's milk protein were provided. CONCLUSIONS: The recommendations endorsed by 20 Mexican pediatricians through this study are applicable to everyday clinical practice, thereby enhancing the diagnosis and treatment of children under 2 years of age with CMPA. This, in turn, will foster improved health outcomes and optimize the utilization of healthcare resources.

Trunk postural reactions to the force perturbation intensity and frequency during sitting astride in children with cerebral palsy.

The purpose of this study was to examine kinematic and neuromuscular responses of the head and body to pelvis perturbations with different intensities and frequencies during sitting astride in children with CP. Sixteen children with spastic CP (mean age 7.4 ± 2.4 years old) were recruited in this study. A custom designed cable-driven robotic horse was used to apply controlled force perturbations to the pelvis during sitting astride. Each participant was tested in four force intensity conditions (i.e., 10%, 15%, 20%, and 25% of body weight (BW), frequency = 1 Hz), and six force frequency conditions (i.e., 0.5 Hz, 1 Hz, 1.5 Hz, 2 Hz, 2.5 Hz, and 3 Hz, intensity = 20% of BW). Each testing session lasted for one minute with a one-minute rest break inserted between two sessions. Kinematic data of the head, trunk, and legs were recorded using wearable sensors, and EMG signals of neck, trunk, and leg muscles were recorded. Children with CP showed direction-specific trunk and neck muscle activity in response to the pelvis perturbations during sitting astride. Greater EMG activities of trunk and neck muscles were observed for the greater intensities of force perturbations (P < .05). Participants also showed enhanced activation of antagonistic muscles rather than direction-specific trunk and neck muscle activities for the conditions of higher frequency perturbations (P < .05). Children with CP may modulate trunk and neck muscle activities in response to greater changes in intensity of pelvis perturbation during sitting astride. Perturbations with too high frequency may be less effective in inducing direction-specific trunk and neck muscle activities.

Environmental surface monitoring as a noninvasive method for SARS-CoV-2 surveillance in community settings: Lessons from a university campus study.

Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, community level case incidence, and university student health data. Environmental swabs were collected from January 2022 to November 2022 from high-touch objects and surfaces from five locations on a large university campus in Florida, USA. RT-qPCR was used to detect and quantify viral RNA, and a subset of positive samples was analyzed by viral genome sequencing to identify circulating lineages. During the study period, we detected SARS-CoV-2 viral RNA on 90.7 % of 162 tested samples. Levels of environmental viral RNA correlated with trends in community-level activity and case reports from the student health center. A significant positive correlation was observed between the estimated viral gene copy number in environmental samples and the weekly confirmed cases at the university. Viral sequencing data from environmental samples identified lineages concurrently circulating in the local community and state based on genomic surveillance data. Further, we detected emerging variants in environmental samples prior to their identification by clinical genomic surveillance. Our results demonstrate the utility of viral monitoring on high-touch environmental surfaces for SARS-CoV-2 surveillance at a community level. In communities with delayed or limited testing facilities, immediate environmental surface testing may considerably inform epidemic dynamics.

Simulation-based mastery learning for intrathecal baclofen pump management in physical medicine and rehabilitation: A pilot study.

