Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign.

Enzymes exhibit diverse conformations, as represented in the free energy landscape (FEL). Such conformational diversity provides enzymes with the ability to evolve towards novel functions. The challenge lies in identifying mutations that enhance specific conformational changes, especially if located in distal sites from the active site cavity. The shortest path map (SPM) method, which we developed to address this challenge, constructs a graph based on the distances and correlated motions of residues observed in nanosecond timescale molecular dynamics (MD) simulations. We recently introduced a template based AlphaFold2 (tAF2) approach coupled with 10 nanosecond MD simulations to quickly estimate the conformational landscape of enzymes and assess how the FEL is shifted after mutation. In this study, we evaluate the potential of SPM when coupled with tAF2-MD in estimating conformational heterogeneity and identifying key conformationally-relevant positions. The selected model system is the beta subunit of tryptophan synthase (TrpB). We compare how the SPM pathways differ when integrating tAF2 with different MD simulation lengths from as short as 10 ns until 50 ns and considering two distinct Amber forcefield and water models (ff14SB/TIP3P versus ff19SB/OPC). The new methodology can more effectively capture the distal mutations found in laboratory evolution, thus showcasing the efficacy of tAF2-MD-SPM in rapidly estimating enzyme dynamics and identifying the key conformationally relevant hotspots for computational enzyme engineering.

Remote Monitoring and Data Collection for Decentralized Clinical Trials.

Importance: Less than 5% of patients with cancer enroll in a clinical trial, partly due to financial and logistic burdens, especially among underserved populations. The COVID-19 pandemic marked a substantial shift in the adoption of decentralized trial operations by pharmaceutical companies. Objective: To assess the current global state of adoption of decentralized trial technologies, understand factors that may be driving or preventing adoption, and highlight aspirations and direction for industry to enable more patient-centric trials. Design, Setting, and Participants: The Bloomberg New Economy International Cancer Coalition, composed of patient advocacy, industry, government regulator, and academic medical center representatives, developed a survey directed to global biopharmaceutical companies of the coalition from October 1 through December 31, 2022, with a focus on registrational clinical trials. The data for this survey study were analyzed between January 1 and 31, 2023. Exposure: Adoption of decentralized clinical trial technologies. Main Outcomes and Measures: The survey measured (1) outcomes of different remote monitoring and data collection technologies on patient centricity, (2) adoption of these technologies in oncology and all therapeutic areas, and (3) barriers and facilitators to adoption using descriptive statistics. Results: All 8 invited coalition companies completed the survey, representing 33% of the oncology market by revenues in 2021. Across nearly all technologies, adoption in oncology trials lags that of all trials. In the current state, electronic diaries and electronic clinical outcome assessments are the most used technology, with a mean (SD) of 56% (19%) and 51% (29%) adoption for all trials and oncology trials, respectively, whereas visits within local physician networks is the least adopted at a mean (SD) of 12% (18%) and 7% (9%), respectively. Looking forward, the difference between the current and aspired adoption rate in 5 years for oncology is large, with respondents expecting a 40% or greater absolute adoption increase in 8 of the 11 technologies surveyed. Furthermore, digitally enabled recruitment, local imaging capabilities, and local physician networks were identified as technologies that could be most effective for improving patient centricity in the long term. Conclusions and Relevance: These findings may help to galvanize momentum toward greater adoption of enabling technologies to support a new paradigm of trials that are more accessible, less burdensome, and more inclusive.

The shortest path method (SPM) webserver for computational enzyme design.

SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.

AlphaFold2 and Deep Learning for Elucidating Enzyme Conformational Flexibility and Its Application for Design.

