The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.

Nucleic acid tests (NATs) are considered as gold standard in molecular diagnosis. To meet the demand for onsite, point-of-care, specific and sensitive, trace and genotype detection of pathogens and pathogenic variants, various types of NATs have been developed since the discovery of PCR. As alternatives to traditional NATs (e.g., PCR), isothermal nucleic acid amplification techniques (INAATs) such as LAMP, RPA, SDA, HDR, NASBA, and HCA were invented gradually. PCR and most of these techniques highly depend on efficient and optimal primer and probe design to deliver accurate and specific results. This chapter starts with a discussion of traditional NATs and INAATs in concert with the description of computational tools available to aid the process of primer/probe design for NATs and INAATs. Besides briefly covering nanoparticles-assisted NATs, a more comprehensive presentation is given on the role CRISPR-based technologies have played in molecular diagnosis. Here we provide examples of a few groundbreaking CRISPR assays that have been developed to counter epidemics and pandemics and outline CRISPR biology, highlighting the role of CRISPR guide RNA and its design in any successful CRISPR-based application. In this respect, we tabularize computational tools that are available to aid the design of guide RNAs in CRISPR-based applications. In the second part of our chapter, we discuss machine learning (ML)- and deep learning (DL)-based computational approaches that facilitate the design of efficient primer and probe for NATs/INAATs and guide RNAs for CRISPR-based applications. Given the role of microRNA (miRNAs) as potential future biomarkers of disease diagnosis, we have also discussed ML/DL-based computational approaches for miRNA-target predictions. Our chapter presents the evolution of nucleic acid-based diagnosis techniques from PCR and INAATs to more advanced CRISPR/Cas-based methodologies in concert with the evolution of deep learning (DL)- and machine learning (ml)-based computational tools in the most relevant application domains.

Interval-specific likelihood ratios and probability-based models for interpreting combined CSF biomarkers for Alzheimer's disease.

BACKGROUND: In Alzheimer's disease (AD) diagnosis, a cerebrospinal fluid (CSF) biomarker panel is commonly interpreted with binary cutoff values. However, these values are not generic and do not reflect the disease continuum. We explored the use of interval-specific likelihood ratios (LRs) and probability-based models for AD using a CSF biomarker panel. METHODS: CSF biomarker (Aß1-42, tTau and pTau181) data for both a clinical discovery cohort of 241 patients (measured with INNOTEST) and a clinical validation cohort of 129 patients (measured with EUROIMMUN), both including AD and non-AD dementia/cognitive complaints were retrospectively retrieved in a single-center study. Interval-specific LRs for AD were calculated and validated for univariate and combined (Aß1-42/tTau and pTau181) biomarkers, and a continuous bivariate probability-based model for AD, plotting Aß1-42/tTau versus pTau181 was constructed and validated. RESULTS: LR for AD increased as individual CSF biomarker values deviated from normal. Interval-specific LRs of a combined biomarker model showed that once one biomarker became abnormal, LRs increased even further when another biomarker largely deviated from normal, as replicated in the validation cohort. A bivariate probability-based model predicted AD with a validated accuracy of 88% on a continuous scale. CONCLUSIONS: Interval-specific LRs in a combined biomarker model and prediction of AD using a continuous bivariate biomarker probability-based model, offer a more meaningful interpretation of CSF AD biomarkers on a (semi-)continuous scale with respect to the post-test probability of AD across different assays and cohorts.

Visibility of esophageal squamous cell carcinoma under iodine staining on texture and color enhancement imaging.

Objective: Iodine staining on white light imaging (WLI) is the gold standard for detecting and demarcating esophageal squamous cell carcinoma (ESCC). We examined the effects of texture and color enhancement imaging (TXI) on improving the endoscopic visibility of ESCC under iodine staining. Methods: Twenty ESCC lesions that underwent endoscopic submucosal dissection were retrospectively included. The color difference between ESCC and the surrounding mucosa (ΔEe) on WLI, TXI, and narrow-band imaging was assessed, and ΔEe under 1% iodine staining on WLI and TXI. Furthermore, the visibility grade determined by endoscopists was evaluated on each imaging. Result: The median ΔEe was greater on TXI than on WLI (14.53 vs. 10.71, respectively; p < 0.005). Moreover, the median ΔEe on TXI under iodine staining was greater than the median ΔEe on TXI and narrow-band imaging (39.20 vs. 14.53 vs. 16.42, respectively; p < 0.005 for both). A positive correlation in ΔEe under iodine staining was found between TXI and WLI (correlation coefficient = 0.61, p < 0.01). Moreover, ΔEe under iodine staining on TXI in each lesion was greater than the corresponding ΔEe on WLI. The visibility grade assessed by endoscopists on TXI was also significantly greater than that on WLI under iodine staining (p < 0.01). Conclusions: The visibility of ESCC after iodine staining was greater on TXI than on WLI.

