Diseased Patients Research Articles

P1315 Decoding microbiome-metabolome interactions: gaining insights into Gastric Cancer, Inflammatory Bowel Disease and Colon Cancer

Abstract Background The gut microbiome and its metabolites are key to understanding the pathogenesis of gastrointestinal diseases (GID) like gastric cancer (GC), inflammatory bowel disease (IBD), and colon cancer (CC), aiding in the identification of shared and disease-specific biomarkers for personalised interventions. This study used machine learning (ML) models, metabolic modelling and network analysis methods to assess the risk of developing one GID following another, especially as IBD patients are at higher risk of CC, and GC patients can develop CC. Methods Microbiome and metabolome datasets from Erawijantari et al. (GC), Franzosa et al. (IBD), and Yachida et al. (CC) were subjected to three ML models, eXtreme gradient boosting (XGBoost), Random forest (RF) and Least absolute shrinkage and selection operator (LASSO). The models were refined using Recursive Feature Elimination & Cross-Validation (RFECV) and LASSO. Trained models were applied for within and cross disease analyses using common microbes and metabolites. Microbial abundance analysis was conducted to identify compositional differences between the diseased and healthy patients. Microbial Community Modelling (MICOM) simulated microbial interactions to evaluate contributions to metabolite production. Using Weighted Gene Co-expression Network Analysis (WGCNA), A cluster dendrogram was generated to identify modules of highly correlated metabolic features based on co-expression patterns. Results ML models for the GC model had LASSO, achieving the highest AUC 0.96 [0.85-1.00]. For IBD, RF performed the best at AUC 0.93 [0.86-0.98]. CC model had XGBoost as the top performer AUC 0.85 [0.75-0.94]. Biomarkers from the GC model were used to predict CC and IBD outcomes, while biomarkers from IBD and CC models were similarly tested across diseases, having strong performance scores (Figure 2). Abundance analysis had lower levels of Bacteroidaceae in GC compared to healthy patients and higher Ruminococcaceae and Lachnospiraceae in IBD and CC. MICOM identified six metabolites in GC (adenosine, alanine, glycerophosphate, methionine, methionine sulfoxide, nicotinate), two in IBD (cholate, cytosine) and seven in CC (1-methyladenosine, alanine, glutamate, histidine, lactate, nicotinamide, tryptophan) all differentially produced by the selected microbes. WGCNA revealed four modules for GC (β=18,R²=0.91), eight modules for IBD (β=16,R²= 0.56), and two modules for CC (β=19,R²=0.27). Conclusion Despite study limitations, results suggest that the gut microbiome and its metabolites influence disease progression and aid in optimising therapeutic strategies, such as faecal microbiota transplantation (FMT), particularly in IBD and CC, potentially addressing both disease prevention and progression.

P0022 Development of primary human fibroblast cell cultures for fibrosis modelling in Inflammatory Bowel Diseases

Abstract Background Inflammatory Bowel Diseases (IBD) are chronic immune-mediated diseases of the gastrointestinal tract. Fibrosis is frequent in IBD driven by inflammatory cytokines. During fibrosis, extracellular matrix proteins accumulate in the tissue, causing loss of epithelial function and stenosis, leading to malabsorption and intestinal motility problems. This can ultimately lead to serious complications, strictures, fistulas, or ileus. Anti-inflammatory drugs cannot target fibrosis, only surgical intervention can be used. No relevant primary in vitro cell culture model is available for intestinal fibrosis modelling. Therefore, we aimed to establish and optimize human primary fibroblast cell culture from intestinal biopsies of control and IBD patients. We characterized and compared the fibrosis phenotype and gene expression as well. Methods Fibroblast cell cultures were generated from colonic biopsy samples by enzymatic digestion. In a suitable medium, the cells attach to the bottom of the vessel and proliferate, at 90% confluence the cultures were passaged. The phenotype was confirmed by immunofluorescent staining. Target proteins: COL1A1 (Collagen type 1 alpha 1), TGF-ß1 (Transforming growth factor beta), PAI-1 (Plasminogen activator inhibitor type 1), α-SMA (Alpha smooth muscle actin), and PHH3 (Phosphohistone H3). For gene expression analysis RNA was isolated and qRT-PCR technique was used for the following target genes: COL1A1, ACTA2 (Actin alpha 2), TGF-ß1, FN1 (Fibronectin 1), PAI-1, H3C4 (H3 clustered histone 4). We evaluated the collected data and performed statistical analysis. Results We can efficiently create and maintain human colon primary fibroblast cell cultures from colonic biopsies of healthy and CD origins. Cell morphology differences were observed from control and diseased patient samples. At the staining, the fluorescent intensity of fibrotic markers (COL1A1, TGF-ß1, PAI1) and the mitosis marker PHH3 were significantly higher in the CD samples, indicating that the cells maintained fibrotic phenotype, and the diseased fibroblasts had a higher proliferation rate. The myofibroblast marker, α-SMA didn’t show a significant difference. Interestingly, significant differences were not noted between the two groups in the qRT-PCR measurements. Conclusion In conclusion, we can generate primary human intestinal fibroblast cell cultures and maintain them to passage number 3. Fibrotic protein markers and morphology distinguish the diseased samples from the healthy subjects, therefore it could be useable for in vitro fibrosis modelling. However, the gene expression analysis doesn’t discriminate between the two groups at passage number 3. In the future, we would like to observe the fibrotic properties in earlier passage numbers.