The recent success of AlphaFold2 (AF2) and other deep learning (DL) tools in accurately predicting the folded three-dimensional (3D) structure of proteins and enzymes has revolutionized the structural biology and protein design fields. The 3D structure indeed reveals key information on the arrangement of the catalytic machinery of enzymes and which structural elements gate the active site pocket. However, comprehending enzymatic activity requires a detailed knowledge of the chemical steps involved along the catalytic cycle and the exploration of the multiple thermally accessible conformations that enzymes adopt when in solution. In this Perspective, some of the recent studies showing the potential of AF2 in elucidating the conformational landscape of enzymes are provided. Selected examples of the key developments of AF2-based and DL methods for protein design are discussed, as well as a few enzyme design cases. These studies show the potential of AF2 and DL for allowing the routine computational design of efficient enzymes.

Estimating conformational heterogeneity of tryptophan synthase with a template-based Alphafold2 approach.

The three-dimensional structure of the enzymes provides very relevant information on the arrangement of the catalytic machinery and structural elements gating the active site pocket. The recent success of the neural network Alphafold2 in predicting the folded structure of proteins from the primary sequence with high levels of accuracy has revolutionized the protein design field. However, the application of Alphafold2 for understanding and engineering function directly from the obtained single static picture is not straightforward. Indeed, understanding enzymatic function requires the exploration of the ensemble of thermally accessible conformations that enzymes adopt in solution. In the present study, we evaluate the potential of Alphafold2 in assessing the effect of the mutations on the conformational landscape of the beta subunit of tryptophan synthase (TrpB). Specifically, we develop a template-based Alphafold2 approach for estimating the conformational heterogeneity of several TrpB enzymes, which is needed for enhanced stand-alone activity. Our results show the potential of Alphafold2, especially if combined with molecular dynamics simulations, for elucidating the changes induced by mutation in the conformational landscapes at a rather reduced computational cost, thus revealing its plausible application in computational enzyme design.

Rotura de aquiles y fractura cerrada de maleolo tibial concomitante / Concommitant achilles tendon rupture and medial malleolus closed fracture

Objetivo: Se presentan dos nuevos casos de rotura de Aquiles y fractura cerrada de maléolo tibial y se realiza una revisión la bibliográfica de dicha lesión. Material y métodos: La asociación de rotura de tendón de Aquiles y fractura del maléolo tibial en un mismo paciente es una entidad muy poco frecuente y con pocas referencias bibliográficas y hasta donde los autores conocen no hay ninguna referencia en Castellano. En muchos de los casos una de las dos lesiones puede pasar desapercibidas inicialmente, produciendo un aumento de morbilidad. Solo se han descrito 9 casos clínicos aislados en revistas de habla inglesa y en 6 casos una de las lesiones paso desapercibida inicialmente. Se presentan 2 casos de rotura de tendón de Aquiles con fractura de maléolo tibial asociado. Resultados: En los dos casos presentados se diagnosticaron inicialmente ambas lesiones, el tendón de Aquiles se trató con sutura abierta, y los maléolos tibiales mediante tratamiento conservador al ser estables bajo radioscopia. Conclusiones: La correcta identificación de ambas lesiones, su correcto tratamiento y la ausencia de complicaciones postoperatorias condujo a un buen resultado final en ambos pacientes.(AU)

Objective: Two new cases of Achilles rupture and closed tibial malleolus fracture are presented and a bibliographic review of that injury is carried out.Material and methods: The association of Achilles tendon rupture and tibial malleolus fracture in the same patient is a rare entity with few bibliographic references and as far as the authors know there are no references in Spanish. In many cases, one of the two lesions may initially go unnoticed, leading to increased morbidity. Only 9 isolated clinical cases have been described in English-language journals and in 6 cases one of the two lesions went unnoticed initially. Two cases of Achilles tendon rupture with associated tibial malleolus fracture are presented. Results: In the two cases presented, both lesions were initially diagnosed, the Achilles tendon was treated with an open suture, and the tibial malleoli fractures by conservative treatment as they were stable under fluoroscopy. Conclusions: The correct identification of both lesions, their correct treatment and the absence of postoperative complications led to a good final result in both patients.(AU)

Correlation Between Early Endpoints and Overall Survival in Non-Small-Cell Lung Cancer: A Trial-Level Meta-Analysis.

