Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease.

Alkaptonuria (AKU, OMIM: 203500) is an autosomal recessive disorder caused by mutations in the Homogentisate 1,2-dioxygenase (HGD) gene. A lack of standardized data, information and methodologies to assess disease severity and progression represents a common complication in ultra-rare disorders like AKU. This is the reason why we developed a comprehensive tool, called ApreciseKUre, able to collect AKU patients deriving data, to analyse the complex network among genotypic and phenotypic information and to get new insight in such multi-systemic disease. By taking advantage of the dataset, containing the highest number of AKU patient ever considered, it is possible to apply more sophisticated computational methods (such as machine learning) to achieve a first AKU patient stratification based on phenotypic and genotypic data in a typical precision medicine perspective. Thanks to our sufficiently populated and organized dataset, it is possible, for the first time, to extensively explore the phenotype-genotype relationships unknown so far. This proof of principle study for rare diseases confirms the importance of a dedicated database, allowing data management and analysis and can be used to tailor treatments for every patient in a more effective way.

Early Steps in C-Type Inactivation of the hERG Potassium Channel.

Fast C-type inactivation confers distinctive functional properties to the hERG potassium channel, and its association to inherited and acquired cardiac arrythmias makes the study of the inactivation mechanism of hERG at the atomic detail of paramount importance. At present, two models have been proposed to describe C-type inactivation in K+-channels. Experimental data and computational work on the bacterial KcsA channel support the hypothesis that C-type inactivation results from a closure of the selectivity filter that sterically impedes ion conduction. Alternatively, recent experimental structures of a mutated Shaker channel revealed a widening of the extracellular portion of the selectivity filter, which might diminish conductance by interfering with the mechanism of ion permeation. Here, we performed molecular dynamics simulations of the wild-type hERG, a non-inactivating mutant (hERG-N629D), and a mutant that inactivates faster than the wild-type channel (hERG-F627Y) to find out which and if any of the two reported C-type inactivation mechanisms applies to hERG. Closure events of the selectivity filter were not observed in any of the simulated trajectories but instead, the extracellular section of the selectivity filter deviated from the canonical conductive structure of potassium channels. The degree of widening of the potassium binding sites at the extracellular entrance of the channel was directly related to the degree of inactivation with hERG-F627Y > wild-type hERG > hERG-N629D. These findings support the hypothesis that C-type inactivation in hERG entails a widening of the extracellular entrance of the channel rather than a closure of the selectivity filter.

Multi-Omics Model Applied to Cancer Genetics.

In this review, we focus on bioinformatic oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. Before providing a deeper insight into the bioinformatics approach and utilities involved in oncology, we must understand what is a system biology framework and the genetic connection, because of the high heterogenicity of the backgrounds of people approaching precision medicine. In fact, it is essential to providing general theoretical information on genomics, epigenomics, and transcriptomics to understand the phases of multi-omics approach. We consider how to create a multi-omics model. In the last section, we describe the new frontiers and future perspectives of this field.

Assessment of Psychopatologic Traits in a Group of Patients with Adult Chronic Periodontitis: Study on 108 Cases and Analysis of Compliance during and after Periodontal Treatment.

