Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fused Protein Kinase Regulates Hedgehog-stimulated Transcriptional Activation in Drosophila Schneider 2 Cells*

The Drosophila segment polarity genefused encodes a putative protein-serine/threonine kinase, and plays a critical role in the signal transduction for Hedgehog (Hh)-dependent gene expression. We show that theDrosophila Schneider 2 (S2) cell line has the potential to transduce the Hh-triggered intracellular signals, leading to the activation of target gene expression, when a transcription factor, Cubitus interruptus (Ci), is provided exogenously. Using S2 cells transfected with the Ci-expressing plasmid and a patchedpromoter reporter construct, we demonstrate that the forced expression of Fused (Fu) stimulates Hh-triggered and Ci-dependent transcriptional activation. The N-terminal kinase domain of Fu is required for this activity, but the C-terminal domain is not. Two kinase-inactive Fu mutants fail to enhance the reporter activation, indicating that the kinase catalytic activity is essential for this function. Negative components of the Hh-signaling pathway, Costal-2 and Suppressor of Fused, strongly antagonize the Fu activity, irrespective of the presence or absence of the Fu C-terminal domain, suggesting an indirect mechanism for the inhibition of Fu by these proteins. Furthermore, mutational analyses of threonine 158 and serine 159, in the activation segment of the Fu protein kinase, indicate that threonine 158 is essential for Fu activity and that phosphorylation of this threonine residue may be involved in the activation of the kinase catalytic activity upon Hh stimulation.
Splicing factor SF2/ASF rescues IL-2 production in T cells from systemic lupus erythematosus patients by activating IL-2 transcription

T cells from patients with systemic lupus erythematosus (SLE) produce insufficient amounts of the vital cytokine IL-2. We previously showed that SLE T cells express decreased levels of the T-cell receptor–CD3ζ chain and forced expression of CD3ζ into SLE T cells restores IL-2 production. We recently showed that the serine arginine protein splicing factor 2/alternative splicing factor (SF2/ASF) enhances the expression of CD3ζ chain by limiting the production of an unstable splice variant. Here we demonstrate that SF2/ASF levels are decreased in patients with SLE and more so in those with active disease. More importantly, we reveal a function of SF2/ASF, independent of T-cell receptor/CD3 signaling, whereby it is recruited to the IL-2 promoter, increases transcriptional activity, and enhances IL-2 production in SLE T cells. Our results demonstrate that SF2/ASF regulates IL-2 production and that decreased SF2/ASF expression in SLE T cells contributes to deficient IL-2 production.
Detection of lesions in endoscopic video using textural descriptors on wavelet domain supported by artificial neural network architectures

Video processing for classification applications in medical imaging is an area with great importance. In this paper a framework for classification of suspicious lesions using the video produced during an endoscopic session is presented. The proposed approach is based on a feature extraction scheme that uses second order statistical information of the wavelet transformation. These features are used as input to a multilayer feedforward neural network (MFNN) architecture, which has been trained using features of normal and tumor regions. The system uses a limited number of frames with a rather small population of training vectors. The classification results are promising, since the system has been proven to be capable to classify and locate regions, that correspond to lesions with a success of 94 up to 99%, in a sequence of the video-frames. The proposed methodology can be used as a valuable diagnostic tool that may assist physicians to identify possible tumor regions or malignant formations.
Vector field mapping of THz-electromagnetic wave transmitted through quadruple square holes

By using terahertz (THz) time-domain spectroscopy we measured THz-electromagnetic pulse passing through a two-by -two subwavelength hole matrix in near-field regime. Our Fourier analysis of measured data shows detection position dependent transmission maxima with respect to the polarization direction of the incident field. By comparing with numerical simulations based on finite element method, we found that the frequency dependent coupling between the transmitted waves through individual holes leads to different transmission maxima directly above and between holes.
Xenopus fibrinogen: characterization of the mRNAs for the three subunits