Rare case of mantle cell lymphoma of the lacrimal sac

ABSTRACT Mantle cell lymphoma of the ocular and periorbital regions is extremely rare but should be considered in the differential diagnosis of lesions affecting the periorbital tissues. In this study, we present a rare case of mantle cell lymphoma of the lacrimal sac in a 65-year-old male presenting with a mass in the lacrimal sac region and epiphora. After clinical examinations and imaging studies, the mucocele was misdiagnosed. Considering the unexpected findings during external dacryocystorhinostomy, a frozen biopsy was performed, which confirmed the diagnosis of lymphoma.

Anterior lamellar corneoscleral keratoplasty for the management of corneal thinning following treatment with mitomycin-C and interferon to treat highly suspected ocular surface squamous neoplasia: a case report

ABSTRACT A patient presented with corneoscleral thinning five months after the treatment of suspected ocular squamous surface neoplasia with mitomycin-C and interferon. For tectonic and aesthetic purposes, we decided to perform lamellar corneoscleral transplantation. The approach used established new tectonic support and corneal homeostasis. This technique might be an option in similar cases.

Clinical, epidemiological, and care profile of hospitalized patients with retinoblastoma in Brazil

ABSTRACT Purpose: To describe the epidemiological and clinical profile of hospitalized patients with retinoblastoma in Brazil. Methods: Using data from the Hospital Cancer Registry of the Instituto Nacional de Câncer, patients with the morphological codes of retinoblastoma who were diagnosed between 2000 to 2018, aged 0-19 years, and followed up in registered hospitals (analytical cases) were selected. The relative and absolute frequencies of demographic, clinical, diagnostic, therapeutic, and outcome variables were described. Hospital performance indicators were calculated and compared between hospitals qualified and not qualified to treat pediatric oncology cases and between hospitals with different case volumes (<20, 20-75, >75 cases). Results: Of the 2,269 identified analytical cases from 86 institutions, 48% were from the Southeast, 54% were male, and 66% were aged <4 years. The proportion of missing data (NA) was too high for several variables. Approximately 84% of the patients were from the public health system, 40% had a positive family history, and 88% had unilateral involvement. The first treatment included surgery in 58.3% of the patients (NA=2), Approximately 36.6% of these patients achieved complete remission, 10.8% achieved partial remission, and 12.7% died (NA=59%). Hospital performance indicators were within the target in >90% of the patients. The median time between the first appointment and diagnosis (6 days, interquartile range [IQR] 1-14) was significantly lower and the median time to death was longer (343 days, IQR, 212-539) in high-volume hospitals (>75 cases) than in medium- and low-volume hospitals. Conclusions: Despite the high proportion of missing data, we found that the delay in diagnosis is due to prehospital factors. Additionally, there is a need for educational programs for healthcare professionals and families that emphasize early identification and referral to specialized centers. Future studies should focus on the impact of Hospital Cancer Registry data completeness on outcomes, causes of delay in diagnosis, regional inequalities, and barriers to accessing specialized services.

AI for BPH Surgical Decision-Making: Cost Effectiveness and Outcomes.

