Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Home Antigen Testing With RT-PCR and Viral Culture During the Course of SARS-CoV-2 Infection.

Importance As self-collected home antigen tests become widely available, a better understanding of their performance during the course of SARS-CoV-2 infection is needed. Objective To evaluate the diagnostic performance of home antigen tests compared with reverse transcription-polymerase chain reaction (RT-PCR) and viral culture by days from illness onset, as well as user acceptability. Design, Setting, and Participants This prospective cohort study was conducted from January to May 2021 in San Diego County, California, and metropolitan Denver, Colorado. The convenience sample included adults and children with RT-PCR-confirmed infection who used self-collected home antigen tests for 15 days and underwent at least 1 nasopharyngeal swab for RT-PCR, viral culture, and sequencing. Exposures SARS-CoV-2 infection. Main Outcomes and Measures The primary outcome was the daily sensitivity of home antigen tests to detect RT-PCR-confirmed cases. Secondary outcomes included the daily percentage of antigen test, RT-PCR, and viral culture results that were positive, and antigen test sensitivity compared with same-day RT-PCR and cultures. Antigen test use errors and acceptability were assessed for a subset of participants. Results This study enrolled 225 persons with RT-PCR-confirmed infection (median [range] age, 29 [1-83] years; 117 female participants [52%]; 10 [4%] Asian, 6 [3%] Black or African American, 50 [22%] Hispanic or Latino, 3 [1%] Native Hawaiian or Other Pacific Islander, 145 [64%] White, and 11 [5%] multiracial individuals) who completed 3044 antigen tests and 642 nasopharyngeal swabs. Antigen test sensitivity was 50% (95% CI, 45%-55%) during the infectious period, 64% (95% CI, 56%-70%) compared with same-day RT-PCR, and 84% (95% CI, 75%-90%) compared with same-day cultures. Antigen test sensitivity peaked 4 days after illness onset at 77% (95% CI, 69%-83%). Antigen test sensitivity improved with a second antigen test 1 to 2 days later, particularly early in the infection. Six days after illness onset, antigen test result positivity was 61% (95% CI, 53%-68%). Almost all (216 [96%]) surveyed individuals reported that they would be more likely to get tested for SARS-CoV-2 infection if home antigen tests were available over the counter. Conclusions and Relevance The results of this cohort study of home antigen tests suggest that sensitivity for SARS-CoV-2 was moderate compared with RT-PCR and high compared with viral culture. The results also suggest that symptomatic individuals with an initial negative home antigen test result for SARS-CoV-2 infection should test again 1 to 2 days later because test sensitivity peaked several days after illness onset and improved with repeated testing.
Association of Somatic Gene Mutations with Risk of Transformation into Acute Myeloid Leukemia in Patients with Myelodysplastic Syndrome: A Systematic Review and Meta-Analysis

