Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and biochemical characterization of Drosophila singed, a homolog of the actin bundling protein fascin

Genetic and biochemical characterization of Drosophila singed, a homolog of the actin bundling protein fascin Kelly Cant Yale University 1996 Drosophila singed mutants were named for their gnarled bristle phenotype, however, severe alleles are also female sterile due to a defect in nurse cell cytoplasm transport. Recently, singed protein was shown to have 35% peptide identity with the actin bundling protein fascin. I present evidence that singed is a homolog of fascin. In vivo, singed is required for actin filament bundle formation in the cytoplasm of nurse cells during oogenesis and in the cellular extension that forms a bristle. In vitro, purified bacterially-expressed singed bundles actin filaments with the same 12 run periodicity and stoichiometry reported for sea urchin fascin. While many homologs of fascin have been described, functional domain organization is not understood. I generated 15 new sn alleles by EMS mutagenesis; surprisingly only 2 of these expressed fascin. singedG409E mutants have multiply bent bristles and are fertile, although nurse cell cytoplasmic actin bundles appear disorganized and cytoplasm transport is partially incomplete. singedS289N mutants have gnarled bristles and are sterile. I used the singedS289N allele in a dominant suppressor of sterility screen and identified an intragenic mutation S251F that appears to restore much of fascin's function. These Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. mutations, G409E, S289N and S251F, draw attention to critical amino acids in fascin. At wild type protein levels, both fascin and quail, a villin-like protein, are required for cytoplasmic actin bundle formation. I looked for genetic interaction between singed and quail. Mutations in quail enhance the intermediate egg chamber phenotype of singedG409E. Furthermore, overexpression of quail protein can rescue the cytoplasmic actin defect and sterility of singedS289N and of the null allele, singed28. In the absence of fascin, overexpression of quail is sufficient for the formation of actin bundles. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.
Highly Selective, CRISPR/Cas9‐Mediated Isolation of Genes and Genomic Loci from Complex Genomes by TAR Cloning in Yeast

Here we describe an updated TAR cloning protocol for the selective and efficient isolation of any genomic fragment or gene of interest up to 280 kb in size from genomic DNA. The method exploits the special recombination machinery of the yeast Saccharomyces cerevisiae. TAR cloning is based on the high level of in vivo recombination that occurs between a specific genomic DNA fragment of interest and targeting sequences (hooks) in a TAR vector that are homologous to the 5′ and 3′ ends of the targeted region. Upon co‐transformation into yeast, this results in the isolation of the chromosomal region of interest as a circular YAC molecule, which then propagates and segregates in yeast cells and can be selected for. In the updated TAR cloning protocol described here, the fraction of region‐positive clones typically obtained is increased from 1% up to 35% by pre‐treatment of the genomic DNA with specifically designed CRISPR/Cas9 endonucleases that create double‐strand breaks (DSBs) bracketing the target genomic DNA sequence, thereby making the ends of the chromosomal region of interest highly recombinogenic. In addition, a new TAR vector was constructed that contains YAC and BAC cassettes, permitting direct transfer of a TAR‐cloned DNA from yeast to bacterial cells. Once the TAR vector with the hooks is constructed and genomic DNA is prepared, the entire procedure takes 3 weeks to complete. The updated TAR protocol does not require significant yeast experience or extensively time‐consuming yeast work because screening only about a dozen yeast transformants is typically enough to find a clone with the region of interest. TAR cloning of chromosomal fragments, individual genes, or gene families can be used for functional, structural, and population studies, for comparative genomics, and for long‐range haplotyping, and has potential for gene therapy. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC.
E2F1 transcriptionally regulates CCNA2 expression to promote triple negative breast cancer tumorigenicity.

