Mapping the Geographical Distribution of the Mucosa-Associated Gut Microbiome in GI-Symptomatic Children with Autism Spectrum Disorder.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by cognitive, behavioral, and communication impairments. In the last few years, it has been proposed that alterations in the gut microbiota may contribute to an aberrant communication between the gut and brain in children with ASD. Consistent with this notion, several studies have demonstrated that children with ASD have an altered fecal microbiota compared to typically developing (TD) children. However, it is unclear where along the length of the gastrointestinal (GI) tract these alterations in microbial communities occur. Additionally, the variation between specific mucosa-associated communities remains unknown. To address this gap in knowledge of the microbiome associated with ASD, biopsies from the antrum, duodenum, ileum, ascending colon, and rectum of children with ASD and age- and sex-matched TD children were examined by 16s rRNA sequencing. We observed an overall elevated abundance of Bacillota and Bacteroidota and decreased abundance of Pseudomonadota in all GI tract regions of both male and female ASD children compared to TD children. Further analysis at the genera level revealed unique differences in the microbiome in the different regions of the GI tract in ASD children compared to TD children. We also observed sex-specific differences in the gut microbiota composition in children with ASD. These data indicate that the microbiota of ASD children is altered at multiple regions of the GI tract and that different anatomic locations have unique alterations in mucosa-associated bacterial genera.

Detection of Bacteria in Bladder Mucosa of Adult Females.

PURPOSE: Interstitial cystitis/bladder pain syndrome is a chronic urological condition diagnosed in nearly 8 million females in the United States. Whether urinary microbiota play an etiological role remains controversial. Most studies assessed the microbiota of interstitial cystitis/bladder pain syndrome patients with voided or catheterized urine as a proxy for bladder urothelium; however, urine may not be a true reflection of the bladder microbiota. Bladder biopsy tissue may provide a more accurate, and thus more clinically relevant, picture of bladder microbiota. MATERIALS AND METHODS: Bladder biopsy tissues were obtained from: (1) 30 females with interstitial cystitis/bladder pain syndrome (18-80 years old) via cystoscopically guided cold-cup biopsy following therapeutic bladder hydrodistention, and (2) 10 non-interstitial cystitis/bladder pain syndrome females undergoing pelvic organ prolapse repair. To detect bacteria, technical duplicates of each RNAlater-preserved biopsy were subjected to 16S rRNA gene sequencing. To visualize bacteria, paraformaldehyde-fixed, paraffin-embedded biopsies were subjected to a combined multiplexed fluorescence in situ hybridization and fluorescence immunohistochemistry assay and confocal microscopy. RESULTS: Bacteria were detected by 16S rRNA gene sequencing in at least 1 technical duplicate of most biopsies. The most abundant genus was Staphylococcus, followed by Lactobacillus; Escherichia was common but not abundant. There was no significant difference between interstitial cystitis/bladder pain syndrome patients and controls (P > .05). Combined fluorescence in situ hybridization and immunohistochemistry reproducibly detected 16S rRNA in epithelial cells and shed cells in the urothelium and lesioned areas and capillary walls in the lamina propria of human bladder biopsy tissue. CONCLUSIONS: We conclude that urothelial and urinary microbiota are similar but not identical in adult females.

Pulsed electromagnetic field (PEMF) as an adjunct therapy for pain management in interstitial cystitis/bladder pain syndrome.

