Enhancing Si3N4 Selectivity over SiO2 in Low-RF Power NF3-O2 Reactive Ion Etching: The Effect of NO Surface Reaction.

Highly selective etching of silicon nitride (Si3N4) and silicon dioxide (SiO2) has received considerable attention from the semiconductor community owing to its precise patterning and cost efficiency. We investigated the etching selectivity of Si3N4 and SiO2 in an NF3/O2 radio-frequency glow discharge. The etch rate linearly depended on the source and bias powers, whereas the etch selectivity was affected by the power and ratio of the gas mixture. We found that the selectivity can be controlled by lowering the power with a suitable gas ratio, which affects the surface reaction during the etching process. X-ray photoelectron spectroscopy of the Si3N4 and QMS measurements support the effect of surface reaction on the selectivity change by surface oxidation and nitrogen reduction with the increasing flow of O2. We suggest that the creation of SiOxNy bonds on the surface by NO oxidation is the key mechanism to change the etch selectivity of Si3N4 over SiO2.

Deployment of a Reservoir-Targeted Vaccine Against Borrelia burgdorferi Reduces the Prevalence of Babesia microti Coinfection in Ixodes scapularis Ticks.

In the Northeast and upper Midwest of the United States, Babesia microti and Borrelia burgdorferi use Ixodes scapularis ticks as vector and Peromyscus leucopus mice as major reservoir host. We previously established, in a 5-year field trial, that a reservoir-targeted outer surface protein A vaccine reduces the prevalence of B. burgdorferi-infected ticks. We accessed ticks and mouse blood samples collected during the trial, extracted total DNA, and amplified the B. microti 18S rRNA gene. Vaccine deployment reduced the prevalence of ticks coinfected with B. microti and that of mice infected with B. microti. Breaking the enzootic cycle of B. burgdorferi may reduce the incidence of babesiosis.

The Commensal Microbe Veillonella as a Marker for Response to an FGF19 Analog in NASH.

BACKGROUND AND AIMS: The composition of the human gut microbiota is linked to health and disease, and knowledge of the impact of therapeutics on the microbiota is essential to decipher their biological roles and to gain new mechanistic insights. Here we report the effect of aldafermin, an analog of the gut hormone FGF19, versus placebo on the gut microbiota in a prospective, phase 2 study in patients with NASH. APPROACH AND RESULTS: A total of 176 patients with biopsy-confirmed nonalcoholic steatohepatitis (NASH) (nonalcoholic fatty liver disease activity score ≥ 4), fibrosis (F1-F3 by NASH Clinical Research Network criteria), and elevated liver fat content (≥ 8% by magnetic resonance imaging-proton density fat fraction) received 0.3 mg (n = 23), 1 mg (n = 49), 3 mg (n = 49), and 6 mg (n = 28) aldafermin or placebo (n = 27) for 12 weeks. Stool samples were collected on day 1 and week 12 and profiled using 16S ribosomal RNA gene sequencing; 122 patients had paired stool microbiome profiles at both day 1 and week 12. Overall, the state of the gut microbial community was distinctly stable in patients treated with aldafermin, with all major phyla and genera unaltered during therapy. Patients treated with aldafermin showed a significant, dose-dependent enrichment in the rare genus Veillonella, a commensal microbe known to have lactate-degrading and performance-enhancing properties, which correlated with changes in serum bile acid profile. CONCLUSIONS: Veillonella may be a bile acid-sensitive bacteria whose enrichment is enabled by aldafermin-mediated suppression of bile acid synthesis and, in particular, decreases in toxic bile acids. This study provides an integrated analysis of gut microbiome, serum bile acid metabolome, imaging, and histological measurements in clinical trials testing aldafermin for NASH. Our results provide a better understanding of the intricacies of microbiome-host interactions (clinicaltrials.gov trial No. NCT02443116).

Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides.

BACKGROUND: Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R. toruloides to produce the polyketide triacetic acid lactone (TAL) directly from unfiltered hydrolysate deconstructed from biomass with minimal unit process operations. RESULTS: Introduction of the 2-pyrone synthase gene into R. toruloides enabled the organism to produce 2.4 g/L TAL from simple media or 2.0 g/L from hydrolysate produced from sorghum biomass. Both of these titers are on par with titers from other better-studied microbial hosts after they had been heavily engineered. We next demonstrate that filtered hydrolysates produced from ensiled sorghum are superior to those derived from dried sorghum for TAL production, likely due to the substantial organic acids produced during ensiling. We also demonstrate that the organic acids found in ensiled biomass can be used for direct synthesis of ionic liquids within the biomass pretreatment process, enabling consolidation of unit operations of in-situ ionic liquid synthesis, pretreatment, saccharification, and fermentation into a one-pot, separations-free process. Finally, we demonstrate this consolidation in a 2 L bioreactor using unfiltered hydrolysate, producing 3.9 g/L TAL. CONCLUSION: Many steps involved in deconstructing biomass into fermentable substrate can be combined into a distinct operation, and directly fed to cultures of engineered R. toruloides cultures for subsequent valorization into gram per liter titers of TAL in a cost-effective manner.