Clinical Relevancies of Sarcopenic Obesity in Patients with Metabolic Dysfunction-Associated Fatty Liver Disease (MASLD).

Sarcopenic obesity (SO) is associated with adverse outcomes in diseased patients. This study aimed to examine the prevalence and risks associated with SO, with a focus on the impact of SO on cardiovascular risk in patients with MASLD. In this cross-sectional study, patients with MASLD were prospectively enrolled. Through dual-energy X-ray absorptiometry (DXA) scans, their body compositions were analyzed to identify who had SO and osteopenia/osteoporosis. The primary aim is to investigate risks associated with SO, followed by analyzing the association between SO and cardiovascular disease (CVD). Two hundred and twenty-three patients with MASLD were enrolled. The prevalence of SO was 47.1%, respectively. Patients coexisted with MASLD and SO had increased visceral adipose tissue (VAT), higher fatty liver index (FLI) and fibrosis 4 (FIB-4) score. Regression analysis revealed higher FLI and FIB-4 score, as well as history of hypertension, were risks associated with SO. The 10-year atherosclerotic cardiovascular disease (ASCVD) risk score was higher in patients coexisted with MASLD and SO compared to those without (10.1% vs. 7.3%, p = 0.006). Regression analysis showed that increased VAT and FIB-4 score were associated with raised risk of ASCVD. Prevalence of SO in MASLD patients is considerable. The presence of SO also linked to higher risk of ASCVD. Therefore, the recognition of SO in patients with MASLD is important in clinical care.

Quantifying spatial and dynamic lung abnormalities with 3D PREFUL FLORET UTE imaging: A feasibility study.

Pulmonary MRI faces challenges due to low proton density, rapid transverse magnetization decay, and cardiac and respiratory motion. The fermat-looped orthogonally encoded trajectories (FLORET) sequence addresses these issues with high sampling efficiency, strong signal, and motion robustness, but has not yet been applied to phase-resolved functional lung (PREFUL) MRI-a contrast-free method for assessing pulmonary ventilation during free breathing. This study aims to develop a reconstruction pipeline for FLORET UTE, enhancing spatial resolution for three-dimensional (3D) PREFUL ventilation analysis. The FLORET sequence was used to continuously acquire data over 7 ± 2 min in 36 participants, including healthy subjects (N = 7) and patients with various pulmonary conditions (N = 29). Data were reconstructed into respiratory images using motion-compensated low-rank reconstruction, and a 3D PREFUL algorithm was adapted to quantify static and dynamic ventilation surrogates. Image sharpness and signal-to-noise ratio were evaluated across different motion states. PREFUL ventilation metrics were compared with static 129Xe ventilation MRI. Optimal image sharpness and accurate ventilation dynamics were achieved using 24 respiratory bins, leading to their use in the study. A strong correlation was found between 3D PREFUL FLORET UTE ventilation defect percentages (VDPs) and 129Xe VDPs (r ≥ 0.61, p < 0.0001), although PREFUL FLORET static VDPs were significantly higher (mean bias = -10.1%, p < 0.0001). In diseased patients, dynamic ventilation parameters showed greater heterogeneity and better alignment with 129Xe VDPs. The proposed reconstruction pipeline for FLORET UTE MRI offers improved spatial resolution and strong correlation with 129Xe MRI, enabling dynamic ventilation quantification that may reveal airflow abnormalities in lung disease.