OBJECTIVES: Although there is nowadays wide agreement on bacteria being the main etiologic agents of periodontal disease, their sole presence cannot damage periodontal tissues in all subjects. This suggests that an individual response and an adaptation to a certain quantity of bacterial biofilm can occur without the disease progressing and vice versa. Depression, stress and anxiety have not been confirmed yet as risk conditions but, in some observational studies, they have been identified as potential risk factors of periodontal disease. The current study aims at investigating the role which these psychological disorder have in the onset and progression of advanced stage periodontitis. MATERIALS AND METHODS: The case selection was carried out by means of clinical and radiological periodontal assessment involving a total of 108 subjects, both male and female, aged between 24 and 67. Patients were then divided in two groups of 54 patients each: the first group included patients with severe periodontal disease, the second group was formed by periodontally healthy subjects. Clinical assessment was performed by a sole examiner who selected and divided periodontopathic patients from non-periodontopathic ones. From the current study were excluded: patients with systemic pathologies; smokers; patients taking antidepressant drugs; pregnant women. RESULTS: For what concerns depression, in the group of periodontopathic patients it was found that the 62.5% of them were depressed, against the 38.86% in the group of periodontally healthy subjects. For the other two psychological conditions taken into consideration, anxiety and stress, it emerged a different percentage of subjects with anxiety in the periodontal group (31.48%) against healthy controls (20.37%). CONCLUSIONS: For each of the psychological variables considered (depression, anxiety, stress), a significant correlation could be observed with periodontal disease, it can be therefore be suggested that the importance these disturbs have in the onset and progress of the dental disease which supports the existing available data in literature. The innovative aspect of this research was the focus on the assessment of compliance, monitoring the ability of periodontal patients to follow oral hygiene instructions aiming at the improving and keeping their own periodontal condition, even though this takes more time than the control group.

Electrophysiology, molecular modelling, and functional analysis of the effects of dietary quercetin and flavonoid analogues on Kir6.1 channels in rat stomach fundus smooth muscle.

Flavonoids, ubiquitously distributed in the plant world, are regularly ingested with diets rich in fruit, vegetables, wine, and tea. During digestion, they are partially absorbed in the stomach. The present work aimed to assess the in vitro effects of quercetin and ten structurally related flavonoids on the rat gastric fundus smooth muscle, focussing on ATP-dependent K+ (Kir6.1) channels, which play a central role in the regulation of resting membrane potential, membrane excitability and, consequently, of gastric motility. Whole-cell currents through Kir6.1 channels (IKir6.1) were recorded with the patch-clamp technique and the mechanical activity of gastric fundus smooth muscle strips was studied under isometric conditions. Galangin ≈ tamarixetin > quercetin > kaempferol > isorhamnetin ≈ luteolin ≈ fisetin > (±)-taxifolin inhibited pinacidil-evoked, glibenclamide-sensitive IKir6.1 in a concentration-dependent manner. Morin, rutin, and myricetin were ineffective. The steric hindrance of the molecule and the number and position of hydroxyl groups on the B ring played an important role in the activity of the molecule. Molecular docking simulations revealed a possible binding site for flavonoids in the C-terminal domain of the Kir6.1 channel subunit SUR2B, in a flexible loop formed by residues 251 to 254 of chains C and D. Galangin and tamarixetin, but not rutin relaxed both high K+- and carbachol-induced contraction of fundus strips in a concentration-dependent manner. Furthermore, both flavonoids shifted to the right the concentration-relaxation curves to either pinacidil or L-cysteine constructed in strips pre-contracted by high K+, rutin being ineffective. In conclusion, IKir6.1 inhibition exerted by dietary flavonoids might counterbalance their myorelaxant activity, affect gastric accommodation or, at least, some stages of digestion.

Medico-legal considerations in immediate loading implantology: risks, responsibilities, and best practices.

The field of immediate loading implantology has grown rapidly, offering quicker solutions for prosthetic rehabilitation. However, the complexity of this technique raises significant medico-legal concerns regarding patient safety, treatment planning, and professional liability. These issues are particularly relevant in elective procedures where failure could lead to litigation. A comprehensive review of current literature, including clinical studies, legal rulings, and malpractice claims, was conducted to assess the legal implications of immediate loading implantology. The analysis focused on professional liability, patient consent, and complications during treatment. The evidence indicates that a high standard of care, including detailed preoperative planning, risk assessment, and clear patient communication, is essential in minimizing legal risks. Malpractice claims often arise from inadequate patient information or failure to follow established protocols. Proper documentation of informed consent and adherence to evidence-based dentistry (EBD) guidelines are crucial to protect both patients and practitioners. Immediate loading implantology offers numerous benefits, but it requires meticulous planning and patient management to avoid medico-legal issues. Ensuring comprehensive patient consent and following evidence-based practices are key to reducing professional liability and improving outcomes. Further studies should explore standardized protocols for reducing complications and legal disputes in implantology.