Effect of multiple rescatterings on continuum harmonics from asymmetric molecules in multicycle lasers.

A wide range of harmonics especially continuum harmonics is a prerequisite for attosecond pulse generation. One can use longer-wavelength lasers to push the cutoff to a higher order. However, this does not translate to the same amount of continuum range extension because multiple rescattering phenomena are also enhanced in the process, potentially affecting the lower end of the continuum harmonics. It is then important to understand exactly how multiple rescatterings affect the harmonic structure and their response to various laser parameters, which is the main theme of this paper. Particularly, by applying the synchrosqueezed time-frequency transform and classical electron trajectory analysis to the asymmetric molecule carbon monoxide (CO), we justify that the multiple rescatterings indeed influence the periodicity of the harmonic spectra and the stable periodicity is, in fact, bounded by the first- and third-order returns. Moreover, for the first time, we find that the high-order rescatterings are asymmetric regarding the molecular rotation of 180°, but always correlate with the first-order returns. Our last result is that by breaking the laser symmetry in an appropriate way, the contribution of multiple rescatterings is removed so that the continuum region is entirely defined by the first-order return energies.

Differential Cytotoxicity of Curcumin-Loaded Micelles on Human Tumor and Stromal Cells.

Although curcumin in the form of nanoparticles has been demonstrated as a potential anti-tumor compound, the impact of curcumin and nanocurcumin in vitro on normal cells and in vivo in animal models is largely unknown. This study evaluated the toxicity of curcumin-loaded micelles in vitro and in vivo on several tumor cell lines, primary stromal cells, and zebrafish embryos. Breast tumor cell line (MCF7) and stromal cells (human umbilical cord vein endothelial cells, human fibroblasts, and human umbilical cord-derived mesenchymal stem cells) were used in this study. A zebrafish embryotoxicity (FET) assay was conducted following the Organisation for Economic Co-operation and Development (OECD) Test 236. Compared to free curcumin, curcumin PM showed higher cytotoxicity to MCF7 cells in both monolayer culture and multicellular tumor spheroids. The curcumin-loaded micelles efficiently penetrated the MCF7 spheroids and induced apoptosis. The nanocurcumin reduced the viability and disturbed the function of stromal cells by suppressing cell migration and tube formation. The micelles demonstrated toxicity to the development of zebrafish embryos. Curcumin-loaded micelles demonstrated toxicity to both tumor and normal primary stromal cells and zebrafish embryos, indicating that the use of nanocurcumin in cancer treatment should be carefully investigated and controlled.

Updates on metaQuantome Software for Quantitative Metaproteomics.

metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

BACKGROUND: The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. METHODS: In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). RESULTS: Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. CONCLUSION: We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics.

BACKGROUND: Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS: In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

The impact of vitamin B12 deficiency on infant gut microbiota.

Although physiologic and neurologic consequences of micronutrient deficiencies have been addressed extensively, less is known about their impact on developing gut microbiota. Vitamin B12 deficiency is a common micronutrient deficiency in infants. We aimed to analyze the gut microbial composition of exclusively breastfed infants aged between 4 and 6 months with and without vitamin B12 deficiency by 16S rRNA gene sequencing. In a subgroup of infants with vitamin B12 deficiency, stool samples are recollected and reanalyzed after vitamin B12 supplementation. A total of 88 infants' stool samples (median age 4 months [IQR 4-5], 50% males) were analyzed, of which 28 (31.8%) were vitamin B12 sufficient and 60 (68.2%) were vitamin B12 insufficient. Comparisons between vitamin B12-sufficient and vitamin B12-insufficient infants revealed no evidence of differences in the microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the most abundant phyla in all groups. There was no difference between the pre- and post-treatment composition of gut microbiota.Conclusion: Vitamin B12-deficient infants have similar gut microbial composition as vitamin B12-sufficient infants. Since the samples were collected at an early period of life and the exposure to deficiency was relatively short, it may be possible that the effects were not fully established.What is Known: • Vitamin B12 is an essential vitamin for humans and also a crucial compound for human gut microbiota. • Vitamin B12 deficiency is common in exclusively breastfed infants. • In contrast to the adult gut microbiota, infant gut microbiota has been shown to have decreased capacity for de novo synthesis of vitamin B12 and depend on dietary source of vitamin B12.What is New: • There is no difference in the gut microbial composition of vitamin B12-deficient and vitamin B12-sufficient infants.

Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection.

BACKGROUND: Despite effective antiretroviral therapy (ART), patients with chronic human immunodeficiency virus (HIV) infection have increased microbial translocation and systemic inflammation. Alterations in the intestinal microbiota may play a role in microbial translocation and inflammation. METHODS: We profiled the fecal microbiota by pyrosequencing the gene encoding 16S ribosomal RNA (rRNA) and measured markers of microbial translocation and systemic inflammation in 21 patients who had chronic HIV infection and were receiving suppressive ART (cases) and 16 HIV-uninfected controls. RESULTS: The fecal microbial community composition was significantly different between cases and controls. The relative abundance of Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Erysipelotrichi, Erysipelotrichales, Erysipelotrichaceae, and Barnesiella was significantly enriched in cases, whereas that of Rikenellaceae and Alistipes was depleted. The plasma soluble CD14 level (sCD14) was significantly higher and the endotoxin core immunoglobulin M (IgM) level lower in cases, compared with controls. There were significant positive correlations between the relative abundances of Enterobacteriales and Enterobacteriaceae and the sCD14 level; the relative abundances of Gammaproteobacteria, Enterobacteriales, and Enterobacteriaceae and the interleukin 1ß (IL-1ß) level; the relative abundances of Enterobacteriales and Enterobacteriaceae and the interferon γ level; and the relative abundances of Erysipelotrichi and Barnesiella and the TNF-α level. There were negative correlations between endotoxin core IgM and IL-1ß levels. CONCLUSIONS: Patients who have chronic HIV infection and are receiving suppressive ART display intestinal dysbiosis associated with increased microbial translocation and significant associations between specific taxa and markers of microbial translocation and systemic inflammation. This was an exploratory study, the findings of which need to be confirmed.

Childhood malnutrition and the intestinal microbiome.

Malnutrition contributes to almost half of all deaths in children under the age of 5 y, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections, and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it toward an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota, and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition.

Preparations and Thermal Properties of PDMS-AlN-Al2O3 Composites through the Incorporation of Poly(Catechol-Amine)-Modified Boron Nitride Nanotubes.

As one of the emerging nanomaterials, boron nitride nanotubes (BNNTs) provide promising opportunities for diverse applications due to their unique properties, such as high thermal conductivity, immense inertness, and high-temperature durability, while the instability of BNNTs due to their high surface induces agglomerates susceptible to the loss of their advantages. Therefore, the proper functionalization of BNNTs is crucial to highlight their fundamental characteristics. Herein, a simplistic low-cost approach of BNNT surface modification through catechol-polyamine (CAPA) interfacial polymerization is postulated to improve its dispersibility on the polymeric matrix. The modified BNNT was assimilated as a filler additive with AlN/Al2O3 filling materials in a PDMS polymeric matrix to prepare a thermal interface material (TIM). The resulting composite exhibits a heightened isotropic thermal conductivity of 8.10 W/mK, which is a ~47.27% increase compared to pristine composite 5.50 W/mK, and this can be ascribed to the improved BNNT dispersion forming interconnected phonon pathways and the thermal interface resistance reduction due to its augmented compatibility with the polymeric matrix. Moreover, the fabricated composite manifests a fire resistance improvement of ~10% in LOI relative to the neat composite sample, which can be correlated to the thermal stability shift in the TGA and DTA data. An enhancement in thermal permanence is stipulated due to a melting point (Tm) shift of ∼38.5 °C upon the integration of BNNT-CAPA. This improvement can be associated with the good distribution and adhesion of BNNT-CAPA in the polymeric matrix, integrated with its inherent thermal stability, good charring capability, and free radical scavenging effect due to the presence of CAPA on its surface. This study offers new insights into BNNT utilization and its corresponding incorporation into the polymeric matrix, which provides a prospective direction in the preparation of multifunctional materials for electric devices.

"Going vaccine hunting": Multilevel influences on COVID-19 vaccination among racialized sexual and gender minority adults-a qualitative study.

