Miracle-dz/UniFAR-FTUs huggingface dataset:
Music Genre Classification: A Multilinear Approach

In this paper, music genre classification is addressed in a multilinear perspective. Inspired by a model of auditory cortical processing, multiscale spectro-temporal modulation features are extracted. Such spectro-temporal modulation features have been successfully used in various content-based audio classification tasks recently, but not yet in music genre classification. Each recording is represented by a third-order feature tensor generated by the auditory model. Thus, the ensemble of recordings is represented by a fourth-order data tensor created by stacking the third-order feature tensors associated to the recordings. To handle large data tensors and derive compact feature vectors suitable for classification, three multilinear subspace techniques are examined, namely the Non-Negative Tensor Factorization (NTF), the High-Order Singular Value Decomposition (HOSVD), and the Multilinear Principal Component Analysis (MPCA). Classification is performed by a Support Vector Machine. Stratified cross-validation tests on the GTZAN dataset and the ISMIR 2004 Genre one demonstrate the advantages of NTF and HOSVD versus MPCA. The best accuracies obtained by the proposed multilinear approach is comparable with those achieved by state-of-the-art music genre classification algorithms.
Prostaglandin E 2 , Interleukin 1 a , and Tumor Necrosis Factor- a Increase Human Osteoclast Formation and Bone Resorption in Vitro *

Prostaglandin E 2 (PGE 2 ) and the cytokines interleukin (IL) 1 a and tumor necrosis factor (TNF) a increase bone resorption in vivo , but the effect of these agents on osteoclastic bone resorption has never been studied in an in vitro human system. Our recently described human bone marrow culture system, in which osteoclasts are generated (vi- tronectin and calcitonin receptor-positive cells which resorb bone), wasusedtostudytheeffectsoftheseagents.Additionofindomethacintomacrophagecolony-stimulatingfactor(M-CSF)-treatedculturesnearlyabolishedosteoclastparameters,indicatingthatprostaglan-dinsarevirtuallyessentialforhumanosteoclastformation.Addi-tionally,PGE 2 dose responsively increased osteoclast numbers and bone resorption. The effects of M-CSF and PGE 2 are independent, as demonstrated by unaltered PGE 2 concentrations in culture supernatants in spite of the dose-responsive increase in osteoclast parameters in response to M-CSF. The generation of osteoclasts in the presence of PGE 2 occurred in favor of CD 14-positive macrophage formation. IL 1 a and TNF a increased osteoclast parameters in a dose-respon-sive manner. Maximum stimulation yielded culture supernatant lev- els of PGE 2 approximately the same as those concentrations of exogenous PGE 2 that dramatically induced osteoclast formation. This osteoclast-inducing effect was inhibited both by indomethacin and by the specific inhibitor of inducible prostaglandin G/H synthase, NS- 398, and this was reversed by addition of exogenous PGE 2 . These results demonstrate unequivocally that IL 1 a and TNF a enhance human osteoclast formation and suggest that they mediate their effects through PGE 2 . ( Endocrinology 139: 3157–3164, 1998) devitalized the of M-CSF at ng/ml days (phase II). The of 2 IL 1 a and TNF a (Genetics ng/ml) tested them phase II of the in the and absenceofindomethacin(10 (PGHS-2)
Non-Sparse Multiple Kernel Fisher Discriminant Analysis

Sparsity-inducing multiple kernel Fisher discriminant analysis (MK-FDA) has been studied in the literature. Building on recent advances in non-sparse multiple kernel learning (MKL), we propose a non-sparse version of MK-FDA, which imposes a general lp norm regularisation on the kernel weights. We formulate the associated optimisation problem as a semi-infinite program (SIP), and adapt an iterative wrapper algorithm to solve it. We then discuss, in light of latest advances in MKL optimisation techniques, several reformulations and optimisation strategies that can potentially lead to significant improvements in the efficiency and scalability of MK-FDA. We carry out extensive experiments on six datasets from various application areas, and compare closely the performance of lp MK-FDA, fixed norm MK-FDA, and several variants of SVM-based MKL (MK-SVM). Our results demonstrate that lp MK-FDA improves upon sparse MK-FDA in many practical situations. The results also show that on image categorisation problems, lp MK-FDA tends to outperform its SVM counterpart. Finally, we also discuss the connection between (MK-)FDA and (MK-)SVM, under the unified framework of regularised kernel machines.
Predicting protein crystallization using a simple scoring card method

