Network medicine-based epistasis detection in complex diseases: ready for quantum computing.

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) (1-3). Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.

Salivary Biomarkers for Alzheimer's Disease: A Systematic Review with Meta-Analysis.

Alzheimer's Disease (AD) is the most common neurodegenerative disease which manifests with progressive cognitive impairment, leading to dementia. Considering the noninvasive collection of saliva, we designed the systematic review to answer the question "Are salivary biomarkers reliable for the diagnosis of Alzheimer's Disease?" Following the inclusion and exclusion criteria, 30 studies were included in this systematic review (according to the PRISMA statement guidelines). Potential biomarkers include mainly proteins, metabolites and even miRNAs. Based on meta-analysis, in AD patients, salivary levels of beta-amyloid42 and p-tau levels were significantly increased, and t-tau and lactoferrin were decreased at borderline statistical significance. However, according to pooled AUC, lactoferrin and beta-amyloid42 showed a significant predictive value for salivary-based AD diagnosis. In conclusion, potential markers such as beta-amyloid42, tau and lactoferrin can be detected in the saliva of AD patients, which could reliably support the early diagnosis of this neurodegenerative disease.

Salivary Alterations of Myeloperoxidase in Patients with Systemic Diseases: A Systematic Review.

Salivary myeloperoxidase (MPO) is a key mediator of the oral immune system, acting as an enzyme that utilises H2O2 to generate molecules with high bactericidal activity. While MPO determination in plasma is quite common, the use of saliva is still rare. Our systematic review was designed to answer the question "Are salivary levels of myeloperoxidase altered in patients with systemic diseases?". Following the inclusion and exclusion criteria, we included twenty-six studies. Altered MPO levels in saliva were most commonly found in patients with cardiovascular and gastrointestinal diseases. Most studies concerned unstimulated whole saliva, and only a few of them stimulated, mainly by chewing paraffin. Enzyme-linked immunosorbent assay (ELISA) was the most common method for determination of MPO concentrations in saliva. Increased salivary MPO levels were more often observed for inflammatory diseases, except patients with inflammatory bowel diseases who were eligible for biologic therapy. In conclusion, MPO could be altered in the saliva of patients with systematic diseases, especially cardiovascular or gastrointestinal diseases. However, further investigations are recommended to validate these outcomes.

Glomangioma in the hand: diagnosis, treatment, and challenges.

INTRODUCTION: In this paper, we have analysed all hand glomangioma cases referred to our clinic in the context of symptoms, time to diagnosis, and the role of surgical resection of the lesion. MATERIAL AND METHODS: We have collected the following data: the presence of risk factors, manifestation, time to diagnosis, the treatment applied, and follow-up of patients. RESULTS: We have collected medical records from six patients, three males and three females. The median age was 45 (IQR: 29.5-65.75). The main symptom in all patients was severe pain and tenderness. The first-choice physician(s) were: general practitioners, general surgeons, and neurologists. The median time to diagnosis was 7 (IQR: 5-10) years. The main complaint of our patients was severe pain - 9 (IQR: 9-10) on the VAS scale, which was significantly alleviated after surgical treatment - 0 (IQR: 0-0; p = 0.043). CONCLUSIONS: Extremely long times to final diagnosis, and excellent outcomes of surgical treatment, highlight the necessity of raising awareness of glomangiomas among clinicians.

The Comparison of InSb-Based Thin Films and Graphene on SiC for Magnetic Diagnostics under Extreme Conditions.

The ability to precisely measure magnetic fields under extreme operating conditions is becoming increasingly important as a result of the advent of modern diagnostics for future magnetic-confinement fusion devices. These conditions are recognized as strong neutron radiation and high temperatures (up to 350 °C). We report on the first experimental comparison of the impact of neutron radiation on graphene and indium antimonide thin films. For this purpose, a 2D-material-based structure was fabricated in the form of hydrogen-intercalated quasi-free-standing graphene on semi-insulating high-purity on-axis 4H-SiC(0001), passivated with an Al2O3 layer. InSb-based thin films, donor doped to varying degrees, were deposited on a monocrystalline gallium arsenide or a polycrystalline ceramic substrate. The thin films were covered with a SiO2 insulating layer. All samples were exposed to a fast-neutron fluence of ≈7×1017 cm-2. The results have shown that the graphene sheet is only moderately affected by neutron radiation compared to the InSb-based structures. The low structural damage allowed the graphene/SiC system to retain its electrical properties and excellent sensitivity to magnetic fields. However, InSb-based structures proved to have significantly more post-irradiation self-healing capabilities when subject to proper temperature treatment. This property has been tested depending on the doping level and type of the substrate.

