Harmonization of CSF and imaging biomarkers in Alzheimer's disease: Need and practical applications for genetics studies and preclinical classification.

In Alzheimer's disease (AD) research, cerebrospinal fluid (CSF) Amyloid beta (Aß), Tau and pTau are the most accepted and well validated biomarkers. Several methods and platforms exist to measure those biomarkers, leading to challenges in combining data across studies. Thus, there is a need to identify methods that harmonize and standardize these values. We used a Z-score based approach to harmonize CSF and amyloid imaging data from multiple cohorts and compared GWAS results using this approach with currently accepted methods. We also used a generalized mixture model to calculate the threshold for biomarker-positivity. Based on our findings, our normalization approach performed as well as meta-analysis and did not lead to any spurious results. In terms of dichotomization, cutoffs calculated with this approach were very similar to those reported previously. These findings show that the Z-score based harmonization approach can be applied to heterogeneous platforms and provides biomarker cut-offs consistent with the classical approaches without requiring any additional data.

L1CAM mediates neuroendocrine phenotype acquisition in prostate cancer cells.

BACKGROUND: A specific type of prostate cancer (PC) that exhibits neuroendocrine (NE) differentiation is known as NEPC. NEPC has little to no response to androgen deprivation therapy and is associated with the development of metastatic castration-resistant PC (CRPC), which has an extremely poor prognosis. Our understanding of genetic drivers and activated pathways in NEPC is limited, which hinders precision medicine approaches. L1 cell adhesion molecule (L1CAM) is known to play an oncogenic role in metastatic cancers, including CRPC. However, the impact of L1CAM on NEPC progression remains elusive. METHODS: L1CAM expression level was investigated using public gene expression databases of PC cohorts and patient-derived xenograft models. L1CAM knockdown was performed in different PC cells to study in vitro cell functions. A subline of CRPC cell line CWR22Rv1 was established after long-term exposure to abiraterone to induce NE differentiation. The androgen receptor-negative cell line PC3 was cultured under the tumor sphere-forming condition to enrich cancer stemness features. Several oxidative stress inducers were tested on PC cells to observe L1CAM-mediated gene expression and cell death. RESULTS: L1CAM expression was remarkably high in NEPC compared to CRPC or adenocarcinoma tumors. L1CAM was also correlated with NE marker expressions and associated with the adenocarcinoma-to-NEPC progression in gene expression databases and CRPC cells with NE differentiation. L1CAM also promoted cancer stemness and NE phenotypes in PC3 cells under cancer stemness enrichment. L1CAM was also identified as a reactive oxygen species-induced gene, by which L1CAM counteracted CRPC cell death triggered by ionizing radiation. CONCLUSIONS: Our results unveiled a new role of L1CAM in the acquisition of the NE phenotype in PC, contributing to the NE differentiation-related therapeutic resistance of CRPC.

A real-world cohort study of first-line afatinib in patients with EGFR-mutant advanced non-small cell lung cancer in Vietnam.