PURPOSE OF REVIEW: Benign prostatic hyperplasia (BPH) is prevalent in nearly 70% of men over the age of 60, leading to significant clinical challenges due to varying symptom presentations and treatment responses. The decision to undergo surgical intervention is not straightforward; the American Urological Association recommends consideration of surgical treatment after inadequate or failed response to medical therapy. This review explores the role of artificial intelligence (AI), including machine learning and deep learning models, in enhancing the decision-making processes for BPH management. RECENT FINDINGS: AI applications in this space include analysis of non-invasive imaging modalities, such as multiparametric Magnetic Resonance Imaging (MRI) and Ultrasound, which enhance diagnostic precision. AI models also concatenate serum biomarkers and histopathological analysis to distinguish BPH from prostate cancer (PC), offering high accuracy rates. Furthermore, AI aids in predicting patient outcomes post-treatment, supporting personalized medicine, and optimizing therapeutic strategies. AI has demonstrated potential in differentiating BPH from PC through advanced imaging and predictive models, improving diagnostic accuracy, and reducing the need for invasive procedures. Despite promising advancements, challenges remain in integrating AI into clinical workflows, establishing standard evaluation metrics, and achieving cost-effectiveness. Here, we underscore the potential of AI to improve patient outcomes, streamline BPH management, and reduce healthcare costs, especially with continued research and development in this transformative field.

Prenatal Sonographic Features of Rubinstein-Taybi Syndrome-A Small Case Series of a Rare Syndrome.

Rubinstein-Taybi syndrome (RSTS) is a rare syndrome characterized by intellectual disability, distinctive facial features and distal limb abnormalities. RSTS is indicated by clinical features and confirmed via genetic testing. In this prenatal case series, we report four cases of RSTS with various sonographic features. Some features, such as corpus callosum dysgenesis, are nonspecific, but they may be the first sign apparent, as they appear early in pregnancy. Others, like beaked nose, shawl scrotum, premature coccygeal ossification, and overly mature scrotal sac with excessive rugae, are distinctive, but they may only be apparent in advanced gestation.

Sclerosing Odontogenic Carcinoma: UPLIFTS and pitfalls.

Sclerosing Odontogrenic Carcinoma (SOC) is a recent addition to the category of odontogenic tumours, which was first described by Koutlas et al. in 2008. It was described as primary intraosseous carcinoma with bland cytology, sclerotic stroma with presence of local infiltration showing aggressive behaviour. Following its discovery and the presentation of first case, only a handful of cases have been reported till date, which may be due to underreporting of the cases or inclusion of the case to other diagnosis since the features of this tumour overlaps with many other lesions of the oral cavity. Due to this factor, the pathogenesis of this category of tumours still remains enigmatic. The clinical features as a result of this factor are also not reported of the consistent type and overlaps with the already existing clinical features of other lesions. This lesion has only appeared till date twice in WHO classification of Odontogenic Cysts and Tumours. Thereby, the literature on this category is still in paucity. Therefore, the present review takes into account all of the features, diagnostic criteria and the markers discovered for this lesion and would provide an insight into whether this lesion is justified as a malignant lesion or should not be considered as a separate category of odontogenic tumour.

[Expert consensus on Tibetan medicine diagnosis and treatment for high altitude polycythemia].

High altitude polycythemia(HAPC) is one of the most common chronic high-altitude diseases and a prominent public health issue in the Qinghai-Xizang Plateau region of China. Tibetan medicine has provided a safe and effective treatment approach for HAPC, but there is currently no expert consensus on Tibetan medicine diagnosis and treatment for the disease. This consensus followed the principles of evidence-based medicine and learned the procedure and methods of Technical specifications on developing expert consensus for clinical practice guideline in traditional Chinese medicine recommended by China Association of Chinese Medicine. Five clinical issues were identified through literature search, expert interviews, clinical research, and conference consensus. The PICO principle was used for evidence retrieval, screening, and synthesis, and the opinions of experts on high-altitude diseases and cardiovascular and cerebrovascular diseases from major Tibetan medical institutions in China, as well as some traditional Chinese medicine(TCM), western medicine, and evidence-based experts, were widely solicited. Recommendations and consensus suggestions were formed through one expert consensus meeting and two rounds of Delphi expert questionnaire surveys. The consensus included disease diagnosis, etiology and pathogenesis, syndrome classification, clinical treatment, outcome evaluation, prevention and care, and other contents. Therapies for HAPC included Tibetan medicine treatments based on syndrome differentiation, single formula or patent medicine, and external treatment. Each treatment had corresponding levels of evidence and recommendations. This consensus was guided by solving clinical problems, combining disease diagnosis and syndrome differentiation and highlighting the characteristics and advantages of Tibetan medicine, with a view to promoting the standardization of Tibetan medicine diagnosis, treatment, and research on HAPC and improving the level of prevention and treatment.

