Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors

N6-methyladenosine (m6A), internal modification of mRNA, has recently been reported to be an important regulatory mechanism affecting tumor proliferation. However, its role in endocrine system tumors is poorly understood. We obtained datasets for four types tumors from the TCGA database, analyzed the GTEx database as a supplement to the control group, and used “Perl” and “R” software to analyze the datasets. Then we differentiated the expression level, used it to cluster consensus. Besides, we established lasso regression model to screen variables, used univariate and multivariate cox analyses to explore the independent risk factors associated with cancer prognosis. The results indicated that except for WTAP, the expression level of METTL3 was negatively correlated with other genes. The expression level of WTAP and METTL16 was positively correlated with overall survival (OS). Moreover, we found that different clinical subtypes of adrenal cortical carcinoma had significant differences in survival status, histologic grading, pathological T grade, and OS. Furthermore, different clinical subtypes of thyroid carcinoma had significant differences in histologic grading and pathological T grade. The differential expression of m6A regulatory genes is closely associated with the presence of endocrine-system-related tumors, and risk scores can be used to assess prognosis.
Transcriptional Responses of the Heat Shock Protein 20 (Hsp20) and 40 (Hsp40) Genes to Temperature Stress and Alteration of Life Cycle Stages in the Harmful Alga Scrippsiella trochoidea (Dinophyceae)

Simple Summary As the greatest contributors to harmful algal blooms, dinoflagellates account for roughly 75% of bloom events, which become an escalating threat to coastal ecosystems and cause substantial economic loss worldwide. Resting cyst production and broad temperature tolerance are well proven as adaptive strategies for blooming dinoflagellates; however, to date, the underlying molecular information is scarce. In the present study, we characterized two heat shock protein genes from the representative dinoflagellate Scrippsiella trochoidea, with the aim to primarily determine their possible roles in response to temperature stress and alteration of the life cycle. The yielded results enhance our knowledge about the functions of cross-talk of different Hsp members in temperature adaptation of dinoflagellates and facilitate further exploration in their potential physiological relevance during different life-stage alternation in this ecological important lineage. Abstract The small heat shock protein (sHsp) and Hsp40 are Hsp members that have not been intensively investigated but are functionally important in most organisms. In this study, the potential roles of a Hsp20 (StHsp20) and a Hsp40 (StHsp40) in dinoflagellates during adaptation to temperature fluctuation and alteration of different life stages were explored using the representative harmful algal blooms (HABs)-causative dinoflagellate species, Scrippsiella trochoidea. We isolated the full-length cDNAs of the two genes via rapid amplification of cDNA ends (RACE) and tracked their differential transcriptions via real-time qPCR. The results revealed StHsp20 and StHsp40 exhibited mRNA accumulation patterns that were highly similar in response to heat stress but completely different toward cold stress, which implies that the mechanisms underlying thermal and cold acclimation in dinoflagellates are regulated by different sets of genes. The StHsp20 was probably related to the heat tolerance of the species, and StHsp40 was closely involved in the adaptation to both higher and lower temperature fluctuations. Furthermore, significantly higher mRNA abundance of StHsp40 was detected in newly formed resting cysts, which might be a response to intrinsic stress stemmed from encystment. This finding also implied StHsp40 might be engaged in resting cyst formation of S. trochoidea. Our findings enriched the knowledge about possible cross-talk of different Hsp members in dinoflagellates and provided clues to further explore the molecular underpinnings underlying resting cyst production and broad temperature tolerance of this group of HABs contributors.
Nuclear Morphological Remodeling in Human Granulocytes Is Linked to Prenylation Independently from Cytoskeleton

