Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis

Development of primary liver cancer is a multistage process. Detailed understanding of sequential epigenetic alterations is largely missing. Here, we performed Infinium Human Methylation 450k BeadChips and RNA-Seq analyses for genome-wide methylome and transcriptome profiling of cirrhotic liver (n = 7), low- (n = 4) and high-grade (n = 9) dysplastic lesions, and early (n = 5) and progressed (n = 3) hepatocellular carcinomas (HCC) synchronously detected in 8 patients with HCC with chronic hepatitis B infection. Integrative analyses of epigenetically driven molecular changes were identified and validated in 2 independent cohorts comprising 887 HCCs. Mitochondrial DNA sequencing was further employed for clonality analyses, indicating multiclonal origin in the majority of investigated HCCs. Alterations in DNA methylation progressively increased from liver cirrhosis (CL) to dysplastic lesions and reached a maximum in early HCCs. Associated early alterations identified by Ingenuity Pathway Analysis (IPA) involved apoptosis, immune regulation, and stemness pathways, while late changes centered on cell survival, proliferation, and invasion. We further validated 23 putative epidrivers with concomitant expression changes and associated with overall survival. Functionally, Striatin 4 (STRN4) was demonstrated to be epigenetically regulated, and inhibition of STRN4 significantly suppressed tumorigenicity of HCC cell lines. Overall, application of integrative genomic analyses defines epigenetic driver alterations and provides promising targets for potentially novel therapeutic approaches.
Predictors of cognitive impairment in pseudotumor cerebri.

AIMS OF THE STUDY We aimed to define the cognitive burden of the largest pseudotumor cerebri syndrome (PTCS) population to date, compare objective to subjective cognitive dysfunction, and determine clinical predictors of cognitive dysfunction amongst an array of previously unstudied factors. CLINICAL RATIONALE Patients with PTCS commonly report cognitive dysfunction, a factor associated with poor quality of life. It is not definitively known whether cognitive impairment is present in these patients, and what features of the syndrome predict impairment. MATERIALS AND METHODS We administered a cognitive battery consisting of the National Adult Reading Test, Mini-Mental Status Exam, Digit Span, Boston Naming Test, Rey Auditory Verbal Learning Test, Clock Drawing, Trail Making Test, Controlled Oral Word Association, and Category Fluency. Cognitive impairment was defined as mild-single domain with one test score, and mild-multiple domain with two scores, more than two standard deviations below the mean for age-, gender-, and education-adjusted norms. RESULTS One-hundred and one prospectively recruited PTCS patients were enrolled. The objective testing showed 30 patients had mild-single domain impairment, and 25 had mild-multi domain impairment. More patients without objective cognitive impairment had transverse venous sinus stenosis, but otherwise the groups did not differ. Two measures of headache severity, the Headache Impact Test and pain on the Numeric Rating Scale, were negatively associated with the composite cognitive score, as was ocular pain, vision-related disability, and mental health. Opening pressure and visual function were not associated with objective cognitive impairment. We found no association between subjective and objective cognitive impairment. CONCLUSIONS AND CLINICAL IMPLICATIONS Patients with PTCS may be cognitively impaired, and this correlates with measures of headache burden. Studies evaluating cognitive impairment before and after remission of the headache disorder would have to be performed to investigate this relationship further. Patients with self-perception of cognitive burden are no more likely to be cognitively impaired.
Predicting dysphagia onset in patients with ALS: the ALS dysphagia risk score