BACKGROUND: Simulation-based mastery learning (SBML) has demonstrated superiority as a procedural learning method. Implementation of SBML in Physical Medicine and Rehabilitation (PM&R) education has not been described and there is a paucity of literature regarding standardized procedural learning in this specialty. OBJECTIVE: To evaluate if implementation of intrathecal baclofen pump management SBML affects knowledge, attitudes, and skills in PM&R residents. DESIGN: Pretest-posttest design. SETTING: Academic rehabilitation hospital. PARTICIPANTS: Twenty-two PM&R residents. INTERVENTIONS: Participants engaged in SBML steps: pre-test, demonstration of proper technique, deliberate practice, and a post-test. MAIN OUTCOME MEASURES: Ability to achieve minimum passing score, quiz scores, and survey scores. Pre- and post-test results were compared using Wilcoxon signed-rank tests. Post graduate year (PGY)-3 and PGY-4 resident results were compared using Mann-Whitney U tests. RESULTS: Based on institutional expert consensus, a simulation procedural checklist was created with a minimum passing score set at correctly performing 30 of 31 items. On pre-test, no learners achieved the minimum passing score (22.5, interquartile range [IQR] 17.0-23.0). Initial post-test score for all learners was 30 (IQR 29.8-31.0). Six learners required additional attempts to reach mastery as defined by reaching the minimum passing score. Quiz scores significantly improved from 9 to 11 (pre-test IQR 9-10; post-test IQR 10-11; p < .05). Confidence in procedure significantly improved (pre-test 2.7/5.9, IQR 2.2-3.8; post-test 4.1/5.0, IQR 3.7-4.5; p < .01). Likelihood to perform procedure in future practice did not change (pre-test 2.2, IQR 1.0-3.8; post-test 3.0, IQR 1.0-4.0; p = .89). CONCLUSION: SBML is an effective tool to improve multiple domains of learning in PM&R residents.

Free Energy Perturbation Approach for Accurate Crystalline Aqueous Solubility Predictions.

Early assessment of crystalline thermodynamic solubility continues to be elusive for drug discovery and development despite its critical importance, especially for the ever-increasing fraction of poorly soluble drug candidates. Here we present a detailed evaluation of a physics-based free energy perturbation (FEP+) approach for computing the thermodynamic aqueous solubility. The predictive power of this approach is assessed across diverse chemical spaces, spanning pharmaceutically relevant literature compounds and more complex AbbVie compounds. Our approach achieves predictive (RMSE = 0.86) and differentiating power (R2 = 0.69) and therefore provides notably improved correlations to experimental solubility compared to state-of-the-art machine learning approaches that utilize quantum mechanics-based descriptors. The importance of explicit considerations of crystalline packing in predicting solubility by the FEP+ approach is also highlighted in this study. Finally, we show how computed energetics, including hydration and sublimation free energies, can provide further insights into molecule design to feed the medicinal chemistry DMTA cycle.

Expression of ERG11, ERG3, MDR1 and CDR1 genes in Candida tropicalis / Expresión de los genes ERG11, ERG3, MDR1 y CDR1 en Candida tropicalis

INTRODUCTION: Drug resistance to azoles is a growing problem in the Candida genus. OBJECTIVE: To analyze molecularly the genes responsible for fluconazole resistance in Candida tropicalis strains. MATERIALS AND METHODS: Nineteen strains, with and without exposure to fluconazole, were selected for this study. The expression of MDR1, CDR1, ERG11, and ERG3 genes was analyzed in sensitive, dose-dependent sensitive, and resistant strains exposed to different concentrations of the antifungal drug. RESULTS: MDR1, ERG11 and ERG3 genes were significantly overexpressed in the different sensitivity groups. CDR1 gene expression was not statistically significant among the studied groups. Seven of the eight fluconazole-resistant strains showed overexpression of one or more of the analyzed genes. In some dose-dependent sensitive strains, we found overexpression of CDR1, ERG11, and ERG3. CONCLUSION: The frequency of overexpression of ERG11 and ERG3 genes indicates that they are related to resistance. However, the finding of dose-dependent resistant/sensitive strains without overexpression of these genes suggests that they are not exclusive to this phenomenon. More basic research is needed to study other potentially involved genes in the resistance mechanism to fluconazole.