Early endpoints, such as progression-free survival (PFS), are increasingly used as surrogates for overall survival (OS) to accelerate approval of novel oncology agents. Compiling trial-level data from randomized controlled trials (RCTs) could help to develop a predictive framework to ascertain correlation trends between treatment effects for early and late endpoints. Through trial-level correlation and random-effects meta-regression analysis, we assessed the relationship between hazard ratio (HR) OS and (1) HR PFS and (2) odds ratio (OR) PFS at 4 and 6 months, stratified according to the mechanism of action of the investigational product. Using multiple source databases, we compiled a data set including 81 phase II-IV RCTs (35 drugs and 156 observations) of patients with non-small-cell lung cancer. Low-to-moderate correlations were generally observed between treatment effects for early endpoints (based on PFS) and HR OS across trials of agents with different mechanisms of action. Moderate correlations were seen between treatment effects for HR PFS and HR OS across all trials, and in the programmed cell death-1/programmed cell death ligand-1 and epidermal growth factor receptor trial subsets. Although these results constitute an important step, caution is advised, as there are some limitations to our evaluation, and an additional patient-level analysis would be needed to establish true surrogacy.

Health-related quality of life in nonvalvular atrial fibrillation patients with controlled or uncontrolled anticoagulation status.

BACKGROUND: There is a dearth of evidence regarding Health-Related Quality of Life (HRQoL) in nonvalvular atrial fibrillation (NVAF) patients undergoing oral anticoagulation therapy. Our objective was to describe HRQoL in NVAF patients on oral anticoagulation, focusing on uncontrolled patients on vitamin K antagonists (VKAs) versus controlled patients on VKAs or non-vitamin K antagonist oral anticoagulants (NOACs), in a real-world setting. Additionally, we assessed the clinical characteristics of patients with uncontrolled anticoagulation. METHODS: An observational, multicentre, and cross-sectional study, enrolling 38 Spanish Hospitals' Internal Medicine Departments. HRQoL was assessed using the validated Spanish version of the Sawicki questionnaire. High self-perceived HRQoL was indicated by high scores in the general treatment satisfaction and self-efficacy dimensions, and by low scores in the strained social network, daily hassles and distress dimensions. RESULTS: Five hundred and one patients were included for assessment. Mean scores ± SD were closer to a high perceived HRQoL in controlled than uncontrolled patients for the five dimensions of the questionnaire: 4.9 ± 1.0 versus 3.6 ± 1.3 for general treatment satisfaction; 4.3 ± 1.0 versus 3.6 ± 1.0 for self-efficacy, 3.1 ± 0.9 versus 3.9 ± 1.1 for strained social network, 2.1 ± 0.8 versus 3.0 ± 1.0 for daily hassles and 1.8 ± 0.9 versus 2.6 ± 1.2 for distress. CONCLUSIONS: HRQoL in patients with controlled anticoagulant status treated with NOACs or VKAs was better than in patients with uncontrolled anticoagulant status. This seems to indicate that anticoagulation control status influences perception of HRQoL, highlighting the importance of its evaluation when assessing HRQoL in NVAF patients.

Three-layered repair with a collagen membrane and a mucosal rotational flap reinforced with fibrine for palatal fistula closure in children.

The incidence of postoperative fistula following primary cleft palate repair ranges from 0% to 58%. The reported recurrence rate is between 33% and 37%, and the prognosis of a successful closure declines with each reoperation. Closure of palatal fistulas can be achieved by different techniques depending on its size and the experience of the surgeon. Local, regional and distant flaps are commonly used. Alternatively, or in addition to the previous ones, synthetic materials are becoming very popular nowadays. However, a scarcity of articles explains in detail a simple and effective method in children. We present a case report and the procedure proposed by our pediatric surgery team consisting of a three-layered repair, with a collagen membrane placed over the reconstructed nasal mucosa, and a rotational palatal mucosa flap reinforced with a fibrine sealant. This method is simple, easy to reproduce, effective and has a low rate of complications.