Abstract Purpose: For patients diagnosed with ALS, dysphagia can result in aspiration, malnutrition, and mortality. The purpose of this study was to develop a clinical prediction model capable of identifying patients with ALS at imminent risk for developing swallowing complications. Methods: A retrospective cohort study using the Pooled Resource Open-Access ALS Clinical Trials Database (PRO-ACT) was conducted. After dividing the PRO-ACT database into development and validation cohorts with dysphagia defined from the ALS Functional Rating Scale (ALSFRS), a multivariable Cox proportional hazards regression model estimated the probability of dysphagia at 3, 6, and 12-months with subsequent evaluation of model discrimination and calibration. Results: With 2057 participants in the development cohort and 1891 in the validation cohort, the Cox model included 7 clinical variables: spinal-onset; bulbar, fine and gross motor ALSFRS subscale scores; respiratory impairment; functional progression rate; and time from diagnosis. The cumulative incidence of dysphagia was 18% at 3-months, 29% at 6-months, and 45% at 12-months. The mean predicted probability of dysphagia development ranged from 4.5% in the bottommost risk decile to 40% in the topmost decile at 3 months, 10%–72% at 6 months, and 25%–93% at 12 months. In the validation cohort, the model had good discrimination and calibration with an optimism corrected c-statistic of 0.70 and calibration slope of 0.96. Conclusions: The ALS dysphagia risk score can be used to identify patients with ALS at high risk for self-reported dysphagia development who would benefit from a comprehensive swallowing assessment and proactive dysphagia management strategies.
The Tudor Domain-Containing Protein BbTdp1 Contributes to Fungal Cell Development, the Cell Cycle, Virulence, and Transcriptional Regulation in the Insect Pathogenic Fungus Beauveria bassiana

In this study, we used Beauveria bassiana as a biological model to report the role of BbTdp1 in entomopathogenic fungi. Our findings indicated that BbTdp1 contributed significantly to cell development, the cell cycle, and virulence in B. bassiana. In addition, deletion of BbTdp1 led to drastic fluctuations in the transcriptional profile. BbTdp1 can be developed as a novel target for B. bassiana development and pathogenicity, which also provides a framework for the study of Tdp1 in other fungi. ABSTRACT Beauveria bassiana is an insect pathogenic fungus that serves as a model system for exploring the mechanisms of fungal development and host-pathogen interactions. Clinical and experimental studies have indicated that SND1 is closely correlated with the progression and invasiveness of common cancers as a potential oncogene, but this gene has rarely been studied in fungi. Here, we characterized the contributions of an SND1 ortholog (Tdp1) by constructing a BbTdp1 deletion strain and a complemented strain of B. bassiana. Compared with the wild-type (WT) strain, the ΔBbTdp1 mutant lost conidiation capacity (∼87.7%) and blastospore (∼96.3%) yields, increased sensitivity to chemical stress (4.4 to 54.3%) and heat shock (∼44.2%), and decreased virulence following topical application (∼24.7%) and hemocoel injection (∼40.0%). Flow cytometry readings showed smaller sizes of both conidia and blastospores for ΔBbTdp1 mutants. Transcriptomic data revealed 4,094 differentially expressed genes (|log2 ratio| > 2 and a q value of <0.05) between ΔBbTdp1 mutants and the WT strain, which accounted for 41.6% of the total genes, indicating that extreme fluctuation in the global gene expression pattern had occurred. Moreover, deletion of BbTdp1 led to an abnormal cell cycle with a longer S phase and shorter G2/M and G0/G1 phases of blastospores, and enzyme-linked immunosorbent assay confirmed that the level of phosphorylated cyclin-dependent kinase 1 (Cdk1) in the ΔBbTdp1 strain was ∼31.5% lower than in the WT strain. In summary, our study is the first to report that BbTdp1 plays a vital role in regulating conidia and blastospore yields, fungal morphological changes, and pathogenicity in entomopathogenic fungi. IMPORTANCE In this study, we used Beauveria bassiana as a biological model to report the role of BbTdp1 in entomopathogenic fungi. Our findings indicated that BbTdp1 contributed significantly to cell development, the cell cycle, and virulence in B. bassiana. In addition, deletion of BbTdp1 led to drastic fluctuations in the transcriptional profile. BbTdp1 can be developed as a novel target for B. bassiana development and pathogenicity, which also provides a framework for the study of Tdp1 in other fungi.
Association between tooth agenesis and cancer: a systematic review

