Miracle-dz/UniFAR-FTUs huggingface dataset:
DHNLDA: A Novel Deep Hierarchical Network Based Method for Predicting lncRNA-Disease Associations

Recent studies have found that lncRNA (long non-coding RNA) in ncRNA (non-coding RNA) is not only involved in many biological processes, but also abnormally expressed in many complex diseases. Identification of lncRNA-disease associations accurately is of great significance for understanding the function of lncRNA and disease mechanism. In this paper, a deep learning framework consisting of stacked autoencoder(SAE), multi-scale ResNet and stacked ensemble module, named DHNLDA, was constructed to predict lncRNA-disease associations, which integrates multiple biological data sources and constructing feature matrices. Among them, the biological data including the similarity and the interaction of lncRNAs, diseases and miRNAs are integrated. The feature matrices are obtained by node2vec embedding and feature extraction respectively. Then, the SAE and the multi-scale ResNet are used to learn the complementary information between nodes, and the high-level features of node attributes are obtained. Finally, the fusion of high-level feature is input into the stacked ensemble module to obtain the prediction results of lncRNA-disease associations. The experimental results of five-fold cross-validation show that the AUC of DHNLDA reaches 0.975 better than the existing methods. Case studies of stomach cancer, breast cancer and lung cancer have shown the great ability of DHNLDA to discover the potential lncRNA-disease associations.
Phase separation of a plant virus movement protein and cellular factors support virus-host interactions

Both cellular and viral proteins can undergo phase separation and form membraneless compartments that concentrate biomolecules. The p26 movement protein from single-stranded, positive-sense Pea enation mosaic virus 2 (PEMV2) separates into a dense phase in nucleoli where p26 and related orthologues must interact with fibrillarin (Fib2) as a pre-requisite for systemic virus movement. Using in vitro assays, viral ribonucleoprotein complexes containing p26, Fib2, and PEMV2 genomic RNAs formed droplets that may provide the basis for self-assembly in planta. Mutating basic p26 residues (R/K-G) blocked droplet formation and partitioning into Fib2 droplets or the nucleolus and prevented systemic movement of a Tobacco mosaic virus (TMV) vector in Nicotiana benthamiana. Mutating acidic residues (D/E-G) reduced droplet formation in vitro, increased nucleolar retention 6.5-fold, and prevented systemic movement of TMV, thus demonstrating that p26 requires electrostatic interactions for droplet formation and charged residues are critical for nucleolar trafficking and virus movement. p26 readily partitioned into stress granules (SGs), which are membraneless compartments that assemble by clustering of the RNA binding protein G3BP following stress. G3BP is upregulated during PEMV2 infection and over-expression of G3BP restricted PEMV2 RNA accumulation >20-fold. Deletion of the NTF2 domain that is required for G3BP condensation restored PEMV2 RNA accumulation >4-fold, demonstrating that phase separation enhances G3BP antiviral activity. These results indicate that p26 partitions into membraneless compartments with either proviral (Fib2) or antiviral (G3BP) factors.
Use of weak DC electric fields to rapidly align mammalian cells

Objective. The ability to modulate cell morphology has clinical relevance in regenerative biology. For example, cells of the skeletal muscle, peripheral nerve and vasculature have specific oriented architectures that emerge from unique structure-function relationships. Methods that can induce similar cell morphologies in vitro can be of use in the development of biomimetic constructs for the repair or replacement of damaged tissues. In this work, we demonstrate that direct current (DC) electric fields (EFs) can be used as a tool to globally align cell populations in vitro. Approach. Using a 2D culture chamber system, we were able to quickly (within hours) align Schwann cells at different culture densities with an application of steady EFs at 200–500 mV mm−1. Main results. Cellular alignment was perpendicular to the field vector and varied proportionately as a function of field magnitude. In addition, the degree of cellular alignment was also dependent on cellular density. Even well-established Schwann cell monolayers were responsive to the applied DC fields with cells retracting parallel oriented processes (with respect to the imposed field) and re-extending them along the perpendicular axis. When the DC field was removed, monolayers retained the aligned morphology for many days afterwards, likely due to contact inhibition. We further show the method is applicable to other field-responsive cells, such as 3T3 fibroblasts. Significance. The patterned cells provided nanoscale haptotactic cues and can be subsequently used as a basal layer for co-culturing or manipulated for other applications. DC fields represent a rapid, simple, and efficient technique compared to other cell patterning methods such as substrate manipulation.
Outbreak of Oropouche Virus in French Guiana