BACKGROUND: This study aimed to evaluate the efficacy and side effects of first-line afatinib treatment in a real-world setting in Vietnam. METHODS: This retrospective study was conducted across nine hospitals in Vietnam. Advanced epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) patients who received afatinib as first-line therapy between April 2018 and June 2022 were included, and patient medical records were reviewed. Key outcomes were overall response rate (ORR), time-to-treatment failure (TTF), and tolerability. RESULTS: A total of 343 patients on first-line afatinib were eligible for the study. EGFR exon 19 deletion (Del19) alone was detected in 46.9% of patients, L858R mutation alone in 26.3%, and other uncommon EGFR mutations, including compound mutations, in 26.8%. Patients with brain metastases at baseline were 25.4%. Patients who received 40 mg, 30 mg, and 20 mg as starting doses of afatinib were 58.6%, 39.9%, and 1.5%, respectively. The ORR was 78.1% in the overall population, 82.6% in the Del19 mutation subgroup, 73.3% in the L858R mutation subgroup, and 75.0% in the uncommon mutation subgroup (p > 0.05). The univariate and multivariate analyses indicate that the ORR increased when the starting dose was 40 mg compared to starting doses below 40 mg (83.9% vs. 74.3%, p = 0.034). The median TTF (mTTF) was 16.7 months (CI 95%: 14.8-18.5) in all patients, with a median follow-up time of 26.2 months. The mTTF was longer in patients in the common EGFR mutation subgroup (Del19/L858R) than in those in the uncommon mutation subgroup (17.5 vs. 13.8 months, p = 0.045) and in those without versus with brain metastases at baseline (17.5 vs. 15.1 months, p = 0.049). There were no significant differences in the mTTF between subgroups based on the starting dose of 40 mg and < 40 mg (16.7 vs. 16.9 months, p > 0.05). The most common treatment-related adverse events (any grade/grade ≥ 3) were diarrhea (55.4%/3.5%), rash (51.9%/3.2%), paronychia (35.3%/5.0%), and stomatitis (22.2%/1.2%). CONCLUSIONS: Afatinib demonstrated clinical effectiveness and good tolerability in Vietnamese EGFR-mutant NSCLC patients. In our real-world setting, administering a starting dose below 40 mg might result in a reduction in ORR; however, it might not have a significant impact on TTF.

Probiotic cell-free supernatant as effective antimicrobials against Klebsiella pneumoniae and reduce antibiotic resistance development.

This study evaluated the antimicrobial activity, resistance development, and synergistic potential of cell-free supernatant (CFSs) derived from Levilactobacillus brevis (Lb-CFS) and Lactiplantibacillus plantarum (Lp-CFS) against Klebsiella pneumoniae. Both CFSs exhibited potent growth inhibition, with minimum inhibitory concentrations (MICs) of 128 µg/mL and 64 µg/mL for Lb-CFS and Lp-CFS, respectively, and demonstrated dose-dependent bactericidal activity, achieving complete bacterial eradication at minimum bactericidal concentrations (MBC) within 6 h. The CFSs suppressed the expression of virulence genes (galF, wzi, and manC) and biofilm formation in a dose-dependent manner. Synergistic interactions were observed when combining CFSs with antibiotics, resulting in 2- to fourfold reductions in antibiotic MICs and MBCs. Notably, adaptive evolution experiments revealed significantly slower resistance development in K. pneumoniae against CFSs (twofold MIC/MBC increase) compared to antibiotics (16- to 128-fold increase) after 21 days. Furthermore, CFS-adapted strains exhibited increased antibiotic susceptibility, while antibiotic-adapted strains displayed cross-resistance to multiple antibiotics. No cross-resistance occurred between Lb-CFS and Lp-CFS, suggesting distinct adaptive mechanisms. These findings highlight the potential of probiotic-derived CFSs as effective antimicrobials with a lower propensity for inducing rapid resistance compared to conventional antibiotics, suggesting their promise in combating multidrug-resistant infections.

Developing a Passive Dosing Method for Acute Aquatic Toxicity Tests of Cationic Surfactant Benzalkoniums (BACs).

Benzalkonium chlorides (BACs) have been of environmental concern due to their widespread use and potential harm. However, challenges arise in defining and controlling the exposure concentration (Cw) in aquatic toxicity tests involving BACs with a long alkyl chain (i.e., #C > 14). To address this, a novel passive dosing method was introduced in the 48 h-acute ecotoxicity test on Daphnia magna and compared to the conventional solvent-spiking method in terms of Cw stability and toxicity results. Among 13 sorbent materials tested for their sorption capacity, poly(ether sulfone) (PES) membrane was an optimal passive dosing reservoir, with equilibrium desorption of BACs to water achieved within 24 h. The Cw of BACs remained constant in both applied dosing methods during the test period. However, the Cw in solvent-spiking tests was lower than the nominal concentration for long-chain BACs, particularly at low exposure concentrations. Notably, the solvent-spiking tests indicated that the toxicity of BACs increased with alkyl chain length from C6 to 14, followed by a decline in toxicity from C14 to 18. In contrast, the passive dosing method displayed similar or slightly increasing toxicity levels of BACs from C14 to C18, indicating higher toxicity of C16 and C18-BACs than that inferred by the solvent spiking test. These findings emphasize the potential of applying this innovative passive dosing approach in aquatic toxicity tests to generate reliable and accurate toxicity data and support a comprehensive risk assessment of cationic surfactants.

