The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
Huanglongbing, a devastating disease of citrus, is caused by the obligate, intracellular bacterium "Candidatus Liberibacter asiaticus" (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid. Development of transmission-blocking strategies to manage huanglongbing relies on knowledge of CLas and D. citri interactions at the molecular level. Prior transcriptome analyses of D. citri point to changes in psyllid biology due to CLas infection but have been hampered by incomplete versions of the D. citri genome, proper host plant controls, and/or a lack of a uniform data analysis approach. In this work, we present lessons learned from a quantitative transcriptome analysis of excised heads, salivary glands, midguts, and bacteriomes from CLas-positive and CLas-negative D. citri using the chromosomal length D. citri genome assembly.
Each organ had a unique transcriptome profile and response to CLas infection. Though most psyllids were infected with the bacterium, CLas-derived transcripts were not detected in all organs. By analyzing the midgut dataset using both the Diaci_v1.1 and v3.0 D. citri genomes, we showed that improved genome assembly led to significant and quantifiable differences in RNA-sequencing data interpretation.
Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue-specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.
Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue-specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.
To compare the performance of the rabbit monoclonal antihuman CD246 antibody (D5F3 clone) with the established ALK1 clone for immunohistochemical assessment of anaplastic large cell lymphoma (ALCL).
Archival cases of ALCL (n = 27) were assessed immunohistochemically by use of ALK1 and D5F3 clones under standard Clinical Laboratory Improvement Amendments-compliant conditions. The intensity of cytoplasmic staining (0 = none; 1 = faint; 2 = moderate; 3+ = strong) and proportion of neoplastic cells (0%, <5%, 5%-50%, >50%) were evaluated and compared with clinical ALK break-apart fluorescence in situ hybridization (FISH) assays.
Nine ALCL specimens were positive for ALK expression by ALK1 staining (33%; 1 = 1+; 0 = 2+; 8 = 3+), while 14 were positive by D5F3 staining (48%; 3 = 1+; 1 = 2+; 10 = 3+). Across the cohort, D5F3 staining showed a significantly greater proportion of cells staining positive (P = .02) and greater intensity (P = .03). Of 3 cases positive for D5F3 only with FISH results, none showed rearrangements, although 1 showed copy number gains at the ALK locus in a subset of cells.
Overall, D5F3 showed greater stain intensity and proportion staining than ALK1 in ALK-positive ALCL cases, which is especially helpful in limited samples. Caution and consideration of orthogonal ALK testing types is recommended, especially for cases with weak or focal staining.
Overall, D5F3 showed greater stain intensity and proportion staining than ALK1 in ALK-positive ALCL cases, which is especially helpful in limited samples. Caution and consideration of orthogonal ALK testing types is recommended, especially for cases with weak or focal staining.
Single-molecule localization microscopy allows studying the dynamics of biomolecules in cells and resolving the biophysical properties of the molecules and their environment underlying cellular function. With the continuously growing amount of data produced by individual experiments, the computational cost of quantifying these properties is increasingly becoming the bottleneck of single-molecule analysis. Mining these data requires an integrated and efficient analysis toolbox.
We introduce TRamWAy, a modular Python library that features (i) a conservative tracking procedure for localization data, (ii) a range of sampling techniques for meshing the spatio-temporal support of the data, (iii) computationally efficient solvers for inverse models, with the option of plugging in user-defined functions and (iv) a collection of analysis tools and a simple web-based interface.
TRamWAy is a Python library and can be installed with pip and conda. The source code is available at https//github.com/DecBayComp/TRamWAy.
TRamWAy is a Python library and can be installed with pip and conda. The source code is available at https//github.com/DecBayComp/TRamWAy.
The Patient Experienced Symptom State (PESS) is a single-question, patient-reported outcome which is validated to assess global disease impact in rheumatoid arthritis (RA). This study addresses its sensitivity to change and reliability.