Oropouche fever is a zoonotic dengue-like syndrome caused by Oropouche virus. In August–September 2020, dengue-like syndrome developed in 41 patients in a remote rainforest village in French Guiana. By PCR or microneutralization, 23 (82.1%) of 28 tested patients were positive for Oropouche virus, documenting its emergence in French Guiana.
Effects of interval‐based inpatient treatment for anorexia nervosa: An observational study

After inpatient treatment for anorexia nervosa (AN), many patients relapse and need to be readmitted. To obtain a sustained improvement, a pre‐planned multistep inpatient procedure might help to improve the patient's skills in dealing with symptoms and transdiagnostic problems, thus decreasing symptoms of AN. However, no data have been reported for such interval treatment yet. Therefore, this study examined effects of interval treatment in inpatients with AN.
Dipeptedyl peptidase-4 (DPP-4) inhibitor downregulates HMGB1/TLR4/NF-κB signaling pathway in a diabetic rat model of non-alcoholic fatty liver disease.

CONTEXT Inflammatory and immune pathways play a crucial role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD). Sitagliptin blocks the dipeptidyl peptidase-4 (DPP-4) enzyme, mechanisms that alter inflammatory pathways and the innate immune system, and by which Sitagliptin affects the pathogenesis of NAFLD weren't previously discussed. OBJECTIVE This study aims to understand the interaction between Sitagliptin and innate immune response in order to meliorate NAFLD. METHODS Thirty- two Wistar male albino rats were categorised into four groups. Rats have received a standard diet or a high-fat diet either with or without Sitagliptin. Serum HMGB1, protein and mRNA expressions of hepatic TLR4 and NF-κB, inflammatory cytokines, and histopathological changes were analysed. RESULTS An ameliorative action of Sitagliptin in NAFLD was demonstrated via decreasing HMGB1-mediated TLR4/NF-κB signalling in order to suppress inflammation and reduce insulin resistance. CONCLUSION Sitagliptin may in fact prove to be a beneficial therapeutic intervention in NAFLD.
The role of oxidative stress in epigenetic changes underlying autoimmunity.

SIGNIFICANCE Epigenetic dysregulation plays an important role in the pathogenesis and development of autoimmune diseases. Oxidative stress is associated with autoimmunity and is also known to alter epigenetic mechanisms. Understanding the interplay between oxidative stress and epigenetics will provide insights into the role of environmental triggers on the development of autoimmunity in genetically susceptible individuals. Recent Advances: Abnormal DNA and histone methylation patterns in genes and pathways involved in interferon and tumor necrosis factor signaling, cellular survival, proliferation and metabolism, organ development, and autoantibody production have been described in autoimmunity. Inhibitors of DNA and histone methyltransferases showed potential therapeutic effects in animal models of autoimmune diseases. Oxidative stress can regulate epigenetic mechanisms via effects on DNA damage repair mechanisms, cellular metabolism and the local redox environment, and redox-sensitive transcription factors and pathways. CRITICAL ISSUES Studies looking into oxidative stress and epigenetics in autoimmunity are relatively limited. The number of available longitudinal studies to explore the role of DNA methylation in the development of autoimmune diseases is small. FUTURE DIRECTIONS Exploring the relationship between oxidative stress and epigenetics in autoimmunity will provide clues for potential preventative measures and treatment strategies. Inception cohorts with longitudinal follow-up would help to evaluate epigenetic marks as potential biomarkers for disease development, progression, and treatment response in autoimmunity.
Bariatric Surgery: It’s Not Just Incretins!