BACKGROUND Triple-negative breast cancer (TNBC) is a highly malignant breast cancer subtype with a poor prognosis. The cell cycle regulator cyclin A2 (CCNA2) plays a role in tumor development. Herein, we explored the role of CCNA2 in TNBC. METHODS We analyzed CCNA2 expression in 15 pairs of TNBC and adjacent tissues and assessed the relationship between CCNA2 expression using the tissue microarray cohort. Furthermore, we used two TNBC cohort datasets to analyze the correlation between CCNA2 and E2F transcription factor 1 (E2F1) and a luciferase reporter to explore their association. Through rescue experiments, we analyzed the effects of E2F1 knockdown on CCNA2 expression and cellular behavior. RESULTS We found that CCNA2 expression in TNBC was significantly higher than that in adjacent tissues with similar observations in MDA-MB-231 and MDA-MB-468 cells. E2F1 was highly correlated with CCNA2 as observed through bioinformatics analysis (R= 0.80, P< 0.001) and through TNBC tissue verification analysis (R= 0.53, P< 0.001). We determined that E2F1 binds the +677 position within the CCNA2 promoter. Moreover, CCNA2 overexpression increased cell proliferation, invasion, and migration owing to E2F1 upregulation in TNBC. CONCLUSION Our data indicate that E2F1 promotes TNBC proliferation and invasion by upregulating CCNA2 expression. E2F1 and CCNA2 are potential candidates that may be targeted for effective TNBC treatment.
Can grape polyphenols affect glycation markers? A systematic review

Abstract Advanced glycation end-products (AGEs) favor inflammation and oxidative stress, playing a role in chronic diseases pathogenesis. Grape polyphenols exert antiglycative and antioxidant effects which may contribute to prevent chronic diseases. However, clinical evidence of grape polyphenols on chronic disease prevention and treatment by glycation markers modulation are limited. Therefore, we aimed to critically analyze studies about that topic to investigate the antiglycative power of dietary grape polyphenol, and to explore the molecular mechanism involved. This systematic review was conducted and reported according to PRISMA guidelines. The following search terms were used: “grape”, “extract”, “grape seed extract”, “grape skin extract”, “polyphenol extract”, “grape polyphenol(s)”, “grape juice”, “resveratrol”, “quercetin”, “catechin”, “epicatechin”, “procyanidin(s)”, and “anthocyanin(s)”. Seven studies were included. Glycated hemoglobin was not affected. The interventions duration may not have been enough to detect changes. Grape polyphenols reduced fructosamine and methylglyoxal (MGO) concentrations, and increased endogenous secretory RAGE (esRAGE) gene expression but did not affect the serum concentration. Resveratrol antiglycative effects are mainly due its ability to trap MGO and downregulate RAGE. In conclusion, grape polyphenols may have a positive impact on early glycation products, AGEs and esRAGE. Future studies are needed to explore how they modulate AGEs and receptors in chronic diseases.
Availability, variety and distribution of healthy and unhealthy foods and beverages sold at street food stands in Mexico City

Abstract Objective: To examine differences in the availability, variety and distribution of foods and beverages sold at street food stands (SFS) across neighbourhood income levels in Mexico City. Design: Cross-sectional. Setting: Twenty neighbourhoods representing low-, middle- and high-income levels in Mexico City. Participants: Direct observations of SFS (n 391). Results: The availability of healthy foods such as fruits/vegetables was high in middle- and high-income neighbourhoods, whereas the availability of unhealthy foods such as processed snacks was higher in low-income neighbourhoods. However, statistically significant differences in food availability across neighbourhoods were only observed for dairy and processed snack items (P < 0·05). Similarly, differences in variety were only observed for cereal and processed snacks (P < 0·05). No statistically significant differences were seen for variety of fruits/vegetable across neighbourhood income levels (P > 0·05). No statistically significant differences across neighbourhood income levels were observed for beverage availability and variety (P > 0·05). Although street foods and beverages were often distributed near homes, public transportation centres and worksites, no differences were observed across neighbourhood income levels (P > 0·05). Conclusions: Findings suggest that SFS can be a source of both unhealthy foods and healthy foods for communities across neighbourhoods in Mexico City. Additional studies are needed to assess the relationship between street food and beverage availability, and consumption.
Machine learning approaches for drug combination therapies

