Miracle-dz/UniFAR-FTUs huggingface dataset:
An Evolutionary-Conserved Function of Mammalian Notch Family Members as Cell Adhesion Molecules

Notch family members were first identified as cell adhesion molecules by cell aggregation assays in Drosophila studies. However, they are generally recognized as signaling molecules, and it was unclear if their adhesion function was restricted to Drosophila. We previously demonstrated that a mouse Notch ligand, Delta-like 1 (Dll1) functioned as a cell adhesion molecule. We here investigated whether this adhesion function was conserved in the diversified mammalian Notch ligands consisted of two families, Delta-like (Dll1, Dll3 and Dll4) and Jagged (Jag1 and Jag2). The forced expression of mouse Dll1, Dll4, Jag1, and Jag2, but not Dll3, on stromal cells induced the rapid and enhanced adhesion of cultured mast cells (MCs). This was attributed to the binding of Notch1 and Notch2 on MCs to each Notch ligand on the stromal cells themselves, and not the activation of Notch signaling. Notch receptor-ligand binding strongly supported the tethering of MCs to stromal cells, the first step of cell adhesion. However, the Jag2-mediated adhesion of MCs was weaker and unlike other ligands appeared to require additional factor(s) in addition to the receptor-ligand binding. Taken together, these results demonstrated that the function of cell adhesion was conserved in mammalian as well as Drosophila Notch family members. Since Notch receptor-ligand interaction plays important roles in a broad spectrum of biological processes ranging from embryogenesis to disorders, our finding will provide a new perspective on these issues from the aspect of cell adhesion.
An Integrated mRNA and microRNA Expression Signature for Glioblastoma Multiforme Prognosis

Although patients with Glioblastoma multiforme (GBM) have grave prognosis, significant variability in patient outcome is observed. The objective of this study is to identify a molecular signature for GBM prognosis. We subjected 355 mRNA and microRNA expression profiles to elastic net-regulated Cox regression for identification of an integrated RNA signature for GBM prognosis. A prognostic index (PI) was generated for patient stratification. Survival comparison was conducted by Kaplan-Meier method and a general multivariate Cox regression procedure was applied to evaluate the independence of the PI. The abilities and efficiencies of signatures to predict GBM patient outcome was assessed and compared by the area under the curve (AUC) of the receiver-operator characteristic (ROC). An integrated RNA prognostic signature consisted by 4 protective mRNAs, 12 risky mRNAs, and 1 risky microRNA was identified. Decreased survival was associated with being in the high-risk group (hazard ratio = 2.864, P<0.0001). The prognostic value of the integrated signature was validated in five independent GBM expression datasets (n = 201, hazard ratio = 2.453, P<0.0001). The PI outperformed the known clinical factors, mRNA-only, and miRNA-only prognostic signatures for GBM prognosis (area under the ROC curve for the integrated RNA, mRNA-only, and miRNA-only signatures were 0.828, 0.742, and 0.757 at 3 years of overall survival, respectively, P<0.0001 by permutation test). We describe the first, to our knowledge, robust transcriptome-based integrated RNA signature that improves the current GBM prognosis based on clinical variables, mRNA-only, and miRNA-only signatures.
Comparison of Real-Time Water Proton Spectroscopy and Echo-Planar Imaging Sensitivity to the BOLD Effect at 3 T and at 7 T

Gradient-echo echo-planar imaging (GE EPI) is the most commonly used approach to assess localized blood oxygen level dependent (BOLD) signal changes in real-time. Alternatively, real-time spin-echo single-voxel spectroscopy (SE SVS) has recently been introduced for spatially specific BOLD neurofeedback at 3 T and at 7 T. However, currently it is not known how neurofeedback based on real-time SE SVS compares to real-time GE EPI-based. We therefore compared both methods at high (3 T) and at ultra-high (7 T) magnetic field strengths. We evaluated standard quality measures of both methods for signals originating from the motor cortex, the visual cortex, and for a neurofeedback condition. At 3 T, the data quality of the real-time SE SVS and GE EPI R2* estimates were comparable. At 7 T, the data quality of the real-time GE EPI acquisitions was superior compared to those of the real-time SE SVS. Despite the somehow lower data quality of real-time SE SVS compared to GE EPI at 7 T, SE SVS acquisitions might still be an interesting alternative. Real-time SE SVS allows for a direct and subject-specific T2* estimation and thus for a physiologically more plausible neurofeedback signal.
Technological properties of glulam beams made from hydrothermally treated poplar wood