Objectives: we aim to conduct a systematic review and meta-analysis in population of adult MDS patients to elucidate the role of these genes in AML transformation risk. Materials and Methods: The protocol for this systematic review and meta-analysis was registered in the international prospective register of systematic reviews (PROSPERO) with ID number of CRD42020218581. Systematic literature search was conducted by all authors up to October 2021 on: (1) PubMed, (2) EBSCOhost, (3) Scopus, (4) JSTOR, and (5) grey literatures. Hand-searching for relevant articles was also conducted. The following keywords with their synonyms and combinations using Boolean operators were applied to all database: “myelodysplastic syndrome”, SRSF2”, “SF3B1”, “U2AF1”, “ASXL1”, “DNMT3A”, “TET2”, “IDH1”, “IDH2”, “RUNX1”, “acute myeloid leukemia progression”, and “leukemia free survival”. Outcome was measured using hazard ratio (HR). Results: We identified 14 articles to be used for this systematic review and meta-analysis. There was no statistically significant difference in AML transformation risk between U2AF1 mutant and U2AF1 wildtype MDS patients (HR: 1.41; 95% CI: 0.95–2.07, p=0.08, I2=0%). Pooled HR showed that patients with SRSF2 mutation had higher risk of AML transformation (HR 2.62; 95% CI: 1.54-4.45; p= .0004; I2= 55%). The pooled HR for SF3B1 was 0.48 (95% CI: 0.22–1.06, p=0.07, I2=55%). Mutations of TET2, ASXL1, and EZH2 were not associated with AML transformation. Meanwhile, DNMT3A mutations were associated with AML transformation with pooled HR of 2.73 (95% CI: 1.43-5.21; p= 0.08; I2: 67%). The pooled HR for IDH genes was smaller (HR: 2.92; 95%CI: 1.21-7.06; p=0.02; I2:65%). Patients with RUNX1 mutation were associated with AML transformation (HR: 1.85; 95%CI: 1.11-3.09; p=0.02; I2:38%). Conclusion: Based from our analyses, MDS patients with mutations of SRSF2, DNMT3A, IDH, and RUNX1 have higher hazard ratio for AML transformation.
Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation

Abstract Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50 = 33.8–38.0 Mb) genome assemblies of seven closely related Drosophila species that belong to the nasuta species group—a poorly studied group of flies that radiated in the last 2 My. We constructed a high-quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare TE insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor bias from reduced fitness impact of TEs inserting near lowly expressed, nonessential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is a nonautonomous DNA element (Drosophila INterspersed Element; DINE) which has gone through multiple bouts of expansions with thousands of full-length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Thus, whereas horizontal transfer followed by the invasion of a naïve genome has been highlighted to explain the long-term survival of TEs, our analysis suggests that evasion of host suppression of resident TEs is a major strategy to persist over evolutionary times. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
Workshop on RanBP2/Nup358 and acute necrotizing encephalopathy

ABSTRACT Dominant missense mutations in RanBP2/Nup358 cause Acute Necrotizing Encephalopathy (ANE), a pediatric disease where seemingly healthy individuals develop a cytokine storm that is restricted to the central nervous system in response to viral infection. Untreated, this condition leads to seizures, coma, long-term neurological damage and a high rate of mortality. The exact mechanism by which RanBP2 mutations contribute to the development of ANE remains elusive. In November 2021, a number of clinicians and basic scientists presented their work on this disease and on the interactions between RanBP2/Nup358, viral infections, the innate immune response and other cellular processes.
Roots In Tradition: Karelian Tradition as a Creative Resource for Finnish Craft Designers

Abstract This paper explores the meaning of tradition as a resource for contemporary craft production. The data were gathered during a qualitative case study call where the call participants elaborated on the role of Karelian tradition in the contemporary Finnish design discourse. In the analysis, three design practices were identified for gaining inspiration from tradition, and using it as a material, ideational, and relational resource in design work: (1) a materially orientated practice which emphasized the use of visual and material resources; (2) a production-orientated practice which drew ideational inspiration from the structure of the artefact; and (3) an interpretative practice which was based on the designer’s personal association and interpretation of tradition. These design practices suggest the socially constructed meanings of tradition, and argue for the importance of material engagement within the process of handing down the tradition itself.
Psoriatic Serum Induce an Abnormal Inflammatory Phenotype and a Decreased Immunosuppressive Function of Mesenchymal Stem Cells