Interleukin 38 as a bio marker for metabolic syndrome in psoriatic patients

Background Metabolic syndrome (MetS) is more common comorbidity in psoriasis and a risk factor for cardiovascular disease. Interleukin 38 (IL-38) is an anti-inflammatory cytokine that has a vital role in MetS. Aim This research aimed to identify the possible relationship between plasma IL-38 levels in psoriatic cases and MetS development. Methods This case-control study included 88 adults aged greater than 18 years, divided into four groups of 22: group (1) cases with psoriasis vulgaris only, group (2) cases with psoriasis vulgaris and MetS, group (3) cases with MetS only, and group (4) healthy control subjects. All participants were subjected to full history taking, clinical assessment, laboratory investigation (fasting blood sugar, fasting triglyceride level, high-density lipoprotein), and plasma levels of IL-38 using ELISA kits. Results IL-38 levels were significantly decreased in each of the diseased patients (psoriasis, MetS, or both) than in controls. patients with psoriasis and MetS had the lowest level of IL-38 than those with psoriasis only or MetS only. There was a highly significant difference in the IL-38 levels among the groups (P&lt;0.0001). In patients with psoriasis there was a significantly negative correlation between the PASI score and IL-38 levels. Conclusion The decreased serum level of IL-38 among psoriatic patients with MetS is more than patients with either disease alone due to its role in the pathogenesis of both conditions. Much decrease in its level in psoriatic patients can be an indicator of development of metabolic abnormalities. This opens a new scope in the treatment of both conditions using IL-38.

Evaluating the Perceived Benefits and Effectiveness of a Government Health Insurance Scheme for Chronic Kidney Disease Patients: A Study in Nellore, Andhra Pradesh.

Background Chronic kidney disease (CKD) is prevalent in India, particularly among underprivileged populations. Government initiatives such as the Dr. YSR Aarogyasri Health Insurance Scheme aim to provide affordable healthcare to economically impoverished individuals with kidney diseases. This study assessed participants' perceptions of the scheme's benefits, effectiveness, and challenges. Methods A cross-sectional study was conducted in Nellore, Andhra Pradesh, involving 100 CKD patients. Data was collected using a structured questionnaire assessing socio-demographic factors, insurance scheme's awareness, perceived benefits, and effectiveness. Multivariable logistic regression analysis was employed to identify factors influencing participants' perceptions. Results Participants aged over 40 years were more likely to perceive the Dr. YSR Aarogyasri Health Insurance Scheme positively (crude odds ratio{COR}: 9.2; 95% CI: 2.6-31.7). Males (adjusted odds ration {aOR} 1.5; 95% CI: 1.1-2.1), married individuals (aOR 1.3; 95% CI: 0.8-1.7), and those with higher education (aOR 1.9; 95% CI: 1.1-3.2) reported greater schemeeffectiveness. However, 32% of CKDpatients lacked awareness of the scheme's enrolment process, 29% believed that the eligibility criteria were too strict, and 17% of insured patients reported gaps in coverage for specific services, treatments, and medications, reducing the scheme's appeal to diseased patients. Discussion Older males and those with diabetes, who require extensive care, perceive the scheme as beneficial. However, gaps in awareness and coverage remain barriers to its full effectiveness. Conclusion While the Dr. YSR Aarogyasri Health Insurance Scheme provides critical financial relief for CKD patients, enhancing its outreach and expanding coverage could improve its impact. These findings can guide policy improvements to optimize the scheme's effectiveness and accessibility.