ABSTRACT In this research, technological properties of glulam beams made from hydrothermally treated poplar (Populus deltoides) wood were investigated. Poplar wood blocks with dimensions of 6 (r) × 10 (t) × 73 (l) cm3 were cut and hydrothermally treated in a stainless steel reactor at temperatures of 140 and 160°C for a holding time of 30 min. The treated wood blocks were initially air seasoned and then they were dried in a semi-pilot scale vacuum dryer to achieve moisture content (MC) of 12%. Conditioning of the treated and the untreated wood blocks was done prior to adhesive bonding. Afterwards the glulam beams (4 ply) were manufactured using polyurethane. In order to evaluate the physico-mechanical properties of the beams, density, equilibrium moisture content, water repellent effect (WRE), anti-swelling effect (ASE), mass loss (ML), wettability as well as surface roughness due to the hydrothermal treatment were determined in the treated wood and delamination, bond shear strength, tensile strength, MC and moisture-induced stresses as well as strains in cross-section of the beams were determined in the glulam beams. The results revealed that density, ML, ASE, WRE, modulus of elasticity, modulus of rupture and delamination were increasing and the others were decreased due to the hydrothermal treatment.
CRF grant “ Molecular study of lysosomal transporters involved in the cystine-depleting effect of cysteamine ”

The long-term objective of this grant is to identify the membrane transporters underlying the cystine-depleting effect of cysteamine as this would provide a rationale to improve its efficiency or discover more efficient, better tolerated drugs. According to the current model of cysteamine therapy, cystine depletion is mediated by an unknown cationic amino acid transporter, which exports a mixed disulfide of cysteine and cysteamine from the lysosomal lumen.
On the location-dependent quality of the sensor pattern noise and its implication in multimedia forensics

Due to its uniqueness and potential in forensic applications, the sensor pattern noise (SPN) has drawn much attention in the digital forensic community and academia in the past few years. While much work has been done on the application of the SPN, little investigation into its characteristics has been reported in the literature. It is our intention to fill this gap by providing insight into the dependency of the SPN quality on the location in images. We have observed that the SPN components at the image periphery are distorted to the extent that when used for source camera identification, they tend to cause higher false positive rates. Empirical evidence is presented in this work. We suspect that this location-dependent SPN quality degradation has strong connection with the vignetting effect as they exhibit the same type of location-dependency. We recommend that when image blocks are to be used for forensic investigation, they should be taken from the image centre before SPN extraction is performed in order to reduce false positive rate. (6 pages)
Mapping the wavelet transform onto silicon: the dynamic translinear approach

In this paper, an analog implementation of the wavelet transform (WT) is presented. The circuit is based on the dynamic translinear (DTL) circuit technique and implements, by means of cascade connected complex first order systems, an analog filter whose impulse response is a Gabor function, a function most widely used for frequency analysis among wavelet functions. From simulations, it is demonstrated that we can scale and shift in time and frequency by simply controlling the capacitance or the control current values. The main advantage of this DTL implementation is its low-power consumption. The circuit operates from a 1 V supply voltage and a bias current of 1 /spl mu/A.
PhosphoPICK‐SNP: quantifying the effect of amino acid variants on protein phosphorylation

Motivation: Genome‐wide association studies are identifying single nucleotide variants (SNVs) linked to various diseases, however the functional effect caused by these variants is often unknown. One potential functional effect, the loss or gain of protein phosphorylation sites, can be induced through variations in key amino acids that disrupt or introduce valid kinase binding patterns. Current methods for predicting the effect of SNVs on phosphorylation operate on the sequence content of reference and variant proteins. However, consideration of the amino acid sequence alone is insufficient for predicting phosphorylation change, as context factors determine kinase‐substrate selection. Results: We present here a method for quantifying the effect of SNVs on protein phosphorylation through an integrated system of motif analysis and context‐based assessment of kinase targets. By predicting the effect that known variants across the proteome have on phosphorylation, we are able to use this background of proteome‐wide variant effects to quantify the significance of novel variants for modifying phosphorylation. We validate our method on a manually curated set of phosphorylation change‐causing variants from the primary literature, showing that the method predicts known examples of phosphorylation change at high levels of specificity. We apply our approach to data‐sets of variants in phosphorylation site regions, showing that variants causing predicted phosphorylation loss are over‐represented among disease‐associated variants. Availability and Implementation: The method is freely available as a web‐service at the website http://bioinf.scmb. uq.edu. au/phosphopick/snp Contact: m.boden@uq.edu. au Supplementary information: Supplementary data are available at Bioinformatics online.
Novel MSH2 splice-site mutation in a young patient with Lynch syndrome