We purified and characterized the mRNAs coding for each of the three subunits of Xenopus fibrinogen. Purification was accomplished by electrophoretic separation of liver polyadenylated RNA in a fully denaturing gel, followed by recovery of the RNA from the gel via transfer to an ion-exchange membrane. This procedure yielded fractions which were highly enriched for the mRNAs for each of the fibrinogen chains. The fibrinogen mRNAs were identified by two methods: (i) in vitro translation followed by subunit-specific cleavage with the proteases thrombin and batroxobin; and (ii) cross-hybridization with cDNA clones for individual subunits of rat fibrinogen. The results demonstrate that the A alpha and gamma chains of frog fibrinogen are each coded by a single mRNA species. The A alpha mRNA is ca. 3,100 nucleotides in length, which is nearly twice the minimum size required to code for the A alpha precursor polypeptide. The gamma chain mRNA comprises about 1,600 bases and includes only a small untranslated region. In contrast, the B beta subunit is synthesized from two mRNAs, one of which is 2,500 and the other 1,800 nucleotides long. The 2,500-base mRNA includes a large noncoding region, whereas the smaller one is near the minimum required size. The larger B beta mRNA is ca, fivefold more abundant that the smaller species.
Cloning and Characterization of a Cryptic Haloacid Dehalogenase from Burkholderia cepacia MBA4

ABSTRACT Burkholderia cepacia MBA4 has been shown to produce a single dehalogenase batch culture. Moreover, other cryptic dehalogenases were also detected when the cells were grown in continuous culture. In this paper, we report the cloning and characterization of one of the cryptic dehalogenases in MBA4. This cryptic haloacid dehalogenase, designated Chd1, was expressed constitutively in Escherichia coli. This recombinant Chd1 had a relative molecular weight of 58,000 and existed predominantly as a dimer. The subunits had a relative molecular weight of 27,000. Chd1 exhibited isomer specificity, being active towards thel-isomer of 2-monochloropropionic acid only. The structural gene, chd1, was isolated on a 1.7-kb PstI fragment. This fragment contains a functional promoter, because expression of chd1 in E. coli is orientation independent. The nucleotide sequence of this fragment was determined and characterized. An open reading frame of 840 bp encoding a putative peptide of 280 amino acids was identified. This corresponds closely with the size of the subunit. The nucleotide sequence of chd1 did not show any homology with those of other dehalogenase genes. Comparison of the predicted amino acid sequence, however, shows significant homology, ranging from 42 to 50%, with the amino acid sequences of many other dehalogenases. Chd1 is unusual in having a long leader sequence, a property of periplasmic enzymes.
Longitudinal changes of mtDNA A3243G mutation load and level of functioning in MELAS

Mitochondrial encephalopathy, lactic acidosis, and stroke‐like episodes (MELAS), one of the most common mitochondrial multisystemic diseases, is most commonly associated with an A‐to‐G transition at nucleotide position 3243 (A3243G) in mitochondrial DNA. We studied 34 individuals harboring the A3243G mutation for up to 7 years; 17 had the full MELAS phenotype and 17 who were classified as “carrier relatives” because they were either asymptomatic or had some symptoms suggestive of mitochondrial disease but no seizures or strokes. Using the sensitive real‐time polymerase chain reaction to quantify the A3243G mutation, we confirmed that the percent mutation decreases progressively in DNA isolated from blood: the average percent decrease was 0.5% per year for fully symptomatic patients and 0.2% per year for oligosymptomatic carrier relatives. We also correlated mutant loads with functional status estimated by the Karnofksky score: even though the mutation load decreases, the level of functioning worsens in fully symptomatic patients, whereas the level of functioning of carrier relatives remains largely unchanged. This study suggests that A3243G mutant load in DNA isolated from blood is neither useful for prognosis nor for functional assessment. © 2009 Wiley‐Liss, Inc.
Differences and similarities in explanatory models of hypertension in the United States of america, Tanzania and Jamaica.