Epithelial and Endothelial Pannexin1 Channels Mediate AKI.

Background Pannexin1 (Panx1), an ATP release channel, is present in most mammalian tissues, but the role of Panx1 in health and disease is not fully understood. Panx1 may serve to modulate AKI; ATP is a precursor to adenosine and may function to block inflammation, or ATP may act as a danger-associated molecular pattern and initiate inflammation.Methods We used pharmacologic and genetic approaches to evaluate the effect of Panx1 on kidney ischemia-reperfusion injury (IRI), a mouse model of AKI.Results Pharmacologic inhibition of gap junctions, including Panx1, by administration of carbenoxolone protected mice from IRI. Furthermore, global deletion of Panx1 preserved kidney function and morphology and diminished the expression of proinflammatory molecules after IRI. Analysis of bone marrow chimeric mice revealed that Panx1 expressed on parenchymal cells is necessary for ischemic injury, and both proximal tubule and vascular endothelial Panx1 tissue-specific knockout mice were protected from IRI. In vitro, Panx1-deficient proximal tubule cells released less and retained more ATP under hypoxic stress.Conclusions Panx1 is involved in regulating ATP release from hypoxic cells, and reducing this ATP release may protect kidneys from AKI.

Real-Time Dynamics and Phase Separation in a Holographic First-Order Phase Transition.

We study the fully nonlinear time evolution of a holographic system possessing a first order phase transition. The initial state is chosen in the spinodal region of the phase diagram, and it includes an inhomogeneous perturbation in one of the field theory directions. The final state of the time evolution shows a clear phase separation in the form of domain formation. The results indicate the existence of a very rich class of inhomogeneous black hole solutions.

Nonequilibrium Dynamics and Phase Transitions in Holographic Models.

We study the poles of the retarded Green's functions of strongly coupled field theories exhibiting a variety of phase structures from a crossover up to a first order phase transition. These theories are modeled by a dual gravitational description. The poles of the holographic Green's functions appear at the frequencies of the quasinormal modes of the dual black hole background. We establish that near the transition, in all cases considered, the applicability of a hydrodynamic description breaks down already at lower momenta than in the conformal case. We establish the appearance of the spinodal region in the case of the first order phase transition at temperatures for which the speed of sound squared is negative. An estimate of the preferential scale attained by the unstable modes is also given. We additionally observe a novel diffusive regime for sound modes for a range of wavelengths.

Immunotargeting of cancer stem cells.

Cancer stem cells (CSCs) represent a distinctive population of tumour cells that control tumour initiation, progression, and maintenance. Their influence is great enough to risk the statement that successful therapeutic strategy must target CSCs in order to eradicate the disease. Because cancer stem cells are highly resistant to chemo- and radiotherapy, new tools to fight against cancer have to be developed. Expression of antigens such as ALDH, CD44, EpCAM, or CD133, which distinguish CSCs from normal cells, together with CSC immunogenicity and relatively low toxicity of immunotherapies, makes immune targeting of CSCs a promising approach for cancer treatment. This review will present immunotherapeutic approaches using dendritic cells, T cells, pluripotent stem cells, and monoclonal antibodies to target and eliminate CSCs.

Salivary Biomarkers for Parkinson's Disease: A Systematic Review with Meta-Analysis.

Parkinson's Disease (PD) is a common neurodegenerative disease which manifests with motor features, such as bradykinesia, resting tremor, rigidity, and postural instability. Using the non-invasive technique of saliva collection, we designed a systematic review to answer the question "Are salivary biomarkers reliable for the diagnosis of Parkinson's Disease?". Following inclusion and exclusion criteria, 30 studies were included in this systematic review (according to the PRISMA statement guidelines). Mostly proteins were reported as potential biomarkers in saliva. Based on meta-analysis, in PD patients, salivary levels of total alpha-synuclein were significantly decreased, and those of oligomeric alpha-synuclein were significantly increased. Also, according to pooled AUC, heme oxygenase-1 demonstrated significant predictive value for saliva-based PD diagnosis. In conclusion, some potential biomarkers, especially alpha-synuclein, can be altered in the saliva of PD patients, which could be reliably useful for early diagnosis of this neurodegenerative disease differentiating other synucleopathies.

Sexually dimorphic renal expression of Klotho is directed by a kidney-specific distal enhancer responsive to HNF1b.