Lynch Syndrome (LS) is associated with germline mutations in one of the mismatch repair (MMR) genes, including MutL homolog 1 (MLH1), MutS homolog 2 (MSH2), MSH6, PMS1 homolog 2, mismatch repair system component (PMS2), MLH3 and MSH3. The mutations identified in MMR genes are point mutations or large rearrangements. The point mutations are certainly pathogenetic whether they determine formation of truncated protein. The mutations that arise in splice sites are classified as ‘likely pathogenic’ variants. In the present study, a novel splicing mutation was identified, (named c.212-1g>a), in the MSH2 gene. This novel mutation in the consensus splice site of MSH2 exon 2 leads to the loss of the canonical splice site, without skipping in-frame of exon 2; also with the formation of 2 aberrant transcripts, due to the activation of novel splice sites in exon 2. This mutation was identified in a young patient who developed colon cancer at the age of 26 years and their belongs to family that met the ‘Revised Amsterdam Criteria’. The present study provided insight into the molecular mechanism determining the pathogenicity of this novel MSH2 mutation and it reaffirms the importance of genetic testing in LS.
Modeling Risk-Factor Trajectories When Measurement Tools Change Sequentially During Follow-up in Cohort Studies: Application to Dietary Habits in Prodromal Dementia

Modeling risk-factor trajectories is critical to understanding the natural history of diseases, yet the measurement tools used to assess risk factors often evolve during follow-up in cohorts, and such change prevents longitudinal analyses using standard models. We addressed this issue with a latent process model. Trajectories of average intakes of 5 food families (fish, meat, fruits, vegetables, and carbohydrate-rich foods) were described in prodromal dementia during the 10 years prior to diagnosis of cases and compared with those of controls, using a case-control sample nested within the Three-City Study, Bordeaux, France (1999-2012). Food intakes were measured by 2 or 3 different subquestionnaires across 5 repeated food frequency questionnaires. The sample comprised 205 incident cases and 410 controls matched for age, sex, education, and number of repeated food frequency questionnaires. Intakes of fish, fruits, and vegetables decreased at the approach of diagnosis among cases, suggesting reverse causation. This study demonstrated that the latent process model approach constitutes a powerful framework for modeling risk-factor trajectories, even when measurement tools change sequentially over time. Coupled with a case-control approach to contrast trajectories in prodromal disease versus healthy status, it can help us to understand the dynamic, causal relationships between risk factors and diseases.
Rapid in vitro regeneration of Gerbera jamesonii (H. Bolus ex Hook. f.) from different explants

Rapid in vitro multiplication of shoots has been described using capitular sections and leaf explants in Gerbera jamesonii. Three types of basal media regimes were used including MS and two of its modified forms⎯MSI and MSA. Shoot induction was achieved on all three regimes but MSI medium supplemented with Kn (4 mg/l) and IAA (0.5 mg/l) was ideal for shoot bud initiation (8-11) from capitular sections and Kn (4 mg/l) and IAA (0.1 mg/l) from leaves (5-8 shoot buds). MSI medium with 2 mg/l Kn+0.5 mg/l PAA was used for rapid multiplication of organogenic callus; 20-25 shoot buds developed from this callus. Rooting of in vitro shoots was achieved on MS medium with 0.5 mg/l IAA. Plantlets were transferred to pots where they matured and flowered.
Effect of thrombopoietin receptor agonists on markers of coagulation and P-selectin in patients with immune thrombocytopenia