Nuclear shape modulates cell behavior and function, while aberrant nuclear morphologies correlate with pathological phenotype severity. Nevertheless, functions of specific nuclear morphological features and underlying molecular mechanisms remain poorly understood. Here, we investigate a nucleus-intrinsic mechanism driving nuclear lobulation and segmentation concurrent with granulocyte specification, independently from extracellular forces and cytosolic cytoskeleton contributions. Transcriptomic regulation of cholesterol biosynthesis is equally concurrent with nuclear remodeling. Its putative role as a regulatory element is supported by morphological aberrations observed upon pharmacological impairment of several enzymatic steps of the pathway, most prominently the sterol ∆14-reductase activity of laminB-receptor and protein prenylation. Thus, we support the hypothesis of a nuclear-intrinsic mechanism for nuclear shape control with the putative involvement of the recently discovered GGTase III complex. Such process could be independent from or complementary to the better studied cytoskeleton-based nuclear remodeling essential for cell migration in both physiological and pathological contexts such as immune system function and cancer metastasis.
Mental Rotation in American Children: Diminished Returns of Parental Education in Black Families

Background: While parental education and family socioeconomic status (SES) are associated with an increase in children’s cognitive functioning, and less is known about racial variation in these effects. Minorities’ Diminished Returns (MDRs) suggest that, under racism and social stratification, family SES and particularly parental education show weaker effects on children’s tangible outcomes for marginalized, racialized, and minoritized families, particularly Blacks, compared to Whites. Aim: We conducted this study to compare the effect of parental education on children’s mental rotation abilities, as an important aspect of cognitive function, by race. Methods: This cross-sectional study included 11,135 9–10-year-old American children. Data came from baseline of the Adolescent Brain Cognitive Development (ABCD) study. The independent variable was parental education. The dependent variable, mental rotation, was measured by the Little Man Task. Ethnicity, gender, age, marital status, and household income were the covariates. Results: Parental education was positively associated with mental rotation. However, parental education showed a weaker association with mental rotation in Black than in White families. This was documented by a significant interaction between race and parental education on children’s efficiency score. Conclusion: Parental education shows a weaker correlation with mental rotation of Black rather than White children, which is probably because of racism, social stratification, and discrimination. This finding is in line with the MDRs phenomenon and suggests that marginalization and racism may interfere with the influences of parental assets and resources and Black American children’s development.
Development and Evaluation of a Novel Oral Mucoadhesive Ointment Containing Pomegranate Peel Extract as an Adjuvant for Oral Hygiene of Dogs

Herbal therapies are used worldwide to treat a variety of health conditions, including dental conditions in veterinary medicine. In this context, the use of medicinal plant-based formulations as potential therapeutics and preventatives in veterinary dentistry is worth highlighting. The objective of the present study was to develop a mucoadhesive ointment formulation, named orabase, that contained pomegranate extract for use in the oral cavity of dogs, with the aim of improving their oral hygiene. The hydroalcoholic extracts of pomegranate peels was incorporated into the orabase in 3 different concentrations. The formulations were subjected to in vitro microbiological testing by a modified disc-diffusion method to study the susceptibility of microorganisms collected from the oral cavities of the dogs. The samples were taken from the buccal mucosa of dogs having the same management and diet. The most effective formulation was submitted to physicochemical tests to evaluate the functionality of the product, namely pH, swelling index, spreadability, and mechanical properties (hardness, cohesiveness, and adhesiveness). The formulation containing 25.0% w/w of the extract was considered most suitable for the intended use as it showed antiseptic activity and demonstrated a swelling index of approximately 35% in the first 20 minutes of the test, high spreadability, and suitable mechanical properties. The results suggest that the product obtained from pomegranate peel extract is a viable option for use to improve oral hygiene, helping to reduce the bacterial component of dental plaque in dogs.
Differential expression of transfer RNA-derived small RNAs in IgA nephropathy