Interactive Effect of UVR and Phosphorus on the Coastal Phytoplankton Community of the Western Mediterranean Sea: Unravelling Eco-Physiological Mechanisms.

Some of the most important effects of global change on coastal marine systems include increasing nutrient inputs and higher levels of ultraviolet radiation (UVR, 280-400 nm), which could affect primary producers, a key trophic link to the functioning of marine food webs. However, interactive effects of both factors on the phytoplankton community have not been assessed for the Mediterranean Sea. An in situ factorial experiment, with two levels of ultraviolet solar radiation (UVR+PAR vs. PAR) and nutrients (control vs. P-enriched), was performed to evaluate single and UVR×P effects on metabolic, enzymatic, stoichiometric and structural phytoplanktonic variables. While most phytoplankton variables were not affected by UVR, dissolved phosphatase (APAEX) and algal P content increased in the presence of UVR, which was interpreted as an acclimation mechanism of algae to oligotrophic marine waters. Synergistic UVR×P interactive effects were positive on photosynthetic variables (i.e., maximal electron transport rate, ETRmax), but negative on primary production and phytoplankton biomass because the pulse of P unmasked the inhibitory effect of UVR. This unmasking effect might be related to greater photodamage caused by an excess of electron flux after a P pulse (higher ETRmax) without an efficient release of carbon as the mechanism to dissipate the reducing power of photosynthetic electron transport.

Síndrome papulopurpúrico en guante y calcetín y trombocitopenia en relación con infección por parvovirus B19 / Papular-purpuric gloves and socks syndrome and thrombocytopenia related to parvovirus B19 infection

No disponible

Tumores carcinoides gástricos: análisis de 24 casos / Gastric carcinoid tumors: an analysis of 24 cases

No disponible

Pancreatic endocrine tumors or apudomas.

INTRODUCTION AND OBJECTIVE: pancreatic endocrine tumors (PET) are difficult to diagnose. Their accurate localization using imaging techniques is intended to provide a definite cure. The goal of this retrospective study was to review a PET series from a private institution. PATIENTS AND METHODS: the medical records of 19 patients with PETs were reviewed, including 4 cases of MEN-1, for a period of 17 years (1994-2010). A database was set up with ten parameters: age, sex, symptoms, imaging techniques, size and location in the pancreas, metastasis, surgery, complications, adjuvant therapies, definite diagnosis, and survival or death. RESULTS: a total of 19 cases were analyzed. Mean age at presentation was 51 years (range: 26-67 y) (14 males, 5 females), and tumor size was 5 to 80 mm (X: 20 mm). Metastatic disease was present in 37% (7/19). Most underwent the following imaging techniques: ultrasounds, computed tomography (CT) an magnetic resonance imaging (MRI). Fine needle aspiration punction (FNA) was performed for the primary tumor in 4 cases. Non-functioning: 7 cases (37%), insulinoma: 2 cases [1 with possible multiple endocrine neoplasia (MEN)], Zollinger-Ellison syndrome (ZES) from gastrinoma: 5 (3 with MEN-1), glucagonoma: 2 cases, 2 somatostatinomas; carcinoid: 1 case with carcinoide-like syndrome. Most patients were operated upon: 14/19 (73%). Four (4/14:28%) has postoperative complications following pancreatectomy: pancreatitis, pseudocyst, and abdominal collections. Some patients received chemotherapy (4), somatostatin (3) and interferon (2) before or after surgery. Median follow-up was 48 months. Actuarial survival during the study was 73.6% (14/19). CONCLUSIONS: age was similar to that described in the literature. Males were predominant. Most cases were non-functioning (37%). Most patients underwent surgery (73%) with little morbidity (28%) and an actuarial survival of 73.6% at the time of the study.

