Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors.

Allosteric regulation plays a crucial role in modulating protein functions and represents a promising strategy in drug development, offering enhanced specificity and reduced toxicity compared to traditional active site inhibition. Existing computational methods for predicting allosteric sites on proteins often rely on static protein surface pocket features, normal mode analysis or extensive molecular dynamics simulations encompassing both the protein function modulator and the protein itself. In this study, we introduce an innovative methodology that employs a per amino acid residue classifier to distinguish allosteric site-forming residues (AFRs) from non-allosteric, or free residues (FRs).

Calcium phosphate and titanium cranioplasty after total angular craniopagus separation.

Craniopagus separation requires careful planning and a multi-staged surgical approach, managed by a multidisciplinary team. Despite growing experience on surgical management, the long-term restoration of the cranial defect has been rarely discussed so far. Several alloplastic materials have been proposed as effective and safe solutions for cranioplasty even for pediatric patients, allowing for bone generation, good aesthetic results, and low complication rates.

Vertical Hemispherotomy: Contribution of Advanced Three-Dimensional Modeling for Presurgical Planning and Training.

Vertical hemispherotomy is an effective treatment for many drug-resistant encephalopathies with unilateral involvement. One of the main factors influencing positive surgical results and long-term seizure freedom is the quality of disconnection. For this reason, perfect anatomical awareness is mandatory during each step of the procedure.

Combining 3-Dimensional Electroanatomic Mapping and Cardiac Magnetic Resonance: A New Tool for Arrhythmogenic Cardiomyopathy.

We present the case of a 17-year-old asymptomatic boy with a diagnosis of arrhythmogenic cardiomyopathy. Merging of cardiac magnetic resonance imaging and three-dimensional electroanatomic mapping provided striking visualization of the association between structural and electrical alterations and guided the decision to implant an implantable cardioverter defibrillator. ().

3D bioprinting in airway reconstructive surgery: A pilot study.

Objectives: Open surgery is a reliable choice for congenital subglottic stenosis, that represents the third most common congenital anomaly of the larynx. One of the procedures performed is anterior laryngotracheal reconstruction (LTR) with anterior rib graft. The objective of this preliminary study was to evaluate the potential of 3D printing technology for the realization of laryngo-tracheal scaffold in Polycaprolactone (PCL) implanted in vivo in ovine animal model.

The Modern Surgical Approach to Pulmonary Atresia with Ventricular Septal Defect and Major Aortopulmonary Collateral Arteries.

Pulmonary atresia with ventricular septal defect and major aortopulmonary collaterals is a complex congenital heart defect that includes a heterogeneous subgroup of patients. Variation in the sources of pulmonary blood flow contributes to the complexity of the lesion and the diversity of approaches to its management. Unifocalization and rehabilitation focus on mobilization of collateral arteries and growth of native pulmonary arteries, respectively, with the ultimate surgical goal of achieving separated systemic and pulmonary circulations with the lowest possible right ventricular pressure.

A Simple Method to Quantify Outward Leakage of Medical Face Masks and Barrier Face Coverings: Implication for the Overall Filtration Efficiency.

Face masking proved essential to reduce transmission of COVID-19 and other respiratory infections in indoor environments, but standards and literature do not provide simple quantitative methods for quantifying air leakage at the face seal. This study reports an original method to quantify outward leakage and how wearing style impacts on leaks and filtration efficiency. The amount of air leakage was evaluated on four medical masks and four barrier face coverings, exploiting a theoretical model and an instrumented dummy head in a range of airflows between 30 and 160 L/min.

Reusability of P3 Facial Filter in a Pandemic Emergency: A 3D Analysis of Filter Microstructure with X-ray Microtomography Images after Dry Heat and UV Sterilization Procedures.

Objective: Our goal is to evaluate the effects of heat and ultraviolet (UV) irradiation on P3 facial respirator microstructure.

Intervention: P3 facial filters were exposed to dry heat and UV sterilization procedures.

Methods: P3 facial filter samples underwent a standardized sterilization process based on dry heat and UV irradiation techniques.

Successful staged separation of total angular craniopagus.

Background: Total craniopagus is an exceedingly rare condition in which surgical treatment is complex and potentially fatal. Over the last decades, a multistep surgical approach, which allows development of venous collateral circulation, has fostered a dramatic improvement of successful separation rates and neurological outcomes. Most of the experience derives from management of vertical craniopagus, as the angular form is even less common and less amenable to successful surgical separation.

Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions.

Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions.

Bioprinting Technology in Skin, Heart, Pancreas and Cartilage Tissues: Progress and Challenges in Clinical Practice.

Bioprinting is an emerging additive manufacturing technique which shows an outstanding potential for shaping customized functional substitutes for tissue engineering. Its introduction into the clinical space in order to replace injured organs could ideally overcome the limitations faced with allografts. Presently, even though there have been years of prolific research in the field, there is a wide gap to bridge in order to bring bioprinting from "bench to bedside".

Strategies for Bone Regeneration: From Graft to Tissue Engineering.

Bone is a regenerative organ characterized by self-renewal ability. Indeed, it is a very dynamic tissue subjected to continuous remodeling in order to preserve its structure and function. However, in clinical practice, impaired bone healing can be observed in patients and medical intervention is needed to regenerate the tissue via the use of natural bone grafts or synthetic bone grafts.