HLA-DPB1*13:01 associates with enhanced, and KIR2DS4*001 with diminished protection from developing severe COVID-19.

Extreme polymorphism of HLA and killer-cell immunoglobulin-like receptors (KIR) differentiates immune responses across individuals. Additional to T cell receptor interactions, subsets of HLA class I act as ligands for inhibitory and activating KIR, allowing natural killer (NK) cells to detect and kill infected cells. We investigated the impact of HLA and KIR polymorphism on the severity of COVID-19. High resolution HLA class I and II and KIR genotypes were determined from 403 non-hospitalized and 1575 hospitalized SARS-CoV-2 infected patients from Italy collected in 2020. We observed that possession of the activating KIR2DS4*001 allotype is associated with severe disease, requiring hospitalization (OR = 1.48, 95% CI 1.20-1.85, pc = 0.017), and this effect is greater in individuals homozygous for KIR2DS4*001 (OR = 3.74, 95% CI 1.75-9.29, pc = 0.003). We also observed the HLA class II allotype, HLA-DPB1*13:01 protects SARS-CoV-2 infected patients from severe disease (OR = 0.49, 95% CI 0.33-0.74, pc = 0.019). These association analyses were replicated using logistic regression with sex and age as covariates. Autoantibodies against IFN-α associated with COVID-19 severity were detected in 26% of 156 hospitalized patients tested. HLA-C*08:02 was more frequent in patients with IFN-α autoantibodies than those without, and KIR3DL1*01502 was only present in patients lacking IFN-α antibodies. These findings suggest that KIR and HLA polymorphism is integral in determining the clinical outcome following SARS-CoV-2 infection, by influencing the course both of innate and adaptive immunity.

Temporomandibular disorders in burning mouth syndrome patients: an observational study.

BACKGROUND: Burning Mouth Syndrome (BMS) is a chronic disease characterized by absence of any lesions and burning of the oral mucosa associated to a sensation of dry mouth and/or taste alterations. The purpose of our study is to estimate signs and symptoms of Temporomandibular Disorders (TMD) in patients with BMS and to investigate for the existence of an association between BMS and TMD. MATERIALS AND METHODS: Forty-four BMS patients were enrolled; BMS subtype was established according to the classification of Lamey. After a gnathological evaluation, according to the protocol of the European Academy of Craniomandibular Disorders, patients were classified by RDC/TMD criteria. The data were compared and analyzed using a chi-square test to describe the existence of an association between BMS and TMD. RESULTS: 65.9% the BMS patients showed disorders classified as primary signs and symptoms of TMD according to RDC / TMD criteria, and 72.7% showed parafunctional habits. The chi-square test revealed a statistically significant association (p = 0.035) between BMS and TMD. CONCLUSION: The data suggest that there is a possible relationship not yet well understood between BMS and TMD, may be for neurophatic alterations assumed for BMS that could be also engaged in TMD pathogenesis.

Immunohistochemical evaluation of neuroreceptors in healthy and pathological temporo-mandibular joint.

AIM: A study was performed on the articular disk and periarticular tissues of the temporo-mandibular joint (TMJ) with immunohistochemical techniques to give evidence to the presence of neuroreceptors (NRec) in these sites. METHODS: The study was carried out on tissue samples obtained from 10 subjects without TMJ disease and from 7 patients with severe TMJ arthritis and arthrosis. We use antibodies directed against following antigens: Gliofibrillary Acidic Protein (GFAP), Leu-7, Myelin Basic Protein (MBP), Neurofilaments 68 kD (NF), Neuron Specific Enolase (NSE), S-100 protein (S-100) and Synaptophysin (SYN). RESULTS: This study revealed that Ruffini's-like, Pacini's-like and Golgi's-like receptors can be demonstrated in TMJ periarticular tissues and that free nervous endings are present in the subsynovial tissues but not within the articular disk. We observed elongated cytoplamic processes of chondrocytes that demonstrated strong S-100 immunoreactivity but they were unreactive with all other antibodies. These cytoplamic processes were more abundant and thicker in the samples obtained from patients with disease TMJ. CONCLUSION: The results of this study confirm that different Nrec are detectable in TMJ periarticular tissues but they are absent within the articular disk. In the latter site, only condrocytic processes are evident, especially in diseased TMJ, and they might have been confused with nervous endings in previous morphological studies. Nevertheless the absence of immunoreactivity for NF, NSE and SYN proves that they are not of neural origin.