BACKGROUND Misperceptions detract from effective disease management in a number of conditions but the nature of underlying illness beliefs and their relative consistency in patients with chronic hypertension (cHTN) who present to the Emergency Department (ED) with poor blood pressure control is not known. OBJECTIVES 1) To explore disease knowledge in ED patients with cHTN using explanatory modelling; and 2) to compare gaps in cHTN knowledge across racially similar but geographically divergent ED patients. METHODS Emergency department patients of African origin with cHTN were recruited from three sites: Detroit Receiving Hospital (DRH - Detroit, MI), the Tanzanian Training Center for International Health (TTCIH - Ifakara, TZ) and the University Hospital of the West Indies (UHWI - Kingston, JA). Demographic and baseline data were collected along with open-ended responses to a series of questions related to cHTN. Qualitative responses were coded into predefined, disease-relevant quantitative domains by two separate, blinded reviewers and multilevel comparisons were performed using Kruskal-Wallis or analysis of variance (ANOVA) tests, where appropriate. RESULTS One hundred and ninety-seven patients were enrolled; mean age (50.5 years vs 51.6 years vs 50.8 years; p = 0.86) and gender distribution (% male: 49.5 vs 44 vs 40; p = 0.53) were similar across sites but patients at DRH (vs TTCIH vs UHWI) were more hypertensive at presentation (mean systolic BP in mmHg: 166.8 vs 153 vs 152.7; p = 0.003), had a longer mean duration of cHTN (12.1 years vs 4.6 years vs 9.1; p < 0.0001), and were less likely to be on antihypertensive therapy (84.5% vs 92% vs 100%, p = 0.001). Explanatory models revealed limited recognition of cHTN as a "disease" (19.6% vs 28% vs 16%; p = 0.31) and consistency in the belief that cHTN was curable (44.3% vs 36% vs 42%; p = 0.62). Stress (48.4% vs 60% vs 50%; p = 0.31) and, especially at DRH, diet (62.2% vs 22% vs 36%; p < 0.0001) were identified most frequently as causes of cHTN and an association with symptoms was common (83.5% vs 98% vs 78%; p = 0.15). Clear differences existed for perceived benefits of treatment and consequences of poor control by site, but in general, both were under-appreciated. CONCLUSIONS Misperceptions related to cHTN are common in ED patients. While specific areas of disconnect exist by geographic region, failure to recognize cHTN as a dire and fixed disease state is consistent, suggesting that a uniform educational intervention may be of benefit in this setting.
A simulated-data adaptation technique for robust speech recognition

This paper proposes an efficient acoustic model adaptation method based on the use of simulated-data in maximum likelihood linear regression (MLLR) adaptation for robust speech recognition. Online MLLR adaptation is an unsupervised process which requires an input speech with phone labels transcribed automatically. Instead of using only the input signal in adaptation, our proposed simulated data method increases the size of adaptation data by adding noise portions extracted from the input speech to a set of pre-recorded clean speech, whose correct transcriptions are known. Various configurations of the proposed method are explored. Evaluations are performed with both additive and real noisy speech. The experimental results show that the proposed system achieves higher recognition rate than the system using only the input speech in adaptation and the system using a multi-conditioned acoustic model.
Nanocarbons in Electrospun Polymeric Nanomats for Tissue Engineering: A Review

Electrospinning is a versatile process technology, exploited for the production of fibers with varying diameters, ranging from nano- to micro-scale, particularly useful for a wide range of applications. Among these, tissue engineering is particularly relevant to this technology since electrospun fibers offer topological structure features similar to the native extracellular matrix, thus providing an excellent environment for the growth of cells and tissues. Recently, nanocarbons have been emerging as promising fillers for biopolymeric nanofibrous scaffolds. In fact, they offer interesting physicochemical properties due to their small size, large surface area, high electrical conductivity and ability to interface/interact with the cells/tissues. Nevertheless, their biocompatibility is currently under debate and strictly correlated to their surface characteristics, in terms of chemical composition, hydrophilicity and roughness. Among the several nanofibrous scaffolds prepared by electrospinning, biopolymer/nanocarbons systems exhibit huge potential applications, since they combine the features of the matrix with those determined by the nanocarbons, such as conductivity and improved bioactivity. Furthermore, combining nanocarbons and electrospinning allows designing structures with engineered patterns at both nano- and microscale level. This article presents a comprehensive review of various types of electrospun polymer-nanocarbon currently used for tissue engineering applications. Furthermore, the differences among graphene, carbon nanotubes, nanodiamonds and fullerenes and their effect on the ultimate properties of the polymer-based nanofibrous scaffolds is elucidated and critically reviewed.
The Border Between the Ultrabithorax and abdominal-A Regulatory Domains in the Drosophila Bithorax Complex