Transcription enhancers are genomic sequences regulating common and tissue-specific genes and their disruption can contribute to human disease development and progression. Klotho, a sexually dimorphic gene specifically expressed in kidney, is well-linked to kidney dysfunction and its deletion from the mouse genome leads to premature aging and death. However, the sexually dimorphic regulation of Klotho is not understood. Here, we characterize two candidate Klotho enhancers using H3K27ac epigenetic marks and transcription factor binding and investigate their functions, individually and combined, through CRISPR-Cas9 genome engineering. We discovered that only the distal (E1), but not the proximal (E2) candidate region constitutes a functional enhancer, with the double deletion not causing Klotho expression to further decrease. E1 activity is dependent on HNF1b transcription factor binding site within the enhancer. Further, E1 controls the sexual dimorphism of Klotho as evidenced by qPCR and RNA-seq. Despite the sharp reduction of Klotho mRNA, unlike germline Klotho knockouts, mutant mice presented normal phenotype, including weight, lifespan, and serum biochemistry. Lastly, only males lacking E1 display more prominent acute, but not chronic kidney injury responses, indicating a remarkable range of potential adaptation to isolated Klotho loss, especially in female E1 knockouts, retaining renoprotection despite over 80% Klotho reduction.

Sexually dimorphic renal expression of mouse Klotho is directed by a kidney-specific distal enhancer responsive to HNF1b.

Transcription enhancers are genomic sequences regulating common and tissue-specific genes and their disruption can contribute to human disease development and progression. Klotho, a sexually dimorphic gene specifically expressed in kidney, is well-linked to kidney dysfunction and its deletion from the mouse genome leads to premature aging and death. However, the sexually dimorphic regulation of Klotho is not understood. Here, we characterize two candidate Klotho enhancers using H3K27ac epigenetic marks and transcription factor binding and investigate their functions, individually and combined, through CRISPR-Cas9 genome engineering. We discovered that only the distal (E1), but not the proximal (E2) candidate region constitutes a functional enhancer, with the double deletion not causing Klotho expression to further decrease. E1 activity is dependent on HNF1b transcription factor binding site within the enhancer. Further, E1 controls the sexual dimorphism of Klotho as evidenced by qPCR and RNA-seq. Despite the sharp reduction of Klotho mRNA, unlike germline Klotho knockouts, mutant mice present normal phenotype, including weight, lifespan, and serum biochemistry. Lastly, only males lacking E1 display more prominent acute, but not chronic kidney injury responses, indicating a remarkable range of potential adaptation to isolated Klotho loss, especially in female E1 knockouts, retaining renoprotection despite over 80% Klotho reduction.

Sexually dimorphic renal expression of Klotho is directed by a kidney-specific distal enhancer responsive to HNF1b.

Transcription enhancers are genomic sequences regulating common and tissue-specific genes and their disruption can contribute to human disease development and progression. Klotho, a sexually dimorphic gene specifically expressed in kidney, is well-linked to kidney dysfunction and its deletion from the mouse genome leads to premature aging and death. However, the sexually dimorphic regulation of Klotho is not understood. Here, we characterize two candidate Klotho enhancers using H3K27ac epigenetic marks and transcription factor binding and investigate their functions, individually and combined, through CRISPR-Cas9 genome engineering. We discovered that only the distal (E1), but not the proximal (E2) candidate region constitutes a functional enhancer, with the double deletion not causing Klotho expression to further decrease. E1 activity is dependent on HNF1b transcription factor binding site within the enhancer. Further, E1 controls the sexual dimorphism of Klotho as evidenced by qPCR and RNA-seq. Despite the sharp reduction of Klotho mRNA, unlike germline Klotho knockouts, mutant mice presented normal phenotype, including weight, lifespan, and serum biochemistry. Lastly, only males lacking E1 display more prominent acute, but not chronic kidney injury responses, indicating a remarkable range of potential adaptation to isolated Klotho loss, especially in female E1 knockouts, retaining renoprotection despite over 80% Klotho reduction.

Salivary markers of aggression - The possible alterations in salivary hormones levels to identify perpetrators of aggression-related violence.