Background and Objectives Mesenchymal stem cells (MSCs) have immunomodulatory function and participate in the pathogenesis of many immunoregulation-related diseases, including psoriasis. Previously, we found that MSCs from psoriatic lesions overexpress the proinflammatory microRNA, miR-155 and exhibit a decreased immunosuppressive capacity. But the origin of these aberrant characteristics is still not clear. To investigate whether inflammatory cytokines in serum and peripheral blood mononuclear cells (PBMCs) from psoriatic patients can regulate the expression patterns of immunoregulation-related cytokines and the immunoregulation function of MSCs. Methods and Results Normal dermal mesenchymal stem cells (nDMSCs) were treated with serum or PBMCs derived from patients with psoriasis or healthy donors. Expression of miR-155 and immunoregulation-related genes in each MSCs were measured using real-time PCR or western-blot. Meanwhile, the immunosuppressive capacity of DMSCs was evaluated by its inhibitory ability on proliferation of activated PBMCs. Compared to control serum, psoriatic serum significantly increased the expression levels of miR-155 (27.19±2.40 vs. 3.51±1.19, p<0.001), while decreased TAB2 expression (0.28±0.04 vs. 0.72±0.20, p<0.01) in DMSCs. Expression levels of immunoregulation-related genes such as PGE2, IL-10, and TLR4 were also markedly down-regulated following the psoriatic serum treatment. Those DMSCs treated with healthy serum could inhibit PBMC proliferation, while those psoriatic serum-treated DMSCs could not inhibit PBMC proliferation effectively. Conclusions Psoriatic serum up-regulate the expression of miR-155, down-regulate the expression of immunoregulation-related genes (PGE2, IL-10, and TLR4) in DMSCs, and along with the inhibition of the immunosuppressive function of MSCs.
Is Indirect Decompression and Fusion More Effective than Direct Decompression and Fusion for Treating Degenerative Lumbar Spinal Stenosis With Instability? A Systematic Review and meta-Analysis

Study design: Systematic Review and Meta-analysis. Objective: Surgical alternatives to treat lumbar spinal stenosis and instability include indirect (ALIF, OLIF, and LLIF) and direct (TLIF or posterior lumbar interbody fusion) decompression and fusion interventions. Although both approaches have proven to be effective in reducing symptoms, it is unknown if there is any difference in effectiveness between them. In this systematic review and meta-analysis, we aimed to evaluate postoperative pain and disability in patients treated whit indirect vs direct decompression and fusion approaches. Methods: We conducted a systematic review of the literature consulting several databases and identified studies that enrolled patients diagnosed with degenerative lumbar spinal stenosis and instability treated with indirect or direct decompression and fusion techniques. Our primary endpoints were the visual analogue scale, Oswestry Disability Index, and the Japanese Orthopedics Association Back Pain Evaluation Questionnaire 1 year after the procedure. Secondary outcomes included complication rate, blood loss, and surgical time. Results: Nine retrospective and comparative studies were included enrolling a total of 1004 participants. Both surgical strategies had satisfactory clinical outcomes with no significant difference at 1 year. Although the complication rate was similar for both groups, the profile of the adverse events was different. In addition, patients treated with indirect decompression and fusion had significantly less blood loss and operative times. Conclusions: Indirect and direct decompression and fusion techniques are similarly effective in treating patients with lumbar spinal stenosis and instability. The ID group had significantly lower intraoperative blood loss and surgical time values.
Exploration of surfactin production by newly isolated Bacillus and Lysinibacillus strains from food‐related sources

As a lipopeptide (LP), surfactin exhibits properties, such as emulsifying and dispersing ability, which are useful in food industry. Discovery of new LP‐producing strains from food sources is an important step towards possible application of surfactin in foods. A total of 211 spore‐forming, Gram‐positive, and catalase‐positive bacterial strains were isolated from fermented African locust beans (iru) and palm oil mill effluents in a screening process and examined for their ability to produce surfactin. This was achieved by a combination of methods, which included microbiological and molecular classification of strains, along with chemical analysis of surfactin production. Altogether, 29 isolates, positive for oil spreading and emulsification assays, were further identified with 16S rDNA analysis. The strains belonged to nine species including less commonly reported strains of Lysinibacillus, Bacillus flexus, B. tequilensis, and B. aryabhattai. The surfactin production was quantitatively and qualitatively analysed by high‐performance thin‐layer chromatography and liquid chromatography‐mass spectrometry (LC–MS). Confirmation of surfactin by MS was achieved in all the 29 strains. Highest surfactin production capability was found in B. subtilis IRB2‐A1 with a titre of 1444·1 mg L−1.
Validation of the Iranian version of the ENDOPAIN-4D questionnaire for measurement of painful symptoms of endometriosis