Efficiency of freeze- and spray-dried microbial preparation as active dried starter culture in kombucha fermentation.

BACKGROUND: Kombucha is a widely consumed fermented beverage produced by fermenting sweet tea with a symbiotic culture of bacteria and yeast (SCOBY). The dynamic nature of microbial communities in SCOBY may pose challenges to production scale-up due to unpredictable variations in microbial composition. Using identified starter strains is a novel strategy to control microorganism composition, thereby ensuring uniform fermentation quality across diverse batches. However, challenges persist in the cultivation and maintenance of these microbial strains. This study examined the potential of microencapsulated kombucha fermentation starter cultures, specifically Komagataeibacter saccharivorans, Levilactobacillus brevis and Saccharomyces cerevisiae, through spray-drying and freeze-drying. RESULTS: Maltodextrin and gum arabic-maltodextrin were employed as carrier agents. Our results revealed that both spray-dried and freeze-dried samples adhered to physicochemical criteria, with low moisture content (2.18-7.75%) and relatively high solubility (65.75-87.03%) which are appropriate for food application. Freeze-drying demonstrated greater effectiveness in preserving bacterial strain viability (88.30-90.21%) compared to spray drying (74.92-78.66%). Additionally, the freeze-dried starter strains demonstrated similar efficacy in facilitating kombucha fermentation, compared to the SCOBY group. The observations included pH reduction, acetic acid production, α-amylase inhibition and elevated total polyphenol and flavonoid content. Moreover, the biological activity, including antioxidant potential and in vitro tyrosinase inhibition activity, was enhanced in the same pattern. The freeze-dried strains exhibited consistent kombucha fermentation capabilities over a three-month preservation, regardless of storage temperature at 30 or 4 °C. CONCLUSION: These findings highlight the suitability of freeze-dried starter cultures for kombucha production, enable microbial composition control, mitigate contamination risks and ensure consistent product quality. © 2024 Society of Chemical Industry.

Alterations to the duodenal microbiota are linked to gastric emptying and symptoms in functional dyspepsia.

OBJECTIVE: Functional dyspepsia (FD) is a complex disorder, with debilitating epigastric symptoms. Evidence suggests alterations in gastrointestinal (GI) motility, visceral hypersensitivity, permeability and low-level immune activation in the duodenum may play a role. However, we still have a relatively poor understanding of how these factors interact to precipitate the onset of FD symptoms which are frequently meal related. The duodenal microbiota, in combination with specific dietary substrates, may be important mediators in disease pathophysiology; however, these interlinked factors have not been thoroughly investigated in FD. DESIGN: Eighty-six individuals (56 FD, 30 controls) undergoing endoscopy were consecutively recruited and underwent detailed clinical assessment, including upper GI symptoms, gastric emptying and dietary assessment. Duodenal biopsies were obtained aseptically, and the mucosa-associated microbiota (MAM) analysed via 16S rRNA gene amplicon sequencing. RESULTS: The relative abundances of predominant members of the Firmicutes, Bacteroidota and Fusobacteriota phyla were linked to symptom burden in FD. Inverse relationships between the relative abundances of Streptococcus and Prevotella, and the relative abundance of Veillonella spp with gastric emptying time, were also observed. No significant differences in long-term nutrient intake or diet quality were found between FD and controls, and there appeared to be limited association between habitual diet and duodenal MAM profiles. CONCLUSION: This study suggests a link between the duodenal MAM, gastric emptying and FD symptoms, and this is largely independent of long-term dietary intake.

Changes in Quality of life Outcomes of Patients with HIV/AIDS Under a Theory-based Mobile Health Intervention.