Ultrastructural characterization of tau pathology in the human post‐mortem Alzheimer’s disease brain

AbstractBackgroundNeuropathological tau tangles in Alzerheimer’s disease (AD) have been roughly characterized into pre‐tangles, mature tangles and ghost tangles. However, to date, their maturation in the human brain is poorly understood. Here, we aimed to define the structure and composition of tangle maturation stages in the AD brain using correlative light and electron microscopy (CLEM).MethodChemically fixed (4% paraformaldehyde, 0.1% glutaraldehyde) entorhinal and hippocampal formation of two diseased AD patients were analyzed using CLEM (6 more cases are currently being analyzed). Vibratome sections were stained with different relevant markers (AT8, AT180, 44744, etc; Amytracker; DAPI) and imaged using a fluorescence microscope. Brain sections were then processed for electron microscopy (heavy metal staining and resin embedding). Ultra‐thin alternate sections were collected on glass slides and electron microscopy grids.ResultWe have characterized the ultrastructure of several mature tangles, dystrophic neurites, a few putative pre‐tangles and one putative ghost tangle. While we observed no tau fibrils in pre‐tangles, high contents of tau fibrils were present in mature tangles that often formed distinct clusters. Multilamellar bodies, damaged mitochondria and small membranous vesicles were present. Dystrophic neurites were swollen and filled with a mix of tau fibrils and multilamellar bodies. Often the twist of individual fibrils was visible. Fibrils in the putative ghost tangle had a fuzzy appearance, were densely packed and compartmentalized by a membrane. Compartmentalized clusters of multilamellar bodies were present as well.ConclusionA prominent difference between mature tangles and neuritic pathology was the increased presence of multilamellar bodies in dystrophic neurites. This could be explained by differences in the aggregation process of tau fibrils, depending on the cellular context (neuron soma vs dendrite). In most previous studies, the staining with amyloid markers suggested the absence of fibrils in pre‐tangles, while one report found fibrils in pre‐tangles using EM. Our results support the hypothesis of the absence of tau fibrils in the earliest form of pre‐tangles. Further work is needed to identify the tau tangle stage at which fibrillar tau first occurs. The here presented preliminary data needs to be expanded with additional earlier and later stages of tau pathology.

MRI trigeminal nerve digitalization for trigeminal neuralgia diagnosis

ObjectiveThis study aimed to determine the affected side in trigeminal neuralgia by examining the digitized angle ratio value between the bilateral trigeminal nerve root axis and the pontine tangent line. MethodsTrigeminal nerve-related MRI from 81 patients with trigeminal neuralgia (TNG) and 20 healthy persons were divided into normal and diseased groups. All the patient's films were scanned to form the images stored in compute. The following skull base MRI parameters were measured by Image J software: 1. bilateral trigeminal nerve root-pontine tangent line angle (T-P angle) values were measured. 2. Clinical symptoms were used to record the affected side of diseased patients, and 3. Nerve vascular confliction (NVC) and the side with NVC were subdivided (none/left/right/both sides). The normal T-test proved that P Value between the normal group and the diseased group. The T-P angle Ratio of the normal group was utilized to estimate the normal patient Ratio to establish the 95% confidence interval (CI). In diseased group, if the ratio was ≥ the reference value, the afflicted side was determined by comparing the max T-P angle with the actual affected side for accuracy. A binomial distribution test verified its statistical significance. ResultsThe T-P angle was significantly different between patients with TNG and normal subjects (p < 0.001). The T-P angle ratio (R) ≥ 1.238 was used to diagnose the affected side, achieving an overall accuracy rate of 82% (95% CI: 75%–89%). For patients without NVC, the accuracy was 78% (95% CI: 60%–95%), while for those with unilateral NVC, it was 91% (95% CI: 82%–100%), and for those with bilateral NVC, it was 69% (95% CI: 52%–86%). For 1 ≤ R < 1.238, the accuracy for diagnosing the affected side using NVC was 80% (95% CI: 67%–93%). ConclusionThe T-P angle is significantly higher in TNG patients than in normal patients (p < 0.001)., making it a valuable diagnostic tool. This measurement aids in guiding microvascular decompression surgery, particularly in non-vascular compression cases, and enhances postoperative evaluation. Future integration into standard protocols could improve surgical outcomes and patient care.

Pathological Mutations D169G and P112H Electrostatically Aggravate the Amyloidogenicity of the Functional Domain of TDP-43.

