Miracle-dz/UniFAR-FTUs huggingface dataset:
A web-based tool for the prediction of rice transcription factor function

Abstract Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.
Reduction Rate of Specific IgE Level as a Predictor of Persistent Egg Allergy in Children

Purpose Egg is the most common food allergen in infants. However, the natural course of egg allergy has not been fully elucidated. This study aimed to describe clinical characteristics and to identify prognostic factors associated with tolerance acquisition of immunoglobulin E (IgE)-mediated egg allergy in children. Methods Children who underwent more than 1 follow-up egg white-specific immunoglobulin E (EWsIgE) test between November 2005 and November 2015 at -Severance Children's Hospital were assessed. Children were diagnosed as having IgE-mediated egg allergy based on immediate allergic reaction after egg consumption and an EWsIgE level of > 0.35 kU/L. The children were divided into “tolerant” and “persistent” groups according to tolerance acquisition defined as egg consumption without adverse allergic reactions. Results Of 124 participants, egg allergy resolved in 101 (81.5%) children. The persistent group had more atopic dermatitis (P = 0.039), and more wheat (P = 0.009) and peanut (P = 0.012) allergies compared to the tolerant group. The EWsIgE levels at diagnosis (EWsIgEdiag) were higher in the persistent group than in the tolerant group (P = 0.001). The trend of the EWsIgE levels in the tolerant group decreased markedly over time compared to the persistent group (P < 0.001). In predicting egg allergy tolerance acquisition, the reduction rate of EWsIgE level after 12 months from diagnosis (ΔEWsIgE12mo) tended to be more accurate than EWsIgEdiag (area under the curve: 0.835 vs. 0.731). When ΔEWsIgE12mo was ≥ 30%, tolerance acquisition was more frequent than that of < 30% (91.9% vs. 57.9%; P < 0.001). Conclusions ΔEWsIgE12mo can be used as an early independent predictor of tolerance acquisition of IgE-mediated egg allergy in children.
Virtual Reality Rehabilitation Versus Conventional Physical Therapy for Improving Balance and Gait in Parkinson’s Disease Patients: A Randomized Controlled Trial

Background The aim of this study was to investigate the effect of virtual reality (VR) technology on balance and gait in patients with Parkinson’s disease (PD). Material/Methods The study design was a single-blinded, randomized, controlled study. Twenty-eight patients with PD were randomly divided into the experimental group (n=14) and the control group (n=14). The experimental group received VR training, and the control group received conventional physical therapy. Patients performed 45 minutes per session, 5 days a week, for 12 weeks. Individuals were assessed pre- and post-rehabilitation with the Berg Balance Scale (BBS), Timed Up and Go Test (TUGT), Third Part of Unified Parkinson’s Disease Rating Scale (UPDRS3), and Functional Gait Assessment (FGA). Results After treatment, BBS, TUGT, and FGA scores had improved significantly in both groups (P<0.05). However, there was no significant difference in the UPDRS3 between the pre- and post-rehabilitation data of the control group (P>0.05). VR training resulted in significantly better performance compared with the conventional physical therapy group (P<0.05). Conclusions The results of this study indicate that 12 weeks of VR rehabilitation resulted in a greater improvement in the balance and gait of individuals with PD when compared to conventional physical therapy.
Breastfeeding duration is associated with offspring’s adherence to prudent dietary pattern in adulthood: results from the Nutritionist’s Health Study

Abstract Little is known about the long-term effect of breastfeeding on dietary habits. We examined the association between breastfeeding duration and adherence to current dietary patterns of young women. This was a cross-sectional analysis of 587 healthy women aged ≤45 years, undergraduates or nutrition graduates. Maternal characteristics and breastfeeding duration [<6; 6–<12; ≥12 months (reference)] were recalled. Diet was assessed using a food frequency questionnaire and patterns were identified using factor analysis by principal component. Adherence to patterns was categorized in tertiles; the first (T1 = reference) was compared to T2 + T3 (moderate-to-high adherence). Logistic regression was performed considering the minimal sufficient adjustment recommended by the directed acyclic graph. Median age was 22 (interquartile range (IQR) 20; 27) years and body mass index (BMI) 22.2 (IQR 20.4; 25.0) kg/m2. The four dietary patterns identified (Processed, Prudent, Brazilian and Lacto-vegetarian) explained 27% of diet variance. Women breastfed for <6 months showed lower chance of moderate-to-high adherence to the Prudent pattern (odds ratio (OR) = 0.53, p = 0.04). Breastfeeding was not associated with the other patterns. Maternal pre-pregnancy BMI was directly associated with moderate-to-high adherence to the Processed pattern (OR = 2.01, p = 0.03) and inversely to the Prudent pattern (OR = 0.52, p = 0.02). Higher adherence to the Brazilian pattern was associated with proxies of low socioeconomic status and the Lacto-vegetarian pattern with the opposite. Confirmation in prospective studies of the association found in this study between breastfeeding with the Prudent pattern in adult offspring could suggest that early feeding practices influence long-term dietary habits, which could then affect the risk of nutrition-related diseases.
Degeneration of Corneal Sensation and Innervation in Patients with Facial Paralysis: A Cross-Sectional Study Using in Vivo Confocal Microscopy