Introducción: La farmacorresistencia a los azoles es un problema creciente en el género Candida. Objetivo: Analizar molecularmente los genes responsables de la resistencia a fluconazol en cepas de Candida tropicalis. Materiales y métodos: Para este estudio, se seleccionaron 19 cepas, con exposición a fluconazol y sin ella. Se analizó la expresión de los genes MDR1, CDR1, ERG11 y ERG3 en cepas sensibles, sensibles dependiente de la dosis, y resistentes, previamente expuestas a diferentes concentraciones del fármaco antifúngico. Resultados: Se encontró que los genes MDR1, ERG11 y ERG3 estaban significativamente sobreexpresados en los diferentes grupos de sensibilidad. La expresión del gen CDR1 no fue estadísticamente significativa entre los grupos estudiados. Siete de las ocho cepas resistentes a fluconazol mostraron sobreexpresión de uno o más de los genes analizados. En algunas cepas sensibles dependientes de la dosis, se encontró sobreexpresión de CDR1, ERG11 y ERG3. Conclusión: La sobreexpresión de los genes ERG11 y ERG3 indica que están relacionados con la resistencia de las cepas de Candida. Sin embargo, el hallazgo de cepas resistentes o sensibles según la dosis, sin sobreexpresión de estos genes, sugiere que pueden existir otros genes involucrados en este fenómeno. Se necesitan más investigaciones básicas que contribuyan al estudio de otros genes potencialmente involucrados en el mecanismo de resistencia al fluconazol.

Rapid population growth and high management costs have created a narrow window for control of introduced hippos in Colombia.

The introduction of hippos into the wild in Colombia has been marked by their rapid population growth and widespread dispersal on the landscape, high financial costs of management, and conflicting social perspectives on their management and fate. Here we use population projection models to investigate the effectiveness and cost of management options under consideration for controlling introduced hippos. We estimate there are 91 hippos in the middle Magdalena River basin, Colombia, and the hippo population is growing at an estimated rate of 9.6% per year. At this rate, there will be 230 hippos by 2032 and over 1,000 by 2050. Applying the population control methods currently under consideration will cost at least 1-2 million USD to sufficiently decrease hippo population growth to achieve long-term removal, and depending on the management strategy selected, there may still be hippos on the landscape for 50-100 years. Delaying management actions for a single decade will increase minimum costs by a factor of 2.5, and some methods may become infeasible. Our approach illustrates the trade-offs inherent between cost and effort in managing introduced species, as well as the importance of acting quickly, especially when dealing with species with rapid population growth rates and potential for significant ecological and social impacts.

Improving Trunk Postural Control Facilitates Walking in Children With Cerebral Palsy: A Pilot Study.

OBJECTIVE: The aim of this study is to determine the effects of bilateral trunk support during walking on trunk and leg kinematics and neuromuscular responses in children with cerebral palsy. DESIGN: Fourteen children with spastic cerebral palsy (Gross Motor Function Classification System level I to III) participated in this study. Children walked on a treadmill under four different conditions, that is, without support (Baseline), with bilateral support applied to the upper trunk (upper trunk support), the lower trunk (lower trunk support), and combined upper and lower trunk (combined trunk support). The trunk and leg kinematics and muscle activity were recorded. RESULTS: Providing bilateral support to the trunk had a significant impact on the displacement of the pelvis and trunk ( P < 0.003) during walking. Children's weaker leg showed greater step length ( P = 0.032) and step height ( P = 0.012) in combined trunk support compared with baseline and greater step length in upper trunk support ( P = 0.02) and combined trunk support ( P = 0.022) compared with lower trunk support. Changes in soleus electromyographic activity during stance phase of gait mirrored the changes in step length across all conditions. CONCLUSIONS: Providing bilateral upper or combined upper and lower trunk support during walking may induce improvements in gait performance, which may be due to improved pelvis kinematics. Improving trunk postural control may facilitate walking in children with cerebral palsy.

A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance.

Mutations of the androgen receptor (AR) associated with prostate cancer and androgen insensitivity syndrome may profoundly influence its structure, protein interaction network, and binding to chromatin, resulting in altered transcription signatures and drug responses. Current structural information fails to explain the effect of pathological mutations on AR structure-function relationship. Here, we have thoroughly studied the effects of selected mutations that span the complete dimer interface of AR ligand-binding domain (AR-LBD) using x-ray crystallography in combination with in vitro, in silico, and cell-based assays. We show that these variants alter AR-dependent transcription and responses to anti-androgens by inducing a previously undescribed allosteric switch in the AR-LBD that increases exposure of a major methylation target, Arg761. We also corroborate the relevance of residues Arg761 and Tyr764 for AR dimerization and function. Together, our results reveal allosteric coupling of AR dimerization and posttranslational modifications as a disease mechanism with implications for precision medicine.