Aggregation of TDP-43 is linked to the pathogenesis of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Notably, electrostatic point mutations such as D169G and P112H, located within the highly conserved functional tandem RNA recognition motif (RRM) domains of the TDP-43 protein (TDP-43tRRM), have been identified in diseased patients as well. In this study, we address how the electrostatic mutations alter both the native state stability and aggregation propensity of TDP-43tRRM. The mutants D169G and P112H show increased chemical stability compared to the TDP-43tRRM at physiological pH. However, at low pH, both the mutants undergo a conformational change to form amyloid-like fibrils, though with variable rates─the P112H mutant being substantially faster than the other two sequences (TDP-43tRRM and D169G mutant) showing comparable rates. Moreover, among the three sequences, only the P112H mutant undergoes a strong ionic strength-dependent aggregability trend. These observations signify the substantial contribution of the excess charge of the P112H mutant to its unique aggregation process. Complementary simulated observables with atomistic resolution assign the experimentally observed sequence-, pH-, and ionic strength-dependent aggregability pattern to the degree of thermal lability of the mutation site-containing RRM1 domain and its extent of dynamical anticorrelation with the RRM2 domain whose combination eventually dictate the extent of generation of aggregation-prone partially unfolded conformational ensembles. Our choice of a specific charge-modulated pathogenic mutation-based experiment-simulation-combination approach unravels the otherwise hidden residue-wise contribution to the individual steps of this extremely complicated multistep aggregation process.

Assisted Reproductive Technology, Pregnancy, and Recurrent Disease in Melanoma Patients: A 30-Year Single Institution Experience.

The primary aim of this study was to assess differences in melanoma recurrence between patients conceiving spontaneously versus those undergoing assisted reproductive technology (ART) and to determine use of ART in post-melanoma patients. A secondary aim was to describe the use of immunotherapy as a novel treatment regimen for metastatic melanoma in a cohort of fertile patients. This study is a 30-year analysis including data from a single-center questionnaire and a retrospective cohort study. Participants/Materials: Women of childbearing age with a history of melanoma were requested to participate in our study. We selected patients who underwent either primary melanoma treatment or treatment of local/distant recurrence at our institute between 1994 and 2021. Each participant received a questionnaire and informed consent form. The questions concerned general health, primary tumor characteristics, utilization of ART, subsequent pregnancies, and development of recurrent melanoma. Additional information was collected from the medical files. The research was conducted in a dedicated oncology center and tertiary referral center for melanoma in The Netherlands. Participants received the questionnaires by mail. Six weeks later a reminder was sent to nonresponders. Analysis was performed using descriptive statistics. For comparisons between groups, chi-square tests were used. p value was considered significant when below 0.05. A clinically relevant difference in recurrence rate was defined as a 10% difference. A total of 498 questionnaires were available for analyses, 449 from living patients and 49 from relatives of diseased patients. One hundred and seventy-nine patients (36%) with a history of melanoma became pregnant following their diagnosis. There was no difference in the recurrence rate between patients who became pregnant after the diagnosis of melanoma and those who never subsequently conceived (37% vs. 35%, p = 0.609). In the total cohort, 28 patients (6%) attempted to conceive using ART, and eight of them experienced disease recurrence. A total of 58 patients (22% of patients since 2006) were treated with immunotherapy. The main limitations of the study are its size, observational design, and questionnaire methodology. Pregnancy did not increase the risk of recurrent melanoma. The group of patients conceiving after ART was small, and therefore, it is difficult to confidently conclude that the recurrence risk is comparable to the other groups. Prospective international registration of these patients, their oncologic follow-up and possible use of assisted reproduction, will provide valuable information to determine any potential association between ART and risk of recurrent melanoma. This would enable health professionals to develop surveillance strategies and preconception counseling of patients wishing to conceive.