High levels of COVID-19 vaccine hesitancy have been reported among Black and Latinx populations, with lower vaccination coverage among racialized versus White sexual and gender minorities. We examined multilevel contexts that influence COVID-19 vaccine uptake, barriers to vaccination, and vaccine hesitancy among predominantly racialized sexual and gender minority individuals. Semi-structured online interviews explored perspectives and experiences around COVID-19 vaccination. Interviews were recorded, transcribed, uploaded into ATLAS.ti, and reviewed using thematic analysis. Among 40 participants (mean age, 29.0 years [SD, 9.6]), all identified as sexual and/or gender minority, 82.5% of whom were racialized. COVID-19 vaccination experiences were dominated by structural barriers: systemic racism, transphobia and homophobia in healthcare and government/public health institutions; limited availability of vaccination/appointments in vulnerable neighborhoods; absence of culturally-tailored and multi-language information; lack of digital/internet access; and prohibitive indirect costs of vaccination. Vaccine hesitancy reflected in uncertainties about a novel vaccine amid conflicting information and institutional mistrust was integrally linked to structural factors. Findings suggest that the uncritical application of "vaccine hesitancy" to unilaterally explain undervaccination among marginalized populations risks conflating structural and institutional barriers with individual-level psychological factors, in effect placing the onus on those most disenfranchised to overcome societal and institutional processes of marginalization. Rather, disaggregating structural determinants of vaccination availability, access, and institutional stigma and mistrust from individual attitudes and decision-making that reflect vaccine hesitancy, may support 1) evidence-informed interventions to mitigate structural barriers in access to vaccination, and 2) culturally-informed approaches to address decisional ambivalence in the context of structural homophobia, transphobia, and racism.

Frequent Disengagement and Subsequent Mortality Among People With HIV and Hepatitis C in Canada: A Prospective Cohort Study.

Background: The cascade of care, commonly used to assess HIV and hepatitis C (HCV) health service delivery, has limitations in capturing the complexity of individuals' engagement patterns. This study examines the dynamic nature of engagement and mortality trajectories among people with HIV and HCV. Methods: We used data from the Canadian HIV-HCV Co-Infection Cohort, which prospectively follows 2098 participants from 18 centers biannually. Markov multistate models were used to evaluate sociodemographic and clinical factors associated with transitioning between the following states: (1) lost-to-follow-up (LTFU), defined as no visit for 18 months; (2) reengaged (reentry into cohort after being LTFU); (3) withdrawn from the study (ie, moved); (4) death; otherwise remained (5) engaged-in-care. Results: A total of 1809 participants met the eligibility criteria and contributed 12 591 person-years from 2003 to 2022. LTFU was common, with 46% experiencing at least 1 episode, of whom only 57% reengaged. One in 5 (n = 383) participants died during the study. Participants who transitioned to LTFU were twice as likely to die as those who were consistently engaged. Factors associated with transitioning to LTFU included detectable HCV RNA (adjusted hazards ratio [aHR], 1.37; 95% confidence interval [CI], 1.13-1.67), evidence of HCV treatment but no sustained virologic response result (aHR, 1.99; 95% CI, 1.56-2.53), and recent incarceration (aHR, 1.94; 95% CI, 1.58-2.40). Being Indigenous was a significant predictor of death across all engagement trajectories. Interpretation: Disengagement from clinical care was common and resulted in higher death rates. People LTFU were more likely to require HCV treatment highlighting a priority population for elimination strategies.

Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics.

Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.

Free satellite image data application for monitoring land use cover changes in the kon ha nung plateau, vietnam.

Remote sensing imagery is the most suitable tool for monitoring, managing, and evaluating land-use overlay fluctuations, especially forest cover for large areas. Free- and medium-resolution satellite imagery is a useful tool that allows scientific researchers and management organizations to monitor forest development in developing countries, such as Vietnam. In this study, we used SPOT 4 and Planet remote sensing data to assess land-use status fluctuations in the Kon Ha Nung Plateau area, Vietnam, between 2000 and 2021 (the overall accuracy was 90.52%, Kappa value = 0.89). The results showed that from 2000 to 2010, the rate of natural forest loss in this area was 0.32%/year, of which, more than 6500 ha were converted to other uses. Between 2010 and 2021, the rate of natural forest loss gradually decreased (0.09%/year) instead of fluctuating between different types of land use. The area of forests, perennial crop land, and annual crop land tended to increase from 2000 to 2010; however, from 2010 to 2021, the area of plantation forests decreased markedly, while the area of perennial crop land and annual crop land continued to expand. The analysis of the policies on forest management, exploitation, and protection was applied locally, to explain the causes of the change in spatiotemporal aspects of the types of land-use cover in the Kon Ha Nung Plateau. Restoring forest areas during 2010-2021 initially improved effectiveness in forest management and protection. Furthermore, the results provide a better understanding of the current position and role of the government apparatus, cadres, and ethnic minorities in socioeconomic development associated with forest protection and development on the Kon Ha Nung Plateau. The results of this study can help managers monitor annual forest-cover fluctuations based on free remote sensing imagery to reduce both the cost of management and surveying, yielding relatively accurate results.