The bithorax complex in Drosophila melanogaster includes three homeobox-containing genes—Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B)—which are required for the proper differentiation of the posterior 10 segments of the body. Each of these genes has multiple distinct regulatory regions; there is one for each segmental unit of the body plan where the genes are expressed. One additional protein- coding gene in the bithorax complex, Glut3, a sugar-transporter homolog, can be deleted without phenotype. We focus here on the upstream regulatory region for Ubx, the bithoraxoid (bxd) domain, and its border with the adjacent infraabdominal-2 (iab-2) domain, which controls abdA. These two domains can be defined by the phenotypes of rearrangement breakpoints, and by the expression patterns of enhancer traps. In D. virilis, the homeotic cluster is split between Ubx and abd-A, and so the border can also be located by a sequence comparison between species. When the border region is deleted in melanogaster, the flies show a dominant phenotype called Front-ultraabdominal (Fub); the first abdominal segment is transformed into a copy of the second abdominal segment. Thus, the border blocks the spread of activation from the bxd domain into the iab-2 domain.
Self-supervised Product Feature Extraction using a Knowledge Base and Visual Clues

This paper presents a novel approach to extract product features from large e-commerce web sites. Starting from a small set of rendered product web pages (typically 5 to 10) and a sample of their corresponding features, the proposed method automatically produces labeled examples. Those examples are then used to induce extraction rules which are finally applied to extract new product features from unseen web pages. We have carried out an evaluation on 10 major French e-commerce web sites (roughly 1 000 web pages) and have reported promising results. Moreover, experiments have shown that our method can handle web site template changes without human intervention.
Effects of noise reduction on speech intelligibility

On percoit souvent la parole en presence de bien d’autres sons. Parfois les interferences sonores atteignent des niveaux tellement eleves que la parole devient inintelligible. Les methodes de renforcement de la parole tentent de reduire les bruits ambiants, mais on en sait tres peu sur l’effet qu’elles produisent sur l’intelligibilite de la parole. Cette these explore les effets des methodes de renforcement de la parole, aussi appelees algorithmes de suppression du bruit, sur la l’intelligibilite.Apres une breve introduction sur les notions de renforcement de la parole et d’intelligibilite, on presente trois etudes qui abordent les effets de ces methodes d’un point de vue empirique. On demontre que le resultat de la suppression du bruit tend a reduire l’intelligibilite et que cet effet est constant pour une grande variete de niveaux sonores. Quand on fait appel a des experts pour mettre en place un systeme commercial de suppression du bruit dans le but d’ameliorer l’intelligibilite, ils proposent des reglages qui degradent l’intelligibilite. Les profanes percoivent bien une amelioration de l’intelligibilite qui resulte des methodes de renforcement de la parole.Trois autres etudes subsequentes tentent de preciser les proprietes du signal, qui ont des effets sur l’intelligibilite et qui sont genere par les methodes de renforcement de la parole. Des metriques physiques basees sur differentes proprietes du signal ont ete utilisees pour estimer l’intelligibilite de la parole renforcee. La plupart de ces mesures fournissent des estimations peu fiables ou biaisees de l’intelligibilite absolue.
Visualizing code profiling line oriented statistics

A visualization technique that makes it possible to display and analyze line count profile data is described. The technique is to make a reduced picture of code with the line execution counts identified with color. Hot spots are shown in red, warm spots in orange, and so on. It is possible to identify nonexecuted code and nonexecutable code such as declarations and static tables. <<ETX>>
Low Level Features for Quality Assessment of Facial Images

An automated system that provides feedback about aesthetic quality of facial pictures could be of great interest for editing or selecting photos. Although image aesthetic quality assessment is a challenging task that requires understanding of subjective notions, the proposed work shows that facial image quality can be estimated by using low-level features only. This paper provides a method that can predict aesthetic quality scores of facial images. 15 features that depict technical aspects of images such as contrast, sharpness or colorfulness are computed on different image regions (face, eyes, mouth) and a machine learning algorithm is used to perform classification and scoring. Relevant features and facial image areas are selected by a feature ranking technique, increasing both classification and regression performance. Results are compared with recent works, and it is shown that by using the proposed low-level feature set, the best state of the art results are obtained.
Cathepsin E enhances anticancer activity of doxorubicin on human prostate cancer cells showing resistance to TRAIL-mediated apoptosis