Abstract Background: IgA nephropathy (IgAN) is one of the most common forms of primary glomerulonephritis. Recent studies have indicated that small noncoding RNAs, such as tRNA-derived small RNAs (tsRNAs), might be novel biomarkers for glomerulonephritis. We therefore investigated the potential roles and possible functions of the tsRNAs in IgAN. Method: Peripheral blood mononuclear cells (PBMCs) were extracted from blood samples of the patients with IgAN and healthy control groups. The expression profiles of tsRNAs were assessed by small RNA sequencing (RNA-Seq) in PBMCs of the IgAN and control groups. Dysregulated tsRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR). Target gene prediction and enrichment were performed by bioinformatics analysis. Results: The results revealed that 143 significantly upregulated and 202 significantly downregulated tsRNAs were differentially altered in the IgAN group compared with the control group. Five upregulated tsRNAs (tRF-Val-AAC-007, tRF-Ala-AGC-063, tRF-Gln-CTG-010, tRF-Tyr-GTA-011 and tRF-Thr-AGT-007) and 3 downregulated tsRNAs (tiRNA-Val-TAC-004, tRF-Gly-CCC-005 and tRF-His-GTG-006) were selected for validation by qRT-PCR; the results were consistent with the sequencing data. Gene Ontology (GO) analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in “nucleic acid metabolic process," “intracellular part," and “ion binding," whereas the target genes predicted by downregulated tsRNAs were mostly enriched in “regulation of cellular component organization," “membrane-bound organelle," and “ion binding. " Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in “herpes simplex virus 1 infection," whereas the target genes predicted by downregulated tsRNAs were mostly enriched in “circadian rhythm Conclusions: The present study confirmed the differential expression of tsRNAs in patients with IgAN, and these dysregulated tsRNAs might be novel potential targets for the diagnosis and treatment of IgAN.
Inhibitory Effect of Lithospermic Acid on the HIV-1 Nucleocapsid Protein

The HIV-1 nucleocapsid protein (NC) is a desirable target in antiretroviral therapy due to its high conservation among HIV-1 strains, and to its multiple and crucial roles in the HIV-1 replication cycle. Natural products represent a valuable source of NC inhibitors, with the catechol group being a privileged scaffold in NC inhibition. By coupling molecular modeling with NMR spectroscopy and fluorescence-based assays, we disclosed lithospermic acid, a catechol derivative extracted from Salvia miltiorrhizza, as a potent and chemically stable non-covalent inhibitor of the NC. Being different from other catechol derivative reported so far, lithospermic acid does not undergo spontaneous oxidation in physiological conditions, thus becoming a profitable starting point for the development of efficient NC inhibitors.
Human Pluripotent Stem Cells-Based Therapies for Neurodegenerative Diseases: Current Status and Challenges

Neurodegenerative diseases are characterized by irreversible cell damage, loss of neuronal cells and limited regeneration potential of the adult nervous system. Pluripotent stem cells are capable of differentiating into the multitude of cell types that compose the central and peripheral nervous systems and so have become the major focus of cell replacement therapies for the treatment of neurological disorders. Human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC)-derived cells have both been extensively studied as cell therapies in a wide range of neurodegenerative disease models in rodents and non-human primates, including Parkinson’s disease, stroke, epilepsy, spinal cord injury, Alzheimer’s disease, multiple sclerosis and pain. In this review, we discuss the latest progress made with stem cell therapies targeting these pathologies. We also evaluate the challenges in clinical application of human pluripotent stem cell (hPSC)-based therapies including risk of oncogenesis and tumor formation, immune rejection and difficulty in regeneration of the heterogeneous cell types composing the central nervous system.
Screening tools for early identification of children with developmental delay in low- and middle-income countries: a systematic review