Covid-19 Vaccine Hesitancy and Under-Vaccination among Marginalized Populations in the United States and Canada: A Scoping Review.

BACKGROUND: Amid persistent disparities in Covid-19 vaccination and burgeoning research on vaccine hesitancy (VH), we conducted a scoping review to identify multilevel determinants of Covid-19 VH and under-vaccination among marginalized populations in the U.S. and Canada. METHODS: Using the scoping review methodology developed by the Joanna Briggs Institute, we designed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020-October 25, 2022. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 VH and under-vaccination among marginalized populations. RESULTS: The search captured 11,374 non-duplicated records, scoped to 103 peer-reviewed articles. Among 14 marginalized populations identified, African American/Black, Latinx, LGBTQ+, American Indian/Indigenous, people with disabilities, and justice-involved people were the predominant focus. Thirty-two factors emerged as influencing Covid-19 VH, with structural racism/stigma and institutional mistrust (structural)(n = 71) most prevalent, followed by vaccine safety (vaccine-specific)(n = 62), side effects (vaccine-specific)(n = 50), trust in individual healthcare provider (social/community)(n = 38), and perceived risk of infection (individual)(n = 33). Structural factors predominated across populations, including structural racism/stigma and institutional mistrust, barriers to Covid-19 vaccine access due to limited supply/availability, distance/lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally- and linguistically-appropriate information. DISCUSSION: We identified multilevel and complex drivers of Covid-19 under-vaccination among marginalized populations. Distinguishing vaccine-specific, individual, and social/community factors that may fuel decisional ambivalence, more appropriately defined as VH, from structural racism/structural stigma and systemic/institutional barriers to vaccination access may better support evidence-informed interventions to promote equity in access to vaccines and informed decision-making among marginalized populations.

Longitudinal Analysis of the Intestinal Microbiota among a Cohort of Children in Rural and Urban Areas of Pakistan.

The profile of the intestinal microbiota is known to be altered in malnourished young children in low- and middle-income countries. However, there are limited studies longitudinally evaluating the intestinal microbiota in malnourished young children in resource-limited settings over the first two years of life. In this longitudinal pilot study, we determined the effect of age, residential location, and intervention on the composition, relative abundance, and diversity of the intestinal microbiota in a representative sample of children under 24 months of age with no diarrhea in the preceding 72 h in the urban and rural areas of Sindh, Pakistan nested within a cluster-randomized trial evaluating the effect of zinc and micronutrients on growth and morbidity (ClinicalTrials.gov Identifier: NCT00705445). The major findings were age-related with significant changes in alpha and beta diversity with increasing age. There was a significant increase in the relative abundance of the Firmicutes and Bacteroidetes phyla and a significant decrease in that of the Actinobacteria and Proteobacteria phyla (p < 0.0001). There were significant increases in the relative abundances of the major genera Bifidobacterium, Escherichia/Shigella and Streptococcus (p < 0.0001), and no significant change in the relative abundance of Lactobacillus. Using the LEfSE algorithm, differentially abundant taxa were identified between children in the first and second years of age, between those residing in rural and urban areas, and those who received different interventions at different ages from 3 to 24 months. The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them. Further longitudinal studies with larger numbers of well-nourished and malnourished children are required to fully characterize the intestinal microbiota of children in this region.

Estimation of the rate and effect of new beneficial mutations in asexual populations.

The rate and effect of available beneficial mutations are key parameters in determining how a population adapts to a new environment. However, these parameters are poorly known, in large part because of the difficulty of designing and interpreting experiments to examine the rare and intrinsically stochastic process of mutation occurrence. We present a new approach to estimate the rate and selective advantage of beneficial mutations that underlie the adaptation of asexual populations. We base our approach on the analysis of experiments that track the effect of newly arising beneficial mutations on the dynamics of a neutral marker in evolving bacterial populations and develop efficient estimators of mutation rate and selective advantage. Using extensive simulations, we evaluate the accuracy of our estimators and conclude that they are quite robust to the use of relatively low experimental replication. To validate the predictions of our model, we compare theoretical and experimentally determined estimates of the selective advantage of the first beneficial mutation to fix in a series of ten replicate populations. We find that our theoretical predictions are not significantly different from experimentally determined selection coefficients. Application of our method to suitably designed experiments will allow estimation of how population evolvability depends on demographic and initial fitness parameters.