Correlation between Diabetes Mellitus and Peri-implantitis: A Systematic Review.

BACKGROUND: Osseo-integrated implants provide effective treatment results for edentulous patients. However, despite the high success and survival rates of dental implants, several factors, such as poor oral hygiene and a history of periodontal disease, and systemic diseases, such as diabetes mellitus, could influence the outcome of the treatment. In fact, poor glycemic control can affect the healing process. Diabetes mellitus is considered a relative contraindication for dental implant therapy due to the fact that the success rates of the implants seem to be lower in diabetic patients, even if there is no total agreement among the results reported in the literature. The analysis of peri-implant inflammation indices, bone loss around the implant and glycemic index can provide us with useful information on the relationship between glycaemia in diabetic patients and the course of peri-implantitis, as well as implant success in the short term. OBJECTIVE: The purpose of this review is to establish how peri-implant inflammation parameters vary in diabetic versus non-diabetic patients. METHODS: This review was conducted on the basis of PRISMA. The search was conducted by three independent reviewers searching for keywords in three databases: PubMed, Scopus, Web Of Sciences (WOS), and the Cochrane Central Register of Controlled Trial. RESULTS: A total of 1159 records were identified, and 11 articles were included in the qualitative analysis. CONCLUSION: The analysis of the extracted data from the included studies suggests that some periimplant inflammation indices, such as bleeding on probing and bone loss around the implant, appear to be increased in diabetic patients with glycometabolic decompensation, compared with control not affected by diabetes mellitus.

Transmission of nonviral sexually transmitted infections and oral sex.

INTRODUCTION: Oral sex is usually considered a lower-risk sexual activity when compared with sex, but it is frequently the cause of sexually transmitted infections (STI). In particular, STI transferred through oral sex might have no visible symptoms, depending on the type of infection. AIMS: The aim of this study is to review the literature about the role of oral sex in the transmission of nonviral STI. MAIN OUTCOME MEASURES: State-of-the-art information in the area of STI in relation to sexual function and self-care, this last important for development of STI prevention products such as vaginal microbicides. Sexual behaviors assessed focusing on receiving oral sex and giving oral sex. METHODS: A search of the main electronic databases including registers of clinical controlled trials was performed in addition to a hand search of the most relevant Journals. The following electronic databases were searched: PubMed, Embase, Google Scholar, literature review of research articles, and public health department Internet Web sites, for the period of 1945-2011. In addition to searching the Clinical Trials Registry at the US National Institutes of Health, we also used the meta Register of Controlled Trials and the Cochrane Central Register of Controlled Trials. RESULTS: STI affect the mucous membranes both directly and indirectly producing characteristic diagnostic signs and lesions. Daily dental clinical activity needs an appropriate knowledge of any kind of oral lesions-related STI. The reader is offered a practical approach with clinically relevant recommendations that may prove useful in his/her daily practice when dealing with STI. CONCLUSIONS: These data provide a foundation for understanding diverse STI. We advise physicians to be receptive to discuss sexuality issues and provide patients with adequate therapy.

Effect of different irrigating solutions and endodontic sealers on bond strength of the dentin-post interface with and without defects.