Objective To systematically review, identify and report the screening tools used for early identification of developmental delay in low- and middle-income countries. Design Systematic review. Data sources Four bibliographic databases: Medline (1946 to 13 July 2020), Embase (1974 to 13 July 2020), Scopus (1823 to 11 July 2020) and PsycINFO (1987 to July week 1 2020). Eligibility criteria Peer-reviewed original articles published in English addressing validated culturally sensitive developmental screening tools among children aged <5 years were included in this review. Data extraction and synthesis One author (CK, medical librarian) developed the search strategy. Three authors conducted the database search (phase I: CK; phase II: IJ and MKI). Three authors (TF, IJ and MKI) independently screened the title and abstracts. TF, MKI and GK independently performed the full-text review of the screened articles. During each step of the study selection process, disagreements were resolved through discussion. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement was used to guide the systematic review. Data extraction and analysis were performed using MS Excel. Meta-analysis was not possible due to heterogeneity of the study findings. Results We identified 3349 articles, of which 18 studies from 10 countries, reporting 16 screening tools, were selected for qualitative synthesis. Six cultural contexts were explored. Twelve general, two motor and two speech-language tools were identified. Seven of them found to be parent-completed ones. Five screening tools (American Speech-Language and Hearing Association, Guide for Monitoring Child Development, Infant Neurological International Battery, New Delhi-Development Screening Questionnaire and Woodside Screening Technique) reported relatively higher sensitivity (82.5%–100%) and specificity (83%–98.93%). Conclusions Limited number of culturally sensitive developmental screening tools were validated for children aged <5 years in low- and middle-income countries. Revising existing screening tools in different ethnic and cultural settings and subsequent validation with normative value should be a research priority.
Twin Pregnancies in Dairy Cattle: Observations in a Large Herd of Holstein-Friesian Dairy Cows

Simple Summary Cows have two ovaries, two uterine horns, two oviducts, and a uterine body. Although they are commonly monovular, they can sustain twin or other multiple pregnancies to term. In cows with a single pregnancy, the embryo implants in the uterine horn that is on the side of ovulation where a corpus luteum develops. Multiple pregnancies are classified into bilateral (one or more embryos in each uterine horn) and unilateral (all embryos in the same uterine horn, right or left) and, in both cases, embryos occur on the side of their corresponding corpus luteum or corpora lutea. Multiple pregnancies are undesirable in dairy herds as they compromise the reproductive performance and productive lifespan of cows. The present study sought to: (a) gain information on the incidence of twin pregnancies, (b) assess and expand information on the relative incidence of bilateral twins compared to unilateral twins, (c) confirm corresponding laterality between embryos and corpora lutea, (d) tabulate the frequency of triplets or quadruplets, and (e) evaluate possible effects of environmental heat stress conditions on the incidence of multiple pregnancies. The data for this study were derived from the ultrasonographic examination of 1130 cows carrying twins, triplets, or quadruplets, and 3160 cows carrying singletons. Abstract Multiple pregnancies have devastating consequences on the herd economy of dairy cattle. This observational study examines incidence patterns based on data from the ultrasonographic examination of 1130 multiple pregnancies in cows in their third lactation or more carrying twins (98.8%), triplets (1.1%), or quadruplets (0.08%), and 3160 of their peers carrying singletons. Cows became pregnant following a spontaneous estrus with no previous hormone treatments. Irrespective of a significant decrease (p < 0.0001) in the conception rate (28–34 days post-insemination) during the warm period of the year, the multiple pregnancy rate was similar for both warm (26.5%) and cool (26.3%) periods. The incidence of unilateral multiple pregnancies (all embryos in the same uterine horn) was higher than that of bilateral pregnancies (at least one embryo in each uterine horn): 54.4% versus 45.6% (p < 0.0001). This difference rose to 17% during the warm season (p = 0.03). Pregnancy was monitored in unilateral multiple pregnancies until abortion or parturition (n = 615). In the warm period, the parturition rate was 43% compared to 61% recorded in the cool period (p < 0.0001). Thus, a warm climate is the main factor compromising the fate of multiple pregnancies. Some clinical suggestions are provided.
The effects of substitutional Fe-doping on magnetism in MoS2 and WS2 monolayers