This study examined the effectiveness of a theory-based mHealth intervention on the quality of life (QOL) of people living with HIV. A randomized controlled trial was performed at two outpatient clinics in Hanoi, Vietnam. There were 428 patients with HIV/AIDs in selected clinics and were divided into the intervention arm (receiving HIV-assisted smartphone application and usual care) and the control arm (receiving only usual care). The WHOQOLHIV-BREF instrument was utilized to measure QOL. An intention-to-treat approach using Generalized Linear Mixed Model analysis was performed. The trial showed significant improvements in Physical health, Psychological health, and Level of Dependence among patients in the intervention arm compared to the control arm. However, the Environment and Spirituality/Personal beliefs improvements would require additional interventions, both individual, organizational, or governmental. This study explored the utility of a smartphone mobile application for individuals with HIV, and how the resultant application could improve the overall QOL.

Effect of Mass Fraction on Leaching Kinetics of Hydrophobic Ultraviolet Stabilizers in Low-Density Polyethylene.

The leaching kinetics of five hydrophobic ultraviolet (UV) stabilizers from low-density polyethylene (LDPE) (micro)fibers into water was evaluated in this study, with variation of the mass fraction (ω = 0.1-2.0 wt %) of the stabilizers. A one-dimensional convection-diffusion model for a cylindrical geometry, requiring partitioning between the LDPE fibers and water (KLDPEw) and the internal diffusion coefficients (DLDPE), was used to evaluate the leaching process and the leaching half-life of the target UV stabilizers at ω < 0.5 wt % (Case I). Diffusion through the aqueous boundary layer is the rate-determining step, and the leaching half-life is predicted to be very long (a few months to years) under unaffected conditions. When the UV stabilizers are supersaturated within LDPE fibers (i.e., ω > 0.5 wt %, Case II), the possible formation of a surficial crystal layer of the additives on the LDPE fiber extends the time scale for leaching compared to that in Case I due to the requirement of overcoming the crystallization energy. This study provides a fundamental understanding of the leaching profiles of plastic additives for assessing their potential chemical risks in aquatic environments; further studies under the relevant environmental conditions are required.

Toward sustainable development goals in gender inequality: an analysis of gender preferences among urban pregnant women in a Southeast Asian country.

BACKGROUND: Gender-biased discrimination and preferences are global phenomena, particularly son preferences. However, updated evidence about this issue in Vietnam has not yet been provided. Therefore, this study aimed to examine the gender preferences among pregnant women and identify associated factors of such preferences. METHODS: A cross-sectional survey was conducted in two hospitals in Vietnam with 732 pregnant women. Gender preferences for their child were asked, along with socio-demographic (e.g., education, occupation) and pregnancy characteristics (e.g., pressure to have a son, gender of first child, the importance to have a son of family members, and information sources on pregnancy care) by using face-to-face interviews and a structured questionnaire. Multinomial logistic regression was performed to determine factors associated with gender preferences. RESULTS: About 51.9% of the participants had no gender preference, while, among those who had a gender preference, 26.5% preferred sons, and 21.6% preferred daughters. Only 6.2% had pressure to have a son. Having the first child who was female (OR = 4.16, 95%CI = 1.54-11.25), having the pressure to have a son (OR = 6.77, 95%CI = 2.06-22.26), and higher self-perceived importance to have a son (OR = 3.05, 95%CI = 1.85-5.02) were positively associated with son preference. Otherwise, women having partners with high school education or above (OR = 2.04, 95%CI = 1.06-3.91), living with parents-in-law (OR = 2.33; 95%CI = 1.25-4.34), the higher number of pregnancies, and a higher degree of importance in having a son regarding parents-in-law (OR = 2.15, 95%CI = 1.38-3.35) associated with higher odds of preferring daughter. CONCLUSION: This study showed that gender preference was common among pregnant women, but the pressure to have a son was low. Further education programs and legal institutions should be implemented to improve gender inequality and gender preference in society.

Efficacy of a Mobile Phone-Based Intervention on Health Behaviors and HIV/AIDS Treatment Management: Randomized Controlled Trial.