Many computational methods have been developed to predict protein crystallization. Most methods use amino acid and dipeptide compositions as part of the informative features. To advance the prediction accuracy, the support vector machine (SVM) based classifiers and ensemble approaches were effective and commonly-used techniques. However, these techniques suffer from the low interpretation ability of insight into crystallization. In this study, we utilize a newly-developed scoring card method (SCM) with a dipeptide composition feature to predict protein crystallization. This SCM classifier obtains prediction results 74%, 0.55 and 0.83 for accuracy, sensitivity and specificity, respectively, which is comparable to the SVM classifier using the same benchmarks. The experimental results show that the SCM classifier has advantages of simplicity, high interpretability, and high accuracy in predicting protein crystallization, compared with existing SVM-basedensemble classifiers.
Mechanisms and implications of the age‐associated decrease in DNA repair capacity

Skin cancer incidence is clearly linked to UV irradiation and increases exponentially with age. We studied the rate of removal of thymine dimers and (6–4) photoproducts in UV‐irradiated human dermal fibroblasts derived from donors of different ages. There was a significant decrease with aging in the repair rates of both thymine dimers and (6–4) photoproducts (P< 0.001). In addition, there was an age‐associated decrease in the protein levels of ERCC3, PCNA, RPA, XPA, and p53 that participate in nucleotide excision repair. Moreover, the mRNA levels of XPA, ERCC3, and PCNA were significantly reduced with aging, suggesting that these decreases are often regulated at the mRNA level. Furthermore, with age induction of p53 after UV irradiation was significantly reduced. Taken together, our data suggest that the age‐associated decrease in the repair of UV‐induced DNA damage results at least in part from decreased levels of proteins that participate in the repair process. —Goukassian, D. , Gad, F. , Yaar, M. , Eller, M. S. , Nehal, U. S. , Gilchrest, B. A. Mechanisms and implications of the age‐associated decrease in DNA repair capacity. FASEB J. 14, 1325–1334 (2000)
Studies on the effects of simple sugars on mammalian cells in culture and characterization of the inhibition of 3T3 fibroblasts by L-fucose.

Summary Studies concerning the effects of naturally occurring simple sugars on the morphology and metabolism of various mammalian cell lines further illustrate the selective effects of different individual sugars on specific cell lines. Attempts to characterize the selective effects of l-fucose on 3T3 fibroblasts showed that the marked changes in morphology and inhibition of incorporation of radioactive precursors were reversible. Also, the plating efficiency of 3T3 cells grown in medium containing l-fucose for 24 hours was not diminished. Studies of the sequence of inhibition of incorporation of radioactive precursors in fucose-containing cultures showed that uridine incorporation was decreased before leucine and thymidine. In contrast to the striking effects of l-fucose on rapidly growing cultures of 3T3 cells, the addition of this sugar to confluent cultures caused no apparent effects. The mechanisms by which l-fucose causes these changes in 3T3 cells are unknown. However, it does not appear to be caused directly by interference with the uptake or utilization of glucose. Furthermore, the selective inhibition by l-fucose appears to require very little of this sugar to be taken up by the cells. Parallelisms between the characteristics of inhibition by l-fucose and those of cell contact inhibition of mitosis raise the possibility that similar mechanisms operate in both phenomena. Regardless of the mechanisms responsible for the selective effects of l-fucose, the results suggest that naturally occurring sugar constituents of cells may play a unique role in influencing cell growth and metabolism.
Twig Pattern Matching Algorithms for XML

The emergence of XML promised significant advances in B2B integration. This is because users can store or transmit structure data using this highly flexible open standard. An effective well-formed XML document structure helps convert data into useful information that can be processed quickly and efficiently. From this point there is need for efficient processing of queries on XML data in XML databases like XML-enabled (MS-SQL Server, Oracle), Native XML (Mark Logic Server, EMC xDB). The research area in XML database is processing of XML tree pattern query (TPQ) called twig with efficient answers . Generally we have parsers that constructs the parse trees for some representation. Similarly, we have XML DOM parser it converts the XML document into XML tree. The XML query languages like XQL(XML Query Language), XML-QL(a query language for XML), Quilt, XPath (Extensible path language), XQuery (Extensible Query language) represent queries on XML data as twigs(small tree patterns). The major operation of XML query processing is to find all the occurrences of twig patterns efficiently on XML database. In the past few years, many algorithms have been proposed to match such tree patterns (twigs). This paper presents an overview of the state of the art in TPQ processing. This overview shall start by providing some background in holistic approaches to process TPQ and then introduce different algorithms for twig pattern matching.
Protection of gerbils from amebic liver abscess by immunization with recombinant Entamoeba histolytica 29-kilodalton antigen

