Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis?

OBJECTIVE: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. METHODS: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. RESULTS: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84-0.89), 91% (95% CI: 0.90-0.92) and 95% (95% CI: 0.93-0.97) in the adult BAL group; 90% (95% CI: 0.88-0.91), 98% (95% CI: 0.97-0.98) and 97% (95% CI: 0.95-0.99) in the adult ES group; 86% (95% CI: 0.84-0.89) and 97% (95% CI: 0.96-0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10-0.19) and 99% (95% CI: 0.97-1.00) in the pediatric ES group; 80% (95% CI: 0.72-0.87) and 94% (95% CI: 0.92-0.95) in the pediatric GA group; 67% (95% CI: 0.62-0.72) and 99% (95% CI: 0.98-0.99) in the pediatric IS group; and 54% (95% CI: 0.43-0.64) and 99% (95% CI: 0.97-0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. CONCLUSION: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations

Soil N-oxide emissions decrease from intensive greenhouse vegetable fields by substituting synthetic N fertilizer with organic and bio-organic fertilizers

In order to reduce soil and environmental quality degradation associated with the use of synthetic nitrogen (N), substituting chemical fertilizer with organic or bio-organic fertilizer has become an increasingly popular option. However, components of this fertilizer strategy related to mitigation of soil N-oxide emissions and maintenance of crop yield remain uncertain. Here, we evaluated the effects of three different fertilizer strategies, with equal amounts of N, on nitrous oxide (N2O) and nitric oxide (NO) emissions, vegetable yield, and yield-scaled N2O and NO emissions under three consecutive cucumber growing seasons. The three treatments were chemical fertilizer (NPK, urea), organic fertilizer (O, composted cattle manure), and bio-organic fertilizer (O + T, O combined with Trichoderma.spp). Results showed that the NPK plot had the highest area-scaled emissions of N2O (13.1 ± 0.48 kg N ha−1 yr−1) and NO (5.01 ± 0.34 kg N ha−1 yr−1), which were 1.3–1.4 and 3.1–3.7 times greater than the O and O + T plots, respectively. The annual direct emission factors for N2O and NO were 2.08% and 0.92% for the NPK plot, which declined to 1.34% and 0.09% in the O plot, and 1.12% and 0.03% in the O + T plot, respectively. The annual vegetable yield was 117 ± 2.9 t ha−1 for NPK plot and 122 ± 2.0 t ha−1 for O + T plot, which was higher than 111 ± 1.7 t ha−1 for O plot. The yield-scaled N2O + NO emissions differed significantly with fertilization treatment, with the lowest value observed in the O + T plot. We attributed the lower soil N-oxide emissions following organic fertilizer application to the slow release of available N and enhanced denitrification caused by the increase of soil dissolved organic carbon and pH. Compared with the use of organic fertilizer alone, the addition of Trichoderma.spp significantly increased the potential denitrification rate but decreased N2O emissions, which may have promoted the reduction of N2O to N2. Therefore, our results suggest that adopting composted organic fertilizer mixtures with microbial inoculants could be a win-win practice to mitigate gaseous N losses and simultaneously improve crop yield in intensively managed vegetable cropping systems

Mining the candidate genes of rice panicle traits via a genome-wide association study

Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding

A hub gene signature as a therapeutic target and biomarker for sepsis and geriatric sepsis-induced ARDS concomitant with COVID-19 infection

BackgroundCOVID-19 and sepsis represent formidable public health challenges, characterized by incompletely elucidated molecular mechanisms. Elucidating the interplay between COVID-19 and sepsis, particularly in geriatric patients suffering from sepsis-induced acute respiratory distress syndrome (ARDS), is of paramount importance for identifying potential therapeutic interventions to mitigate hospitalization and mortality risks.MethodsWe employed bioinformatics and systems biology approaches to identify hub genes, shared pathways, molecular biomarkers, and candidate therapeutics for managing sepsis and sepsis-induced ARDS in the context of COVID-19 infection, as well as co-existing or sequentially occurring infections. We corroborated these hub genes utilizing murine sepsis-ARDS models and blood samples derived from geriatric patients afflicted by sepsis-induced ARDS.ResultsOur investigation revealed 189 differentially expressed genes (DEGs) shared among COVID-19 and sepsis datasets. We constructed a protein-protein interaction network, unearthing pivotal hub genes and modules. Notably, nine hub genes displayed significant alterations and correlations with critical inflammatory mediators of pulmonary injury in murine septic lungs. Simultaneously, 12 displayed significant changes and correlations with a neutrophil-recruiting chemokine in geriatric patients with sepsis-induced ARDS. Of these, six hub genes (CD247, CD2, CD40LG, KLRB1, LCN2, RETN) showed significant alterations across COVID-19, sepsis, and geriatric sepsis-induced ARDS. Our single-cell RNA sequencing analysis of hub genes across diverse immune cell types furnished insights into disease pathogenesis. Functional analysis underscored the interconnection between sepsis/sepsis-ARDS and COVID-19, enabling us to pinpoint potential therapeutic targets, transcription factor-gene interactions, DEG-microRNA co-regulatory networks, and prospective drug and chemical compound interactions involving hub genes.ConclusionOur investigation offers potential therapeutic targets/biomarkers, sheds light on the immune response in geriatric patients with sepsis-induced ARDS, emphasizes the association between sepsis/sepsis-ARDS and COVID-19, and proposes prospective alternative pathways for targeted therapeutic interventions