INTRODUCTION AND HYPOTHESIS: Patients with interstitial cystitis/bladder pain syndrome (IC/BPS) often experience chronic pelvic and even systemic pain that can be difficult to clinically manage. Pulsed electromagnetic field (PEMF) therapy, a non-invasive strategy that has shown significant efficacy for pain reduction in other chronic pain conditions, may provide benefit for pain management in patients with IC/BPS. METHODS: PEMF delivery to patients occurs via a bio-electromagnetic-energy device which consists of a flexible mat (180 × 50 cm) that the patient lies on for systemic, full-body delivery and/or a flexible pad (50 × 15 cm) for targeted delivery to a specific body region (e.g., pelvic area). The duration of individual sessions, number of sessions per day, total number of sessions, and follow-up observation period vary between previously published studies. Positive outcomes are typically reported as a significant reduction in visual analog scale (VAS) pain score and functional improvement assessed using validated questionnaires specific to the condition under study. RESULTS AND CONCLUSIONS: The use of PEMF has been evaluated as a therapeutic strategy for pain management in several clinical scenarios. Randomized, double-blinded, placebo-controlled trials have reported positive efficacy and safety profiles when PEMF was used to treat non-specific low back pain, patellofemoral pain syndrome, chronic post-operative pain, osteoarthritis-related pain, rheumatoid arthritis-related pain, and fibromyalgia-related pain. Based on these positive outcomes in a variety of pain conditions, clinical trials to evaluate whether PEMF can provide a safe, non-invasive therapeutic approach to improve symptoms of chronic pain and fatigue in patients with IC/BPS are warranted.

Functional genomic analyses of IC/BPS patient subgroups: a pilot study.

INTRODUCTION: To further facilitate understanding of disease pathophysiology and patient stratification in interstitial cystitis/bladder pain syndrome (IC/BPS), we utilized molecular phenotyping to compare three clinically distinct IC/BPS patient subgroups. MATERIALS AND METHODS: Total RNA (miRNA and mRNA) was isolated via standard protocols from IC/BPS patient bladder biopsies and assayed on whole genome and microRNA expression arrays. Data from three patient subgroups (n = 4 per group): (1) low bladder capacity (BC; ≤ 400 cc) without Hunner's lesion, (2) low BC with Hunner's lesion, and (3) non-low BC (> 400 cc) were used in comparative analyses to evaluate the influence of BC and HL on gene expression profiles in IC/BPS. RESULTS: The BC comparison (Group 1 v 3) identified 54 miRNAs and 744 mRNAs. Eleven miRNAs mapped to 40 genes. Hierarchical clustering of miRNA revealed two primary clusters: (1) 3/4 low BC patients; (2) 4/4 non-low and 1/4 low BC patients. Clustering of mRNA provided clear separation based on BC. The HL comparison (Group 1 v 2) identified 16 miRNAs and 917 mRNAs. 4 miRNAs mapped to 13 genes. Clustering of miRNA and mRNA revealed clear separation based on HL status. CONCLUSIONS: Significant molecular differences in IC/BPS were found to be associated with the low BC phenotype (e.g., an upregulation of cell proliferation and inflammation marker genes), as well as additional molecular findings that further define the HL+ phenotype (e.g., upregulation of genes involved in bioenergetics reactions) and suggest oxidative stress may play a role.

Hydrodistention does not alter bladder gene expression profiles in patients with non-Hunner lesion interstitial cystitis/bladder pain syndrome.

AIMS: Gene expression profiling of bladder biopsies in patients with interstitial cystitis/bladder pain syndrome (IC/BPS), typically obtained following therapeutic bladder hydrodistention (HOD), is used to improve our understanding of molecular phenotypes. The objective of this study was to determine if the HOD procedure itself impacts the biopsy gene expression profile and, by extension, whether biopsies from non-HOD bladders are appropriate controls. METHODS: Bladder biopsies were obtained just before HOD and immediately following HOD from 10 consecutively recruited IC/BPS patients undergoing therapeutic HOD. Biopsies were also obtained from four non-IC/BPS patients who did not undergo HOD (controls). Total RNA was isolated from each of the 24 samples and used to query whole-genome microarrays. Differential gene expression analysis was performed to compare expression profiles of IC/BPS biopsies before and after HOD, and between IC/BPS and control biopsies. RESULTS: Principal component analysis revealed complete separation between gene expression profiles from IC/BPS and control samples (q ≤ 0.05) and while IC/BPS samples before and after HOD showed no significant differences in expressed genes, 68 transcripts were found to be significantly different between IC/BPS and control samples (q ≤ 0.05). CONCLUSIONS: The bladder HOD procedure itself does not significantly change gene expression within the IC/BPS patient bladder, a finding that provides evidence to support the use of biopsies from non-IC/BPS patients that have not undergone HOD as controls for gene expression studies.