The goal of our study was to obtain a highly conserved Entamoeba histolytica recombinant antigen for study as a subunit amebiasis vaccine. We screened a Uni-Zap cDNA library of E. histolytica (strain HM1:IMSS) with human immune sera and isolated a dominant 804-bp cDNA clone. A 33-kDa fusion protein expressed from the cDNA clone was determined by monoclonal antibody binding, DNA hybridization, and nucleotide sequence to be the complete E. histolytica 29-kDa antigen. Serum antibodies to the recombinant protein were detected by enzyme-linked immunosorbent assay in 80% of subjects from Egypt and South Africa with amebic liver abscess. Similar results were found with the native 29-kDa protein. Native and recombinant 29-kDa antigens induced proliferation of lymphocytes harvested from patients with amebic liver abscess (P < 0.01 compared with controls). Intraperitoneal immunization of gerbils with the recombinant fusion protein (10 micrograms) with Titermax adjuvant elicited an antigen-specific serum immunoglobulin G antibody response and was partially protective (54%) against intrahepatic challenge with 5 x 10(5) virulent axenic trophozoites (strain HM1:IMSS). In summary, the recombinant form of the E. histolytica 29-kDa antigen demonstrated serologic specificity for amebic liver abscess, exhibited conserved T-cell epitopes, and was effective as a subunit vaccine in an experimental animal model of amebic liver abscess.
Tourette’s syndrome: a cross sectional study to examine the PANDAS hypothesis

Background: The classical neurological disorder after group A β haemolytic streptococcal infection is Sydenham’s chorea. Recently a tic disorder occurring after group A streptococcal infection has been described and termed PANDAS (paediatric autoimmune neuropsychiatric disorders associated with streptococcal infection). It is proposed that antibodies induced after group A streptococcal infection react with basal ganglia neurones in Sydenham’s chorea and PANDAS. Anti-basal ganglia antibodies (ABGA) are present in most cases of acute Sydenham’s chorea, but rarely in controls. Objective: To investigate the hypothesis that Tourette’s syndrome may be associated with group A streptococcal infection and ABGA. Methods: 100 patients with Tourette’s syndrome (DSM-IV-TR) were enrolled in a cross sectional study. Children with neurological disease (n = 50) and recent uncomplicated streptococcal infection (n = 40), adults with neurological disease (n = 50), and healthy adults (n = 50) were studied as controls. Recent group A streptococcal infection was defined using antistreptolysin O titre (ASOT). ABGA were detected using western immunoblotting and indirect immunofluorescence. Results: ASOT was raised in 64% of children with Tourette’s syndrome compared with 15% of paediatric neurological disease controls (p < 0.0001), and in 68% of adults with Tourette’s syndrome compared with 12% of adult neurological controls and 8% of adult healthy controls (p < 0.05). Western immunoblotting showed positive binding in 20% of children and 27% of adults with Tourette’s syndrome, compared with 2–4% of control groups (p < 0.05). The most common basal ganglia binding was to a 60 kDa antigen, similar to the proposed antigen in Sydenham’s chorea. Indirect immunofluorescence revealed autoantibody binding to basal ganglia neurones. Serological evidence of recent group A streptococcal infection, assessed by a raised ASOT, was detected in 91% (21/23) of Tourette’s syndrome patients with positive ABGA compared with 57% (44/77) with negative ABGA (p < 0.01). Conclusions: The results support a role of group A streptococcal infection and basal ganglia autoimmunity in a subgroup of patients with Tourette’s syndrome and suggest a pathogenic similarity between Sydenham’s chorea and some patients with Tourette’s syndrome.
Low Vitamin D Levels Predict Stroke in Patients Referred to Coronary Angiography

