Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and application of multiplex targeted-sequencing approaches to identify Phytophthora species associated with root rot and wilting complex of red raspberry

Phytophthora species are primary causal agents of raspberry root rot and wilting complex (RRWC), a disease complex that is of major concern to raspberry producers worldwide. Accurate identification of the causal agents is a first step for effective disease management. Advancements in molecular diagnostics can facilitate the detection of multiple pathogen species associated with this disease complex. We developed multiplex targeted-sequencing methods using degenerate primers for heat shock protein 90, elongation factor 1α and β-tubulin genes to identify Phytophthora species causing RRWC. One hundred and twenty-eight isolates recovered during 2018 to 2020 from diverse fields in major raspberry growing areas of British Columbia (BC) were sequenced and identified by comparing with known reference sequences of 142 Phytophthora species, 111 Pythium species, and nine Phytopythium species in the NCBI database. This multiplex targeted-sequencing method was highly specific and identified two species of Phytophthora associated with RRWC. These were P. rubi (85% of isolates) and P. gonapodyides (15% of isolates). Phytophthora rubi was predominantly isolated from the cultivars ‘Chemainus’ (51%), ‘Rudi’ (27%) and ‘Meeker’ (15%), whereas P. gonapodyides was predominately isolated from the moderately resistant cultivar ‘Cascade Bounty’. Pathogenicity studies on intact plants and detached leaves confirmed that P. rubi and P. gonapodyides can cause symptoms of RRWC on raspberry, thus fulfilling Koch’s postulates. To our knowledge, this is the first report of P. gonapodyides as a causal agent of RRWC on raspberry in BC. This study provides novel insights into the identification and species composition of Phytophthora associated with RRWC in raspberry production systems.
Do multiple types of confirmatory tests improve performance in predicting subtypes of primary aldosteronism?

The clinical practice guideline for primary aldosteronism (PA) places a high value on confirmatory tests to sparing patients with false‐positive results in case detection from undergoing adrenal venous sampling (AVS). However, it is unclear whether multiple types of confirmatory tests are more useful than a single type. To evaluate whether the machine‐learned combination of two confirmatory tests is more useful in predicting subtypes of PA than each test alone.
sanon : An R Package for Stratified Analysis with Nonparametric Covariable Adjustment

Kawaguchi, Koch, and Wang (2011) provide methodology and applications for a stratified Mann-Whitney estimator that addresses the same comparison between two randomized groups for a strictly ordinal response variable as the van Elteren test statistic for randomized clinical trials with strata. The sanon package provides the implementation of the method within the R programming environment. The usage of sanon is illustrated with five examples. The first example is a randomized clinical trial with eight strata and a univariate ordinal response variable. The second example is a randomized clinical trial with four strata, two covariables, and four ordinal response variables. The third example is a crossover design randomized clinical trial with two strata, one covariable, and two ordinal response variables. The fourth example is a randomized clinical trial with seven strata (which are managed as a categorical covariable), three ordinal covariables with missing values, and three ordinal response variables with missing values. The fifth example is a randomized clinical trial with six strata, a categorical covariable with three levels, and three ordinal response variables with missing values.
A Zn‐dependent structural transition of SOD1 modulates its ability to undergo phase separation

The misfolding and mutation of Cu/Zn superoxide dismutase (SOD1) is commonly associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress granules (SGs), a type of membraneless organelle, which is believed to form via liquid–liquid phase separation (LLPS). Using wild‐type, metal‐deficient, and different ALS disease mutants of SOD1 and computer simulations, we report here that the absence of Zn leads to structural disorder within two loop regions of SOD1, triggering SOD1 LLPS and amyloid formation. The addition of exogenous Zn to either metal‐free SOD1 or to the severe ALS mutation I113T leads to the stabilization of the loops and impairs SOD1 LLPS and aggregation. Moreover, partial Zn‐mediated inhibition of LLPS was observed for another severe ALS mutant, G85R, which shows perturbed Zn‐binding. By contrast, the ALS mutant G37R, which shows reduced Cu‐binding, does not undergo LLPS. In addition, SOD1 condensates induced by Zn‐depletion exhibit greater cellular toxicity than aggregates formed by prolonged incubation under aggregating conditions. Overall, our work establishes a role for Zn‐dependent modulation of SOD1 conformation and LLPS properties that may contribute to amyloid formation.
EphA4/ephrinA3 reverse signaling mediated downregulation of glutamate transporter GLAST in Müller cells in an experimental glaucoma model