Abstract Endometriosis is one of the leading gynecological disorders in reproductive ages. About two-thirds of women with endometriosis experience chronic pelvic pain. There are different methods for the assessment of pain in endometriosis. One of these questionnaires is endometriosis painful symptoms-4 dimensions (ENDOPAIN-4D) questionnaire, which has not been validated in Iran. Therefore, we decided to conduct a study to determine the psychometric properties of this questionnaire. In this study, we randomly selected 169 women with endometriosis from two educational-medical centres of Al-Zahra and Taleghani in Tabriz, Iran, in 2020. We evaluated the validity of ENDOPAIN-4D in terms of face, content, and structure (through exploratory and confirmatory factor analyses). We used internal consistency assessment and test-retest reliability to determine the questionnaire reliability. In this study, the CVI and CVR for the ENDOPAIN-4D instrument were obtained as 0.99 and 0.98, respectively. In the exploratory factor analysis, we extracted a four-factor structure, and the confirmatory factor analysis gave a good fit for the extracted model. We obtained Cronbach's alpha coefficient as 0.96 and the intra-class correlation coefficient (ICC) (at 95% confidence interval) as 0.94 (0.85 to 0.98). The Persian version of ENDOPAIN-4D has acceptable content validity, construct validity and reliability for the evaluation of pelvic pain and gynaecology in Iranian women with endometriosis. Impact Statement What is already known on this subject? There are different methods for the assessment of pain in endometriosis. But there is no specific psychometric instrument to determine the painful symptoms of endometriosis in Iran so far. What do the results of this study add? The Persian version of ENDOPAIN-4D is a valid and reliable instrument for the evaluation of pelvic pain and gynaecology in Iranian women with endometriosis. What are the implications of these findings for clinical practice and/or future research? The validation of the Persian version of the ENDOPAIN-4D questionnaire leads to correct assessment of painful symptoms in Iranian women with endometriosis and will be useful in evaluating the patients' pain intensity and the response to treatment in practice.
Livogrit Prevents Methionine-Cystine Deficiency Induced Nonalcoholic Steatohepatitis by Modulation of Steatosis and Oxidative Stress in Human Hepatocyte-Derived Spheroid and in Primary Rat Hepatocytes

ABSTRACT The prevalence of nonalcoholic steatohepatitis (NASH), characterized by fatty liver, oxidative injury, and inflammation, has considerably increased in the recent years. Due to the complexity of NASH pathogenesis, compounds which can target different mechanisms and stages of NASH development are required. A robust screening model with translational capability is also required to develop therapies targeting NASH. In this study, we used HepG2 spheroids and rat primary hepatocytes to evaluate the potency of Livogrit, a tri-herbal Ayurvedic prescription medicine, as a hepatoprotective agent. NASH was developed in the cells via methionine and cystine-deficient cell culture media. Livogrit at concentration of 30 µg/mL was able to prevent NASH development by decreasing lipid accumulation, ROS production, AST release, NFκB activation and increasing lipolysis, GSH (reduced glutathione), and mitochondrial membrane potential. This study suggests that Livogrit might reduce the lipotoxicity-mediated ROS generation and subsequent production of inflammatory mediators as evident from the increased gene expression of FXR, FGF21, CHOP, CXCL5, and their normalization due to Livogrit treatment. Taken together, Livogrit showed the potential as a multimodal therapeutic formulation capable of attenuating the development of NASH. Our study highlights the potential of Livogrit as a hepatoprotective agent with translational possibilities. Graphical abstract
Deterioration of glycemic control in youth-onset type 2 diabetes: what are the early and late predictors?