Vitamin B12 Levels in Methamphetamine Addicts

Objective: It has been established that reduced vitamin B12 serum levels are associated with cognitive decline and mental illness. The chronic use of methamphetamine (MA), which is a highly addictive drug, can induce cognitive impairment and psychopathological symptoms. There are few studies addressing the association of MA with vitamin B12 serum levels. This study examined whether the serum levels of B12 are associated with MA addiction.Methods: Serum vitamin B12, homocysteine (Hcy), glucose and triglyceride concentrations were measured in 123 MA addicts and 108 controls. In addition, data were collected on their age, marital status, level of education and Body Mass Index (BMI) for all participants. In the patient group, the data for each subject were collected using the Fagerstrom Test for Nicotine Dependence (FTND), the Alcohol Use Disorders Identification Test (AUDIT), and a drug use history, which included the age of onset, total duration of MA use, the number of relapses and addiction severity.Results: Our results showed that MA addicts had lower vitamin B12 levels (p < 0.05) than those of healthy controls, but Hcy levels were not significantly different between the two groups (p > 0.05). Serum B12 levels were negatively correlated with the number of relapses in the MA group. Furthermore, binary logistics regression analysis indicated that the B12 was an influencing factor contributing to addiction severity.Conclusion: The findings of this study suggest that some MA addicts might have vitamin B12 deficiency, and serum B12 levels may be involved in the prognosis of MA addiction

A novel single nucleotide polymorphism within the NOD2 gene is associated with pulmonary tuberculosis in the Chinese Han, Uygur and Kazak populations

<p>Abstract</p> <p>Background</p> <p>The present study aimed to investigate the genetic polymorphisms in exon 4 of the <it>NOD2 </it>gene in tuberculosis patients and healthy controls, in order to clarify whether polymorphisms in the <it>NOD2 </it>gene is associated with tuberculosis.</p> <p>Methods</p> <p>A case-control study was performed on the Chinese Han, Uygur and Kazak populations. Exon 4 of the <it>NOD2 </it>gene was sequenced in 425 TB patients and 380 healthy controls to identify SNPs.</p> <p>Results</p> <p>The frequency of T/G genotypes for the Arg587Arg (CGT → CGG) single nucleotide polymorphism (SNP) in <it>NOD2 </it>was found to be significantly higher in the Uygur (34.9%) and Kazak (37.1%) populations than the Han population (18.6%). Also, the frequency of G/G genotypes for the Arg587Arg SNP was significantly higher in the Uyghur (8.3%) and Kazak (5.4%) populations than the Han population (0.9%). Meanwhile, no significant difference was found in the Arg587Arg polymorphism between the tuberculosis patients and healthy controls in the Uyghur and Kazak populations (<it>P </it>> 0.05) whereas, a significant difference was observed in the Arg587Arg polymorphism between the tuberculosis patients and healthy controls in the Han population (<it>P </it>< 0.01). The odd ratio of 2.16 (95% CI = 1.31-3.58; <it>P </it>< 0.01) indicated that the Arg587Arg SNP in <it>NOD2 </it>may be associated with susceptibility to tuberculosis in the Chinese Han population.</p> <p>Conclusions</p> <p>Our study is the first to demonstrate that the Arg587Arg SNP in <it>NOD2 </it>is a new possible risk factor for tuberculosis in the Chinese Han population, but not in the Uyghur and Kazak populations. Our results may reflect racial differences in genetic susceptibility to tuberculosis.</p

Monetary incentives and peer referral in promoting secondary distribution of HIV self-testing among men who have sex with men in China: A randomized controlled trial