Best clinical practice experience at University of Gondar Comprehensive specialized Hospital Emergency and critical care Medicine department, A Case Study Under a resource limited set up

Abstract Background The emergency department (ED) is unique unstable environment where someone faces unscheduled and undifferentiated diseased patients, stressed families, unsettled staffs and unequitable resources.UoGCSH is the oldest in the Ethiopia and the only referral hospital for more than 13 million people from the five-zone north-west Ethiopia with 950 beds capacity. During the 2020 G.C a proposal paper was submitted to the administration bodies of the college and the hospital. The proposal was suggesting short term, mid-term and long-term quality improvement segments implemented in institutionally convenient manner. Objective To describe the transformation of emergency and critical care medical services at University of Gondar Comprehensive specialized hospital from scratch to the current status. Method A descriptive case study design was applied to narrate critical care service transformation at UoG Comprehensive Specialized Hospital. Since this case study is a data review from gathered secondary data, desk reviews of the emergency department, quality directorate data review, and the annual audit report review, there was no need for IRB approval. Result and recommendation After a year of renovation, we were able to organize a newly refurbished emergency room having a triage area with adequate reception space, Red resuscitation area with 10 beds (considering patient overflow), Orange with 18 beds, Yellow with 10 beds and floater area, isolation room, decontamination room, ED laboratory, main store, disaster store and piped oxygen system to all beds. we have gone a long journey in bringing those promised practices into demonstrable practice and finally replicable prototypic best practice. Even though we paced extra miles in achieving this status. Standard emergency room work flow implementation enable us to control the day-to-day patient and attendant crowding that impedes the anticipated medical treatment outcome and result in a significant dissatisfaction.Despite this achievement the trauma center establishment and high-quality patient care is recommended.

Capillary Blood Docosahexaenoic Acid Levels Predict Electrocardiographic Markers in a Sample Population of Premenopausal Women.

Introduction: The relationship between blood N-3 polyunsaturated fatty acid (PUFA) levels and cardiovascular health is known, but direct evidence that N-3 PUFA levels influence electrocardiographic (ECG) parameters is non-existent. In the study described herein, we investigated the relationship between anthropometric biomarkers and capillary blood PUFAs with ECG outputs in a sample population of healthy pre-menopausal women. Method: Twenty-three consenting females were recruited, with the study power analysis sufficiently demonstrated. Food intake, anthropometric and cardiovascular parameters were obtained. Capillary blood was collected for fatty acid chromatographic analysis. Results: Body mass index, haematocrit, heart rate (HR), mean arterial pressure (MAP) and ECG readings all fell within healthy ranges. Principal component analysis-mediated correlations were carried out controlling for combined Components 1 (age, body fat % and waist-to-hip ratio) and 2 (height, HR and MAP) as control variables. Docosahexaenoic acid (DHA) unequivocally decreased the QRS area under the curve (AUC-QRS) regardless of the impact of control variables, with each unit increase in DHA corresponding to a 2.3-unit decrease in AUC-QRS. Mediation analysis revealed a significant overall effect of DHA on AUC-QRS, with the impact of DHA on R wave amplitude accounting for 77% of the total observed effect. Discussion: Our new findings revealed an inverse relationship between AUC-QRS with capillary blood DHA, suggesting that the association between ventricular mass and its QRS depolarising voltage is mediated by DHA. Our findings bridge a knowledge gap on the relationship between ventricular mass and ventricular efficiency. Further research will confirm whether the relationship identified in our study also exists in diseased patients.

Applying queueing theory to evaluate wait-time-savings of triage algorithms

In the past decade, artificial intelligence (AI) algorithms have made promising impacts in many areas of healthcare. One application is AI-enabled prioritization software known as computer-aided triage and notification (CADt). This type of software as a medical device is intended to prioritize reviews of radiological images with time-sensitive findings, thus shortening the waiting time for patients with these findings. While many CADt devices have been deployed into clinical workflows and have been shown to improve patient treatment and clinical outcomes, quantitative methods to evaluate the wait-time-savings from their deployment are not yet available. In this paper, we apply queueing theory methods to evaluate the wait-time-savings of a CADt by calculating the average waiting time per patient image without and with a CADt device being deployed. We study two workflow models with one or multiple radiologists (servers) for a range of AI diagnostic performances, radiologist’s reading rates, and patient image (customer) arrival rates. To evaluate the time-saving performance of a CADt, we use the difference in the mean waiting time between the diseased patient images in the with-CADt scenario and that in the without-CADt scenario as our performance metric. As part of this effort, we have developed and also share a software tool to simulate the radiology workflow around medical image interpretation, to verify theoretical results, and to provide confidence intervals for the performance metric we defined. We show quantitatively that a CADt triage device is more effective in a busy, short-staffed reading setting, which is consistent with our clinical intuition and simulation results. Although this work is motivated by the need for evaluating CADt devices, the evaluation methodology presented in this paper can be applied to assess the time-saving performance of other types of algorithms that prioritize a subset of customers based on binary outputs.