Molecular Pathways Underlying Adaptive Repair of the Injured Kidney: Novel Donation After Cardiac Death and Acute Kidney Injury Platforms.

OBJECTIVE: To test the hypothesis that gene expression profiling in peripheral blood from patients who have undergone kidney transplantation (KT) will provide mechanistic insights regarding graft repair and regeneration. BACKGROUND: Renal grafts obtained from living donors (LD) typically function immediately, whereas organs from donation after cardiac death (DCD) or acute kidney injury (AKI) donors may experience delayed function with eventual recovery. Thus, recipients of LD, DCD, and AKI kidneys were studied to provide a more complete understanding of the molecular basis for renal recovery. METHODS: Peripheral blood was collected from LD and DCD/AKI recipients before transplant and throughout the first 30 days thereafter. Total RNA was isolated and assayed on whole genome microarrays. RESULTS: Comparison of longitudinal gene expression between LD and AKI/DCD revealed 2 clusters, representing 141 differentially expressed transcripts. A subset of 11 transcripts was found to be differentially expressed in AKI/DCD versus LD. In all recipients, the most robust gene expression changes were observed in the first day after transplantation. After day 1, gene expression profiles differed depending upon the source of the graft. In patients receiving LD grafts, the expression of most genes did not remain markedly elevated beyond the first day post-KT. In the AKI/DCD groups, elevations in gene expression were maintained for at least 5 days post-KT. In all recipients, the pattern of coordinate gene overexpression subsided by 28 to 30 days. CONCLUSIONS: Gene expression in peripheral blood of AKI/DCD recipients offers a novel platform to understand the potential mechanisms and timing of kidney repair and regeneration after transplantation.

Injection location does not impact botulinum toxin A efficacy in interstitial cystitis/bladder pain syndrome patients.

INTRODUCTION: Botulinum toxin A (BTX-A) is currently used as a fourth-line therapeutic option for interstitial cystitis/bladder pain syndrome (IC/BPS) management. The purpose of this study was to determine if BTX-A injection can mitigate pain and if injection location (i.e. trigone-including versus trigone-sparing injection template) impacts treatment efficacy and/or treatment complications profile. MATERIALS AND METHODS: Female IC/BPS patients refractory to conservative management strategies were prospectively enrolled and asked to complete a baseline history and physical exam, post-void residual (PVR) urine volume determination, O'Leary Sant (OLS) questionnaire, and Pelvic Pain and Urgency/Frequency Symptom Scale (PUF) questionnaire. Participants were randomly assigned to one of two treatment groups and received either: 1) a trigone-including BTX-A injection template or 2) a trigone-sparing injection template. Following therapy, patients were examined in clinic at 30 and 90 day post-treatment with symptom re-assessment via repeat questionnaires and for evidence of post-procedural complications. RESULTS: Compared to baseline, patients in both treatment groups experienced significant improvement in OLS and PUF scores at both 30 and 90 days post-treatment with BTX-A, regardless of which injection template was used (p < 0.05). Complications resulting from BTX-A were minimal (most commonly urinary tract infection (UTI) and urinary retention) and not significantly different between the treatment groups (p > 0.05). No distant spread of BTX-A was observed in any patient in either treatment group. CONCLUSIONS: BTX-A treatment using either a trigone-sparing or trigone-including injection template resulted in significant, but not location-dependent, improvement in IC/BPS symptom scores at 30 and 90 day points post-procedure with no significant difference in post-treatment complication profiles.

Non-bladder centric interstitial cystitis/bladder pain syndrome phenotype is significantly associated with co-occurring endometriosis.