Abstract Drug combination therapy is a promising strategy to treat complex diseases such as cancer and infectious diseases. However, current knowledge of drug combination therapies, especially in cancer patients, is limited because of adverse drug effects, toxicity and cell line heterogeneity. Screening new drug combinations requires substantial efforts since considering all possible combinations between drugs is infeasible and expensive. Therefore, building computational approaches, particularly machine learning methods, could provide an effective strategy to overcome drug resistance and improve therapeutic efficacy. In this review, we group the state-of-the-art machine learning approaches to analyze personalized drug combination therapies into three categories and discuss each method in each category. We also present a short description of relevant databases used as a benchmark in drug combination therapies and provide a list of well-known, publicly available interactive data analysis portals. We highlight the importance of data integration on the identification of drug combinations. Finally, we address the advantages of combining multiple data sources on drug combination analysis by showing an experimental comparison.
Dimerization underlies the aggregation propensity of intrinsically disordered coiled‐coil domain‐containing 124

Coiled‐coil domain‐containing 124 (CCDC124) is a recently discovered ribosome‐binding protein conserved in eukaryotes. CCDC124 has regulatory functions on the mediation of reversible ribosomal hibernation and translational recovery by direct attachment to large subunit ribosomal protein uL5, 25S rRNA backbone, and tRNA‐binding P/A‐site major groove. Moreover, it independently mediates cell division and cellular stress response by facilitating cytokinetic abscission and disulfide stress‐dependent transcriptional regulation, respectively. However, the structural characterization and intracellular physiological status of CCDC124 remain unknown. In this study, we employed advanced in silico protein modeling and characterization tools to generate a native‐like tertiary structure of CCDC124 and examine the disorder, low sequence complexity, and aggregation propensities, as well as high‐order dimeric/oligomeric states. Subsequently, dimerization of CCDC124 was investigated with co‐immunoprecipitation (CO‐IP) analysis, immunostaining, and a recent live‐cell protein–protein interaction method, bimolecular fluorescence complementation (BiFC). Results revealed CCDC124 as a highly disordered protein consisting of low complexity regions at the N‐terminus and an aggregation sequence (151‐IAVLSV‐156) located in the middle region. Molecular docking and post‐docking binding free energy analyses highlighted a potential involvement of V153 residue on the generation of high‐order dimeric/oligomeric structures. Co‐IP, immunostaining, and BiFC analyses were used to further confirm the dimeric state of CCDC124 predominantly localized at the cytoplasm. In conclusion, our findings revealed in silico structural characterization and in vivo subcellular physiological state of CCDC124, suggesting low‐complexity regions located at the N‐terminus of disordered CCDC124 may regulate the formation of aggregates or high‐order dimeric/oligomeric states.
Clinical characterization of NTCP deficiency in paediatric patients : A case‐control study based on SLC10A1 genotyping analysis

Na+‐taurocholate cotransporting polypeptide deficiency (NTCPD) is a newly described disorder arising from biallelic mutations of the SLC10A1 gene. As a result of a lack of compelling evidence from case‐control studies, its genotypic and phenotypic features remain open for in‐depth investigation. This study aimed to explore the genotypic and clinical phenotypic characteristics of paediatric patients with NTCPD. The SLC10A1 genotypes of all NTCPD patients were confirmed by screening for the prevalent variant c.800C>T and Sanger sequencing when necessary. The clinical presentations and laboratory changes were collected, reviewed and analysed, and then qualitatively and quantitatively compared with the relevant controls. A total of 113 paediatric NTCPD patients were diagnosed while c.374dupG and c. 682_683delCT were detected as two novel pathogenic mutations. Hypercholanemia was observed in 99.12% of the patients. Indirect hyperbilirubinemia in affected neonates exhibited higher positive rates in comparison to controls. Moreover, transient cholestatic jaundice, elevated liver enzymes and 25‐hydroxyvitamin D (Vit D) deficiency during early infancy were more commonly observed in patients than in controls. All NTCPD patients exhibited favourable clinical outcomes as a result of symptomatic and supportive treatment. The findings enriched the SLC10A1 mutation spectrum and provided comprehensive insights into the phenotypic characteristics of NTCPD. NTCPD should be considered and SLC10A1 gene should be analysed in patients with above age‐dependent clinical features. Furthermore, over investigation and intervention should be avoided in the management of NTCPD patients.
Functional characterization of CDK10 and cyclin M truncated variants causing severe developmental disorders