Background Digital network–based methods may enhance peer distribution of HIV self-testing (HIVST) kits, but interventions that can optimize this approach are needed. We aimed to assess whether monetary incentives and peer referral could improve a secondary distribution program for HIVST among men who have sex with men (MSM) in China. Methods and findings Between October 21, 2019 and September 14, 2020, a 3-arm randomized controlled, single-blinded trial was conducted online among 309 individuals (defined as index participants) who were assigned male at birth, aged 18 years or older, ever had male-to-male sex, willing to order HIVST kits online, and consented to take surveys online. We randomly assigned index participants into one of the 3 arms: (1) standard secondary distribution (control) group (n = 102); (2) secondary distribution with monetary incentives (SD-M) group (n = 103); and (3) secondary distribution with monetary incentives plus peer referral (SD-M-PR) group (n = 104). Index participants in 3 groups were encouraged to order HIVST kits online and distribute to members within their social networks. Members who received kits directly from index participants or through peer referral links from index MSM were defined as alters. Index participants in the 2 intervention groups could receive a fixed incentive ($3 USD) online for the verified test result uploaded to the digital platform by each unique alter. Index participants in the SD-M-PR group could additionally have a personalized peer referral link for alters to order kits online. Both index participants and alters needed to pay a refundable deposit ($15 USD) for ordering a kit. All index participants were assigned an online 3-month follow-up survey after ordering kits. The primary outcomes were the mean number of alters motivated by index participants in each arm and the mean number of newly tested alters motivated by index participants in each arm. These were assessed using zero-inflated negative binomial regression to determine the group differences in the mean number of alters and the mean number of newly tested alters motivated by index participants. Analyses were performed on an intention-to-treat basis. We also conducted an economic evaluation using microcosting from a health provider perspective with a 3-month time horizon. The mean number of unique tested alters motivated by index participants was 0.57 ± 0.96 (mean ± standard deviation [SD]) in the control group, compared with 0.98 ± 1.38 in the SD-M group (mean difference [MD] = 0.41),and 1.78 ± 2.05 in the SD-M-PR group (MD = 1.21). The mean number of newly tested alters motivated by index participants was 0.16 ± 0.39 (mean ± SD) in the control group, compared with 0.41 ± 0.73 in the SD-M group (MD = 0.25) and 0.57 ± 0.91 in the SD-M-PR group (MD = 0.41), respectively. Results indicated that index participants in intervention arms were more likely to motivate unique tested alters (control versus SD-M: incidence rate ratio [IRR = 2.98, 95% CI = 1.82 to 4.89, p-value < 0.001; control versus SD-M-PR: IRR = 3.26, 95% CI = 2.29 to 4.63, p-value < 0.001) and newly tested alters (control versus SD-M: IRR = 4.22, 95% CI = 1.93 to 9.23, p-value < 0.001; control versus SD-M-PR: IRR = 3.49, 95% CI = 1.92 to 6.37, p-value < 0.001) to conduct HIVST. The proportion of newly tested testers among alters was 28% in the control group, 42% in the SD-M group, and 32% in the SD-M-PR group. A total of 18 testers (3 index participants and 15 alters) tested as HIV positive, and the HIV reactive rates for alters were similar between the 3 groups. The total costs were $19,485.97 for 794 testers, including 450 index participants and 344 alter testers. Overall, the average cost per tester was$24.54, and the average cost per alter tester was $56.65. Monetary incentives alone (SD-M group) were more cost-effective than monetary incentives with peer referral (SD-M-PR group) on average in terms of alters tested and newly tested alters, despite SD-M-PR having larger effects. Compared to the control group, the cost for one more alter tester in the SD-M group was$14.90 and $16.61 in the SD-M-PR group. For newly tested alters, the cost of one more alter in the SD-M group was$24.65 and $49.07 in the SD-M-PR group. No study-related adverse events were reported during the study. Limitations include the digital network approach might neglect individuals who lack internet access. Conclusions Monetary incentives alone and the combined intervention of monetary incentives and peer referral can promote the secondary distribution of HIVST among MSM. Monetary incentives can also expand HIV testing by encouraging first-time testing through secondary distribution by MSM. This social network–based digital approach can be expanded to other public health research, especially in the era of the Coronavirus Disease 2019 (COVID-19). Trial registration Chinese Clinical Trial Registry (ChiCTR) ChiCTR190002543

JWST CEERS probes the role of stellar mass and morphology in obscuring galaxies

A population of massive galaxies invisible or very faint in deep optical/near-infrared surveys, but brighter at longer wavelengths has been uncovered in the past years. However, the nature of these optically dark/faint galaxies (OFGs, among other nomenclatures) is highly uncertain. In this work, we investigate the drivers of dust attenuation in the JWST era. Particularly, we study the role of stellar mass, size, and orientation in obscuring star-forming galaxies (SFGs) at $3 < z < 7.5$, focusing on understanding why galaxies like OFGs are so faint at optical/near-infrared wavelengths. We find that stellar mass is the primary proxy of dust attenuation among those studied. Effective radius and axis ratio do not show a clear link with dust attenuation, with the effect of orientation close to random. However, there is a subset of highly dust attenuated ($A_V > 1$, typically) SFGs, of which OFGs are a specific case. For this subset, we find that the key distinctive feature is their compact size (for massive systems with $\log (M_{*}/M_{\odot}) > 10$), exhibiting 30% smaller effective radius than the average SFGs at the same stellar mass and redshift. On the contrary, they do not exhibit a preference for low axis ratios (i.e., edge-on disks). The results in this work show stellar mass as a primary proxy of dust attenuation and compact stellar light profiles behind thick dust columns obscuring typical massive SFGs.Comment: Submitted to A&A. 13 pages, 9 figure