INTRODUCTION: Interstitial cystitis/bladder pain syndrome (IC/BPS) and endometriosis are coexistent diagnoses in 48%-65% of women with chronic pelvic pain (CPP), suggesting that dual screening may be warranted. To further investigate the clinical relationship and risk factors between these two conditions, we performed a retrospective review of our large IC/BPS patient data registry. MATERIALS AND METHODS: We evaluated IC/BPS patients who were prospectively enrolled into our registry who completed validated questionnaires and underwent therapeutic hydrodistension, during which anesthetic bladder capacity (BC) and Hunner's lesion (HL) status were recorded. Demographic/medical history were reviewed. IC/BPS patients with co-occurring endometriosis diagnosis versus those without were compared using descriptive statistics as well as multivariate regression analyses to determine predictors of co-occurring disease. RESULTS: Of 431 IC/BPS participants, 82 (19%) were also diagnosed with endometriosis. These women were significantly younger, had increased prevalence of non-low BC (> 400 cc), and decreased prevalence of HL (p < 0.05). Patients with co-occurring endometriosis also had increased prevalence of irritable bowel syndrome (IBS), CPP, fibromyalgia, and vulvodynia (p < 0.05). On multivariate analysis, non-low BC (OR 4.53, CI 1.004-20.42, p = 0.049), CPP (OR 1.84, CI 1.04-3.24, p = 0.04), and fibromyalgia (OR 1.80, CI 1.03-3.14, p < 0.04) were significantly associated with a diagnosis of endometriosis. CONCLUSIONS: Patients with IC/BPS and co-occurring endometriosis were significantly more likely to carry a non-bladder centric IC/BPS phenotype as well as several comorbid, systemic pain diagnoses. This study characterizes features of a target IC/BPS phenotype that could potentially benefit from endometriosis and systemic pain syndrome screening.

Small fiber polyneuropathy as a potential therapeutic target in interstitial cystitis/bladder pain syndrome.

INTRODUCTION AND HYPOTHESIS: Interstitial cystitis/bladder pain syndrome (IC/BPS) and fibromyalgia (FM) are frequently co-occurring medical diagnoses in patients referred to the urology clinic for secondary and tertiary treatment options. METHODS: Abundant literature has shown that many patients with FM have small fiber polyneuropathy (SFPN) that can be confirmed via skin punch biopsy and immunological staining to measure nerve density. RESULTS AND CONCLUSIONS: This finding of SFPN provides a therapeutic target for FM and in this article we hypothesize and provide rationale for the idea that this same phenomenon (SFPN) might explain, in some IC/BPS patients, the finding of widespread pain and likewise provide a therapeutic target for these patients.

Histological evidence supports low anesthetic bladder capacity as a marker of a bladder-centric disease subtype in interstitial cystitis/bladder pain syndrome.

INTRODUCTION AND HYPOTHESIS: Low anesthetic bladder capacity has been shown to be a biomarker for bladder-centric interstitial cystitis/bladder pain syndrome (IC/BPS). The goal of this study was to determine if histopathological evidence from bladder biopsies supports anesthetic bladder capacity (BC) as a marker to distinguish a bladder-centric IC/BPS subtype. METHODS: From a review of our large IC/BPS cohort of patients undergoing hydrodistention, we identified a total of 41 patients with low BC (≤ 400 ml); an additional 41 consecutive patients with BC > 400 ml were selected as the comparator group. The original bladder mucosal biopsy pathology slides were re-reviewed by a single pathologist (blinded to patient information) using a standardized grading scale developed for this study. RESULTS: Histologically, the low BC subjects exhibited higher levels of acute inflammation (p = 0.0299), chronic inflammation (p = 0.0139), and erosion on microscopy (p = 0.0155); however, there was no significant difference in mast cell count between groups (p = 0.4431). There was no significant gender difference between the groups; female patients were the majority in both groups (low BC: 94.12%, non-low BC: 100%; p = 0.1246). Individuals in the low BC group were older (p < 0.0001), had a higher incidence of Hunner's lesions on cystoscopy (p < 0.0001), and had significantly higher scores, i.e., more bother symptoms, on two IC/BPS questionnaires (ICPI, p = 0.0154; ICSI, p = 0.0005). CONCLUSIONS: IC/BPS patients with low anesthetic bladder capacity have histological evidence of significantly more acute and chronic inflammation compared with patients with a non-low bladder capacity. These data provide additional evidence to support low bladder capacity as a marker of a distinct bladder-centric IC/BPS phenotype.