ABSTRACT Purpose: Facial paralysis (FP) leads to diverse periocular complications which threats visual acuity and affects corneal nerve functionally and morphologically. This study aims to summarize the clinical ophthalmic outcomes, corneal sensation, and morphological alterations of subbasal nerve and dendritic cells (DCs) in patients with facial paralysis. Methods: We performed a cross-sectional study of 48 consecutive patients with facial paralysis at one tertiary hospital. Forty-eight healthy participants were enrolled as controls. The images of corneal nerves and epithelial DCs were detected by in vivo confocal microscopy (IVCM). Each patient received thorough ophthalmic examination, tear film function tests, corneal fluorescence staining and Cochet-Bonnet esthesiometry test. Clinical and morphologic data were compared with controls. Results: Forty patients (83.3%) showed corneal injuries from punctate epithelial defects to corneal ulcers and scars. Visual impairment and eyelid malposition were observed. Corneal sensitivity remarkably decreased (25.1 ± 23.8 mm) in the affected eyes and was correlated to diminished subbasal nerve density (P = .019, r = 0.387). Numbers of corneal main nerve trunks and branches were significantly reduced (P < .0001) while DCs were increased (P < .0001) in patients with FP when compared with controls. Nerve fiber density showed inverse association with DC density (P = .019, r = −0.389). Conclusions: Ocular complications including corneal erosions, loss of corneal sensation, visual impairment and eyelid malposition have largely affected patients with facial paralysis. Morphological changes of diminished corneal subbasal nerve and increased DCs were detected by IVCM. Corneal epithelial defect, corneal opacity, corneal sensation, dendritic cell density are factors associated with corneal subbasal nerve density. Patients with FP are suggested to have complete ophthalmic evaluation and early instruction on ocular prevention.
Platelet Apoptosis Can Be Triggered Bypassing the Death Receptors

In nucleated cells, the extrinsic pathway of the programmed cell death (apoptosis) is triggered by interaction of death ligands of the tumor necrosis factor superfamily with the death receptors on external cell surface membrane. In this review, we present evidence that, in contrast to nucleated cells, apoptosis in anucleate platelets can be induced through bypassing the death receptors, using instead specific receptors on the platelet surface mediating platelet activation, aggregation, and blood coagulation. These platelet surface receptors include the protease-activated receptor 1 of thrombin and glycoproteins IIbIIIa and Ibα, receptors of fibrinogen, and von Willebrand factor. The pro-apoptotic BH3 mimetic ABT-737 and calcium ionophore A23187 also trigger platelet apoptosis without using death receptors. These agents induce the intrinsic pathway of platelet apoptosis by direct targeting mitochondrial and extra-mitochondrial apoptotic responses.
Monitoring of Air-Dispersed Formaldehyde and Carbonyl Compounds as Vapors and Adsorbed on Particulate Matter by Denuder-Filter Sampling and Gas Chromatographic Analysis

Carbonyl compounds (CCs) are products present both as vapors and as condensed species adsorbed on the carbonaceous particle matter dispersed in the air of urban areas, due to vehicular traffic and human activities. Chronic exposure to CCs is a potential health risk given the toxicity of these chemicals. The present study reports on the measurement of the concentrations of 14 CCs in air as vapors and 2.5 µm fraction PM by the ENVINT GAS08/16 gas/aerosol sampler, a serial sampler that uses annular denuder, as sampling device. The 14 CCs were derivatized during sampling prior to gas-chromatographic separation and multiple detection by mass spectrometry, nitrogen-phosphorus thermionic, electron capture detection. Outdoor air multiple samples were collected in four locations in the urban area of Florence. The results evidenced that formaldehyde, acetaldehyde, and acetone were the more abundant CCs in the studied areas. The data collected was discussed considering the particle to vapor ratio of each CC found. The CCs pollution picture obtained was tentatively related to the nature and intensity of the traffic transiting by the sampling sites. This approach allowed to determine 14 CCs in both concentrated and diluted samples and is proposed as a tool for investigating outdoor and indoor pollution.
Expression and Distribution of PIEZO1 in the Mouse Urinary Tract.

