MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis.

MOTIVATION: Microbiota analyses have important implications for health and science. These analyses make use of 16S/18S rRNA gene sequencing to identify taxa and predict species diversity. However, most available tools for analyzing microbiota data require adept programming skills and in-depth statistical knowledge for proper implementation. While long-read amplicon sequencing can lead to more accurate taxa predictions and is quickly becoming more common, practitioners have no easily accessible tools with which to perform their analyses. RESULTS: We present MOCHI, a GUI tool for microbiota amplicon sequencing analysis. MOCHI preprocesses sequences, assigns taxonomy, identifies different abundant species and predicts species diversity and function. It takes either taxonomic count table or FASTQ of partial 16S/18S rRNA or full-length 16S rRNA gene as input. It performs analyses in real time and visualizes data in both tabular and graphical formats. AVAILABILITY AND IMPLEMENTATION: MOCHI can be installed to run locally or accessed as a web tool at https://mochi.life.nctu.edu.tw. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dysregulation of glutamine/glutamate metabolism in COVID-19 patients: A metabolism study in African population and mini meta-analysis.

Coronavirus disease 2019 (COVID-19) remains a serious global threat. The metabolic analysis had been successfully applied in the efforts to uncover the pathological mechanisms and biomarkers of disease severity. Here we performed a quasi-targeted metabolomic analysis on 56 COVID-19 patients from Sierra Leone in western Africa, revealing the metabolomic profiles and the association with disease severity, which was confirmed by the targeted metabolomic analysis of 19 pairs of COVID-19 patients. A meta-analysis was performed on published metabolic data of COVID-19 to verify our findings. Of the 596 identified metabolites, 58 showed significant differences between severe and nonsevere groups. The pathway enrichment of these differential metabolites revealed glutamine and glutamate metabolism as the most significant metabolic pathway (Impact = 0.5; -log10P = 1.959). Further targeted metabolic analysis revealed six metabolites with significant intergroup differences, with glutamine/glutamate ratio significantly associated with severe disease, negatively correlated with 10 clinical parameters and positively correlated with SPO2 (rs = 0.442, p = 0.005). Mini meta-analysis indicated elevated glutamate was related to increased risk of COVID-19 infection (pooled odd ratio [OR] = 2.02; 95% confidence interval [CI]: 1.17-3.50) and severe COVID-19 (pooled OR = 2.28; 95% CI: 1.14-4.56). In contrast, elevated glutamine related to decreased risk of infection and severe COVID-19, the pooled OR were 0.30 (95% CI: 0.20-0.44), and 0.44 (95% CI: 0.19-0.98), respectively. Glutamine and glutamate metabolism are associated with COVID-19 severity in multiple populations, which might confer potential therapeutic target of COVID-19, especially for severe patients.

Modeling and spectroscopic investigation of U(VI) removal on porous amidoxime-functionalized metal organic framework derived from macromolecular carbohydrate.

The investigation of interaction mechanism of U(VI) selective removal on amidoxime-functionalized metal organic framework (i.e., UiO-66(Zr)-AO) derived from macromolecular carbohydrate is conducive to apply metal organic frameworks in actual environmental remediation. The batch experiments showed that UiO-66(Zr)-AO displayed the fast removal rate (equilibrium time of 0.5 h), high adsorption capacity (384.6 mg/g), excellent regeneration performance (<10 % decrease after three cycles) towards U(VI) removal due to the unprecedented chemical stability, large surface area and simple fabrication. U(VI) removal at different pH can be satisfactorily fitted by diffuse layer modeling with cation exchange at low pH and an inner-sphere surface complexation at high pH. The inner-sphere surface complexation was further demonstrated by X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis. These findings revealed that UiO-66(Zr)-AO can be an effective adsorbent to remove the radionuclides from aqueous solution, which is crucial for recycling of uranium resource and decreasing the uranium harm to the environment.

Effects of Dietary Selenium Sources on Physiological Status of Laying Hens and Production of Selenium-Enriched Eggs.