On disease and healing: a theoretical sketch

The onset and progression of a neurological disease can often be explained in terms of brain-network alteration. They can be formalized as the action of an operator representing the disease, the so-called K-operator, acting on the network. The healing process can thus be seen as the inverse of the disease mechanism. However, perfect healing is often impossible to achieve. Here, we formalize the ideal healing in terms of perturbative variation of the possible partial healing. The modeling and analytical strategy is based on techniques from theoretical physics, with the language of matrix operators. In addition, using the language of category theory, we also formalize the progressive abstraction from the reality of diseased patients to the definition of a disease and the comparison between different diseases as a natural transformation between colimits. This theoretical presentation can provide a new, interdisciplinary perspective on neurological investigation and possibly foster new theoretical-experimental developments.

Joint meta-analysis of two diagnostic tests accounting for within and between studies dependence.

There is an extensive literature on methods for meta-analysis of diagnostic test accuracy, but it mainly focuses on a single test. A multinomial generalised linear mixed model was recently proposed for the joint meta-analysis of studies comparing two tests on the same participants in a paired tests design with a gold standard. In this setting, we propose a novel model for joint meta-analysis of studies comparing two diagnostic tests which assumes independent multinomial distributions for the counts of each combination of test results in diseased and non-diseased patients, conditional on the latent vector of probabilities of each combination of test results in diseased and non-diseased patients. For the random effects distribution of the latent proportions, we employ a one-truncated D-vine copula that can provide tail dependence or asymmetry. The proposed model includes the multinomial generalised linear mixed model as a special case, accounts for the within-study dependence induced because the tests are applied to the same participants, allows for between-studies dependence, and can also operate on the original scale of the latent proportions. The latter enables the derivation of summary receiver operating characteristic curves. Our methodology is demonstrated with simulation studies and a meta-analysis of screening for Down's syndrome with two tests: shortened humerus and shortened femur.

Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.

Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help to predict cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters. We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created in silico datasets by simulating various protocols applied to a population of models with known conductance variations, and then fitted parameters to those datasets. We found that calibrating to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation also held when the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses.

Serum mRNA levels of cytokeratin-19 and vascular endothelial growth factor in oral squamous cell carcinoma and oral potentially malignant disorders using RT-PCR

BackgroundOral cancers, which include tumors of the oral cavity, salivary glands, and pharynx, are becoming increasingly prevalent worldwide. Squamous cell carcinoma accounts for over 90% of malignant oral lesions, with oral squamous cell carcinoma (OSCC) being notably common in the Indian subcontinent and other regions of Asia. This is especially true in South-Central Asia, including Sri Lanka, where it is particularly prevalent among men. This study aims to evaluate the levels of Vascular Endothelial Growth Factor-A (VEGF-A) and Cytokeratin-19 (CK-19) mRNAs in whole blood as a potential method for the early detection of OSCC.MethodsThe study included 40 patients (each from OSCC, Oral Submucous Fibrosis (OSF), Oral Leukoplakia (OLK), Oral Lichen Planus (OLP), and 10 healthy controls. The expression levels of VEGF-A and CK-19 mRNAs were measured from extracellular RNA extracted from whole blood samples using real-time reverse transcription polymerase chain reaction (RT-PCR) with sequence-specific primers. Receiver operating characteristic (ROC) curve analysis was used to evaluate the effectiveness of these biomarkers in detecting OSCC.ResultsThe results demonstrated a significant increase in blood transcripts of the candidate mRNAs CK-19 and VEGF-A in patients with OSCC, OSF, OLK, and OLP. The Wilcoxon signed-rank test revealed a p-value of 0.002 for each specific comparison between diseased patients and healthy controls (i.e., OSCC vs. HC, OSF vs. HC, OLP vs. HC, OLK vs. HC) for both CK-19 and VEGF-A. When these two biomarkers were used together, they provided a 60% predictive probability for patients with OSCC (p = 0.023).ConclusionThis study highlights the efficacy of blood mRNA transcriptome diagnostics in detecting OSCC. This innovative clinical approach has the potential to be a robust, efficient, and reliable tool for early cancer detection. Blood-based transcriptomes could be further explored for their effectiveness in various health contexts and for routine health monitoring.