Chemoinformatic modelling of the antioxidant activity of phenolic compounds.

BACKGROUND: Antioxidants are chemicals used to protect foods from deterioration by neutralizing free radicals and inhibiting the oxidative process. One approach to investigate the antioxidant activity is to develop quantitative structure-activity relationships (QSARs). RESULTS: A curated database of 165 structurally heterogeneous phenolic compounds with the Trolox equivalent antioxidant capacity (TEAC) was developed. Molecular geometries were optimized by means of the GFN2-xTB semiempirical method and diverse molecular descriptors were obtained afterwards. For model development, V-WSP unsupervised variable reduction was used before performing the genetic algorithms-variable subset selection (GAs-VSS) to construct the best five-descriptor multiple linear regression model. The coefficient of determination and the root mean square error were used to measure the performance in calibration (R2 = 0.789 and RMSEC = 0.381), and test set prediction (Q2 = 0.748 and RMSEP = 0.416), along several cross-validation criteria. To thoroughly understand the TEAC prediction, a fully explained mechanism of action of the descriptors is provided. In addition, the applicability domain of the model defined a theoretical chemical space for reliable predictions of new phenolic compounds. CONCLUSION: This in silico model conforms to the five principles stated by the Organisation for Economic Co-operation and Development. The model might be useful for virtual screening of the antioxidant chemical space and for identifying the most potent molecules related to an experimental measurement of TEAC activity. In addition, the model could assist chemists working on computer-aided drug design for the synthesis of new targets with improved activity and potential uses in food science. © 2023 Society of Chemical Industry.

Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum α-Glucosidase I with Anti-SARS-CoV-2 Activity.

Enveloped viruses depend on the host endoplasmic reticulum (ER) quality control (QC) machinery for proper glycoprotein folding. The endoplasmic reticulum quality control (ERQC) enzyme α-glucosidase I (α-GluI) is an attractive target for developing broad-spectrum antivirals. We synthesized 28 inhibitors designed to interact with all four subsites of the α-GluI active site. These inhibitors are derivatives of the iminosugars 1-deoxynojirimycin (1-DNJ) and valiolamine. Crystal structures of ER α-GluI bound to 25 1-DNJ and three valiolamine derivatives revealed the basis for inhibitory potency. We established the structure-activity relationship (SAR) and used the Site Identification by Ligand Competitive Saturation (SILCS) method to develop a model for predicting α-GluI inhibition. We screened the compounds against SARS-CoV-2 in vitro to identify those with greater antiviral activity than the benchmark α-glucosidase inhibitor UV-4. These host-targeting compounds are candidates for investigation in animal models of SARS-CoV-2 and for testing against other viruses that rely on ERQC for correct glycoprotein folding.

Antioxidant pectins from eggplant (Solanum melongena) fruit exocarp, calyx and flesh isolated through high-power ultrasound and sodium carbonate.

Dried and milled eggplant fruit peel and calyces (PC) and mesocarp, placenta and core (Mes) were utilized as natural sources of valuable chemicals. Pectins were extracted with 0.1 M Na2CO3 (1 h; 23 °C). A high-power ultrasound (US) pretreatment (10 min net time; 12.76 W/cm2 power intensity) in 10:200 (g/mL) powder:water ratio led to the lowest solvent and energy consumptions after the subsequent 0.1 M Na2CO3 stirring, permitting the highest recoveries of uronic acid (UA) from PC and Mes (80.25 and 93.8 %, respectively). Homogalacturonans (>65 % w/w UA) of low degree of methylesterification, of acetylation, and 90,214-138,184 Da molecular weights with low polydispersity (≈1.32-1.40) were obtained. They included released ferulate (≈3.5 mg/100 g) esterified pectins. Antioxidants (caffeoylquinic acid, putrescine and spermidine derivatives, ß-carotene, lutein) gave additional technological value to their thickening effect as pectins protected tryptophan, tyrosine, alkyl side chains and sulfhydryl of skim milk proteins from UV-C photo-oxidation.