Background and Purpose— Vitamin D deficiency is common among the elderly and may contribute to cerebrovascular diseases. We aimed to elucidate whether low vitamin D levels are predictive for fatal stroke. Methods— The LUdwigshafen RIsk and Cardiovascular Health (LURIC) study includes 3316 patients who were referred to coronary angiography at baseline between 1997 and 2000. 25-Hydroxyvitamin D [25(OH)D] and 1,25-dihydroxyvitamin D [1,25(OH)2D] were measured in 3299 and 3315 study participants, respectively. To account for the seasonal variation of vitamin D metabolites, we calculated z values for the 25(OH)D and 1,25(OH)2D concentrations within each month of blood draw. Results— During a median follow-up time of 7.75 years, 769 patients died, including 42 fatal (ischemic and hemorrhagic) strokes. When compared with survivors in binary logistic-regression analyses, the odds ratios (with 95% CIs) for fatal stroke were 0.58 (0.43 to 0.78; P<0.001) per z value of 25(OH)D and 0.62 (0.47 to 0.81; P<0.001) per z value of 1,25(OH)2D. After adjustment for several possible confounders, these odds ratios remained significant for 25(OH)D at 0.67 (0.46 to 0.97; P=0.032) and for 1,25(OH)2D at 0.72 (0.52 to 0.99; P=0.047). Z values of 25(OH)D and 1,25(OH)2D were also reduced in the 274 patients who had a history of previous cerebrovascular disease events at baseline. Conclusions— Low levels of 25(OH)D and 1,25(OH)2D are independently predictive for fatal strokes, suggesting that vitamin D supplementation is a promising approach in the prevention of strokes.
Frontline Science: Nasal epithelial GM‐CSF contributes to TLR5‐mediated modulation of airway dendritic cells and subsequent IgA response

Flagellin, as a TLR5 agonist, is an established mucosal adjuvant for enhancing mucosal IgA responses by i.n. immunization. Nasal epithelial cells (NECs) are the first sentinel cells to be exposed to antigen and adjuvant in i.n. immunization, and it is suggested that they play an important role in the mucosal adjuvant activity of flagellin. However, the molecular mechanism leading to modulation and the response by flagellin‐activated NECs remain unknown. We aimed to identify the soluble mediator(s) from flagellin‐activated NECs that modulate the functions of airway dendritic cells (DCs) and enhance subsequent IgA response. In vitro studies showed that compared with the TLR4 agonist LPS, flagellin directly triggered slight up‐regulation of CD80 on airway DCs but was insufficient to affect CD86 expression and DC‐mediated IgA response. With the use of an in vitro system for culturing mouse primary NECs (mNECs), we demonstrated that flagellin‐activated mNECs could functionally modulate airway DCs, which manifested as significant up‐regulation of CD80/CD86 and enhancement of IgA production. The functional modulation of airway DCs was dependent on TLR5 activation of mNECs rather than direct TLR5 activation of airway DCs. With the use of cytokine array and antibody‐blocking assays, we further identified that GM‐CSF, a cytokine secreted from TLR5‐activated mNECs, contributes to the activation of mNECs to airway DCs and subsequent IgA enhancement. In vivo blocking experiments confirmed that GM‐CSF is an important factor in recombinant flagellin derived from Salmonella typhi (FliC)‐induced airway DC activation and antigen‐specific IgA enhancement. Our data directly demonstrate that nasal epithelial GM‐CSF contributes to TLR5‐mediated modulation of airway DCs and a subsequent IgA response.
Skinned Fibers of Human Atrium and Ventricle: Myosin Isoenzymes and Contractility

Different myosin isoenzymes of pig and human atrium and ventricle and rat ventricle were characterized by two approaches: pyrophosphate polyacrylamide gel electrophoresis (PP-PAGE) and analysis of the myosin P light chains by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). We further investigated the relation between atrial and ventricular myosin isoenzymes of human, pig, and rat, and the maximum (unloaded) shortening velocity (Vmax and the Ca2+ sensitivity of chemically skinned fibers of the same species. The myosin isoenzymes of both human and pig atrium comigrated in the PP-PAGE with rat V2 isomyosin, whereas the ventricle of human and pig comigrated with rat V3 In both human and pig ventricle, a myosin P light chain polymorphism exists (two phosphorylatable P light chains with the same molecular weight but different isoelectric points). In contrast, we found no P light chain polymorphism in the atrium of human and pig and in the ventricle of rat (one phosphorylatable P light chain only). A correlation exists between Vmax, Ca2+ sensitivity, and atrium- and ventricle-specific myosin isoenzymes of human and pig. Vmax was determined by the slack-test method. Plots of Al versus At of atrial and ventricular skinned fibers were well fitted by a single straight line up to Δl = 15% and Δl = 13%, respectively. Vmax of skinned ventricular fibers was lower than Vmax of skinned atrial fibers in both human and pig. Ca2+ sensitivity of skinned fibers of ventricle, however, was higher than Ca2+ sensitivity of atrial skinned fibers in both human and pig.
Facet Tropism and Interfacet Shape in the Thoracolumbar Vertebrae: Characterization and Biomechanical Interpretation