Abstract The congenital absence of multiple teeth may share the same genetic background of the development of some types of cancer. Objective: This systematic review aimed to investigate the possible association between dental agenesis and cancer, and the perspective of agenesis as an early predictor for cancer risk. Methodology: The electronic databases PubMed, Scopus, Web of Science, Cochrane Library, LILACS, and OpenGrey were searched and the risk of bias was evaluated using the Newcastle-Ottawa tool. The GRADE tool was used to evaluate the certainty of the evidence. Results: Six studies met the eligibility criteria. A positive co-occurrence between ovarian cancer and hypodontia was found in two articles. Three studies evaluated the association between dental agenesis and colorectal cancer and only one showed common genes for these conditions. One paper found individuals with hypodontia had a higher risk of family history of cancer. Five studies had a fair quality and one a good quality. The certainty of evidence was classified as very low. Conclusion: Notwithstanding the limited scientific evidence, there may be a possible association between dental agenesis and cancer due to genes involved in both conditions. Agenesis of multiple teeth could be an early indicator of cancer risk. Nevertheless, studies with a better level of evidence are needed to confirm this possible association.
Relation between anti-Porphyromonas gingivalis antibody titers and HLA-DRB1 neutral alleles in individuals with rheumatoid arthritis

Abstract Objective This study aimed to determine the relation between titres of anti-Porphyromonas gingivalis (P. gingivalis) antibody and rheumatoid arthritis (RA) HLA-DRB1 susceptibility region associated with shared epitope (SE) using the Gregersen’s and de Vries’s classification methods. Material and Methods In this cross-sectional study, results of immunoglobulin G1 (IgG1) and immunoglobulin G2 (IgG2) anti-P. gingivalis antibodies, anti-citrullinated protein antibodies (ACPA), diagnosis for RA, and periodontal disease (PD), and a genetic study of the HLA DRB1 region were obtained from 50 patients with RA and 50 control individuals. Results Anti-P. gingivalis antibody levels and PD parameters were similar in control and RA groups. Anti-P. gingivalis antibodies were not associated with SE or ACPA. There was no association between ACPA and SE. However, de Vries’ classification in RA patients revealed an association between the HLA DRB1 neutral alleles and higher titres of anti-P. gingivalis antibodies as follows: IgG1 anti-P. gingivalis ≥ 1:400 (p = .039); IgG2 anti-P. gingivalis ≥ 1:400 with neutral/neutral genotype (N/N), being exclusive for RA (p = .008); and IgG2 anti-P. gingivalis ≥ 1:200 and N/N (p = .016). Conclusions Although no association was found between SE and anti-P. gingivalis antibodies; according to the de Vries’ classification, there was an existing association between HLA DRB1 neutral alleles, with high titres of IgG anti-P.gingivalis antibodies for RA, focussing on novel associations between P.gingivalis and RA.
Bioactivity of a Fraction Rich in Linoleic Acid of Ricinus communis L. (Euphorbiaceae) Leaves against the Yellow Sugarcane Aphid, Sipha flava (Hemiptera: Aphididae).

The insecticidal activity of the hexane extract and fractions of Ricinus communis leaves against the yellow sugarcane aphid ( Sipha flava ) was evaluated in adults using contact bioassays by fumigation. The n -hexane extract at a concentration of 10,000 ppm achieved the highest mortality rate (80%), the positive control exhibited 100% mortality and the negative control only presented 4% mortality over the 72-hour experimental time. By means a chemical fractionation of the hexanic extract of R. communis leaves, it was possible to obtain an F4 fraction with an aphid mortality of 92% at 10,000 ppm in 72 hours. F4 GC-MS identified linoleic acid as the major compound (84.5%). The extract of R. communis and linoleic acid could be considered for integrated pest control as a more ecologically friendly alternative to synthetic chemical insecticides.
Stepwise improvement in limb shaking achieved by staged angioplasty for severe carotid stenosis