Taken together, however, these data suggest that additional factors beyond sustained increases in plasma levels of GLP1, OXM, and PYY are required to produce the full impact of RYGB. While the tripeptide GOP infusion yielded improvements in glucose metabolism superior to RYGB or VLCD, there was little effect on the plasma metabolome. This suggests that the more robust and acute caloric restriction and weight loss observed with both RYGB and VLCD, together with additional intestinal and microbiome adaptations, changes in feeding behavior, and alterations in amino acid and bile acid metabolism over time, provide additional and sustained benefits for systemic metabolism and weight loss not observed with incretin infusion alone. Additional studies will be required to understand the unique and potent mediators of bariatric/metabolic surgery, and to identify those combinations of “bariatric-mimetics” which can lead us one step closer to more effective nonsurgical solutions for obesity and T2D.
Impaired social perception from eyes and face visual cues: evidence from prefrontal cortex damage

ABSTRACT Despite the key role that decoding of social-perceptual cues from faces plays in interpersonal communication, it is only recently that the potential of prefrontal cortex damage to disrupt this ability has been recognized. In fact, few studies to date had assessed whether the ability to identify the state of mind of others from the whole or part of the face is disrupted after prefrontal cortex damage and whether these two abilities are associated and share overlapped neural systems. In the present study, 30 patients with focal prefrontal lesions and 30 matched control subjects were assessed on their ability to recognize six basic emotions from facial expressions of the whole face and to identify states of mind of others from photographs of only the eyes using the “Reading the Mind in the Eyes Task”. Results showed that frontal patients were significantly impaired compared with control subjects on both tasks. Moreover, regression analyses showed that these two abilities are associated and reciprocally predictive of one another. Finally, using voxel-based lesion analysis; we identified a partially common bilaterally distributed prefrontal network in the decoding of both emotional cues from both the whole face and eyes centered within the dorsomedial and ventral regions with extension to the lateral frontal pole.
Validity of the Wechsler Abbreviated Scale of Intelligence, Second Edition (WASI-II) as an Indicator of Neurological Disease/Injury: A Pilot Study

ABSTRACT Purpose Although the Wechsler Abbreviated Scale of Intelligence, Second Edition is commonly used by neuropsychologists in the assessment of intellectual functioning, there is a paucity of published literature examining its utility in detecting neurological disease/injury. This study constitutes an attempt to validate the four-subtest WASI-II (4-FSIQ) for use with patients with neurological disease/injury. Method Participants were 59 patients referred for outpatient neuropsychological evaluation. Thirty-two individuals with diagnoses of dementia, stroke, traumatic brain injury, and other neurological disorders constituted the neurological group. A control group was comprised of 27 individuals with diagnoses of psychiatric disorders or age-related cognitive decline. Results The WASI-II subtest and composite scores of the neurological group were all significantly (ps < .0001) lower than those of the control sample, but pattern differences between the groups were absent. When premorbid IQs and WASI-II IQs were compared, neurological patients with neurological disease/injury displayed evidence of intellectual deterioration; whereas, control participants did not. Conclusions Findings suggest that the 4-WASI-II is sensitive to the biological condition of the brain and provide preliminary validation for its use in the neuropsychological assessment of a diagnostically heterogeneous sample of patients with neurological disorders.
An ECG Delineation and Arrhythmia Classification System Using Slope Variation Measurement by Ternary Second-Order Delta Modulators for Wearable ECG Sensors