Disease activity, disease impact in the 7 domains of RAID and PESS were assessed in patients with RA from the NOR-DMARD registry, at two visits, six-months apart. The PESS over the last week was scored in five levels, from "very bad" to "very good".Disease impact and disease activity were compared between patients who improved, maintained or worsened PESS over time, through one-way analysis of variance (ANOVA), with post-hoc Bonferroni correction. Correlations between changes in these parameters were assessed through SpearmaĆs correlation coefficient. Sensitivity to change was assessed by standardized response mean (SRM) between the two visits. Reliability was analyzed through intraclass correlation coefficient between the two visits in patients with stable disease activity and impact.
In 353 patients (76.8% females, 9.9(9.6) years disease duration), patients who improved their PESS level was associated with substantial improvements in mean impact in all domains as well as disease activity. (p< 0.02). PESS change was moderately to strongly correlated with RAID domains and disease activity (rho 0.4-0.7). https://www.selleckchem.com/products/LBH-589.html PESS was responsive to change (SRM 0.65, 95%CI 0.54-0.76), particularly among RAID responders (SRM 1.79, 95%CI 1.54-1.99). PESS was moderately reliable in patients with stable condition (ICC 0.72, 95%CI 0.52-0.83).
PESS is valid, feasible, reliable and responsive, representing an opportunity to improve the assessment of disease impact with minimal questionnaire burden.
PESS is valid, feasible, reliable and responsive, representing an opportunity to improve the assessment of disease impact with minimal questionnaire burden.
Patients with systemic lupus erythematosus (SLE) have increased prevalence of clinical cardiovascular disease (CVD) and subclinical atherosclerosis. Although 30-40% of patients with SLE have vascular plaque on ultrasound scanning, this study is the first to consider the relationship between total burden of plaque and subsequent CVD risk.
One hundred patients with SLE and without any previous clinical CVD underwent vascular ultrasound scans of both carotid and both common femoral bifurcations between 2011 and 2013. Clinical, serological, demographic and treatment data were collected at baseline. Patients were followed till 2020 to identify those who developed new onset coronary disease or stroke. Statistical analysis to identify factors associated with increased risk of developing CVD events was carried out.
Thirty-six patients had plaque at baseline. During follow-up five patients (all had baseline plaque) developed coronary disease and two, without baseline plaque, developed lacunar strokes. Mean (SD) age of these patients was 46.5 (4.5) years. Patients with three or more baseline bifurcations with plaque were 10 times more likely to develop CVD than those with 0-2 bifurcations with plaques (OR 9.9, p= 0.009). TPA > 16mm2 was associated with six-fold increased risk of CVD (OR = 6.44, p= 0.028). Patients with disease duration > 14 years were more likely than those with disease duration < 14 years to develop CVD (OR 8.3 p= 0.043).
The number of bifurcations with plaque and TPA in patients with SLE may be valuable in assessing risk of CVD and deciding on clinical measures to reduce this risk.
The number of bifurcations with plaque and TPA in patients with SLE may be valuable in assessing risk of CVD and deciding on clinical measures to reduce this risk.Advocacy organizations have played a significant role in the field of nutrition in recent years. However, why are some advocates viewed as more effective than others? This paper derives metrics for assessing advocacy efficacy by first drawing on key insights from the nutrition and public policy scholarship. A set of metrics is proposed to capture the constitutive elements of three concepts that often emerge as critical from that literature organizational capacity, strong networks and external outreach. Based on a survey of 66 nutrition stakeholders in Nigeria, including at the federal level and within the states of Kaduna and Kano, the metrics are then applied to a set of advocacy organizations within the country. We show that the metrics can provide insights into why some advocacy organizations are perceived as more effective than others by policymakers. Specifically, we find that geographical reach, the share of budget allocated to advocacy, action plans with clear objectives, large networks that include government and non-governmental policy champions, multiple media and dissemination outputs and numerous training events collectively increase nutrition advocates' visibility to, and influence on, policymakers.