Recent advances in two-dimensional materials for the diagnosis and treatment of neurodegenerative diseases.

With the size of the aging population increasing worldwide, the effective diagnosis and treatment of neurodegenerative diseases (NDDs) has become more important. Two-dimensional (2D) materials offer specific advantages for the diagnosis and treatment of NDDs due to their high sensitivity, selectivity, stability, and biocompatibility, as well as their excellent physical and chemical characteristics. As such, 2D materials offer a promising avenue for the development of highly sensitive, selective, and biocompatible theragnostics. This review provides an interdisciplinary overview of advanced 2D materials and their use in biosensors, drug delivery, and tissue engineering/regenerative medicine for the diagnosis and/or treatment of NDDs. The development of 2D material-based biosensors has enabled the early detection and monitoring of NDDs via the precise detection of biomarkers or biological changes, while 2D material-based drug delivery systems offer the targeted and controlled release of therapeutics to the brain, crossing the blood-brain barrier and enhancing treatment effectiveness. In addition, when used in tissue engineering and regenerative medicine, 2D materials facilitate cell growth, differentiation, and tissue regeneration to restore neuronal functions and repair damaged neural networks. Overall, 2D materials show great promise for use in the advanced treatment of NDDs, thus improving the quality of life for patients in an aging population.

Benign glomus tumor of prostate: a case report.

Glomus tumor (GT) is a neoplastic lesion of mesenchymal origin arising from the neuromyoarterial canal or glomus body. Although most GT occur in the peripheral soft tissue and extremities, these tumors can grow anywhere in the body. Here, we describe an uncommon case of GT involving the prostate.

When an inguinal hernia is more than just a hernia with ovary and fallopian tube involvement: a case report.

BACKGROUND: Finding an ovary and/or fallopian tube within an indirect inguinal hernia is a rare occurrence that can be detected incidentally during elective surgery or present as a medical emergency requiring immediate intervention. Hence, it poses a difficult clinical picture in a reproductive-age woman with groin mass. CLINICAL PRESENTATION: We describe the case of a 45-year-old Ethiopian woman of Amhara ethnicity who presented with a left inguinal swelling that persisted for 5 years. Physical examination revealed an irreducible, non-tender lump in the left groin and an ultrasonography scan confirmed the presence of an indirect inguinal hernia. The patient was then scheduled for elective hernia repair. During the surgery, both her left ovary and fallopian tube were found within the hernial sac. The contents were released from the sac, high ligation performed, and the inguinal floor repaired with mesh. DISCUSSION: Inguinal hernias in women are rare and often present a diagnostic challenge. Although the exact pathogenesis of inguinal hernias containing female genital organs is unknown, some risk factors have been postulated. Diagnosis should start with a physical exam and imaging, but many of the cases have been intraoperative surprises. Management is primarily surgical, ranging from simple reduction and hernia repair to salpingo-oophorectomy depending on the status of the hernia contents. CONCLUSION: This report emphasizes the importance of maintaining a high index of suspicion when examining females with inguinal hernias to ensure accurate diagnosis and management of tubo-ovarian hernias. Although rare, inguinal hernias containing female genital organs should be considered in the differential diagnosis of inguinal hernias, as early detection and appropriate surgical management can prevent potential complications.

A Challenging Case of Recurrent Fever.

Syndrome of undifferentiated recurrent fever (SURF) includes heterogeneous episodes of systemic inflammation without documented infection, without response to antibiotherapy, and characterized by a paucity of specific clinical or molecular criteria. Colchicine is an effective treatment with an impact on morbimortality. We describe a case of a previously healthy one-year-old male, with consanguineous ancestry, admitted four times due to recurrent fever, associated with nonspecific symptoms and an increase of inflammatory markers in a sepsis-like pattern. No consistent infection was documented, and there was no response to broad-spectrum antibiotics. The evolution revealed corticosteroid dependency. The autoinflammatory syndrome-targeted next-generation sequencing (NGS) gene panel didn't detect relevant pathogenic variants. SURF was postulated as a diagnosis of exclusion, and the effectiveness of colchicine supports an autoinflammatory etiology. We aimed to draw attention to recurrent fevers associated with autoinflammatory disorders due to their challenging diagnosis. Improved understanding of immune pathways and advances in genetic testing will enable greater accuracy in the approach.