BACKGROUND: Antiretroviral therapy (ART) is considered the most important intervention for HIV-positive patients; thus, encouraging the use of and adherence to ART are vital to HIV treatment outcomes. Advances in web and mobile technologies hold potential in supporting HIV treatment management. OBJECTIVE: The aim of this study was to evaluate the feasibility and efficacy of a theory-based mobile health (mHealth) intervention on health behaviors and HIV treatment adherence among patients with HIV/AIDS in Vietnam. METHODS: We performed a randomized controlled trial on 425 HIV patients in two of the largest HIV clinics in Hanoi, Vietnam. Both the intervention group (238 patients) and the control group (187 patients) received regular consultations with doctors and then participated in 1-month and 3-month follow-up visits. Patients in the intervention group received a theory-driven smartphone app to facilitate medication adherence and self-efficacy in HIV patients. Measurements were developed based on the Health Belief Model, which included the visual analog scale of ART Adherence, HIV Treatment Adherence Self-Efficacy Scale, and HIV Symptom Management Self-Efficacy Scale. We also included the 9-item Patient Health Questionnaire (PHQ-9) to assess patients' mental health throughout treatment. RESULTS: In the intervention group, the adherence score increased significantly (ß=1.07, 95% CI .24-1.90) after 1 month, whereas the HIV adherence self-efficacy was significantly higher after 3 months (ß=2.17, 95% CI 2.07-2.27) compared to the control group. There was a positive but low level of change in risk behaviors such as drinking, smoking, and drug use. Factors related to positive change in adherence were being employed and having stable mental well-being (lower PHQ-9 scores). Factors associated with self-efficacy in treatment adherence and symptom management were gender, occupation, younger age, and having no other underlying conditions. A longer duration of ART increased treatment adherence but decreased self-efficacy in symptom management. CONCLUSIONS: Our study demonstrated that the mHealth app could improve the overall ART adherence self-efficacy of patients. Further studies with larger sample sizes and longer follow-up periods are needed to support our findings. TRIAL REGISTRATION: Thai Clinical Trials Registry TCTR20220928003; https://www.thaiclinicaltrials.org/show/TCTR20220928003.

Examination of host genetic effects on nasal microbiome composition.

BACKGROUND: Genetic predisposition increases risk for asthma, and distinct nasal microbial compositions are associated with asthma. Host genetics might shape nasal microbiome composition. OBJECTIVE: We examined associations between host genetics and nasal microbiome composition. METHODS: Nasal samples were collected from 584 participants from the Mount Sinai Health System, New York. Seventy-seven follow-up samples were collected from a subset of 40 participants. 16S rRNA sequencing and RNA sequencing were performed on nasal samples. Beta diversity was calculated, variant calling on RNA sequencing data was performed, and genetic relatedness between individuals was determined. Using linear regression models, we tested for associations between genetic relatedness and nasal microbiome composition. RESULTS: The median age of the cohort was 14.6 (interquartile range 11.2-19.5) years, with participants representing diverse ancestries and 52.7% of the cohort being female. For participants who provided follow-up samples, the median time between samples was 5.1 (interquartile range 1.4-7.2) months. Nasal microbiome composition similarity as reflected by beta diversity was significantly higher within subjects over time versus between subjects (coefficient = 0.091, P = 2.84-7). There was no significant association between genetic relatedness and beta diversity (coefficient = -0.05, P = .29). Additional analyses exploring the relationship between beta diversity and genetic variance yielded similar results. CONCLUSION: Host genetics has little influence on nasal microbiome composition.

Cervical Secretion Methylation Is Associated with the Pregnancy Outcome of Frozen-Thawed Embryo Transfer.