Deficiency of glutamate transporter GLAST in Müller cells may be culpable for excessive extracellular glutamate, which involves in retinal ganglion cell (RGC) damage in glaucoma. We elucidated how GLAST was regulated in rat chronic ocular hypertension (COH) model. Western blot and whole‐cell patch‐clamp recordings showed that GLAST proteins and GLAST‐mediated current densities in Müller cells were downregulated at the early stages of COH. In normal rats, intravitreal injection of the ephrinA3 activator EphA4‐Fc mimicked the changes of GLAST in COH retinas. In purified cultured Müller cells, EphA4‐Fc treatment reduced GLAST expression at mRNA and protein levels, which was reversed by the tyrosine kinase inhibitor PP2 or transfection with ephrinA3‐siRNA (Si‐EFNA3), suggesting that EphA4/ephrinA3 reverse signaling mediated GLAST downregulation. EphA4/ephrinA3 reverse signaling‐induced GLAST downregulation was mediated by inhibiting PI3K/Akt/NF‐κB pathways since EphA4‐Fc treatment of cultured Müller cells reduced the levels of p‐Akt/Akt and NF‐κB p65, which were reversed by transfecting Si‐EFNA3. In Müller cells with ephrinA3 knockdown, the PI3K inhibitor LY294002 still decreased the protein levels of NF‐κB p65 in the presence of EphA4‐Fc, and the mRNA levels of GLAST were reduced by LY294002 and the NF‐κB inhibitor SN50, respectively. Pre‐injection of the PI3K/Akt pathway activator 740 Y‐P reversed the GLAST downregulation in COH retinas. Western blot and TUNEL staining showed that transfecting of Si‐EFNA3 reduced Müller cell gliosis and RGC apoptosis in COH retinas. Our results suggest that activated EphA4/ephrinA3 reverse signaling induces GLAST downregulation in Müller cells via inhibiting PI3K/Akt/NF‐κB pathways, thus contributing to RGC damage in glaucoma.
Domain inversion and electrochromism in congruent RuO2:LiNbO3 crystal

The domain inversion and electrochromism in congruent RuO2:LiNbO3 crystals are investigated at room temperature, and the relations between them are proposed. During electric poling process, the electrochromism accompanies the ferroelectric domain inversion simultaneously, and is localized to the same region with domain inversion. As domain inversion, the electrochromism is completely reversible when the domain is inverted from the reverse direction. The properties, coincidence and localization, between domain inversion and electrochromism are proved solidly by the digital holographic interferometry, the real-time measurement of optical transmittance change and poling current, and the micrographic analysis after being etched in hydrofluoric acid. The influences of annealing conditions on electrochromism are also discussed. We provide the reasonable assumptions and analyses that the charge redistribution within the crystal caused by domain inversion is the source for electrochemically oxidation and reduction of Ru ion, and the intervalence electron transference between Ru4+ and Ru3+ plays a key role in the spectrum shift within different spectral range by the change of the photon absorption.
Space Rather than Seasonal Changes Explained More of the Spatiotemporal Variation of Tropical Soil Microbial Communities

The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). ABSTRACT Soil microbiomes play an essential role in maintaining soil geochemical cycle and function. Although there have been some reports on the diversity patterns and drivers of the tropical forest soil microbial community, how space and seasonal changes affect spatiotemporal distribution at the regional scales are poorly understood. Based on 260 soil samples, we investigated the spatiotemporal patterns of rubber plantations and rainforest soil microbial communities across the whole of Hainan Island, China during the dry and rainy seasons. We examined soil bacterial and fungal composition and diversity and the main drivers of these microbes using Illumina sequencing and assembly. Our results revealed that the diversity (both alpha and beta) spatiotemporal variation in microbial communities is highly dependent on regional location rather than seasonal changes. For example, the site explained 28.5% and 37.2% of the variation in alpha diversity for soil bacteria and fungi, respectively, and explained 34.6% of the bacterial variance and 14.3% of the fungal variance in beta diversity. Soil pH, mean annual temperature, and mean annual precipitation were the most important factors associated with the distribution of soil microbial communities. Furthermore, we identified that variations in edaphic (e.g., soil pH) and climatic factors (e.g., mean annual temperature [MAT] and mean annual precipitation [MAP]) were mainly caused by regional sites (P < 0.001). Collectively, our work provides empirical evidence that space, rather than seasonal changes, explained more of the spatiotemporal variation of soil microbial communities in tropical forests, mediated by regional location-induced changes in climatic factors and edaphic properties. IMPORTANCE The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). Moreover, the environmental factors were mainly explained by geographic location effect rather than by seasonal effect, and environmental dissimilarity significantly increased with geographic distance. In conclusion, our study provides solid empirical evidence that space rather than season explained more of the spatiotemporal variation of soil microbial communities in the tropical forest.
Interaction mechanism of benzophenone-type UV filters on bovine serum albumin: Insights from structure-affinity relationship