Abstract Thrombopoietin-receptor-agonists (TPO-RA) are effective treatments of immune thrombocytopenia (ITP). Previous long-term TPO-RA clinical trials have shown that thrombotic events occurred in 6% of TPO-RA-treated ITP patients. To explore the increased risk of thrombosis, the effects of TPO-RA on markers of coagulation and P-selectin were studied. The study comprised two ITP cohorts and controls. Cohort 1 included 26 patients with sequential samples acquired before and during treatment with TPO-RA. Cohort 2 included a single sample in 18 patients on TPO-RA for more than one year. Thrombin generation (endogenous thrombin potential (ETP)) prothrombin fragments 1 + 2 (F1+2), D-dimer, and plasminogen-activator-inhibitor-1 (PAI-1) were measured as well as soluble P-selectin (sP-selectin). Sequential expression of encoding genes for P-selectin (SELP) and PAI-1 (SERPINE1) was determined in four patients in cohort 1. Significantly higher levels of F1+2, D-dimer, and PAI-1 were found in ITP patients before TPO-RA treatment and in patients on long-term TPO-RA treatment than in controls. Pre-treatment levels of sP-selectin did not differ from controls. Analysis of longitudinal trends showed an increase in platelet count, sP-selectin, and PAI-1 after initiation of TPO-RA, followed by gradual decline. Platelet count and sP-selectin remained at higher levels throughout the study, whereas PAI-1 did not. Levels of other studied parameters did not show significant changes after initiation of treatment. Expression of SELP was up-regulated after initiation of TPO-RA, while the expression of SERPINE1 showed no significant changes. In conclusion, elevated pre-treatment levels of F1+2, D-dimer and PAI-1 are compatible with ITP being an intrinsically pro-thrombotic condition. After TPO-RA treatment, there were no significant changes in markers of coagulation activation or fibrinolysis, except for an initial increase in PAI-1 and a significant increase in sP-selectin both of which may contribute to increased thrombotic risk associated with TPO-RA treatment in ITP.
EMBRYO SEXING IN CATTLE : REVIEW

Predetermination of sex is of commercial importance since economic value of each livestock species is different for different sex. Embryo sexing enables the producers to run a fewer recipient female and thus quickly increase the size of their herd. The widespread use of embryo transfer technology has created an alternative approach in controlling the sex of offspring. The methods used can be grouped under two main categories: invasive and non-invasive. The latter is generally considered optimal, since embryonic integrity is maintained and the capacity for normal development should be optimized. Non-invasive sexing, however, is not as accurate as invasive techniques and recent advances in DNA probing have minimized the losses in embryonic viability inherent in all invasive techniques. With recent progress in molecular biology, more rapid and reliable embryo sexing techniques are being evolved like PCR (Polymerase Chain Reaction) and fluorescent in-situ hybridization (FISH). A routine method of embryo sexing must include an accurate sexing procedure and survival of embryos. Sexing methods must also be easy to use and inexpensive to operate. The dairy industry eagerly awaits the perfection of this scientific advancement. The sexing of embryo is likely to find a widespread application in embryo transfer industry in near future.
Relationship of Aortic Wall Distensibility to Mitral and Aortic Valve Calcification: The Multi-Ethnic Study of Atherosclerosis

Data are limited on whether valvular calcification is associated with aortic wall stiffness. We tested whether aortic valve calcification (AVC) and/or mitral valve calcification (MVC) is inversely associated with aortic distensibility (AD). Cross-sectional study conducted in a subset of the Multi-Ethnic Study of Atherosclerosis (MESA) included 3676 MESA participants aged 44 to 84 years with AD measured with magnetic resonance imaging and with AVC and MVC measured with noncontrast cardiac computed tomography scans. Both AVC and MVC were divided into 3 categories: zero, < median values (low), and ≥ median values (high) for patients with nonzero values. Overall, 88% (n = 3256) and 92% (n = 3365) of participants had zero AVC and MVC, while 6% (n = 211) and 4% (n = 156) had low, and 6% (n = 209) and 4% (n = 155) had high values of AVC and MVC, respectively. The AVC was independently associated with AD after adjusting for age, gender, and ethnicity (P = .035). No association was noted between AVC groups and AD after adjustment for all covariates or MVC groups and AD in any model.
Clinical relevance of the primary findings of the MTA: success rates based on severity of ADHD and ODD symptoms at the end of treatment.