The causes of implantation failure remain a black box in reproductive medicine. The exact mechanism behind the regulation of endometrial receptivity is still unknown. Epigenetic modifications influence gene expression patterns and may alter the receptivity of human endometrium. Cervical secretions contain endometrial genetic material, which can be used as an indicator of the endometrial condition. This study evaluates the association between the cervical secretion gene methylation profile and pregnancy outcome in a frozen-thawed embryonic transfer (FET) cycle. Cervical secretions were collected from women who entered the FET cycle with a blastocyst transfer (36 pregnant and 36 non-pregnant women). The DNA methylation profiles of six candidate genes selected from the literature review were measured by quantitative methylation-specific PCR (qMSP). Bioinformatic analysis of six selected candidate genes showed significant differences in DNA methylation between receptive and pre-receptive endometrium. All candidate genes showed different degrees of correlation with the pregnancy outcomes in the logistic regression model. A machine learning approach showed that the combination of candidate genes' DNA methylation profiles could differentiate pregnant from non-pregnant samples with an accuracy as high as 86.67% and an AUC of 0.81. This study demonstrated the association between cervical secretion methylation profiles and pregnancy outcomes in an FET cycle and provides a basis for potential clinical application as a non-invasive method for implantation prediction.

Effects of Roasting Conditions on Antibacterial Properties of Vietnamese Turmeric (Curcuma longa) Rhizomes.

Processing with heat treatment has been reported to alter several therapeutic effects of turmeric. In Vietnamese traditional medicine, turmeric has been long used for bacterial infections, and roasting techniques are sometimes applied with this material. However, there have been no studies investigating the effects of these thermal processes on the plant's antibacterial properties. Our study was therefore performed to examine the changes that roasting produced on this material. Slices of dried turmeric were further subjected to light-roasting (80 °C in 20 min) or dark-roasting (160 °C in 20 min) processes. Broth dilution and agar-well diffusion methods were applied to examine and compare the effects of ethanol extracts obtained from non-roasted, light-roasted and dark-roasted samples, on a set of 6 gram-positive and gram-negative bacteria. In both investigations, dark-roasted turmeric was significantly less antibacterial than non-roasted and light-roasted materials, as evident by the higher values of minimum inhibitory concentrations and the smaller diameters of induced inhibitory zones. In addition, dark-roasting was also found to clearly reduce curcumin contents, total polyphenol values and antioxidant activities of the extracts. These results suggest that non-roasting or light-roasting might be more suitable for the processing of turmeric materials that are aimed to be applied for bacterial infections.

Effect of thickness and CAD-CAM material on fatigue resistance of endodontically treated molars restored with occlusal veneers.

PURPOSE: To evaluate the influence of the thickness and type of computer-aided design and computer-aided manufacturing (CAD-CAM) material on the fatigue resistance and failure mode of endodontically treated teeth (ETT) restored with occlusal veneers (OV). MATERIALS AND METHODS: Seventy-five (N = 75) ETT were restored with Herculite XRV in the endodontic access. Five experimental groups (n = 15) were tested. Four groups had two different thicknesses (0.6-0.7 mm or 1.4-1.6 mm) and two different CAD-CAM materials: zirconia-reinforced lithium-silicate (LS/Celtra Duo) and composite resin (RC/Cerasmart). The fifth group (control) did not have occlusal veneers. All the specimens were subjected to accelerated fatigue (5 Hz frequency) with an occlusal load increasing up to 1800 N and 131,000 cycles. The number of cycles was recorded when the machine stopped or at the completion of the test. Fatigue resistance was analyzed using the Kaplan-Meier survival test (95% significance level, log-rank post hoc pairwise comparisons). The samples were categorized according to failure mode. The CAD-CAM materials were examined through scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). RESULTS: No differences were found between the thicknesses, regardless of the type of the CAD-CAM material. The thick LS OV outperformed the RC and control groups. The thin RC OV and control groups showed a higher percentage of repairable and possibly repairable failures than the other groups. LS was more homogeneous under SEM, and the EDS analysis detected Si and Zr, but not Li. CONCLUSIONS: A larger thickness did not improve the resistance of the CAD-CAM materials. Thick LS showed a higher cumulative survival rate to fatigue than the RC and control groups. The direct composite alone (control) survived similarly to the experimental groups, except for the thick LS.

Evaluation of a Multidisciplinary Integrated Treatment Approach Versus Standard Model of Care for Functional Gastrointestinal Disorders (FGIDS): A Matched Cohort Study.