Doping of two-dimensional (2D) semiconductors has been intensively studied toward modulating their electrical, optical, and magnetic properties. While ferromagnetic 2D semiconductors hold promise for future spintronics and valleytronics, the origin of ferromagnetism in 2D materials remains unclear. Here, we show that substitutional Fe-doping of MoS2 and WS2 monolayers induce different magnetic properties. The Fe-doped monolayers are directly synthesized via chemical vapor deposition. In both cases, Fe substitutional doping is successfully achieved, as confirmed using scanning transmission electron microscopy. While both Fe:MoS2 and Fe:WS2 show PL quenching and n-type doping, Fe dopants in WS2 monolayers are found to assume deep-level trap states, in contrast to the case of Fe:MoS2, where the states are found to be shallow. Using μm- and mm-precision local NV− magnetometry and superconducting quantum interference device, we discover that, unlike MoS2 monolayers, WS2 monolayers do not show a magnetic phase transition to ferromagnetism upon Fe-doping. The absence of ferromagnetism in Fe:WS2 is corroborated using density functional theory calculations.
Behavioral Outcomes in Children With an Orofacial Cleft in a National Study in New Zealand

Objective: To determine whether children with an orofacial cleft have higher levels of behavioral problems than the general population and whether this differs by cleft phenotype. Design: A cohort of children with cleft lip and/or palate (CL/P) born in New Zealand from January 1, 2000. Setting: Cleft clinics in New Zealand participating in a larger outcomes study between 2014 and 2017. Participants: Children (N = 378) aged 5 to 12 years of age and their parents. Main Outcomes: The Strengths and Difficulties Questionnaire (SDQ) and Pediatric Quality of Life Inventory (PedsQL) Generic Core Scales 4.0 and Family Impact Module 2.0. Results: Compared to standardized norms, children with a cleft had higher than expected (defined as 20%) levels of abnormal/borderline SDQ scores for conduct problems (27.4%, P = .0003) and peer relationship problems (31.6%, P < .0001) but lower than expected levels of problems with pro-social skills (6.3%, P < .0001). There were no significant differences by age-group and or cleft phenotype other than an increased risk of hyperactivity in children with CP compared to children with CL. Total difficulties SDQ scores had moderate correlations with the PedsQL. Conclusions: While over 90% of children with CL/P had normal prosocial skills, they may not be easily accepted by their peers which may result in behavioral problems. These concerns were moderately related to lower quality of life. Support for establishment and maintenance of peer relationships is important to address externalizing and peer difficulties in children with CL/P. Community knowledge and understanding of CL/P needs to continue to be promoted.
Heavy metals concentration, and antioxidant activity of the essential oil of the wild mint (Mentha longifolia L.) in the Egyptian watercourses

Abstract In the present study, we assessed seasonal variation in the accumulation potential of wild mint (Mentha longifolia) to heavy metals as well as the chemical composition and antioxidant activity of the essential oil of mint in polluted and unpolluted watercourses. The results indicated that the wild mint showed seasonal fluctuations in accumulation potential for heavy metals proved by bioaccumulation factor (BF) and translocation factor (TF). The all measured heavy metals, except Pb were retained in the underground parts. Summer plants accumulated the highest concentrations of Al, Cd, Cr and Fe in their root, while the lowest concentration of Ni in their shoot. The bioaccumulation factor for Cd, Cu, Mn, Ni, Zn and Co was greater than one, while the translocation factor of the investigated metals (except Pb) did not exceed one, indicating the potential of wild mint for phytostabilization of these metals in contaminated wetlands. The yield and composition of mint essential oil (MEO) were affected by harvesting season and heavy metals pollution. GC/MS showed that isomenthone, cis-piperitenone oxide, menthone and pulegone, were the main oil constituents. Mint essential oil show promising antioxidant activity by 2,2′-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay under pollution stress. The maximum reducing power of MEO were obtained during autumn and summer seasons (polluted canals). In conclusion, summer is the ideal season for harvesting wild mint plants for the maximum plant biomass, oil yield, high radical scavenging activity of MEO and to monitor pollution in contaminated wetlands.