Cerebral hyperperfusion syndrome is a rare but severe complication of carotid artery stenting or carotid endarterectomy. Staged angioplasty is reportedly an effective strategy to avoid cerebral hyperperfusion syndrome. We encountered a case of internal carotid artery stenosis with a rare clinical presentation of limb shaking that was successfully improved by staged angioplasty. To our knowledge, there are no reported cases of limb shaking treated with staged angioplasty. A 76-year-old woman presented with continuous chorea in her left lower limb and shoulder. Medical examination revealed a tiny cerebral infarction in the right corona radiata and severe right internal carotid artery stenosis. Angiography showed near occlusion of the right internal carotid artery. Staged angioplasty was performed to avoid the risk of cerebral hyperperfusion syndrome. The first angioplasty resulted in an expanded diameter of 2.5 mm and was followed by definitive carotid artery stenting using a closed-cell stent 3.5 weeks later. Limb shaking improved in a stepwise manner along with an improvement in internal carotid artery stenosis and distal flow state with no signs of cerebral hyperperfusion syndrome. Patients with internal carotid artery stenosis or occlusion presenting with limb shaking have been suggested to have impaired cerebrovascular reactivity, which is also thought to be a risk factor for cerebral hyperperfusion syndrome. The stepwise improvement in limb shaking observed in this case supports the idea that the pathophysiology of limb shaking is related to cerebral haemodynamic impairment. Measures to prevent cerebral hyperperfusion syndrome, including staged angioplasty, should be actively considered in patients with limb shaking because the symptoms themselves suggest severe hypoperfusion.
Region-Specific Differences in the Apoe4-dependent Response to Focal Brain Injury

Apolipoprotein E (apoE) plays a role in various physiological functions including lipid transport, synaptic plasticity, and immune modulation. Epidemiological studies suggest that the apoE4 allele increases the risk of post-traumatic sequelae. This study was performed to investigate region-specific effects of the apoE4 isoform on post-traumatic neurodegeneration. Two focal brain injuries were introduced separately in the motor cortex and hippocampus of apoE4 knock-in, apoE3 knock-in, apoE knockout, and wild-type (WT) mice. Western blotting showed that the expression levels of pre-synaptic and post-synaptic markers at the recovery stage were lower in the hippocampal injury core in apoE4 mice, compared with apoE3 and WT mice. Fast glial activation (determined by immunohistochemistry with glial fibrillary acidic protein, ionized calcium binding adaptor molecule 1, and cluster of differentiation 45 antibodies) was characteristic of apoE4 mice with hippocampal injury penumbra. apoE4-specific changes were not observed after cortical injury. The intensity of microglial activation in the hippocampus was inversely correlated with the volume of injury reduction on sequential magnetic resonance imaging examinations, when validated using matched samples. These findings indicate that the effects of the interaction between apoE4 and focal brain damage are specific to the hippocampus. Manipulation of inflammatory cell responses could be beneficial for reducing post-traumatic hippocampal neurodegeneration in apoE4 carriers.
Patients with diabetes mellitus and atrial fibrillation treated with non-vitamin K antagonist oral anticoagulants

Dear Editor, We read with interest Jin et al. titled “A network metaanalysis of non-vitamin K antagonist oral anticoagulants versus warfarin in patients with atrial fibrillation and diabetes mellitus” [1] highlighting that direct oral anticoagulants (DOACs) are effective and safe in diabetic (DM) patients with atrial fibrillation (AF). Since 2009, DOACs are drugs used in clinical practice while the amount of information on their efficacy compared to vitamin K antagonists in different indications is currently growing. The prevalence of therapeutic complications in the “real world” is difficult to assess especially in subjects hospitalised in internal medicine wards, where patients are often elderly, affected by poly-morbidities as DM and renal insufficiency [2]. In our opinion, is important to underline that aspirin is also indicated for the prevention of cardiovascular disease in subjects with DM [3] and diabetic subjects with AF usually take it together with DOACs. About the bleeding risk, data presented by Jin et al. [1] agree with Plitt et al. metanalysis [4], although this second meta-analysis was included 35.3% of diabetic patients in combination of oral anticoagulants and aspirin (excluding subject enrol in the RE-LY trial) therapy. In these case reductions of DOACs dosage is recommended to limit the higher risk of bleeding [2]. To note that the significant benefit of DOACs for the primary safety endpoint of mayor bleeding reported by Plitt et al. [4] identifies endoxaban as the potentially safest drug but with the limitation to compared it with dabigatran 150mg per day without knowing the concomitant use of aspirin. We are agreed with Jin et al. [1] that, in clinical practice, dabigatran 100mg (bid) may be the most considered choice to balance embolism and bleeding risks in diabetic patients with atrial fibrillation. Therefore, a deeper evaluation of these aspects could be very useful to better define the safety profile of DOACs and particular attention to drug–drug interactions avoiding unnecessary association between DOACs and antiplatelet agents [5] to improve the patients’ safety. Disclosure statement
The 20-minute whole blood clotting test (20WBCT) for snakebite coagulopathy—A systematic review and meta-analysis of diagnostic test accuracy