BACKGROUND: Functional gastrointestinal disorders (FGID) are linked to a variety of potential causes, and treatments include reassurance, life-style (including diet), psychological, or pharmacologic interventions. AIMS: To assess whether a multidisciplinary integrated treatment approach delivered in a dedicated integrated care clinic (ICC) was superior to the standard model of care in relation to the gastrointestinal symptom burden. METHODS: A matched cohort of 52 consecutive patients with severe manifestation of FGID were matched with 104 control patients based upon diagnosis, gender, age, and symptom severity. Patients in the ICC received structured assessment and 12-weeks integrated treatment sessions provided as required by gastroenterologist and allied health team. Control patients received standard medical care at the same tertiary center with access to allied health services as required but no standardized interprofessional team approach. Primary outcome was reduction in gastrointestinal symptom burden as measured by the Structured Assessment of Gastrointestinal Symptoms Scale (SAGIS). Secondary outcome was reduction in anxiety and depressive symptoms as measured by the Hospital Anxiety and Depression Scale (HADS). RESULTS: Mixed models estimated the within ICC change in SAGIS total as -9.7 (95% CI -13.6, -5.8; p < 0.0001), compared with -1.7 (95% CI -4.0, 0.6; p = 0.15) for controls. The difference between groups reached statistical significance, -7.6 (95% CI -11.4, -3.8; p < 0.0001). Total HADS scores in ICC patients were 3.4 points lower post-intervention and reached statistical significance (p = 0.001). CONCLUSION: This matched cohort study demonstrates superior short-term outcomes of FGID patients in a structured multidisciplinary care setting as compared to standard care.

Establishment of an in-house real-time RT-PCR assay for the detection of severe acute respiratory syndrome coronavirus 2 using the first World Health Organization international standard in a resource-limited country.

BACKGROUND: The COVID-19 pandemic caused by SARS-CoV-2 remains public health burdens and many unresolved issues worldwide. Molecular assays based on real-time RT-PCR are critical for the detection of SARS-CoV-2 in clinical specimens from patients suspected of COVID-19. OBJECTIVE: We aimed to establish and validate an in-house real-time RT-PCR for the detection of SARS-CoV-2. METHODOLOGY: Primers and probes sets in our in-house real-time RT-PCR assay were designed in conserved regions of the N and E target genes. Optimized multiplex real-time RT-PCR assay was validated using the first WHO International Standard (NIBSC code: 20/146) and evaluated clinical performance. RESULTS: The limit of detection validated using the first WHO International Standard was 159 IU/ml for both E and N target genes. The evaluation of clinical performance on 170 clinical samples showed a positive percent agreement of 100% and the negative percent agreement of 99.08% for both target genes. The Kappa value of 0.99 was an excellent agreement, the strong correlation of Ct values observed between two tests with r2  = 0.84 for the E gene and 0.87 for the N gene. Notably, we assessed on 60 paired saliva and nasopharyngeal samples. The overall agreement was 91.66%, and Kappa value of 0.74 showed a high agreement between two types of samples. When using nasopharyngeal swabs as the reference standard, positive percent agreement, and negative percent agreement were 91.83% and 90.90%, respectively. CONCLUSION: In the present study, we established and validated an in-house real-time RT-PCR for molecular detection of SARS-CoV-2 in a resource-limited country.

The nasal microbiome, nasal transcriptome, and pet sensitization.