Simultaneous Detection of Collagen I Alpha II and Cytokeratin 19 mRNA by Multiplex qPCR in Liquid Biopsy in Diagnosis of Patients with Resectable Solid Tumors.

The early detection of tumors is one of the key factors in increasing overall survival in cancer patients. A wide range of cancers still do not have a system of early diagnosis; therefore, the development of new non-invasive tools in this line is essential. Accordingly, the objective of our work was to develop a non-invasive screening method for the early detection of various carcinomas in plasma using a panel that combines two markers using RT-qPCR. A retrospective case-control study was conducted to develop a cancer screening test based on the detection of stromal and epithelial biomarkers (COL1A2 and KRT19) in plasma. The expression of biomarkers was evaluated using multiplex quantitative PCR applied to 47 cases with non-metastatic tumors and 13 control participants. For both biomarkers, a cut-off value was stablished using Youden's J index through ROC curve analysis and areas under the curve (AUC) were calculated. The plasma mRNA expression level of both biomarkers was significantly higher in diseased versus healthy patients. Moreover, ROC curve analysis showed an AUC value of 0.897 for the combined model. This model also resulted in a cutoff value of 0.664, as well as a sensitivity of 83% and a specificity of 84.6%. These results suggest that the plasma expression levels of COL1A2 and KRT19 could a have potential role in detecting various types of cancer at the early stages. The combined analysis of both stromal and epithelial biomarkers would provide a non-invasive screening method that would allow us to differentiate patients with an active neoplastic process.

Partial reconstruction of sparse and incomplete point clouds applied to the generation of corneal topographic maps of healthy and diseased patients

The presence of unmeasured areas or areas with missing data in corneal topographies greatly affect the quality of digital corneal models. These are more frequent in posterior than in anterior corneal surface. This work seeks to complete and improve digital corneal models generated from incomplete point clouds obtained with commercial tomographic equipment, applying three interpolation/extrapolation techniques based on population data (Polynomial, Biharmonic Splines and Cubic Radial Base Functions). 43 personalized corneal models of patients with different grades of keratoconus were used to test each interpolation method. All interpolation results were compared using the Mean Average Percentage Error (MAPE) index, observing that it is possible to interpolate/extrapolate up to the radius 5.2 mm on the anterior face and up to 4.2 mm on the posterior face in general, but none of the methods stand out above the others for all the situations considered. Consequently, extrapolation method must be chosen carefully.

γH2AX as an Indicator for DNA Double-Strand Breaks in Helicobacter pylori-Associated Chronic Gastritis among Jordanian Patients: A Retrospective Study

Background and Aims: Serine 139 phosphorylation of H2AX (γH2AX) is a biomarker for an early response to DNA double-strand breaks (DSB) and to monitor DNA damage and resolution. This study aimed to measure the rate of γH2AX expression associated with H. pylori infection in Jordanian patients with chronic gastritis. Materials and Methods: A retrospective case-control study was designed to evaluate the rate of γH2AX expression in the epithelium of gastric tissue in subjects chronically infected with H. pylori. A total of 75 gastric biopsy samples embedded in paraffin were chosen from the library, including 50 samples with chronic H. pylori infection and 25 negative samples for H. pylori and any other gastric pathologies. PCR and immunohistochemistry were used to confirm the diagnosis of H. pylori-infected and noninfected gastric biopsies, and the rate of γH2AX formation was analyzed in the mucosa using immunohistochemical staining analyses. Results: PCR and immunohistochemistry proved H. pylori infection in the gastric biopsies of diseased patients (n = 50) and the absence of H. pylori infection in negative samples (n = 25). A strong nuclear signal of γH2AX was detected in the positive samples using immunohistochemistry compared to the undetected signal in the noninfected samples of the gastric mucosa. Conclusion: Our findings show that H. pylori infection is accompanied with high levels of DSBs. This may play a role in the increased risk for tumor initiation associated with H. pylori carriage.