Study Design. Thoracolumbar facet and interfacet linear dimensions were measured and analyzed. Objective. To characterize and analyze the thoracolumbar facet and interfacet size and shape in relation to gender, ethnic group, and age and to detect the extent of normal facet tropism along the thoracolumbar spine. Summary of Background Data. Knowledge on facet tropism and interfacet shape is limited in the literature as most data are based on 2-dimensional measurements, small samples, or isolated vertebrae. Methods. Facet shape as represented by width, length, width/length ratio and interfacet distances was obtained directly from dry vertebrae of 240 adult human spines. The specimen’s osteologic material is part of the Hamann-Todd Osteological Collection housed at the Cleveland Museum of Natural History, Cleveland, OH. A total of 4080 vertebrae (T1–L5) from the vertebral columns of individuals 20 to 80 years of age were measured, using a Microscribe 3-dimensional apparatus (Immersion Co., San Jose, CA). Data were recorded directly on computer software. Statistical analysis included paired t tests and ANOVA. Results. A significant correlation was found between all thoracolumbar facet dimensions and an individual’s height and weight. Facet tropism is a major characteristic of the thoracolumbar spine, the left being longer in the thorax while the right is longer in the lumbar. In general, facet size is age-independent and greater in males compared with females with a significant ethnic component. Facet length is similar for all thoracic vertebrae, whereas it sharply and continuously increases in the lumbar vertebrae. Facet dimension manifests a bipolar distribution along the thoracolumbar vertebrae. Width/length ratio indicates that facets are longer than wider for most verte-brae. The interarticular area manifests a marked inverted trapezoidal shape at T1–T2, a rectangular shape at T3–L3, and an ordinary trapezoidal shape at L4–L5. Conclusions. Facet tropism is a normal characteristic in humans, yet it varies along the thoracolumbar spine.
Inhibition of the sodium potassium adenosine triphosphatase pump sensitizes cancer cells to anoikis and prevents distant tumor formation.

Normal epithelial cells undergo apoptosis upon detachment from the extracellular matrix, a process termed "anoikis. " However, malignant epithelial cells with metastatic potential resist anoikis and can survive in an anchorage-independent fashion. Molecules that sensitize resistant cells to anoikis will be useful chemical probes to understand this pathway. To identify novel anoikis sensitizers in anoikis-resistant PPC-1 prostate adenocarcinoma cells, a library of 2,000 off-patent drugs and natural products was screened for their ability to preferentially induce cell death in suspension over adherent culture conditions. This screen identified five members of the family of cardiac glycosides as anoikis sensitizers, including ouabain, peruvoside, digoxin, digitoxin, and strophanthidin. We conducted further studies with ouabain to discern the mechanism of cardiac glycoside-induced anoikis sensitization. Ouabain initiated anoikis through the mitochondrial pathway of caspase activation. In addition, ouabain sensitized cells to anoikis by inhibiting its known target, the Na(+)/K(+) ATPase pump, and inducing hypoosmotic stress. Resistance to anoikis permits cancer cells to survive in the circulation and facilitates their metastasis to distant organs, so we tested the effects of Na(+)/K(+) ATPase inhibition on distant tumor formation in mouse models. In these mouse models, ouabain inhibited tumor metastases but did not alter the growth of subcutaneous tumors. Thus, we have identified a novel mechanism to sensitize resistant cells to anoikis and decrease tumor metastasis. These results suggest a potential mechanism for the observed clinical reduction in metastasis and relapse in breast cancer patients who have undergone treatments with cardiac glycosides.