Developing new sources of organic selenium (Se) has potential benefits for animal production and human nutrition via animal-based foods enriched with Se. The objective of this study was to evaluate the effects of Se-enriched insect protein (SEIP) in comparison with other sources, such as sodium selenite (SS) and selenium-enriched yeast (SEY), on performance, egg quality, selenium concentration in eggs, serum biochemical indices, immune capacity, and intestinal morphology of laying hens. Four hundred and fifty 24-week-old Hy-Line Brown laying hens with 94.0 ± 1.5% laying rate were randomly allocated to five groups with six replicates of 15 hens each. The control diet was prepared without adding exogenous selenium (calculated basal Se content of 0.08 mg/kg). The normal group was fed basal diets supplemented with 0.3 mg/kg of Se provided by sodium selenite. Three treatment groups (SS, SEY, and SEIP, respectively) were fed basal diets supplemented with 2 mg/kg of Se provided by sodium selenite, Se-enriched yeast, and SEIP, respectively. The feeding trial lasted for 12 weeks. Results revealed that dietary supplementation of 2 mg/kg of Se increased egg weight, decreased feed conversion ratio, and enhanced the antioxidant capacity of eggs in laying hens relative to the control group, whereas no significant differences were observed among SS, SEY, and SEIP treatment groups for the same. The organic source of Se provided by SEY or SEIP showed higher bio efficiency, as indicated by higher selenium content in eggs of SEY and SEIP compared with SS, although higher content was observed in SEY compared with SEIP. Also, the organic Se source significantly improved antioxidant capacity and immune functions of laying hens than the inorganic Se source. Diets supplemented with SEIP and SS significantly improved jejunal morphology of the laying hens compared with SEY, whereas SEIP was more effective than SEY to improve the oviduct health of laying hens. The results of this work evidently points the additive effect and nontoxicity of SEIP. Thus, SEIP could be used as another organic source of Se in the diet of laying hens and production of selenium-enriched eggs for humans.

Secondary analysis of malaria rapid diagnostic tests from rounds 5-8 of WHO product testing with a focus on false-negative results.

Despite the widespread use of malaria rapid diagnostic test (RDT) in clinical practice, there are a lot of challenges. We conducted a secondary analysis of 129 malaria RDT data from rounds 5-8 of the World Health Organization (WHO) product testing summary and discuss the causes of false-negative (FN) results with a focus on low parasite density, improper RDT storage, operation and interpretation, and plasmodium falciparum with a pfhrp2/3 gene deletion. The results demonstrated that the malaria RDTs currently commercially available might cause FN results in practice.

Predictive factors for pituitary response to pulsatile GnRH therapy in patients with congenital hypogonadotropic hypogonadism.

Pulsatile gonadotropin-releasing hormone (GnRH) may induce spermatogenesis in most patients with congenital hypogonadotropic hypogonadism (CHH) by stimulating gonadotropin production, while the predictors for a pituitary response to pulsatile GnRH therapy were rarely investigated. Therefore, the aim of our study is to investigate predictors of the pituitary response to pulsatile GnRH therapy. This retrospective cohort study included 82 CHH patients who received subcutaneous pulsatile GnRH therapy for at least 1 month. Patients were categorized into poor or normal luteinizing hormone (LH) response subgroups according to their LH level (LH <2 IU l-1 or LH ≥2 IU l-1) 1 month into pulsatile GnRH therapy. Gonadotropin and testosterone levels, testicular size, and sperm count were compared between the two subgroups before and after GnRH therapy. Among all patients, LH increased from 0.4 ± 0.5 IU l-1 to 7.5 ± 4.4 IU l-1 and follicle-stimulating hormone (FSH) increased from 1.1 ± 0.9 IU l-1 to 8.8 ± 5.3 IU l-1. A Cox regression analysis showed that basal testosterone level (ß = 0.252, P = 0.029) and triptorelin-stimulated FSH60min(ß = 0.518, P = 0.01) were two favorable predictors for pituitary response to GnRH therapy. Nine patients (9/82, 11.0%) with low LH response to GnRH therapy were classified into the poor LH response subgroup. After pulsatile GnRH therapy, total serum testosterone level was 39 ± 28 ng dl-1 versus 248 ± 158 ng dl-1 (P = 0.001), and testicular size was 4.0 ± 3.1 ml versus 7.9 ± 4.5 ml (P = 0.005) in the poor and normal LH response subgroups, respectively. It is concluded that higher levels of triptorelin-stimulated FSH60minand basal total serum testosterone are favorable predictors of pituitary LH response to GnRH therapy.

A Review of the Functional and Anatomical Default Mode Network in Schizophrenia.