Abstract Benzophenone (BP)-type UV filters can cause structural changes of carrier protein in plasma. The binding process of five BP-type UV filters with bovine serum albumin (BSA) was investigated by multiple characterization methods, along with their structure-affinity relationship involving the structure of the five BP-type UV filters and their binding affinity for BSA. The BP-type UV filters investigated bound to BSA spontaneously, and altered conformation of BSA. The binding constants and number of binding sites between BP-type UV filters and BSA were 103–106 M−1 and 0.82–1.26, respectively. These BP-type UV filters and BSA interacted with the same binding forces and went through the similar binding process, suggesting that the benzophenone skeleton structure was primarily responsible for the BP-type UV filters and BSA binding, and changes in the structure of the BSA. The BP-type UV filters with hydroxyl substituent (BP-1 and BP-9) and non-polar molecules (BP-6) had a high affinity for binding BSA and had a greater impact on BSA conformation.
Multi-component mathematical models in multilayer fields by the transformation operators method

The vector transform operators are investigated; these operators are used at the solution of boundary value problems in piecewise homogeneous spherically symmetric areas. In particular, examples of transformation operators for vector boundary value problems are given for third vector boundary value problem in the the right half-plane and for the Dirichlet problem in the the right half-plane.
Understanding the role of race in abortion stigma in the United States: a systematic scoping review

Abstract The impact of abortion stigma is broad. Stigma impacts abortion providers, abortion patients and the broader community. Understanding how race and culture affect aspects of abortion stigma may be an important piece of expanding access to and support of abortion. We conducted a systematic search for studies involving abortion stigma and race in PubMed, PubMed Central, Embase, PsycINFO, Sociological Abstracts, Social Services Abstracts, GenderWatch and Ethnic NewsWatch on 7 January 2020. Articles were eligible for inclusion if they explored stigma and included participant race and/or ethnicity, were in English, and included original research. Thirty studies were included in the final review, including 11 quantitative studies, 9 qualitative studies, 4 mixed methods studies and 6 dissertations. Most studies provided basic racial and demographic data but did not provide racial differences in experiences of abortion stigma. Three quantitative studies found that women of colour had different experiences of abortion stigma compared to White women. Non-peer-reviewed studies of qualitative PhD-level dissertation research found that race, culture, religion and immigration had unique and complex effects on abortion stigma experienced by Latinx women. While abortion stigma is common, we found that there is a lack of research contextualising the racialisation of the United States. Quantitative studies found that women of colour experience abortion stigma at lower levels compared to White women. However, qualitative analyses of experiences suggest that quantitative measures of abortion stigma may not capture unique aspects of abortion stigma as experienced by women of colour.
Marker-free characterization of full-length transcriptomes of single live circulating tumor cells

The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analyses. These include a novel method of scRNA-seq clustering, named deep dictionary learning using k-means clustering cost (DDLK), expression-based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell FX and Polaris workflow that works by the principles of size-based separation of CTCs and marker-based WBC depletion.
Fixed‐order optimal deconvolution filter with irregular missing data

In general, the reconstruction performance of the conventional deconvolution filter is deteriorated by the missing data. In this paper, a fixed‐order deconvolution filter design method is proposed for the signal reconstruction from received signal with irregular missing data. The missing data model is based on a probabilistic structure. The probability of occurrence of missing data is unknown a prior. In this situation, the deconvolution filter design problem becomes a complicated nonlinear estimation problem. In this study, a design method based on genetic algorithms is proposed to treat the signal reconstruction design problem with irregular missing data. Finally, two examples are given to illustrate the simulation results of the proposed deconvolution filter. The results show that the reconstruction performance is improved significantly if the missing probability is considered in the deconvolution filter design procedure. Copyright © 2009 John Wiley & Sons, Ltd.
Genetic ablation of Toll‐like Receptor 4 seems to activate the apoptosis pathway in the skeletal muscle of mice after acute physical exercise