AIMS: To investigate how the interfacial shear strength of the dentin-post interface with and without defects changes for different combinations irrigant/sealer. METHODS: In forty human decoronated and instrumented teeth, fibreglass posts were inserted. The obtained root segments were randomly assigned to four different groups according to the irrigant adopted and the cement used to seal the root canal. The root segments were processed for metyl-methacrylate embedding. Serial sections were obtained and submitted to histomorphometric analyses in order to observe any defect of adhesion at the dentin-post interface and to measure the defects' dimension. The serial sections were also submitted to micro-push-out test. The measured shear strength values were subjected to statistical analysis by one-way ANOVA. The values of bond strength determined for the defective samples were correlated with the dimension of the defects. Finite element models were built to interpret and corroborate the experimental findings. RESULTS: ANOVA showed that the generic combination irrigant/sealer does not affect the interfacial shear strength values. The bond strength of the samples without defects was averagely twice as large as that of the defective samples. The defects occupying more than 12% of the total transverse section area of the endodontic cement layer led to a reduction of the bond strength of about 70%. The predictions of the finite element models were in agreement with the experimental results. CONCLUSION: Defects occupying less than 2% of the total transverse section area of the cement layer were shown to be acceptable as they have rather negligible effects on the shear strength values. Technologies/protocols should be developed to minimize the number and the size of the defects.

Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93.

The transmembrane glycoprotein CD93 has been identified as a potential new target to inhibit tumor angiogenesis. Recently, Multimerin-2 (MMRN2), a pan-endothelial extracellular matrix protein, has been identified as a ligand for CD93, but the interaction mechanism between these two proteins is yet to be studied. In this article, we aim to investigate the structural and functional effects of induced mutations on the binding domain of CD93 to MMRN2. Starting from experimental data, we assessed how specific mutations in the C-type lectin-like domain (CTLD) affect the binding interaction profile. We described a four-step workflow in order to predict the effects of variations on the inter-residue interaction network at the PPI, based on evolutionary information, complex network metrics, and energetic affinity. We showed that the application of computational approaches, combined with experimental data, allowed us to gain more in-depth molecular insights into the CD93-MMRN2 interaction, offering a platform for developing innovative therapeutics able to target these molecules and block their interaction. This comprehensive molecular insight might prove useful in drug design in cancer therapy.

Proton Pump Inhibitors Directly Block hERG-Potassium Channel and Independently Increase the Risk of QTc Prolongation in a Large Cohort of US Veterans.

[Figure: see text].

Treatment of oroantral fistula with autologous bone graft and application of a non-reabsorbable membrane.

AIM: The aim of the current report is to illustrate an alternative technique for the treatment of oroantral fistula (OAF), using an autologous bone graft integrated by xenologous particulate bone graft. BACKGROUND: Acute and chronic oroantral communications (OAC, OAF) can occur as a result of inadequate treatment. In fact surgical procedures into the maxillary posterior area can lead to inadvertent communication with the maxillary sinus. Spontaneous healing can occur in defects smaller than 3 mm while larger communications should be treated without delay, in order to avoid sinusitis. The most used techniques for the treatment of OAF involve buccal flap, palatal rotation - advancement flap, Bichat fat pad. All these surgical procedures are connected with a significant risk of morbidity of the donor site, infections, avascular flap necrosis, impossibility to repeat the surgical technique after clinical failure, and patient discomfort. CASE PRESENTATION: We report a 65-years-old female patient who came to our attention for the presence of an OAF and was treated using an autologous bone graft integrated by xenologous particulate bone graft. An expanded polytetrafluoroethylene titanium-reinforced membrane (Gore-Tex) was used in order to obtain an optimal reconstruction of soft tissues and to assure the preservation of the bone graft from epithelial connection. CONCLUSIONS: This surgical procedure showed a good stability of the bone grafts, with a complete resolution of the OAF, optimal management of complications, including patient discomfort, and good regeneration of soft tissues. CLINICAL SIGNIFICANCE: The principal advantage of the use of autologous bone graft with an expanded polytetrafluoroethylene titanium-reinforced membrane (Gore-Tex) to guide the bone regeneration is that it assures a predictable healing and allows a possible following implant-prosthetic rehabilitation.

Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions.

BACKGROUND: Identification of Protein-Protein Interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. OBJECTIVE: Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. METHODS: Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. RESULTS: In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/ inhibitor molecules. CONCLUSION: A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention.