Does hope mediate the relationship between parent's resolution of their child's autism diagnosis and parental stress.

Introduction: Resolution of a child's diagnosis, the process of accepting and adjusting to the reality of a child's significant diagnosis, has been often associated with decreased parental stress. Hope, a potential buffer against psychological distress, has been suggested as a potential explanation for this relationship. However, the mediating role of hope in the relationship between resolution of diagnosis and parental stress has not been explored. Methods: This study aimed to examine whether four types of hope (child, parental, societal, denial of diagnosis) mediated the relationship between resolution to an autism diagnosis and reduced parental stress. Participants included 73 parents (Mage = 43.22, SD = 7.69, female 97.3%) of autistic children (Mage = 11.15, SD = 4.56, male = 67.1%). Results: Resolution to diagnosis was negatively and significantly correlated with resolution to diagnosis, as well as child, parental and societal hope. These three hopes were also significantly and negatively correlated with parental stress. Importantly, when controlling for level of support and autism awareness, parental hope mediated the relationship between resolution to diagnosis and parental stress. Denial of diagnosis was not correlated with resolution or parental stress but did have significant but weak associate with the other hopes. Discussion: These findings suggest that hope based on parent's abilities to support their child and be supported themselves play an important role in parental stress once parents are more resolved to their child's diagnosis. Supporting parents to manage factors associated with supporting their child's needs, may benefit parents of autistic children.

Analysis of urine cell-free DNA in bladder cancer diagnosis by emerging bioactive technologies and materials.

Urinary cell-free DNA (UcfDNA) is gaining recognition as an important biomarker for diagnosing bladder cancer. UcfDNA contains tumor derived DNA sequences, making it a viable candidate for non-invasive early detection, diagnosis, and surveillance of bladder cancer. The quantification and qualification of UcfDNA have demonstrated high sensitivity and specificity in the molecular characterization of bladder cancer. However, precise analysis of UcfDNA for clinical bladder cancer diagnosis remains challenging. This review summarizes the history of UcfDNA discovery, its biological properties, and the quantitative and qualitative evaluations of UcfDNA for its clinical significance and utility in bladder cancer patients, emphasizing the critical role of UcfDNA in bladder cancer diagnosis. Emerging bioactive technologies and materials currently offer promising tools for multiple UcfDNA analysis, aiming to achieve more precise and efficient capture of UcfDNA, thereby significantly enhancing diagnostic accuracy. This review also highlights breakthroughs in detection technologies and substrates with the potential to revolutionize bladder cancer diagnosis in clinic.

Pulp Sensitivity Testing in Multiple Sclerosis: Disease Duration and Sensory/Motor Associations-A Cross-Sectional Study.

Introduction: This study explores a relatively unexplored aspect of multiple sclerosis (MS) by examining the sensitivity threshold of dental pulp as a potential indicator of neuropathy in MS patients. Building upon earlier research that focused on assessing the response to electrical pulp testing in MS patients who did not have a history of trigeminal neuralgia, this survey is aimed at delving into the relationship between MS duration and the threshold for stimulation in response to pulp sensitivity tests. Materials and Methods: This study encompassed a total of 124 maxillary central incisors from patients diagnosed with relapsing-remitting multiple sclerosis (RRMS). The participants were uniform in terms of age, falling within the 18-50 years range, and all had RRMS with no history of trigeminal neuralgia. The electric pulp sensitivity test was conducted on all samples, and the results of the electric pulp testing (EPT) were recorded according to the grade of the pulp tester that elicited a response. The threshold was considered reached when the patient first experienced a burning sensation after EPT application and the use of 1,1,1,2-tetrafluoroethane spray. Data analysis employed paired t-tests, Fisher's exact test, and Spearman correlation, with a significance level set at p < 0.05. Results: Based on the study's findings, the average response value to EPT was 2.69 ± 1.17, while the response time to the cold test was 2.61 ± 1.03 s. There was no statistically significant difference in the response to the cold test based on age (p = 0.45). However, it was observed that the mean response time to the cold test was significantly longer among male participants (p = 0.001). No significant differences were identified in the pulpal response to EPT or the cold test between patients with and without sensory-motor involvement (p > 0.05). Furthermore, Spearman's analysis revealed a noteworthy positive correlation between the electrical pulp threshold and the time taken to respond to the cold test (p = 0.025, r = 0.2). Conclusions: The utilization of the pulpal sensitivity test in MS patients holds promise for practical clinical use. Notably, individuals with a more extended duration of the disease exhibited a notably elevated threshold for both the EPT and the cold test conducted on their maxillary central incisors.