Characterization and bioavailability of a novel coenzyme Q10 nanoemulsion used as an infant formula supplement.

Supplementation with Coenzyme Q10 (CoQ10), in patients with its deficiency, has greater odds of success if the treatment is carried out early with an appropriate formulation. For neonatal CoQ10 deficiency, infant formula supplementation could be an attractive option. However, solid CoQ10 cannot be solubilized or dispersed in milk matrix leading to an inefficient CoQ10 dosage and poor intestinal absorption. We developed and characterized a high-dose CoQ10 oil-in-water (O/W) nanoemulsion suitable to supplement infant formula without modifying its organoleptic characteristics. CoQ10 powder and soy lecithin were solubilized in an oil phase consisted of Labrasol® and LabrafacTM. The aqueous phase was Tween 80, TPGS, methylparaben and propylparaben. O/W nanoemulsion was prepared by adding dropwise the oil phase to the aqueous phase under stirring to a final concentration of CoQ10 9.5 % w/w followed by ultrasonic homogenization. Pharmacotechnical parameters were determined. This formulation resulted to be easily to be dispersed in milk matrix, stable for at least 90 days, with no cytotoxicity in in vitro assays, and higher bioavailability than CoQ10 powder. CoQ10 nanoemulsion supplementation in the infant formula facilitates the individualized administration for the child with accurate dosage, overcome swallowing difficulties and in turn could increase the treatment adherence and efficacy.

The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities.

The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. We identify four distinct homodimerization interfaces on the GR-LBD surface, which can associate into 20 topologically different homodimers. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution, quantitative fluorescence microscopy in living cells, and transcriptomic analyses. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work illustrates the unique flexibility of GR's LBD and suggests different dimeric conformations within cells. In addition, we unveil pathophysiologically relevant quaternary assemblies of the receptor with important implications for glucocorticoid action and drug design.

CT-based pathological lung opacities volume as a predictor of critical illness and inflammatory response severity in patients with COVID-19.

Objective: The aim of the study was to assess the impact of CT-based lung pathological opacities volume on critical illness and inflammatory response severity of patients with COVID-19. Methods: A retrospective, single center, single arm study was performed over a 30-day period. In total, 138 patients (85.2%) met inclusion criteria. All patients were evaluated with non-contrast enhanced chest CT scan at hospital admission. CT-based lung segmentation was performed to calculate pathological lung opacities volume (LOV). At baseline, complete blood count (CBC) and inflammation response biomarkers were obtained. The primary endpoint of the study was the occurrence of critical illness, as defined as, the need of mechanical ventilation and/or ICU admission. Mann-Whitney U test was performed for univariate analysis. Logistic regression analysis was performed to determine independent predictors of critical illness. Spearman analysis was performed to assess the correlation between inflammatory response biomarkers serum concentrations and LOV. Results: Median LOV was 28.64% (interquartile range [IQR], 6.33-47.22%). Correlation analysis demonstrated that LOV was correlated with higher levels of D-dimer (r = 0.51, p < 0.01), procalcitonin (r = 0.47, p < 0.01) and IL6 (r = 0.48, p < 0.01). Critical illness occurred in 51 patients (37%). Univariate analysis demonstrated that inflammatory response biomarkers and LOV were associated with critical illness (p < 0.05). However, multivariate analysis demonstrated that only D-dimer and LOV were independent predictors of critical illness. Furthermore, a ROC analysis demonstrated that a LOV equal or greater than 60% had a sensitivity of 82.1% and specificity of 70.2% to determine critical illness with an odds ratio of 19.4 (95% CI, 4.2-88.9). Conclusion: Critical illness may occur in up to 37% of the patients with COVID-19. Among patients with critical illness, higher levels of inflammatory response biomarkers with larger LOVs were observed. Furthermore, multivariate analysis demonstrated that pathological lung opacities volume was an independent predictor of critical illness. In fact, patients with a pathological lung opacities volume equal or greater than 60% had 19.4-fold increased risk of critical illness.