Many conditions, such as inflammation and physical exercise, can induce endoplasmic reticulum (ER) stress. Toll‐like Receptor 4 (TLR4) can trigger inflammation and ER stress events. However, there are still no data in the literature regarding the role of TLR4 in ER stress during exercise in skeletal muscle. Therefore, the current investigation aimed to verify the responses of ER stress markers in wild‐type (WT) and Tlr4 global knockout (KO) mice after acute and chronic physical exercise protocols. Eight‐week‐old male WT and KO mice were submitted to acute (moderate or high intensity) and chronic (4‐week protocol) treadmill exercises. Under basal conditions, KO mice showed lower performance in the rotarod test. Acute high‐intensity exercise increased eIF2α protein in the WT group. After the acute high‐intensity exercise, there was an increase in Casp3 and Ddit3 mRNA for the KO mice. Acute moderate exercise increased the cleaved Caspase‐3/Caspase‐3 in the KO group. In response to chronic exercise, the KO group showed no improvement in any performance evaluation. The 4‐week chronic protocol did not generate changes in ATF6, CHOP, p‐IRE1α, p‐eIF2α/eIF2α, and cleaved Caspase‐3/Caspase‐3 ratio but reduced BiP protein compared with the KO‐Sedentary group. These results demonstrate the global deletion of Tlr4 seems to have the same effects on UPR markers of WT animals after acute and chronic exercise protocols but decreased performance. The cleaved Caspase‐3/Caspase‐3 ratio may be activated by another pathway other than ER stress in Tlr4 KO animals.
The variation of the scalelengths of galaxies at different wavelengths

We develop model profiles of spiral galaxies with different amounts and geometries of disc absorption and different bulge sizes. These are used to investigate whether there are any systematic changes in the profiles of absorbed galaxies at different wavelengths, and whether measurement of the scalelength of disc galaxies at different wavelengths can be used as a test of whether galaxies are optically thick or thin. Using models with realistic geometries where the dust vertical scaleheight is less than the stars' vertical scaleheight, and including a bulge component, we find very little difference in the B-band and I- or H-band scalelengths, even for optical depths as high as τ B =20
Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections

Sensitive and specific genotyping of human papillomaviruses (HPVs) is critical for the surveillance and monitoring of the vaccine effectiveness. Here, HPV genotypes were identified in 137 cervical samples with different histology (79 ≤CIN1 and 58 CIN3+) using Nested-PCR followed by Next-Generation sequencing (NGS) and relative proportions for each genotype in multiple infections were computed. All samples had been previously genotyped by PCR-Reverse Blotting Hybridization (PCR-RBH) thus allowing for a concordance analysis between both techniques. Multiple infections were present in 85% of ≤CIN1 cases compared to only 41% in CIN3+ cases (p<0.001). Among ≤CIN1 cases a towering genotypic diversity was observed, considering both low (LR-) and high risk (HR-) HPV genotypes; while among CIN3+, diversity was lower, HR-HPVs prevailing in most cases, especially HPV16. Furthermore, the predominance of HR-HPV genotypes in the proportions identified in each sample was higher in CIN3+ cases [(HPV16 (62.5%), followed by HPV31 and HPV58 (8.3% each)], than in ≤CIN1 cases [(HPV16 (17.7%), followed by HPV52 (14.7%) and HPV31 (10.3%)]. Agreement between PCR-RBH and NGS was higher than 90% for all genotypes (with an overall Kappa of 0.7), even though NGS identified eighty-nine positive results for HPV genotypes that had not been detected by PCR-RBH, evidencing its greater sensitivity. These results suggest that a reduction in genotypic diversity and/or an increase in the relative proportion of HR-HPVs in multiple infections can be considered as a biomarker for the potential risk of malignant progression.
HLA-DQ genotype distribution and risk evaluation of celiac disease in Northwest China

Abstract Background Celiac disease (CD) is an autoimmune small bowel disease. Genetic susceptibility for CD is mainly determined by the human leukocyte antigen (HLA)-DQ haplotypes. The risk of CD conferred by HLA genotypes varies geographically and across populations, however, this has not yet been documented in Chinese patients with CD. Aims To investigate the distribution of HLA-DQ and the related risks of CD development in Northwest China. Methods A total of 75 CD patients and 300 healthy individuals were genotyped for HLA-DQ using the Illumina NextSeq, and the relative risks of the different genotypes were evaluated. Results In total, 68.00% of CD patients and 21.00% of controls carried HLA-DQ2.5 heterodimers (p < 0.001). We identified four CD risk gradients. Individuals carrying a double dose of DQB1*02 had the highest risk of developing CD (1:16); however, with heterozygosis (DQB1*02:02/DQB1*02:01) having the highest risk (1:9). HLA-DQ2.5 individuals with a single copy of HLA-DQB1*02, in either the cis or trans configuration, were at a medium risk (1:38). Non-DQ2.5 carriers of DQ8 or DQ2.2 were at low risk, while only carriers of DQ7.5 or DQX.5 were at very low risk. Patients with the HLA-DQ2.5 genotype had more severe mucosal damage compared with the HLA-DQ2.5 genotype negative CD patients (70.59% vs. 41.67%, p = 0.016). Conclusion Genetic susceptibility to CD is highly prevalent in the Northwest Chinese population and the highest risk of developing CD was associated with the DQ2.5/DQ2.2 genotype. The DQ2.5 allele is involved in the severity of mucosal injury.