Tumores endocrinos o apudomas pancreáticos / Pancreatic endocrine tumors or apudomas

Introducción y objetivo: los tumores endocrinos pancreáticos (TEP) son difíciles de diagnosticar. Su localización exacta mediante métodos de imagen tiene el propósito de lograr una curación definitiva. El objetivo de este trabajo retrospectivo fue revisar una serie institucional privada de TEP. Pacientes y métodos: se revisaron las historias clínicas de 19 pacientes con TEP, 4 casos con NEM-1, observados durante 17 años (1994-2010). Se creó una base de datos con diez parámetros: edad y sexo, síntomas, métodos diagnósticos de imagen, tamaño y situación en el páncreas, metástasis, cirugía, complicaciones, tratamientos complementarios, diagnóstico definitivo, supervivencia o éxitus. Resultados: en total se analizaron 19 casos. La edad media de presentación fue 51 años (intervalo: 26-67 años) (14 varones y 5 mujeres), con un tamaño del tumor de 5 a 80 mm (X: 20 mm). El 37% (7/19) tenían metástasis. En la mayoría se practicaron los siguientes métodos de imagen: ecografía, TAC y RM. La PAAF del tumor primitivo se practicó en 4 casos. No funcionantes: 7 casos (37%), insulinomas: 2 casos (1 con posible NEM), SZE por gastrinomas: 5 (3 con NEM-1), glucagonoma: 2 casos, 2 somatostatinomas, carcinoide: 1 caso con síndrome carcinoide-like. La mayoría de los enfermos fueron intervenidos quirúrgicamente 14/19 (73%). En cuatro (4/14: 28%) pacientes hubo complicaciones postoperatorias después de pancreatectomías: páncreas, seudoquiste y colecciones abdominales. Algunos casos fueron tratados con quimioterapia (4), somatostatina (3) e interferón (2) antes o después de la cirugía. La mediana de seguimiento fue de 48 meses. La supervivencia actuarial en el momento del estudio fue del 73,6% (14/19). Conclusiones: la edad fue similar a lo descrito en la literatura. El sexo predominante fue el masculino. La mayoría fueron no funcionantes (37%). La mayoría fueron intervenidos quirúrgicamente (73%), con escasa morbilidad (28%) y con una supervivencia actuarial en el momento de cerrar el estudio del 73,6%(AU)

Introduction and objective: pancreatic endocrine tumors (PET) are difficult to diagnose. Their accurate localization using imaging techniques is intended to provide a definite cure. The goal of this retrospective study was to review a PET series from a private institution. Patients and methods: the medical records of 19 patients with PETs were reviewed, including 4 cases of MEN-1, for a period of 17 years (1994-2010). A database was set up with ten parameters: age, sex, symptoms, imaging techniques, size and location in the pancreas, metastasis, surgery, complications, adjuvant therapies, definite diagnosis, and survival or death. Results: a total of 19 cases were analyzed. Mean age at presentation was 51 years (range: 26-67 y) (14 males, 5 females), and tumor size was 5 to 80 mm (X: 20 mm). Metastatic disease was present in 37% (7/19). Most underwent the following imaging techniques: ultrasounds, computed tomography (CT) and magnetic resonance imaging (MRI). Fine needle aspiration punction (FNA) was performed for the primary tumor in 4 cases. Nonfunctioning: 7 cases (37%), insulinoma: 2 cases [1 with possible multiple endocrine neoplasia (MEN)], Zollinger-Ellison syndrome (ZES) from gastrinoma: 5 (3 with MEN-1), glucagonoma: 2 cases, 2 somatostatinomas; carcinoid: 1 case with carcinoide-like syndrome. Most patients were operated upon: 14/19 (73%). Four (4/14: 28%) has postoperative complications following pancreatectomy: pancreatitis, pseudocyst, and abdominal collections. Some patients received chemotherapy (4), somatostatin (3) and interferon (2) before or after surgery. Median follow-up was 48 months. Actuarial survival during the study was 73.6% (14/19). Conclusions: age was similar to that described in the literature. Males were predominant. Most cases were non-functioning (37%). Most patients underwent surgery (73%) with little morbidity (28%) and an actuarial survival of 73.6% at the time of the study(AU)