Structural investigation of Rett-inducing MeCP2 mutations.

X-ray structure of methyl-CpG binding domain (MBD) of MeCP2, an intrinsically disordered protein (IDP) involved in Rett syndrome, offers a rational basis for defining the spatial distribution for most of the sites where mutations responsible of Rett syndrome, RTT, occur. We have ascribed pathogenicity for mutations of amino acids bearing positively charged side chains, all located at the protein-DNA interface, as positive charge removal cause reduction of the MeCP2-DNA adduct lifetime. Pathogenicity of the frequent proline replacements, outside the DNA contact moiety of MBD, can be attributed to the role of this amino acid for maintaining both unfolded states for unbound MeCP2 and, at the same time, to favor some higher conformational order for stabilizing structural determinants required by protein activity. These hypotheses can be extended to transcription repressor domain, TRD, the other MeCP2-DNA interaction site and, in general, to all the IDP that interact with nucleic acids.

Maxillary Overdenture Retained with an Implant Support CAD-CAM Bar: A 4 Years Follow Up Case.

INTRODUCTION: Oral rehabilitation with overdenture on implants of upper jaw must be taken into consideration a variety of anatomical and biomechanical issues. It is possible to provide for rehabilitation with two or more implants, in different positions, solidarizing them with a bar. MATERIALS & METHODS: The present study involved a patient rehabilitated with 4 Xive implants (Friadent GmbH, Mannheim, Germany) solidarized with a titanium bar crafted with CAD-CAM technology for maximal comfort, precision and structural lightness. RESULTS & DISCUSSION: The follow-up was 54 months, with an implant survival of 100%. Based on our clinical evidence, bars engineered with CAD-CAM technology are promising in terms of precision and comfort despite higher costs.

An Optical System to Monitor the Displacement Field of Glass-fibre Posts Subjected to Thermal Loading.

Endocanalar posts are necessary to build up and retain coronal restorations but they do not reinforce dental roots. It was observed that the dislodgement of post-retained restorations commonly occurs after several years of function and long-term retention may be influenced by various factors such as temperature changes. Temperature changes, in fact, produce micrometric deformations of post and surrounding tissues/materials that may generate high stress concentrations at the interface thus leading to failure. In this study we present an optical system based on the projection moiré technique that has been utilized to monitor the displacement field of endocanalar glass-fibre posts subjected to temperature changes. Measurements were performed on forty samples and the average displacement values registered at the apical and middle region were determined for six different temperature levels. A total of 480 displacement measurements was hence performed. The values of the standard deviation computed for each of the tested temperatures over the forty samples appear reasonably small which proves the robustness and the reliability of the proposed optical technique. The possible implications for the use of the system in the applicative context were discussed.

Human papilloma virus (HPV) genotypes prevalence in a region of South Italy (Apulia).

INTRODUCTION: Since human papillomavirus (HPV) is the central casual factor in cervical cancer, understanding the epidemiology and geographical area distribution of the most prevalent HPV genotypes constitutes an important step towards development of strategies of prevention. AIM: The aim of this study was to investigate the prevalence of HPV infection and to determine HPV types distribution among 822 HPV positive women and some sexual male partners in Apulia (Italy). METHODS: HPV DNA detection and genotyping was performed by nested-PCR for the L1 region and reverse line blot hybridization allowing the specific detection of 24 HPV genotyping both high risk (HR) and low risk (LR). RESULTS: The most prevalent HPV genotypes were HPV 16 (35%), HPV 31 (16%) HPV 6 (9%), HPV 58 and 66 (7%), followed by HPV 33 (6%), HPV 18 and 56 (4%), HPV 70 and 45 (3%), HPV 53 and 11 (2%). Currently 1.5% of tested specimens remained unclassified. Multiple infections with at last two different high- risk HPV genotypes were observed in 10% of specimens. CONCLUSIONS: This finding adds knowledge to HPV epidemiological investigation, and addresses further studies aimed to consider public health for identifying groups at risk for cervical cancer.