Aggression, understood as intentional actions aimed at causing harm, remains in a direct relation with the phenomenon of interpersonal violence, especially its physical form. Creating an objective marker of aggression would be an important tool for preventing, protecting the victims and maintaining control over suspects. There have been attempts to link aggression with shifts in hormone levels, including those that can be measured in saliva, especially testosterone and cortisol. The systematic review aimed to assess changes in salivary hormone levels among perpetrators of violence, with particular emphasis on physical violence, as parameters pointing to perpetrators of violence. Following the inclusion and exclusion criteria, 22 studies were included. Most of the papers included in the analysis came from the USA and Europe. Studies typically included adults as well as children, while focusing mainly on men. Among the hormones, salivary testosterone levels were the ones analyzed most frequently. On the basis of the included studies, a meta-analysis was conducted on the relationship between aggressive behavior and the levels of concentration of testosterone and cortisol measured in saliva. Regardless of gender, individuals exhibiting aggressive behavior were proved to have significantly higher testosterone levels and lower cortisol concentrations in saliva measurements. The obtained results indicate the feasibility of using the examined parameters for initial detection of perpetrators of aggression-related violence. However, further research is necessary to more precisely determine the relationship between aggressive behavior and hormonal changes in order to determine the feasibility of using these parameters as an objective marker for early identification of perpetrators.

Periodontal disease in patients with thyroid diseases: A systematic review with meta-analysis.

PURPOSE: The imbalance of thyroid hormones affects the metabolic activity of various tissues, including periodontium. Also, autoimmune diseases present an increased tendency to suffer from periodontal disease. Therefore, our systematic review was designed to answer the question "Is there a relationship between thyroid diseases and periodontal disease?". MATERIALS AND METHODS: Following the inclusion and exclusion criteria, 10 studies were included in this systematic review using the databases PubMed, Scopus and Web of Science (according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement guidelines). RESULTS: Based on the meta-analysis, patients with thyroid diseases (especially with hypothyroidism) demonstrated significantly worse periodontal status than systemically healthy controls. Moreover, according to the cross-sectional studies, 5.74 â€‹% of periodontitis patients reported the concomitance of thyroid diseases. CONCLUSIONS: In summary, the included studies suggest a potential relationship between thyroid diseases and periodontal disease. However, further research is necessary to reliably assess the oral health in patients with hypothyroidism and hyperthyroidism.

Potential Immunohistochemical Biomarkers for Grading Oral Dysplasia: A Literature Review.

Oral cancer is a prevalent global health issue, with significant morbidity and mortality rates. Despite available preventive measures, it remains one of the most common cancers, emphasising the need for improved diagnostic and prognostic tools. This review focuses on oral potentially malignant disorders (OPMDs), precursors to oral cancer, specifically emphasising oral epithelial dysplasia (OED). The World Health Organisation (WHO) provides a three-tier grading system for OED, and recent updates have expanded the criteria to enhance diagnostic precision. In the prognostic evaluation of OED, histological grading is presently regarded as the gold standard; however, its subjectivity and unreliability in anticipating malignant transformation or recurrence pose notable limitations. The primary objective is to investigate whether specific immunohistochemical biomarkers can enhance OED grading assessment according to the WHO classification. Biomarkers exhibit significant potential for comprehensive cancer risk evaluation, early detection, diagnosis, prognosis, and treatment optimisation. Technological advancements, including sequencing and nanotechnology, have expanded detection capabilities. Some analysed biomarkers are most frequently chosen, such as p53, Ki-67, cadherins/catenins, and other proteins used to differentiate OED grades. However, further research is needed to confirm these findings and discover new potential biomarkers for precise dysplasia grading and minimally invasive assessment of the risk of malignant transformation.

Clinical Difficulties Related to Direct Composite Restorations: A Multinational Survey.

AIMS: Composite materials are widely used in dentistry for direct tooth restorations. However, they are highly sensitive to the working technique employed during the restorative procedure. Even minor procedural errors can have a significant impact on the quality including the longevity of the restoration. Hence the aim of this study was to determine the material preferences and analyse the clinical problems associated with direct composite restorations in a cohort of dentists. METHODS: A 20-item online questionnaire was created in English and administered 1830 general dentists and specialists in 13 countries. The first section of the questionnaire included four questions to elicit demographic data, and the second section comprised 16 questions focused on material preferences for conservative restorations, durability of composite restorations, and the most challenging stages the dentists faced during the composite restorative procedures. RESULTS: Respondents decided most often to use composite materials for the tooth restorations (OR 997.4, 95% CI 233.8-4254.8, P value <.001). Most respondents indicated that the durability of composite restorations was approximately 7 to 10 years (41.5%). Among the factors affecting durability, maintenance of a dry cavity was the most often reported reason (47.1%) and the foremost challenge faced by dentists (61.0%) during the composite restorative procedures. CONCLUSIONS: Our study confirmed that resin-based composites are the most popular material for direct restoration in many countries. Although working with this material is difficult and involves multiple steps, maintaining a dry cavity during bonding, and material application may affect the therapeutic success and durability of these restorations. Clinicians need to be attentive to this issue and be prepared to adapt their decision-making and consider opting for alternative restorative materials, if appropriate.