Schizophrenia is a severe mental disorder characterized by impaired perception, delusions, thought disorder, abnormal emotion regulation, altered motor function, and impaired drive. The default mode network (DMN), since it was first proposed in 2001, has become a central research theme in neuropsychiatric disorders, including schizophrenia. In this review, first we define the DMN and describe its functional activity, functional and anatomical connectivity, heritability, and inverse correlation with the task positive network. Second, we review empirical studies of the anatomical and functional DMN, and anti-correlation between DMN and the task positive network in schizophrenia. Finally, we review preliminary evidence about the relationship between antipsychotic medications and regulation of the DMN, review the role of DMN as a treatment biomarker for this disease, and consider the DMN effects of individualized therapies for schizophrenia.

Pulsatile gonadotropin-releasing hormone therapy is associated with earlier spermatogenesis compared to combined gonadotropin therapy in patients with congenital hypogonadotropic hypogonadism.

Both pulsatile gonadotropin-releasing hormone (GnRH) infusion and combined gonadotropin therapy (human chorionic gonadotropin and human menopausal gonadotropin [HCG/HMG]) are effective to induce spermatogenesis in male patients with congenital hypogonadotropic hypogonadism (CHH). However, evidence is lacking as to which treatment strategy is better. This retrospective cohort study included 202 patients with CHH: twenty had received pulsatile GnRH and 182 had received HCG/HMG. Patients had received therapy for at least 12 months. The total follow-up time was 15.6 ± 5.0 months (range: 12-27 months) for the GnRH group and 28.7 ± 13.0 months (range: 12-66 months) for the HCG/HMG group. The median time to first sperm appearance was 6 months (95% confidence interval [CI]: 1.6-10.4) in the GnRH group versus 18 months (95% CI: 16.4-20.0) in the HCG/HMG group (P < 0.001). The median time to achieve sperm concentrations ≥5 × 10 6 ml-1 was 14 months (95% CI: 5.8-22.2) in the GnRH group versus 27 months (95% CI: 18.9-35.1) in the HCG/HMG group (P < 0.001), and the median time to concentrations ≥10 × 10 6 ml-1 was 18 months (95% CI: 10.0-26.0) in the GnRH group versus 39 months (95% CI unknown) in the HCG/HMG group. Compared to the GnRH group, the HCG/HMG group required longer treatment periods to achieve testicular sizes of ≥4 ml, ≥8 ml, ≥12 ml, and ≥16 ml. Sperm motility (a + b + c percentage) evaluated in semen samples with concentrations >1 × 10 6 ml-1 was 43.7% ± 20.4% (16 samples) in the GnRH group versus 43.2% ± 18.1% (153 samples) in the HCG/HMG group (P = 0.921). Notably, during follow-up, the GnRH group had lower serum testosterone levels than the HCG/HMG group (8.3 ± 4.6 vs 16.2 ± 8.2 nmol l-1 , P < 0.001). Our study found that pulsatile GnRH therapy was associated with earlier spermatogenesis and larger testicular size compared to combined gonadotropin therapy. Additional prospective randomized studies would be required to confirm these findings.

Short-term Effects of Risperidone Monotherapy on Spontaneous Brain Activity in First-episode Treatment-naïve Schizophrenia Patients: A Longitudinal fMRI Study.

It is unclear whether abnormal spontaneous neural activation patterns found in chronic schizophrenia patients (CSP) are part of the pathogenesis of disease, consequences of chronic illness, or effects of antipsychotic treatment. We performed a longitudinal resting-state functional magnetic resonance imaging (fMRI) study in 42 treatment-naïve first-episode schizophrenia patients (FESP) at baseline and then after 8-weeks of risperidone monotherapy, and compared the findings to 38 healthy volunteers. Spontaneous brain activity was quantified using the fractional amplitude of low-frequency fluctuations (fALFF) and regional homogeneity (ReHo) and compared between patients and controls. Pretreatment, patients exhibited higher fALFF in left caudate compared with controls. After treatment, patients had elevated fALFF in bilateral putamen and right caudate, and increased ReHo in right caudate and left putamen. Greater increase of fALFF in the left putamen correlated with less improvement in positive symptoms. Thus, abnormalities of spontaneous neural activity in chronic schizophrenia is at least partly due to a medication effect. The observed post-treatment increase in striatal intrinsic activity may reflect counter-therapeutic functional adaptation to dopamine D2 receptor occupancy required for medication effects on psychosis.