Metabolic reprogramming-related gene classifier distinguishes malignant from the benign pulmonary nodules.

The current existing classifiers for distinguishing malignant from benign pulmonary nodules is limited by effectiveness or clinical practicality. In our study, we aimed to develop and validate a gene classifier for lung cancer diagnosis. To identify the genes involved in this process, we used the weighted gene co-expression network analysis to analyze gene expression datasets from Gene Expression Omnibus (GEO). We identified the three most relevant modules associated with malignant nodules and performed functional enrichment analysis on them. The results indicated significant involvement in metabolic, immune-related, cell cycle, and viral-related processes. All three modules showed enrichment in metabolic reprogramming pathways. Based on these genes, we intersected genes from the three modules with metabolic reprogramming-related genes and further intersected with differentially expressed genes to get 78 genes. After machine learning algorithms and manual selection, we finally got a nine-gene classifier consisting of SEC24D, RPSA, PSME3, PSMD8, PSMB7, NCOA1, MED12, LPCAT1, and AKR1C3. Our developed and validated classifier-based model demonstrated good discrimination, with an area under the curve (AUC) of 0.763 in the development cohort, 0.744 in the internal validation cohort, and 0.718 in the external validation cohort, and outperformed previous clinical models. Moreover, the addition of nodule size improved the predictive capability of the classifier. We further verify the expression of the gene in the classifier using TCGA lung cancer samples and found eight of the genes showed significant differential expression in lung adenocarcinoma while all nine genes showed significant differential expression in lung squamous carcinoma. Our findings underscore the significance of metabolic reprogramming pathways in patients with malignant pulmonary nodules, and our gene classifier can assist clinicians in differentiating benign from malignant pulmonary nodules in clinical settings.

A novel super-resolution microscopy platform for cutaneous alpha-synuclein detection in Parkinson's disease.

Alpha-synuclein (aSyn) aggregates in the central nervous system are the main pathological hallmark of Parkinson's disease (PD). ASyn aggregates have also been detected in many peripheral tissues, including the skin, thus providing a novel and accessible target tissue for the detection of PD pathology. Still, a well-established validated quantitative biomarker for early diagnosis of PD that also allows for tracking of disease progression remains lacking. The main goal of this research was to characterize aSyn aggregates in skin biopsies as a comparative and quantitative measure for PD pathology. Using direct stochastic optical reconstruction microscopy (dSTORM) and computational tools, we imaged total and phosphorylated-aSyn at the single molecule level in sweat glands and nerve bundles of skin biopsies from healthy controls (HCs) and PD patients. We developed a user-friendly analysis platform that offers a comprehensive toolkit for researchers that combines analysis algorithms and applies a series of cluster analysis algorithms (i.e., DBSCAN and FOCAL) onto dSTORM images. Using this platform, we found a significant decrease in the ratio of the numbers of neuronal marker molecules to phosphorylated-aSyn molecules, suggesting the existence of damaged nerve cells in fibers highly enriched with phosphorylated-aSyn molecules. Furthermore, our analysis found a higher number of aSyn aggregates in PD subjects than in HC subjects, with differences in aggregate size, density, and number of molecules per aggregate. On average, aSyn aggregate radii ranged between 40 and 200 nm and presented an average density of 0.001-0.1 molecules/nm2. Our dSTORM analysis thus highlights the potential of our platform for identifying quantitative characteristics of aSyn distribution in skin biopsies not previously described for PD patients while offering valuable insight into PD pathology by elucidating patient aSyn aggregation status.