Bladder Capacity is a Biomarker for a Bladder Centric versus Systemic Manifestation in Interstitial Cystitis/Bladder Pain Syndrome.

PURPOSE: Interstitial cystitis/bladder pain syndrome presents a significant clinical challenge due to symptom heterogeneity and the myriad associated comorbid medical conditions. We recently reported that diminished bladder capacity may represent a specific interstitial cystitis/bladder pain syndrome subphenotype. The objective of this study was to investigate the relationship between anesthetic bladder capacity, and urological and nonurological clinical findings in a cohort of patients with interstitial cystitis/bladder pain syndrome who had undergone therapeutic urinary bladder hydrodistention. MATERIALS AND METHODS: This is a retrospective chart review of prospectively collected data on women diagnosed with interstitial cystitis/bladder pain syndrome between 2011 and 2015 who underwent bladder hydrodistention. Assessments in each patient included a detailed history and physical examination, ICPI (Interstitial Cystitis Problem Index), ICSI (Interstitial Cystitis Symptom Index) and PUF (Pelvic Pain and Urgency/Frequency Patient Symptom Scale). Bladder capacity was determined during bladder hydrodistention with the patient under general anesthesia. RESULTS: Mean age was 45.8 years and mean bladder capacity was 857 ml in the 110 enrolled patients. We found a significant inverse correlation between bladder capacity and scores on 3 gold standard interstitial cystitis/bladder pain syndrome metrics, including ICPI (p = 0.0014), ICSI (p = 0.0022) and PUF (p = 0.0009) as well as urination frequency (p = 0.0025). Women with higher bladder capacity were significantly more likely to report depression (p = 0.0059) and irritable bowel syndrome (p = 0.022). CONCLUSIONS: Low bladder capacity while under anesthesia was significantly associated with high symptom scores on 3 validated interstitial cystitis/bladder pain syndrome questionnaires as well as with urinary frequency. However, it was not associated with depression or other common systemic pain problems. These results suggest that low bladder capacity is a marker for a bladder centric manifestation of interstitial cystitis/bladder pain syndrome.

Evaluation of the efficacy of postmortem human bladder tissue as a normal comparator for case-controlled gene expression studies in urology.

AIMS: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a poorly understood disease with no absolute diagnostic marker. A molecular-based tool (biomarker) for IC/BPS diagnosis would have immediate clinical utility. We have generated a bank of bladder biopsy tissue from IC/BPS patients and require a control group for comparative gene expression studies. The objective of this pilot study was to investigate the feasibility of cadaveric bladder specimens as a viable source of control tissue. METHODS: Cryopreserved cadaveric bladder specimens were obtained through the National Disease Research Interchange (NDRI) tissue repository. Decedent demographics, postmortem interval to autopsy, necropsy location and size were recorded. At least two punch biopsies were taken from each bladder sample and total RNA was extracted. Nucleic acid concentration and quality were measured as was the RNA integrity number (RIN). RESULTS: We purchased 15 necropsy bladder specimens that had been harvested from women postmortem and flash-frozen. For each bladder specimen, RNA was isolated from multiple sites for comparison both within and between individuals. Bioanalyzer results revealed severe degradation in the majority of samples as indicated by RINs ranging from "n/a" to 6.6, with most samples yielding RINs ≤2.5. Shorter postmortem interval did not correlate with an increase in RNA quantity or quality. CONCLUSIONS: Cadaver-derived bladder tissue from the NDRI does not routinely yield high-quality RNA needed for downstream gene expression applications, such as microarray and next-generation sequencing and, therefore, cannot be used as a reliable source for control samples.