Abstract We previously described that cathepsin E specifically induces growth arrest and apoptosis in several human prostate cancer cell lines in vitro by catalyzing the proteolytic release of soluble tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) from the tumor cell surface. It also prevents tumor growth and metastasis in vivo through multiple mechanisms, including induction of apoptosis, angiogenesis inhibition and enhanced immune responses. Using the prostate cancer cell line PPC-1, which is relatively resistant to cell death by doxorubicin (40–50% cytotoxicity), we first report that a combination treatment with cathepsin E can overcome resistance of the cells to this agent. In vitro studies showed that combined treatment of PPC-1 cells with the two agents synergistically induces viability loss, mainly owing to down-regulation of a short form of the FLICE inhibitory protein FLIP. The enhanced antitumor activity was corroborated by in vivo studies with athymic mice bearing PPC-1 xenografts. Intratumoral application of cathepsin E in doxorubicin-treated mice results in tumor cell apoptosis and tumor regression in xenografts by enhanced TRAIL-induced apoptosis through doxorubicin-induced c-FLIP down-regulation and by a decrease in tumor cell proliferation. These results indicate that combination of cathepsin E and doxorubicin is sufficient to overcome resistance to TRAIL-mediated apoptosis in chemoresistant prostate cancer PPC-1 cells, thus indicating therapeutic potential for clinical use.
Spaceflight-Relevant Challenges of Radiation and/or Reduced Weight Bearing Cause Arthritic Responses in Knee Articular Cartilage

There is little known about the effect of both reduced weight bearing and exposure to radiation during spaceflight on the mechanically-sensitive cartilage lining the knee joint. In this study, we characterized cartilage damage in rat knees after periods of reduced weight bearing with/without exposure to solar-flare-relevant radiation, then cartilage recovery after return to weight bearing. Male Sprague Dawley rats (n = 120) were either hindlimb unloaded (HLU) via tail suspension or remained weight bearing in cages (GROUND). On day 5, half of the HLU and GROUND rats were 1 Gy total-body X-ray irradiated during HLU, and half were sham irradiated (SHAM), yielding 4 groups: GROUND-SHAM; GROUND-IR; HLU-SHAM; and HLU-IR. Hindlimbs were collected from half of each group of rats on day 13. The remaining rats were then removed from HLU or remained weight bearing, and hindlimbs from these rats were collected on day 62. On day 13, glycosaminoglycan (GAG) content in cartilage lining the tibial plateau and femoral condyles of HLU rats was lower than that of the GROUND animals. Likewise, on day 13, immunoreactivity of the collagen type II-degrading matrix metalloproteinase-13 (MMP-13) and of a resultant metalloproteinase-generated neoepitope VDIPEN was increased in all groups versus GROUND-SHAM. Clustering of chondrocytes indicating cartilage damage was present in all HLU and IR groups versus GROUND-SHAM on day 13. On day 62, after 49 days of reloading, the loss of GAG content was attenuated in the HLU-SHAM and HLU-IR groups, and the increased VDIPEN staining in all treatment groups was attenuated. However, the increased chondrocyte clustering remained in all treatment groups on day 62. MMP-13 activity also remained elevated in the GROUND-IR and HLU-IR groups. Increased T2 relaxation times, measured on day 62 using 7T MRI, were greater in GROUND-IR and HLU-IR knees, indicating persistent cartilage damage in the irradiated groups. Both HLU and total-body irradiation resulted in acute degenerative and pre-arthritic changes in the knee articular cartilage of rats. A return to normal weight bearing resulted in some recovery from cartilage degradation. However, radiation delivered as both a single challenge and when combined with HLU resulted in chronic cartilage damage. These findings suggest that radiation exposure during spaceflight leads to and/or impairs recovery of cartilage upon return to reloading, generating long-term joint problems for astronauts.
Human mulipotential mesenchymal/stromal stem cells are derived from a discrete subpopulation of STRO-1bright/CD34−/CD45−/glycophorin-A-bone marrow cells

Magnetic and flow cytometry-based methods were used to characterize clonogenic stromal cells in human bone marrow. STRO-1bright stromal cells were found to lack expression of CD34, CD45 and glycophorin-A markers associated with hematopoietic progenitor cells. These studies support the view that these are two distinct stem cell compartments in adult bone marrow.