This paper presents a system for electrocardiogram (ECG) delineation and arrhythmia classification. The proposed system consists of a front-end integrated circuit, a delineation algorithm implemented on an FPGA board, and an arrhythmia classification algorithm. The front-end circuit applies a ternary second-order Delta modulator to measure the slope variation of the input analog ECG signal. The circuit converts the analog inputs into a pulse density modulated bitstream, whose pulse density is proportional to the slope variation of the input analog signal regardless of the instantaneous amplitude. The front-end chip can detect the minimum slope variation of 3.2 mV/ms$^2$ within a 3 ms timing error. The front-end integrated circuit was fabricated with a 180 nm CMOS process occupying a 0.25 mm$^2$ area with a 151 nW power consumption at the sampling rate of 1 kS/s. Based on the slope variation obtained from the front-end circuit, a delineation algorithm is designed to detect fiducial points in the ECG waveform. The delineation algorithm was tested on a Spartan-6 FPGA. The delineation system can detect the intervals, slopes, and morphology of the QRS/PT waves and form a feature set that contains 22 features. Based on these features, a rotate linear kernel support vector machine (SVM) is applied for patient-specific arrhythmia classification of the ventricular ectopic beat (VEB), supraventricular ectopic beat (SVEB), and heartbeats originating in sinus node. The performance of the proposed system is comparable to the recently published methods while providing a promising solution for the low-complexity implementation of future wearable ECG monitoring systems.
Three-Dimensional Motion Capture of a Smile in Repaired Unilateral Cleft Lip: What's Our Vector, Victor?

Introduction: Following surgical repair, patients with unilateral cleft lip (UCL) exhibit dynamic asymmetry during facial expressions compared to healthy individuals. Previous studies using Euclidean distances to describe this asymmetry fail to take the direction of the movement into account. The aim of this study is to compare differences in participants with UCL and controls using analysis of motion vectors during facial expressions. Methods: In this cross-sectional study, twenty-six pediatric participants were recruited: 13 participants with repaired left UCL and 13 participants with no craniofacial diagnosis. Participants were recorded performing a maximal smile by a 4D stereophotogrammetric system. Phases of the smile were divided into closed lip and open lip smiles. Ten regions of interest were analyzed: subnasal area, upper lip, lower lip, oral commissure, and ala on both sides. The motion vectors were calculated and vector magnitude and direction for each region was compared. Results: Between cleft and control groups, the differences in vector direction were greater than the magnitude differences. Significant differences in vector direction were identified at both oral commissures in the closed lip smile; and at the oral commissure, subnasal, upper lip, and lower lip regions during open lip smile. Conclusions: Vector analysis demonstrated significant movement asymmetry during facial animation in participants following UCL repair, not previously identified when analyzing magnitude of skin displacement.
Expression Analysis of GD2 by Immunohistochemistry in Invasive Breast Carcinoma: Clinical and Pathologic Correlation

The glycosphingolipid disialoganglioside GD2 is a cell surface–associated antigen expressed on tumors of neuroectodermal origin that serves as a target of immunotherapy in select cancer types. Information about the expression of GD2 in breast cancer is limited. In the present study, we investigate the utility of GD2 as a potential biomarker for targeted treatment. The study cohort consists of 386 breast carcinomas of several histologic types. GD2 expression was assessed in both whole tumor sections and tissue microarrays with anti-GD2 3F8 monoclonal antibody immunohistochemistry and correlated with clinicopathologic features and survival outcomes. A total of 134 (35%) breast carcinomas were positive for GD2, with a median H-score of 100. 3F8 staining displayed granular and predominantly cytoplasmic or perinuclear patterns, which was confined to the neoplastic tissue in nearly all cases. GD2 positivity was significantly associated with tumor histologic type (P=0.0015), low grade (P<0.0001), estrogen receptor positivity (P<0.0001), low stage (P=0.0014), and multifocality (P=0.022). Event-free survival and overall survival of patients with GD2-positive and GD2-negative tumors were not significantly different. Our results support further assessment of GD2 using the 3F8 antibody as a predictive and prognostic biomarker in breast cancer.
Neuronal development in the cochlea of a nonhuman primate model, the common marmoset