CDK10 is a poorly known cyclin M (CycM)‐dependent kinase. Loss‐of‐function mutations in the genes encoding CycM or CDK10 cause, respectively, STAR or Al Kaissi syndromes, which present a constellation of malformations and dysfunctions. Most reported mutations abolish gene expression, but two mutations found in 3’ exons could allow the expression of CDK10 and CycM truncated variants.
Developing an International Standard Set of Patient-Reported Outcome Measures for Psychotic Disorders.

OBJECTIVE The objective of this project was to develop a set of patient-reported outcome measures for adolescents and adults who meet criteria for a psychotic disorder. METHODS A research team and an international consensus working group, including service users, clinicians, and researchers, worked together in an iterative process by using a modified Delphi consensus technique that included videoconferencing calls, online surveys, and focus groups. The research team conducted systematic literature searches to identify outcomes, outcome measures, and risk adjustment factors. After identifying outcomes important to service users, the consensus working group selected outcome measures, risk adjustment factors, and the final set of outcome measures. International stakeholder groups consisting of >100 professionals and service users reviewed and commented on the final set. RESULTS The consensus working group identified four outcome domains: symptoms, recovery, functioning, and treatment. The domains encompassed 14 outcomes of importance to service users. The research team identified 131 measures from the literature. The consensus working group selected nine measures in an outcome set that takes approximately 35 minutes to complete. CONCLUSIONS A set of patient-reported outcome measures for use in routine clinical practice was identified. The set is free to service users, is available in at least two languages, and reflects outcomes important to users. Clinicians can use the set to improve clinical decision making, and administrators and researchers can use it to learn from comparing program outcomes.
DeepFeature: feature selection in nonimage data using convolutional neural network

Abstract Artificial intelligence methods offer exciting new capabilities for the discovery of biological mechanisms from raw data because they are able to detect vastly more complex patterns of association that cannot be captured by classical statistical tests. Among these methods, deep neural networks are currently among the most advanced approaches and, in particular, convolutional neural networks (CNNs) have been shown to perform excellently for a variety of difficult tasks. Despite that applications of this type of networks to high-dimensional omics data and, most importantly, meaningful interpretation of the results returned from such models in a biomedical context remains an open problem. Here we present, an approach applying a CNN to nonimage data for feature selection. Our pipeline, DeepFeature, can both successfully transform omics data into a form that is optimal for fitting a CNN model and can also return sets of the most important genes used internally for computing predictions. Within the framework, the Snowfall compression algorithm is introduced to enable more elements in the fixed pixel framework, and region accumulation and element decoder is developed to find elements or genes from the class activation maps. In comparative tests for cancer type prediction task, DeepFeature simultaneously achieved superior predictive performance and better ability to discover key pathways and biological processes meaningful for this context. Capabilities offered by the proposed framework can enable the effective use of powerful deep learning methods to facilitate the discovery of causal mechanisms in high-dimensional biomedical data.
Daratumumab Immunopolymersome‐Enabled Safe and CD38‐Targeted Chemotherapy and Depletion of Multiple Myeloma