OBJECTIVE We examined predictors of early and late loss of glycemic control in individuals with youth-onset type 2 diabetes, as well as predictors of short-term deterioration in youth from the Treatment Options for type 2 Diabetes in Adolescents and Youth (TODAY) study. METHODS Demographic, physical, and biochemical measures at baseline and 48 months, and change over time, were examined in 584 participants separated into those with loss of glycemic control (sustained HbA1c ≥8%) before 48 months or at 48 months or later, and those who remained in control until the end of the study (median 6.8 years). Univariate and multivariate models, and Receiver Operating Characteristic curve analyses were performed. RESULTS ~45% of youth remained in control at 48 months; of these, 30% subsequently lost glycemic control prior to the end of follow-up. Predictors of early loss of glycemic control included baseline HbA1c, C-peptide index, oral disposition index, proinsulin, and proinsulin to insulin ratio. Predictors of late loss included baseline measures of insulin secretion and change in HbA1c and insulin processing at 48 months. A baseline HbA1c cutoff of ≥6.2% was optimally predictive of loss of glycemic control at any time, while an absolute rise in HbA1c >0.5% related to loss of glycemic control within 3-6 months. CONCLUSIONS This analysis demonstrate that youth with type 2 diabetes at risk for loss of glycemic control, including impending rapid deterioration, can be identified using available clinical measures, allowing for closer monitoring of at-risk youth, and facilitating the design of research on better therapeutic options.
Comprehensive transcriptome profiling of BET inhibitor-treated HepG2 cells

Hepatocellular carcinoma (HCC) is the most common primary liver cancer and poor prognosis. Emerging evidence suggests that epigenetic alterations play a crucial role in HCC, suggesting epigenetic inhibition as a promising therapeutic approach. Indeed, the bromodomain and extra-terminal (BET) inhibitors inhibit the proliferation and invasion of various cancers but still lack a strong mechanistic rationale. Here, we identified the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in human HCC cell line HepG2 treated with the BET inhibitors, JQ1, OTX015, or ABBV-075. We analyzed the correlation between DEmRNAs and DElncRNAs in common for the three inhibitors based on their expression profiles and performed functional annotation pathway enrichment analysis. Most of these shared DEmRNAs and DElncRNAs, including some novel transcripts, were downregulated, indicating decreased proliferation/adhesion and increased apoptosis/inflammation. Our study suggests that BET proteins play a crucial role in regulating cancer progression-related genes and provide a valuable resource for novel putative biomarkers and therapeutic targets in HCC.
Atypical Sexual Interests in Compulsive Sexual Behavior: Results From a Phallometric Study

The link between Compulsive Sexual Behavior (CSB) and atypical sexual interests is elusive. This study aimed to provide preliminary insights into the relationship between both aspects. The study sample comprised 61 self-identified straight men. CSB was measured through a composite self-report index assessing symptoms of CSB, whereas sexual interests –atypical and normophilic– were assessed objectively through penile plethysmography. The CSB index had small, non-significant correlation with greater sexual response to different sexual stimuli (rgeneral sexual responsiveness=.127 [95% CI: −.137, .384]). In terms of overall sexual interest, increased scores on the CSB index had small, non-significant correlation with a higher preference for younger sexual stimuli (r = −.098 [95% CI: −.499, .215]) and persuasive sex (r = .10 [95% CI: −.168, .316]). Finally, CSB had a moderate correlation with sexual response when presented with stimuli depicting “female toddler coercive” (r = .27 [95% CI: −.083, .544]). We conclude that our findings do not support the hypotheses that CSB is significantly related to an increased arousability across sexual stimuli. The study findings also suggest that CSB may be, to a small degree, predisposed to experience sexual attraction toward children. Given the preliminary nature of the study, these conclusions warrant further research. Alternative explanations for the study findings related to the particular components of CSB that may be related to typical and atypical sexual interests are also considered.