Precise cochlear neuronal development is vital to hearing ability. Understanding the developmental process of the spiral ganglion is useful for studying hearing loss aimed at aging or regenerative therapy. Although interspecies differences have been reported between rodents and humans, to date, most of our knowledge about the development of cochlear neuronal development has been obtained from rodent models because of the difficulty in using human fetal samples in this field. In this study, we investigated cochlear neuronal development in a small New World monkey species, the common marmoset (Callithrix jacchus). We examined more than 25 genes involved in the neuronal development of the cochlea and described the critical developmental steps of these neurons. We also revealed similarities and differences between previously reported rodent models and this primate animal model. Our results clarified that this animal model of cochlear neuronal development is more similar to humans than rodents and is suitable as an alternative for the analysis of human cochlear development. The time course established in this report will be a useful tool for studying primate‐specific neuronal biology of the inner ear, which could eventually lead to new treatment strategies for human hearing loss.
Elevated Expressions of BTN3A1 and RhoB in Psoriasis Vulgaris Lesions by an Immunohistochemical Study

Psoriasis is a chronic, immune-mediated inflammatory disease which pathogenesis is closely linked to γδ T cells. Recently, a critical role for butyrophilin 3A1 (BTN3A1) in mediating the activation of Vγ9Vδ2 T cells, which are reported to redistribute from blood to the perturbed skin lesions in psoriasis, has been proposed. Additional molecular partners, including RhoB and periplakin, have also been speculated to interact with BTN3A1 in modulating Vγ9Vδ2 T-cell activation. Immunohistochemical staining was performed to examine the expressions of BTN3A1, RhoB, and the plakin family members, including periplakin, epiplakin, and envoplakin in the psoriasis vulgaris lesions as compared with the normal control. The expressions of BTN3A1 and RhoB were found significantly upregulated in the psoriatic lesions. Besides, a downregulation of periplakin and an upregulation of epiplakin were noticed in the psoriasis vulgaris lesions. Our data suggest that BTN3A1 and RhoB might participate in the pathogenesis of psoriasis through Vγ9Vδ2 T-cell responses. In addition, a potential involvement of the plakin protein family, especially periplakin and epiplakin, in psoriasis pathology was proposed.
Triple Inhaler versus Dual Bronchodilator Therapy in COPD: Real-World Effectiveness on Mortality

Abstract Randomized trials of triple therapy including an inhaled corticosteroid (ICS) for chronic obstructive pulmonary disease (COPD) reported remarkable benefits on mortality compared with dual bronchodilators, likely resulting from ICS withdrawal at randomization. We compared triple therapy with dual bronchodilator combinations on major COPD outcomes in a real-world clinical practice setting. We identified a cohort of COPD patients, age 50 or older, treated during 2002-2018, from the United Kingdom’s Clinical Practice Research Datalink. Patients initiating treatment with a long-acting muscarinic antagonist (LAMA), a long-acting beta2-agonist (LABA) and an ICS on the same day, were compared with patients initiating a LAMA and LABA, weighted by fine stratification of propensity scores. Subjects were followed-up one year for all-cause mortality, severe exacerbation and pneumonia. The cohort included 117,729 new-users of LAMA-LABA-ICS and 26,666 of LAMA-LABA. The adjusted hazard ratio (HR) of all-cause mortality with LAMA-LABA-ICS compared with LAMA-LABA was 1.17 (95% CI: 1.04-1.31) while for severe exacerbation and pneumonia it was 1.19 (1.08-1.32) and 1.29 (1.16-1.45) respectively. However, mortality was not elevated with triple therapy among patients with asthma diagnosis (HR 0.99; 95% CI: 0.74-1.34), with two or more prior exacerbations (HR 0.88; 95% CI: 0.70-1.11), and with FEV1 percent predicted >30%. In a real-world setting of COPD treatment, triple therapy initiation was not more effective than dual bronchodilators at preventing all-cause mortality and severe COPD exacerbations. Triple therapy may be unsafe among patients without prior exacerbations, in whom ICS are not recommended, with no asthma diagnosis and with very severe airflow obstruction. Supplemental data for this article is available online at https://doi.org/10.1080/15412555.2021.1977789 .