Correlation of gene expression with bladder capacity in interstitial cystitis/bladder pain syndrome.

PURPOSE: Interstitial cystitis and bladder pain syndrome are terms used to describe a heterogeneous chronic pelvic and bladder pain disorder. Despite its significant prevalence, our understanding of disease etiology is poor. We molecularly characterized interstitial cystitis/bladder pain syndrome and determined whether there are clinical factors that correlate with gene expression. MATERIALS AND METHODS: Bladder biopsies from female subjects with interstitial cystitis/bladder pain syndrome and female controls without signs of the disease were collected and divided into those with normal and low anesthetized bladder capacity, respectively. Samples then underwent RNA extraction and microarray assay. Data generated by these assays were analyzed using Omics Explorer (Qlucore, Lund, Sweden), GeneSifter® Analysis Edition 4.0 and Ingenuity® Pathway Analysis to determine similarity among samples within and between groups, and measure differentially expressed transcripts unique to each phenotype. RESULTS: A total of 16 subjects were included in study. Principal component analysis and unsupervised hierarchical clustering showed clear separation between gene expression in tissues from subjects with low compared to normal bladder capacity. Gene expression in tissue from patients with interstitial cystitis/bladder pain syndrome who had normal bladder capacity did not significantly differ from that in controls without interstitial cystitis/bladder pain syndrome. Pairwise analysis revealed that pathways related to inflammatory and immune response were most involved. CONCLUSIONS: Microarray analysis provides insight into the potential pathological condition underlying interstitial cystitis/bladder pain syndrome. This pilot study shows that patients with this disorder who have low compared to normal bladder capacity have significantly different molecular characteristics, which may reflect a difference in disease pathophysiology.

Correction to: Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism.

[This corrects the article DOI: 10.14740/jmc4209.].

Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism.

This case report describes a novel therapy for patients with severe autism spectrum disorder (ASD) that is worth further investigation. A 19-year-old male adolescent with ASD, who was not responding to standard treatment received fecal microbiota transplant (FMT) using donor material from his typically developing female sibling. The patient's ASD symptoms were assessed by assessors who were blind to the patient's past ASD symptomatology. Assessors used the Childhood Autism Rating Scale (CARS), an observation-based rating scale to assess developmental delay in children with autism (range of CARS scores is 15 - 60; a score > 28 is indicative of autism; higher score is positively correlated with degree of severity), at baseline and again at six timepoints post-FMT. The patient experienced marked improvements in microbiome diversity and composition over the year and a half period that followed the FMT procedure. Additionally, the patient who was previously nonverbal said his first two words and experienced a reduction in aggression 1-month post-FMT. To the authors' knowledge, this is the first report to demonstrate the use of familial FMT in an adolescent patient with ASD. Given that ASD symptom improvements post-FMT tend to occur in younger patients, the authors hypothesize that the use of a familial donor may be an important factor that contributed to the improved outcomes experienced by this older child.

Symptomatic Autonomic Dysfunction in Interstitial Cystitis/Bladder Pain Syndrome.