Awareness of possible complications associated with direct composite restorations: A multinational survey among dentists from 13 countries with meta-analysis.

OBJECTIVES: Resin-based composites (RBCs) evolved into favoured materials for teeth restorations, marking a significant change in dental practice. Despite many advantages, RBCs exhibit various limitations in their physical and chemical properties. Therefore, we assessed the dentists' awareness of possible complications after direct composite restorations and their opinions about this material. METHODS: The online questionnaire was created in English in May 2023. A 16-item survey was dedicated to general dentists and specialists. The first section included four questions related to demographic characteristics. The second section comprised twelve questions and focused on awareness of potential side effects of composite restorations, the most crucial advantages and disadvantages of composite resins, and the frequency of experienced clinical complications after the application of composite materials. RESULTS: A total of 1830 dentists from 13 countries took part in the survey. Dentists most often declared awareness of low adhesion to the dentine (77.5 %) and, most rarely, solubility in oral fluids (42.6 %). Aesthetics was identified as the main advantage of composite fillings (79 %), followed by the possibility of repair (59 %) and adhesion to enamel (57 %). Polymerisation shrinkage was a major disadvantage for most countries (70 % overall). Analysing the declared potential clinical complications for all countries, statistically significant findings were obtained for marginal discolouration (OR=2.982, 95 % CI: 1.321-6.730, p-value=0.009) and borderline significance for secondary caries (OR=1.814, 95 % CI: 0.964-3.415, p-value=0.065). CONCLUSIONS: Dentists value aesthetics and repairability but are aware of shrinkage and experience discolouration. The issue of toxicity and solubility seems to be the least known to dentists. CLINICAL SIGNIFICANCE: Dentists should use RBCs with critical caution due to possible side effects. Despite the undoubted aesthetics of direct composite restorations, it is necessary to remember potential clinical complications such as marginal discolouration or secondary caries.

Kleefstra Syndrome-Dental Manifestations and Needs: A Case Report with a Literature Review.

Kleefstra syndrome (KS) is a rare genetic disorder (prevalence < 1/1 000 000) characterised by autistic spectrum disorder (ASD), childhood hypotonia, and seizures. A typical facial appearance includes microcephaly, arched eyebrows, synophrism, hypertelorism, a short nose, midface hypoplasia, prognathism, and tongue protrusion. This case report presents a 19-year-old female with KS from a dentist's perspective. The patient demonstrates limited mouth opening with a slight deviation of the mandible on the left side. The mandibular prognathism and anterior open bite are visible. A generalised inflammatory gingival enlargement is most likely a response to local irritants like plaque and calculus but is enhanced by the patient's mouth breathing habit. Also, the tongue is unusually large-macroglossia. Dental anomalies were diagnosed by digital panoramic radiograph, including dilaceration of the maxillary left second premolar and taurodontism. The patient was qualified to be treated under general anaesthesia with multiple extractions, restorations, hygienisation procedures, and tooth remineralisation. This individual should also be considered for orthodontic treatment and an eventual tongue reduction procedure. In the case of KS, multidisciplinary cooperation as well as frequent dental check-ups with fluoride prophylaxis are recommended. Unfortunately, dental treatment is still not an integral part of taking care of disabled children and youth with rare diseases.

Eating Disorders and Dental Erosion: A Systematic Review.

Both eating disorders and dental erosion are increasingly affecting adolescents and young adults. Thus, our systematic review was designed to answer the question: "Is there a relationship between dental erosion and eating disorders?" Following the inclusion and exclusion criteria, 31 studies were included in this systematic review (according to the PRISMA statement guidelines). Based on the meta-analysis, 54.4% of patients with bulimia nervosa and 26.7% with anorexia nervosa experienced tooth erosion. For the whole group of 1699 patients with eating disorders, erosive lesions were observed in 42.1% of patients. Bulimics were more than 10 times more likely to experience dental erosion compared to healthy individuals (OR = 10.383 [95%CI: 4.882-22.086]). Similarly, more than 16 times increased odds of tooth erosion were found in patients with self-induced vomiting (OR = 16.176 [95%CI: 1.438-181.918]). In conclusion, eating disorders are associated with an increased risk of developing erosive lesions, especially in patients with bulimia nervosa.