Multiple myeloma (MM) is a second ranking hematological malignancy. Despite the fast advancement of new treatments such as bortezormib and daratumumab, MM patients remain incurable and tend to eventually become relapsed and drug‐resistant. Development of novel therapies capable of depleting MM cells is strongly needed. Here, daratumumab immunopolymersomes carrying vincristine sulfate (Dar‐IPs‐VCR) are reported for safe and high‐efficacy CD38‐targeted chemotherapy and depletion of orthotopic MM in vivo. Dar‐IPs‐VCR made by postmodification via strain‐promoted click reaction holds tailored antibody density (2.2, 4.4 to 8.7 Dar per IPs), superb stability, small size (43–49 nm), efficacious VCR loading, and glutathione‐responsive VCR release. Dar4.4‐IPs‐VCR induces exceptional anti‐MM activity with an IC50 of 76 × 10−12 m to CD38‐positive LP‐1 MM cells, 12‐ and 20‐fold enhancement over nontargeted Ps‐VCR and free VCR controls, respectively. Intriguingly, mice bearing orthotopic LP‐1‐Luc MM following four cycles of i.v. administration of Dar4.4‐IPs‐VCR at 0.25 mg VCR equiv. kg−1 reveal complete depletion of LP‐1‐Luc cells, superior survival rate to all controls, and no body weight loss. The bone and histological analyses indicate bare bone and organ damage. Dar‐IPs‐VCR appears as a safe and targeted treatment for CD38‐overexpressed hematological malignancies.
Association of maternal intake of nitrate and risk of birth defects and preterm birth: a systematic review and dose-response meta-analysis

Abstract In this study, the high versus low analysis method was applied to evaluate the association of maternal nitrate intake and risk of heart defect, limb deficiency, cleft lip, and preterm birth. Also, linear and non-linear dose-response associations between maternal intake of nitrate and risk of heart defects were investigated. In high versus low intake, the risk of heart defects in infants is directly associated with the level of nitrate exposure, but no significant relationship was found between the cleft lip, limb deficiency, and preterm birth. The linear dose-response meta-analysis was associated with risk of heart defects (RR: 1.03; 95% CI: 1.00 to 1.05, P = 0.400, I2= 0%, P heterogeneity= 0.602, n = 3) and nonlinear dose-response meta-analysis showed that maternal intake of nitrate higher than ∼4 mg/day is positively associated with heart defects risk (P non-linearity= 0.012).
Fruiting of "Keitte" Mango Trees in Relation to Application of Glutathione and Boron

This study was conducted during 2014 and 2015 seasons to examine the effect of spraying boric acid and/or glutathione each at (0.05 up to 0.1%) three times at monthly intervals starting from the first March, on growth, tree nutritional status, yield and fruit quality of "Keitte" mango trees grown under sandy calcareous soil. An obvious promotion was revealed on all growth aspects, leaves pigments and nutrients content, fruit retention%, yield and fruit quality as affected by the tested treatments. Glutathione was appreciably superior to boric acid in this respect and using both together was preferable than using them individually. The promising treatment was the application of boric acid plus the antioxidant glutathione each at 0.1and 0.05%without significant differences among them. Therefore, from the economical point of view, it is advised to use this treatment at 0.05%, to obtain acceptable yield and fruit quality of "Keitte" mango trees grown under sandy calcareous soil.
Effect of aging on surface chemistry of rice husk‐derived biochar

Herein, we aimed to determine the physicochemical properties of biochar produced from rice husk at 350 and 550°C, to characterize changes in the biochar properties during aging and to identify the effect of aging time on these changes. To simulate different stages in the aging process, samples were incubated at a constant temperature in the dark and maintained at 60% water holding capacity for 100–300 d. The transformation and morphology of the biochar particles were monitored by diffuse‐reflectance Fourier transform infrared spectroscopy (DRIFTS), scanning electron microscopy (SEM) coupled with energy X‐ray dispersive spectroscopy, and X‐ray photoelectron spectroscopy (XPS). During aging, a layer formed on the surface and the content of easily oxidized substances increased with increased aging time. In addition, SEM indicated that oxidation occurred close to the biochar surface rather than in the biochar particle interior. Furthermore, the DRIFTS and XPS results indicated that the biochar surface produced at 550°C underwent decarboxylation and hydroxylation, while for the 350°C biochar, the increase in surface oxygen content was associated with the presence of hydroxyl moieties. © 2017 American Institute of Chemical Engineers Environ Prog, 37: 410–417, 2018