IMPORTANCE: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a highly prevalent condition with incompletely understood pathophysiology, especially in relation to the systemic symptoms experienced. The role of autonomic nervous system dysfunction in IC/BPS remains poorly understood. OBJECTIVE: The purpose of this study was to assess the relationship between autonomic symptom severity and clinical characteristics of patients with IC/BPS. STUDY DESIGN: This is a retrospective cohort study of 122 IC/BPS patients who completed the Composite Autonomic Symptoms Score (COMPASS-31) questionnaire. Data were collected on anesthetic bladder capacity (BC), Hunner lesion (HL) status, results for validated IC/BPS symptom questionnaires (O'Leary Sant Interstitial Cystitis Symptom Index and Interstitial Cystitis Problem Index (ICSI/ICPI) and the Pelvic Pain and Urgency/Frequency (PUF) scale), and comorbid nonurologic associated syndromes. Using the first quartile of COMPASS-31 scores as the cutoff, we compared patients within the first quartile (low symptom load; n = 30), to the remainder of the patients (high symptom load; n = 92). RESULTS: Patients scoring ≥20.36 were significantly less likely to be HL positive (10.9% vs 26.7%; P = 0.043) and had a significantly higher BC (823.10 ± 396.07 vs 635.00 ± 335.06; P = 0.027), higher scores on the PUF questionnaire (23.80 ± 4.98 vs; 19.61 ± 5.22 P < 0.001), and a higher number of nonurologic associated syndromes (5.65 ± 2.90 vs 2.60 ± 1.89; P < 0.001). CONCLUSIONS: Patients with IC/BPS experience widespread symptoms associated with autonomic nervous system dysfunction. A higher symptom load strongly correlates with a nonbladder-centric phenotype. These findings provide further evidence that total body nervous system dysfunction is present in patients with nonbladder centric IC/BPS.

Analysis of gene expression dynamics and differential expression in viral infections using generalized linear models and quasi-likelihood methods.

Introduction: Our study undertakes a detailed exploration of gene expression dynamics within human lung organ tissue equivalents (OTEs) in response to Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV3) infections. Through the analysis of RNA-Seq data from 19,671 genes, we aim to identify differentially expressed genes under various infection conditions, elucidating the complexities of virus-host interactions. Methods: We employ Generalized Linear Models (GLMs) with Quasi-Likelihood (QL) F-tests (GLMQL) and introduce the novel Magnitude-Altitude Score (MAS) and Relaxed Magnitude-Altitude Score (RMAS) algorithms to navigate the intricate landscape of RNA-Seq data. This approach facilitates the precise identification of potential biomarkers, highlighting the host's reliance on innate immune mechanisms. Our comprehensive methodological framework includes RNA extraction, library preparation, sequencing, and Gene Ontology (GO) enrichment analysis to interpret the biological significance of our findings. Results: The differential expression analysis unveils significant changes in gene expression triggered by IAV, MPV, and PIV3 infections. The MAS and RMAS algorithms enable focused identification of biomarkers, revealing a consistent activation of interferon-stimulated genes (e.g., IFIT1, IFIT2, IFIT3, OAS1) across all viruses. Our GO analysis provides deep insights into the host's defense mechanisms and viral strategies exploiting host cellular functions. Notably, changes in cellular structures, such as cilium assembly and mitochondrial ribosome assembly, indicate a strategic shift in cellular priorities. The precision of our methodology is validated by a 92% mean accuracy in classifying respiratory virus infections using multinomial logistic regression, demonstrating the superior efficacy of our approach over traditional methods. Discussion: This study highlights the intricate interplay between viral infections and host gene expression, underscoring the need for targeted therapeutic interventions. The stability and reliability of the MAS/RMAS ranking method, even under stringent statistical corrections, and the critical importance of adequate sample size for biomarker reliability are significant findings. Our comprehensive analysis not only advances our understanding of the host's response to viral infections but also sets a new benchmark for the identification of biomarkers, paving the way for the development of effective diagnostic and therapeutic strategies.

A comparative analysis of RNA-Seq and NanoString technologies in deciphering viral infection response in upper airway lung organoids.