OBJECTIVES To develop a categorical outcome measure related to clinical decisions and to perform secondary analyses to supplement the primary analyses of the NIMH Collaborative Multisite Multimodal Treatment Study of Children With Attention-Deficit/Hyperactivity Disorder (MTA). METHOD End-of-treatment status was summarized by averaging the parent and teacher ratings of attention-deficit/hyperactivity disorder and oppositional defiant disorder symptoms on the Swanson, Nolan, and Pelham, version IV (SNAP-IV) scale, and low symptom-severity ("Just a Little") on this continuous measure was set as a clinical cutoff to form a categorical outcome measure reflecting successful treatment. Three orthogonal comparisons of the treatment groups (combined treatment [Comb], medication management [MedMgt], behavioral treatment [Beh], and community comparison [CC]) evaluated hypotheses about the MTA medication algorithm ("Comb + MedMgt versus Beh + CC"), multimodality superiority ("Comb versus MedMgt"), and psychosocial substitution ("Beh versus CC"). RESULTS The summary of SNAP-IV ratings across sources and domains increased the precision of measurement by 30%. The secondary analyses of group differences in success rates (Comb = 68%; MedMgt = 56%; Beh = 34%; CC = 25%) confirmed the large effect of the MTA medication algorithm and a smaller effect of multimodality superiority, which was now statistically significant (p < .05). The psychosocial substitution effect remained negligible and nonsignificant. CONCLUSION These secondary analyses confirm the primary findings and clarify clinical decisions about the choice between multimodal and unimodal treatment with medication.
Epidural fibrosis post laminectomy is the unappreciated cause of spinal cord compression post chronic spinal cord injury

Spinal cord injury is the result of extreme trauma to the spinal cord. The trauma often results in a series of lasting and significant symptoms which reduce patients’ quality of life. In the present research, thirty healthy adult Sprague-Dawley rats were randomly divided into three groups: (1) mild injury group (laminectomy and spinal cord impacting, force value=100 kdyn), (2) severe injury group (laminectomy and spinal cord impacting, force value=200 kdyn), (3) control group (laminectomy only). In order to prove the creation of spinal cord injury and epidural fibrosis within the animal model, BBB score tests were performed weekly and MRI scans were done at 4 weeks post-operation. Macroscopic evaluation and histology were used to evaluate the correlation between spinal cord injury and epidural fibrosis formation. Spinal cord injury can instigate epidural fibrosis. The higher grades of spinal cord injury were associated with more widespread epidural adhesion and greater spinal cord compression. Epidural fibrosis is an unappreciated cause of spinal cord compression post laminectomy in spinal cord injury rats. Epidural scarring has been noted to easily form in spinal cord injury model rats. The present study suggests the necessity of preventing epidural fibrosis post-surgery in patients with spinal cord injury.
Single-shot autocorrelator for KrF subpicosecond pulses based on two-photon fluorescence of cadmium vapor at lambda = 508 nm.

By excitation of cadmium vapor with a high-peak-power KrF excimer laser pulse, fluorescence of an atomic transition at lambda = 508 nm is induced by a two-photon ionization process followed by fast recombination. The nonlinear response of the medium is used to develop a simple single-shot autocorrelator for subpicosecond KrF excimer laser pulses operating down to intensities of less than 10(9)W/cm. (2) We have measured 360-fs (FWHM) pulses at lambda = 248 nm with a time resolution of 15 fs.
Color stability of aesthetic composite restoration using LED and halogen light cure

Aim: To determine color stability of two different composites resins with same shade using LED and halogen light cure upon exposure to different types of staining media. Methods: The colors of all specimens before and after storage in the solutions were measured by a spectrophotometer based on CIE Lab system, and the color differences thereby calculated. Data were analyzed by two-way analysis of variance (ANOVA) and Scheffe’s post hoc test. Results: Overall, the highest ΔE was observed with Z350 material, halogen light cure, mustard staining media, and at 30 days time. There was statistically significant mean difference (ΔE) between all the staining media except between ketchup and distilled water. Similarly, a statistically significant mean difference (ΔE) was found between all time periods except between one day and baseline. Conclusion: It can be concluded that all staining media used in this study affected the color stability of the tested materials with time. Further studies with longer period of aging are warranted by the findings of this study.