A comparison between internal protein nanoenvironments of α-helices and β-sheets.

Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more β-sheets than α helices found inside the protein structures. For example, considering the PDB, DSSP and Stride definitions for secondary structure elements and by using the consensus among those, we found 60,727 helices in 4,376 chains identified in all-α structures and 129,440 helices in 7,898 chains identified in all-α and α + β structures.

Advanced 3D "Modeling" and "Printing" for the Surgical Planning of a Successful Case of Thoraco-Omphalopagus Conjoined Twins Separation.

Background: The surgical separation of two Conjoined Twins is a particularly complex operation. Surgical times are particularly long and post-operative complications are very frequent in this type of procedure. We report a clinical case of surgical separation of two thoraco-omphalopagus conjoined twins in which, thanks to the use of (3D) three dimensional technologies, we were able to significantly reduce operative times and improve clinical outcomes.

Multiparametric Imaging for Presurgical Planning of Craniopagus Twins: The Experience of Two Tertiary Pediatric Hospitals with Six Sets of Twins.

Conjoined twins are rare and pose a challenge to radiologists and surgeons. Craniopagus twins, where conjunction involves the cranium, are especially rare. Even in large pediatric centers, radiologists are unlikely to encounter more than one such event in their medical careers.

The role of air conditioning in the diffusion of Sars-CoV-2 in indoor environments: A first computational fluid dynamic model, based on investigations performed at the Vatican State Children's hospital.

Background: About 15 million people worldwide were affected by the Sars-Cov-2 infection, which already caused 600,000 deaths. This virus is mainly transmitted through exhalations from the airways of infected persons, so that Heating, Ventilation and Air Conditioning (HVAC) systems might play a role in increasing or reducing the spreading of the infection in indoor environments.

Methods: We modeled the role of HVAC systems in the diffusion of the contagion through Computational Fluid Dynamics (CFD) simulations of cough at the "Bambino Gesù" Vatican State Children's Hospital.

Quantitative Assessment of Parenchymal Involvement Using 3D Lung Model in Adolescent With Covid-19 Interstitial Pneumonia.

Amount of parenchymal involvement in patients with interstitial pneumonia Covid-19 related, seems to be associated with a worse prognosis. Nowadays 3D reconstruction imaging is expanding its role in clinical medical practice. We aimed to use 3D lung reconstruction of a young lady affected by Sars-CoV2 infection and interstitial pneumonia, to better visualize, and quantitatively assess the parenchymal involvement.

Anomalous aortic origin of the pulmonary arteries: Case series and literature review.

Anomalous origin of the pulmonary arteries from the ascending aorta is a rare, but severe clinical entity necessitating a scrupulous evaluation. Either the right or the left pulmonary arteries can arise directly from the ascending aorta while the other pulmonary artery retains its origin from the right ventricular outflow tract. Such a finding can be isolated or can coexist with several congenital heart lesions.

Study of specific nanoenvironments containing α-helices in all-α and (α+β)+(α/β) proteins.

Protein secondary structure elements (PSSEs) such as α-helices, β-strands, and turns are the primary building blocks of the tertiary protein structure. Our primary interest here is to reveal the characteristics of the nanoenvironment formed by both PSSEs and their surrounding amino acid residues (AARs), which might contribute to the general understanding of how proteins fold. The characteristics of such nanoenvironments must be specific to each secondary structure element, and we have set our goal here to gather the fullest possible description of the α-helical nanoenvironment.

Citrus bioflavonoid, hesperetin, as inhibitor of two thrombin-like snake venom serine proteases isolated from Crotalus simus.

Around 5.5 million people suffer from snakebites per year, with about 400,000 cases with some type of sequelae, such as amputation, and 20,000 to 125,000 cases with the fatal end. Usually, the victim outcome depends on correct, agile and many times in situ intervention based on the proper identification of the snake venom type and its potential effects, among other factors.

Discovery of small molecule inhibitors for the snake venom metalloprotease BaP1 using in silico and in vitro tests.

Snakebites represent an important public health problem, with a great number of victims with permanent sequelae or fatal outcomes, particularly in rural, agriculturally active areas. The snake venom metalloproteases (SVMPs) are the principal proteins responsible for some clinically-relevant effects, such as local and systemic hemorrhage, dermonecrosis, and myonecrosis. Because of the difficulties in neutralizing them rapidly and locally by antivenoms, the search and design of small molecules as inhibitors of SVMPs are proposed.

Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.

Motivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a web-based tool called multiple structure single parameter (MSSP) was developed and here presented.

Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design.

The term "agrochemicals" is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A "drug" on the other side is a term that is used for compounds designed for controlling human diseases.

Microscopic investigation of the use of gallium nitrate for root surface treatment in rat teeth submitted to delayed replantation.

The aim of this study was to investigate the effect of gallium nitrate solution, an anti-resorption substance, when applied for root surface treatment in rat teeth submitted to delayed replantation, in order to inhibit the root resorption process and enhance repair. For such purpose, 20 maxillary right central incisors of rats were randomly assigned to 2 groups (n=10). In group I, root surface was treated with 10-4M gallium nitrate solution for 20 min, while in group II root surface was treated with 2% sodium fluoride for 20 min.