The proper function of the organs that make up the urinary tract (kidneys, ureters, bladder, and urethra) depends on their ability to sense and respond to mechanical forces including shear stress and wall tension. Yet, we have limited understanding of the mechanosensors that function in these organs and the tissue sites in which these molecules are expressed. Possible candidates include the stretch-activated PIEZO channels (PIEZO1 and PIEZO2), which are implicated in mechanically regulated body functions including touch sensation, proprioception, lung inflation, and blood pressure regulation. Using reporter mice expressing PIEZO1-tdTomato, we find that PIEZO1 is expressed in the kidneys, ureters, bladder, and urethra, as well as organs in close proximity including the prostate, seminal vesicles and ducts, ejaculatory ducts, and the vagina. We further find that PIEZO1 expression is not limited to one cell type: it is observed in the endothelial and parietal cells of the renal corpuscle, the basolateral surfaces of many of the epithelial cells that line the urinary tract, the interstitial cells of the bladder and ureters, and populations of smooth and striated muscle cells. We propose that in the urinary tract PIEZO1 likely functions as a mechanosensor that triggers responses to wall tension.
The Relationship between Nutrient Patterns and Bone Mineral Density in Postmenopausal Women

In women, the menopausal transition is characterized by acid-base imbalance, estrogen deficiency and rapid bone loss. Research into nutritional factors that influence bone health is therefore necessary. In this study, the relationship between nutrient patterns and nutrients important for bone health with bone mineral density (BMD) was explored. In this cross-sectional analysis, 101 participants aged between 54 and 81 years were eligible. Body composition and BMD analyses were performed using dual-energy X-ray absorptiometry (DXA). Nutrient data were extracted from a 3-day diet diary (3-DDD) using Foodworks 9 and metabolic equivalent (MET-minutes) was calculated from a self-reported New Zealand physical activity questionnaire (NZPAQ). Significant positive correlations were found between intakes of calcium (p = 0.003, r = 0.294), protein (p = 0.013, r = 0.246), riboflavin (p = 0.020, r = 0.232), niacin equivalent (p = 0.010, r = 0.256) and spine BMD. A nutrient pattern high in riboflavin, phosphorus and calcium was significantly positively correlated with spine (p < 0.05, r = 0.197) and femoral neck BMD (p < 0.05, r = 0.213), while the nutrient pattern high in vitamin E, α-tocopherol, β-carotene and omega 6 fatty acids was negatively correlated with hip (p < 0.05, r = −0.215) and trochanter BMD (p < 0.05, r = −0.251). These findings support the hypothesis that a nutrient pattern high in the intake of vitamin E, α-tocopherol and omega 6 fatty acids appears to be detrimental for bone health in postmenopausal women.
The modulation of endometriosis by lncRNA MALAT1 via NF-κB/iNOS.

OBJECTIVE Endometriosis (Ems) is one benign disorder that frequently leads to chronic pelvic pain, dysmenorrhea or even infertility. Featured as the ectopic growth of active endometrial tissues on tissues beyond the muscular layer, Ems has complicated pathogenesis mechanisms that are not fully illustrated. Long non-coding (lnc) RNA MALAT1 participates in various biological activities, including cell growth, proliferation, apoptosis, organogenesis, inflammation, and tumors. However, its expression and function in Ems are not clear yet. PATIENTS AND METHODS Real-time PCR measured differential expression of MALAT1 in normal and ectopic endometrial tissues. Cultured endometrial cells were transfected with siRNA for MALAT1, whose expression was measured by real-time PCR. MTT assay measured endometrial cell proliferation, whose invasion was measured by transwell assay. Western blot tested the expression and NF-κB/iNOS, and MMP9 proteins. RESULTS LncRNA MALAT1 showed upregulation in ectopic endometrial tissues (p<0.05 comparing to control group). Transfection of MALAT1 siRNA suppressed its expression in endometrial cells, inhibited cell proliferation or invasion, enhanced caspase 3 activity, decreased NF-κB/iNOS or MMP-9 expression (p<0.05 comparing to control group). CONCLUSIONS LncRNA MALAT1 can facilitate endometrial cell apoptosis and modulate MMP-9 expression via NF-κB/iNOS pathway, thus, mediating Ems pathogenesis.
A comparison of voluntary and involuntary measures of electromechanical delay.