Background The 20-minute whole blood clotting test (20WBCT) has been used to detect coagulopathy following snakebite for almost 50 years. A systematic review and meta-analysis of the 20WBCT was conducted to evaluate the accuracy of the 20WBCT to detect coagulopathy, indicative of systemic envenoming. Methods and findings Databases were searched from inception up to 09/12/2020 to identify studies that compared the 20WBCT and INR/fibrinogen on five or more subjects. Data was extracted from full-text articles by two reviewers using a predetermined form. Authors of 29 studies that lacked sufficient details in the manuscript were contacted and included if data meeting the inclusion criteria were provided. Included studies were evaluated for bias using a tailored QUADAS-2 checklist. The study protocol was prospectively registered on PROSPERO database (CRD42020168953). The searches identified 3,599 studies, 15 met the inclusion criteria and 12 were included in the meta-analysis. Data was reported from 6 countries and included a total of 2,270 patients. The aggregate weighted sensitivity of the 20WBCT at detecting INR >1.4 was 0.84 (CI 0.61 to 0.94), the specificity was 0.91 (0.76 to 0.97) and the SROC AUC was 0.94 (CI 0.91 to 0.96). The aggregate weighted sensitivity of the 20WBCT at detecting fibrinogen <100 mg/dL was 0.72 (CI 0.58 to 0.83), the specificity was 0.94 (CI 0.88 to 0.98) and the SROC AUC was 0.93 (0.91 to 0.95). Both analyses that used INR and fibrinogen as the reference test displayed considerable heterogeneity. Conclusions In the absence of laboratory clotting assays, the 20WBCT remains a highly specific and fairly sensitive bedside test at detecting coagulopathy following snakebite. However, clinicians should be aware of the importance of operator training, standardized equipment and the lower sensitivity of the 20WBCT at detecting mild coagulopathy and resolution of coagulopathy following antivenom.
Towards an integrative self: a digital photo elicitation study of resilience among key marginalized populations of sexual and gender minority youth

ABSTRACT Purpose: Sexual and gender minority youth (SGMY) experience unique challenges related to identity and disclosure, and cope in vibrant ways. Qualitative research has not yet fulsomely explored the risk, resilience, and identity intersections that impact vulnerable SGMY wellbeing. Methods: This digital photo-elicitation study (QueerView) recruited thirty SGMY (aged 14–29) from priority populations that had one or more of the following experiences: trans and gender diverse, homelessness, child welfare, and immigration. From submission of fifteen photos representing resilience and a semi-structured interview via web conferencing, constructivist grounded theory was utilized for multimodal analysis of photos, interview video, and interview transcript. Triangulation, an audit trail, and member checking were employed to support trustworthiness. Results: A visual model emerged showing how participants work towards an integrative self, with themes of reflecting and knowing, discrimination and intersectional challenges, connecting, performing, curating, coping, (re)defining and (re)creating, growing and being. Sub-themes of the impact of family dynamic and values, mental health and trauma, and the cathartic benefit from advocacy and leadership offered insight. Participant images were captured in a digital gallery. Conclusions: QueerView animates the complex lives of multiply marginalized SGMY and their intersectional strengths and challenges while demonstrating the utility of a digital multimodal approach.