In this study, we delved into the comparative analysis of gene expression data across RNA-Seq and NanoString platforms. While RNA-Seq covered 19,671 genes and NanoString targeted 773 genes associated with immune responses to viruses, our primary focus was on the 754 genes found in both platforms. Our experiment involved 16 different infection conditions, with samples derived from 3D airway organ-tissue equivalents subjected to three virus types, influenza A virus (IAV), human metapneumovirus (MPV), and parainfluenza virus 3 (PIV3). Post-infection measurements, after UV (inactive virus) and Non-UV (active virus) treatments, were recorded at 24-h and 72-h intervals. Including untreated and Mock-infected OTEs as control groups enabled differentiating changes induced by the virus from those arising due to procedural elements. Through a series of methodological approaches (including Spearman correlation, Distance correlation, Bland-Altman analysis, Generalized Linear Models Huber regression, the Magnitude-Altitude Score (MAS) algorithm and Gene Ontology analysis) the study meticulously contrasted RNA-Seq and NanoString datasets. The Magnitude-Altitude Score algorithm, which integrates both the amplitude of gene expression changes (magnitude) and their statistical relevance (altitude), offers a comprehensive tool for prioritizing genes based on their differential expression profiles in specific viral infection conditions. We observed a strong congruence between the platforms, especially in identifying key antiviral defense genes. Both platforms consistently highlighted genes including ISG15, MX1, RSAD2, and members of the OAS family (OAS1, OAS2, OAS3). The IFIT proteins (IFIT1, IFIT2, IFIT3) were emphasized for their crucial role in counteracting viral replication by both platforms. Additionally, CXCL10 and CXCL11 were pinpointed, shedding light on the organ tissue equivalent's innate immune response to viral infections. While both platforms provided invaluable insights into the genetic landscape of organoids under viral infection, the NanoString platform often presented a more detailed picture in situations where RNA-Seq signals were more subtle. The combined data from both platforms emphasize their joint value in advancing our understanding of viral impacts on lung organoids.

Autism Spectrum Disorder in the Dominican Republic: A Mini Review of the Current Situation.

As the recognition of autism spectrum disorder (ASD) increases, and the prevalence estimates of ASD continue to rise throughout the world, it has become apparent that access to diagnostic and treatment services is highly dependent on geography. Even within countries such as the United States, which has received significant interest and investment in understanding, diagnosing, treating, and providing programs for those with ASD over the last 20+ years, access to information and services is uneven. In poorer countries such as the Dominican Republic (DR), where >40% of citizens live below the poverty level and access to quality healthcare overall continues to be a challenge, issues associated with ASD are not yet being adequately addressed. The objective of this review is to provide a realistic synopsis of the resources currently available to Dominicans who have a family member or loved one with ASD. We examine the challenges these families face in finding care, the stigma associated with ASD, and programs available for people with ASD. We conclude that while the DR is making progress in its efforts to address ASD, there is still much work to be done.

Postsurgery Opiate Use Is Significantly Lower in Patients With Interstitial Cystitis/Bladder Pain Syndrome Following Cystectomy With Urinary Diversion.

OBJECTIVE: To compare pre-and post-operative opiate use in a large cohort of interstitial cystitis/bladder pain syndrome (IC/BPS) patients who underwent cystectomy with urinary diversion (CWUD). METHODS: A retrospective analysis was completed using a database of IC/BPS patients who underwent CWUD at a single institution from 2014 to 2022. In addition to demographic information, bladder capacity and Hunner lesion status were documented for each patient. Opiate use (milligram morphine equivalents [MME]) was calculated for each patient and change in MME (ΔMME) was calculated by subtracting pre-CWUD MME from post-CWUD MME. Paired t test was used to compare ΔMME for all parameters except age, where a Pearson's correlation was used. RESULTS: The analysis included 82 patients (17 M; 65 F) that underwent CWUD as follows: 53 ileal conduit diversions, 11 neobladders, and 18 Indiana Pouches. Mean pre-CWUD MME use was 4509.57 and mean post-CWUD MME was 1788.48 with a ΔMME of - 2721.09 (P < .001). ΔMME was not significantly different based on gender (P = .597), bladder capacity (P = .754), age (P = .561), or Hunner lesion status (P = .085). CONCLUSION: IC/BPS patients using opiates primarily for relief of pain directly related to their condition show a significant decrease in opiate use following CWUD, which likely represents significant pain reduction and implicates the bladder as the primary source of that pain.