Electromechanical delay (EMD) is a measurement used to assess the mechanical lag between muscle activation onset and force production. EMD measurements may be performed by voluntary or electrically evoked muscle activation. This study compared gastrocnemius EMD during voluntary and involuntary contractions and assessd the intrasession reliability of each set of measurements. Subjects were 15 volunteers (age 21 +/- 2 years, ht 171.8 +/- 10.0 cm, mass 76.1 +/- 13.4 kg). EMD measurements were recorded from the medial head of the gastrocnemius of each subject during voluntary and involuntary contractions. Order was counterbalanced between subjects. Subjects stood with the dominant leg on a force plate, the nondominant next to the force plate, and with their hands in contact with a bar in front of them. A supramaximal percutaneous stimulus was applied to the tibial nerve in the popliteal fossa for involuntary (electrically evoked) contractions. For voluntary contractions, subjects were instructed to rise up on the toes as quickly as possible. Four trials were collected for each condition with 30 s of rest between each. Repeated measures ANOVAs were performed for each condition to calculate an ICC (2,1). Means of the 4 trials for each condition were used to detect differences between groups. EMD was greater in the voluntary condition (22.8 +/- 8.2 ms) compared to the involuntary condition (9.7 +/- 3.1 ms; p < .001). Intrasession reliability for each condition was very strong (involuntary ICC (2,1) = . 977; voluntary ICC (2,1) = . 972). EMD measured during a single leg stance is much shorter when measured during an electrically evoked (voluntary) contraction. The difference in EMD between conditions is likely the result of differences in recruitment during the two types of contractions. Reliability within a measurement session was very strong for each of the conditions.
Single-Session Manualized Ego State Therapy (EST) for Combat Stress Injury, PTSD, and ASD, Part 1: The Theory

Abstract Ego state therapy (EST) evolved from a psychodynamic understanding of personality as a product of an individual's ego states to a conceptualization of how ego-energized and object-energized elements are bound together to cope with a traumatic event. Neurobiological studies now substantiate Watkins's war neuroses conceptualizations. Because of their severity, trauma memories are encoded in the subcortical-subconscious brain regions that are accessed by the single-session manualized EST procedure but not by the popular cognitive-behavioral management therapies. The imprint of the trauma is not accessible or resolvable by such top-down verbal understanding or reframing; EST is a bottom-up therapy. Abreactive hypnosis facilitates ego state expression at physiologically and psychologically intense levels sufficient to activate subcortical processes to release affect in the presence of the therapist, who adds ego strength to the patient. This is followed by interpretation and reintegration. The result is a reconstructed personality that is adaptive and resilient.
Broadband Absorption Tailoring of SiO2/Cu/ITO Arrays Based on Hybrid Coupled Resonance Mode

Sub-wavelength artificial photonic structures can be introduced to tailor and modulate the spectrum of materials, thus expanding the optical applications of these materials. On the basis of SiO2/Cu/ITO arrays, a hybrid coupled resonance (HCR) mechanism, including the epsilon-near-zero (ENZ) mode of ITO, local surface plasmon resonance (LSPR) mode and the microstructural gap resonance (GR) mode, was proposed and researched by systematically regulating the array period and layer thickness. The optical absorptions of the arrays were simulated under different conditions by the finite-difference time-domain (FDTD) method. ITO films were prepared and characterized to verify the existence of ENZ mode and Mie theory was used to describe the LSPR mode. The cross-sectional electric field distribution was analyzed while SiO2/Cu/ITO multilayers were also fabricated, of which absorption was measured and calculated by Macleod simulation to prove the existence of GR and LSPR mode. Finally, the broad-band tailoring of optical absorption peaks from 673 nm to 1873 nm with the intensities from 1.8 to 0.41 was realized, which expands the applications of ITO-based plasmonic metamaterials in the near infrared (NIR) region.
Leishmania infantum induces expression of the negative regulatory checkpoint, CTLA‐4, by human naïve CD8+ T cells

CD8+ T cells are important in mediating protective responses to intracellular pathogens. However, an uncontrolled response may lead to pathology. The role of CD8+ T cells in different clinical manifestations of human leishmaniasis is controversial and poorly understood. We aim to study the response of CD8+ T cells to the first exposure to different strains of Leishmania, seeking to correlate these findings with clinical manifestations of disease.
MiR-455-3p, miR-150 and miR-375 are aberrantly expressed in salivary gland adenoid cystic carcinoma and polymorphous adenocarcinoma.

BACKGROUND Adenoid cystic carcinoma (AdCC) and polymorphous adenocarcinoma (PAC) are included among the most common salivary gland cancers. They share clinical and histological characteristics, making their diagnosis challenging in specific cases. MicroRNAs (miRNA) are short, non-coding RNA sequences of 19-25 nucleotides in length that are involved in post-transcriptional protein expression. They have been shown to play important roles in neoplastic and non-neoplastic processes and have been suggested as diagnostic and prognostic markers. METHODS This study, using quantitative RT-PCR, investigated miR-150, miR-455-3p and miR-375 expression, in order to identify a possible molecular distinction between AdCC and PAC. RESULTS miRNA-150 and miRNA-375 expression was significantly decreased in AdCC and PAC compared with salivary gland tissue controls, whilst miRNA-455-3p showed significantly increased expression in AdCC when compared to PAC, (P < 0.05). miR-150, miR-357 and miR-455-3p expression in AdCC, PAC and control was not associated with age, gender nor with anatomic site (major and minor salivary glands) (P > 0.05). CONCLUSION MiR-455-3p could be used as a complimentary tool in the diagnosis of challenging AdCC cases.