BACKGROUND: Pet allergies are common in children with asthma. Microbiota and host responses may mediate allergen sensitization. OBJECTIVE: We sought to uncover host-microbe relationships in pet allergen sensitization via joint examination of the nasal microbiome and nasal transcriptome. METHODS: We collected nasal samples from 132 children with asthma for parallel 16S rRNA and RNA sequencing. Specific IgE levels for cat and dog dander were measured. Analyses of the nasal microbiome, nasal transcriptome, and their correlations were performed with respect to pet sensitization status. RESULTS: Among the 132 children, 91 (68.9%) were cat sensitized and 96 (72.7%) were dog sensitized. Cat sensitization was associated with lower nasal microbial diversity by Shannon index (P = .021) and differential nasal bacterial composition by weighted UniFrac distance (permutational multivariate ANOVA P = .035). Corynebacterium sp and Staphylococcus epidermidis were significantly less abundant, and the metabolic process "fatty acid elongation in mitochondria" was lower in pet-sensitized versus unsensitized children. Correlation networks revealed that the nasal expression levels of 47 genes representing inflammatory processes were negatively correlated with the relative abundances of Corynebacterium sp and S epidermidis. Thus, these species were directly associated not only with the absence of pet sensitization but also with the underexpression of host gene expression of inflammatory processes that contribute to allergen sensitization. Causal mediation analyses revealed that the associations between these nasal species and pet sensitization were mediated by nasal gene expression. CONCLUSIONS: Higher abundances of nasal Corynebacterium sp and S epidermidis are associated with absence of pet sensitization and correlate with lower expression of inflammatory genes.

Network study of nasal transcriptome profiles reveals master regulator genes of asthma.

BACKGROUND: Nasal transcriptomics can provide an accessible window into asthma pathobiology. OBJECTIVE: Our goal was to move beyond gene signatures of asthma to identify master regulator genes that causally regulate genes associated with asthma phenotypes. METHODS: We recruited 156 children with severe persistent asthma and controls for nasal transcriptome profiling and applied network-based and probabilistic causal methods to identify severe asthma genes and their master regulators. We then took the same approach in an independent cohort of 190 adults with mild/moderate asthma and controls to identify mild/moderate asthma genes and their master regulators. Comparative analysis of the master regulator genes followed by validation testing in independent children with severe asthma (n = 21) and mild/moderate asthma (n = 154) was then performed. RESULTS: Nasal gene signatures for severe persistent asthma and for mild/moderate persistent asthma were identified; both were found to be enriched in coexpression network modules for ciliary function and inflammatory response. By applying probabilistic causal methods to these gene signatures and validation testing in independent cohorts, we identified (1) a master regulator gene common to asthma across severity and ages (FOXJ1); (2) master regulator genes of severe persistent asthma in children (LRRC23, TMEM231, CAPS, PTPRC, and FYB); and (3) master regulator genes of mild/moderate persistent asthma in children and adults (C1orf38 and FMNL1). The identified master regulators were statistically inferred to causally regulate the expression of downstream genes that modulate ciliary function and inflammatory response to influence asthma. CONCLUSION: The identified master regulator genes of asthma provide a novel path forward to further uncovering asthma mechanisms and therapy.

Lactobacillus rhamnosus JB3 inhibits Helicobacter pylori infection through multiple molecular actions.

BACKGROUND: Eradication of Helicobacter pylori infection is the most direct and effective way for preventing gastric cancer. Lactic acid bacteria are considered as alternative therapeutic agents against H. pylori infection. METHODS: Effects of Lactobacillus rhamnosus JB3 (LR-JB3) on the virulence gene expression of H. pylori and infection-induced cellular responses of AGS cells were investigated by co-cultivating infected AGS cells with different multiplicity of infections (MOIs) of LR-JB3. RESULTS: LR-JB3, specifically at a MOI of 25, suppressed the association ability of H. pylori and its induced IL-8 levels, as well as the mRNA levels of vacA, sabA, and fucT of H. pylori, infection-induced Lewis (Le)x antigen and Toll-like receptor 4 (TLR4) expressions in AGS cells. However, the apoptosis mediated by infection was inhibited by LR-JB3 in a dose-dependent manner. In addition, autoinducer (AI)-2 was observed to have increased the association ability and fucT expression of H. pylori, and Lex antigen and TLR4 expression of AGS cells. Interestingly, an unknown bioactive cue was hypothesized to have been secreted from LR-JB3 at a MOI of 25 to act as an antagonist of AI-2. CONCLUSIONS: LR-JB3 possesses various means to interfere with H. pylori pathogenesis and infection-induced cellular responses of AGS cells to fight against infection.