Experiencia con la utilización del ócido nitroso en procesos dolorosos en urgencias / Experience with the use of nitrous oxide in painful procedures in the emergency department

Fundamento. El óxido nitroso (N2O) es un gas con efecto analgésico, ansiolítico y amnésico que se utiliza mezclado con 50% de oxígeno en técnicas diagnóstico-terapéuticas que provocan dolor y/o ansiedad. Objetivo. 1) Evaluar la efectividad del N2O en procedimientos dolorosos realizados en urgencias. 2) Describir los efectos secundarios detectados. Método. Estudio prospectivo descriptivo de una serie de casos recogidos desde el 1/05/08 al 31/12/08 en los cuales se utilizó N2O. Resultados. Se recogieron 74 casos, 48 (64%) de ellos eran del sexo masculino, siendo la mediana de edad de 7,5 años. Fue utilizado en los siguientes procedimientos: punciones lumbares (33; 45%), reducción de fracturas (16; 22%), venopunciones (10; 13%), drenaje de abscesos (9; 12%) y sutura de heridas (6; 8%). En 60 casos (81%) se asoció con analgesia local, en 11 (15%) con analgesia sistémica y en 3 (4%) se utilizó el N2O como único analgésico. La efectividad se valoró según el análisis de la conducta del paciente durante el procedimiento; se clasificó cualitativamente como mala en 4 casos (5%), aceptable en 16 (22%) y buena o muy buena en 54 (73%). Cabe decir que los casos valorados como malos o aceptables se trataban de procedimientos muy dolorosos. La valoración del efecto analgésico por parte del equipo médico fue muy satisfactoria en 60 casos (81%). Se constataron efectos secundarios en 10 casos (13,5%): mareo (3), vómitos (2), ansiedad (2), euforia (2) y cefalea (1). En todos los casos estos efectos se resolvieron en pocos minutos. Conclusiones. 1) Según nuestra experiencia, el N2O es un método analgésico y ansiolítico coadyuvante efectivo en muchos procedimientos dolorosos realizados en urgencias pediátricas. 2) Los efectos secundarios en nuestra serie son leves. 3) El equipo médico está muy satisfecho, aunque se deben consensuar las indicaciones para optimizar su uso(AU)

Background. Nitrous oxide (N2O) is a gas with analgesic, ansiolytic and amnesic effect. 50% nitrous oxide oxygen mixture is used in procedures that cause pain or anxiety. Objective. 1) To evaluate the efficacy of N2O in painful procedures in a pediatric emergency department. 2) To determine the adverse effects of this treatment. Method. Prospective descriptive study from May 2008 to December 2008. Results. 74 cases were analyzed; 48 (64%) were male and the median age was 7.5 years. The procedures performed with N2O inhalation were: lumbar punctures (33; 45%), reduction of fractures (16; 22%), venipunctures (10; 13%), abscess drainage (9; 12%) and laceration repairs (6; 8%). Local analgesia was given in 60 (81%) cases; systemic analgesia in 11 (15%) and N2O alone in 3 (4%). A behavioral scale was used to evaluate efficacy; it was bad in 4 cases (5%), acceptable in 16 (22%) and good or very good in 54 (73%). All cases assessed as bad o acceptable were very painful procedures. Medical staff was very satisfied with the sedation effect in 60 cases (81%). Adverse effects were observed in 10 cases (13.5%): dizziness (3), emesis (2), anxiety (2), euphoria (2) and headache (1). All these side effects resolved in a few minutes. Conclusions. 1) In our experience, the N2O is an effective analgesic and ansiolytic coadjuvant method to provide analgesia in a variety of procedures; 2) Side effects are infrequent and minor; 3) Medical staff was very satisfied; however, it is necessary to define specific indications for an optimum use(AU)