gebhart/patrepeval huggingface dataset:
Genetically Detoxified Pertussis Toxin Induces Th1/Th17 Immune Response through MAPKs and IL-10-Dependent Mechanisms (2009)

Genetically detoxified pertussis toxin (dPT) maintains the protein structure and the immunological properties, but not the enzymatic activity. In search of an adjuvant able to direct polarization of T cells to induce/potentiate protective immune response to a variety of infectious disease, we investigated the role played by dPT on human dendritic cell-driven Th polarization and analyzed the intracellular signaling events. To reach these aims, we used a highly purified dPT preparation devoid of contamination and monocyte-derived dendritic cells, a well-characterized model to study ex vivo the polarization of the immune responses. First, we analyzed dPT-induced monocyte-derived dendritic cell maturation, longevity, and cytokine production and, in a second step, we analyzed TLR4/2 engagement by dPT, the connected signaling events, and their relevance to the skewing of Th cell polarization. These approaches allowed us to clarify some of the mechanisms that are responsible for dPT-driven regulation of T cell polarization. We demonstrated that dPT acts utilizing TLR4/TLR2 engagement, being the signaling induced by the former stronger. dPT, through a crucial role played by MAPK and IL-10, favors the expansion of the Th1/Th17 immunity. Indirect evidences indicated that dPT-induced Th17 expansion is counterregulated by the PI3K pathway. For its properties and being already used in humans as vaccine Ag in pertussis, dPT may represents a valid candidate adjuvant to foster immune protective response in vaccines against infectious diseases where Th1/Th17 are mediating host immunity.
A Potent and Highly Efficacious Bcl-2/Bcl-xL Inhibitor (2013)

Our previously reported Bcl-2/Bcl-xL inhibitor, 4, effectively inhibited tumor growth but failed to achieve complete regression in vivo. We have now performed extensive modifications on its pyrrole core structure, which has culminated in the discovery of 32 (BM-1074). Compound 32 binds to Bcl-2 and Bcl-xL proteins with K(i) values of <1 nM and inhibits cancer cell growth with IC50 values of 1-2 nM in four small-cell lung cancer cell lines sensitive to potent and specific Bcl-2/Bcl-xL inhibitors. Compound 32 is capable of achieving rapid, complete, and durable tumor regression in vivo at a well-tolerated dose schedule. Compound 32 is the most potent and efficacious Bcl-2/Bcl-xL inhibitor reported to date.
The blackboard model of problem solving (1986)

The first system was the HEARSAY-II speech understanding system (Erman et al.,1980) that evolved between 1971 and 1976. Subsequently, many have been built that have similar system organization and run-time behavior. The objectives of this article are (1) to define what is meant by blackboard systems and (2) to show the richness and diversity of system designs. The article begins with a discussion of the underlying concept behind all systems, the model of problem solving. In order to bridge the gap between a model and working systems, the framework, an extension of the basic model is introduced, including a detailed description of the model's components and their behavior. A model does not come into existence on its own, and is usually an abstraction of many examples. In Section 2 the history of ideas is traced, and the designs of some application that helped shape the model are detailed. Part 2 of this article which will appear in the next issue of AI Magazine, describes and contrasts some and discusses the characteristics of application problems suitable for the method of problem solving.
Subcutaneous immunoglobulin: opportunities and outlook (2009)

Immunoglobulin (Ig) administration via the subcutaneous (s.c.) route has become increasingly popular in recent years. The method does not require venous access, is associated with few systemic side effects and has been reported to improve patients' quality of life. One current limitation to its use is the large volumes which need to be administered. Due to the inability of tissue to accept such large volumes, frequent administration at multiple sites is necessary. Most studies conducted to date have investigated the use of subcutaneous immunoglobulin (SCIg) in patients treated previously with the intravenous (i.v.) formulation. New data now support the use of s.c. administration in previously untreated patients with primary immunodeficiencies. SCIg treatment may further be beneficial in the treatment of autoimmune neurological conditions, such as multi-focal motor neuropathy; however, controlled trials directly comparing the s.c. and i.v. routes are still to be performed for this indication. New developments may further improve and facilitate the s.c. administration route. For example, hyaluronidase-facilitated administration increases the bioavailability of SCIg, and may allow for the administration of larger volumes at a single site. Alternatively, more concentrated formulations may reduce the volume required for administration, and a rapid-push technique may allow for shorter administration times. As these developments translate into clinical practice, more physicians and patients may choose the s.c. administration route in the future.
[Expression and clinical significance of the genes of Wnt signaling pathway in keratocystic odontogenic tumor of the jaw bones]. (2015)

There are abnormal expressions of genes of Wnt pathway in KCOT. Genes of Wnt pathway plays certain roles in KCOT.
Directional Discrete Cosine Transforms—A New Framework for Image Coding (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Nearly all block-based transform schemes for image and video coding developed so far choose the 2-D discrete cosine transform (DCT) of a square block shape. With almost no exception, this conventional DCT is implemented separately through two 1-D transforms, one along the vertical direction and another along the horizontal direction. In this paper, we develop a new block-based DCT framework in which the first transform may choose to follow a direction other than the vertical or horizontal one. The coefficients produced by all directional transforms in the first step are arranged appropriately so that the second transform can be applied to the coefficients that are best aligned with each other. Compared with the conventional DCT, the resulting directional DCT framework is able to provide a better coding performance for image blocks that contain directional edges-a popular scenario in many image signals. By choosing the best from all directional DCTs (including the conventional DCT as a special case) for each image block, we will demonstrate that the rate-distortion coding performance can be improved remarkably. Finally, a brief theoretical analysis is presented to justify why certain coding gain (over the conventional DCT) results from this directional framework. </para>
Angiogenesis and mast cell density with tryptase activity increase simultaneously with pathological progression in B-cell non-Hodgkin's lymphomas (2000)

Node biopsies of 16 benign lymphadenopathies and 72 B-cell non-Hodgkin's lymphomas (B-NHLs) were investigated for counts of microvessels, total metachromatic mast cells (MCs) and MCs expressing tryptase, an angiogenesis-inducing molecule. Counts were higher in B-NHLs. When grouped according to the Working Formulation (WF) malignancy grades, they were significantly higher in low-grade B-NHLs vs. lymphadenopathies and intermediate-grade vs. low-grade tumors and there was a further increase in the high-grade tumors. A high correlation was demonstrated in all groups of tissues between microvessel counts and both total metachromatic and tryptase-reactive MCs. These results suggest that angiogenesis in B-NHLs increases with their progression, and that MCs cooperate in its induction via the tryptase contained in their secretory granules. Int. J. Cancer 85:171–175, 2000. ©2000 Wiley-Liss, Inc.
First report of intramyocardial pH in man: I. Methodology and initial results. (1984)

Continuous in vivo measurements of intramyocardial pH (MpH) have not been previously obtained in man. To achieve this goal, we developed in our laboratory a new, steel-jacketed, glass electrode, and circumvented temperature-related problems by recording the output in millivolts along with the adjacent myocardial temperature. A computer program was devised to calculate MpH in accordance with the Nernst equation. The need in this system for a remote, subcutaneous, reference electrode prompted two sets of experiments. The first set of experiments demonstrated in vitro that the adverse effect of varying the temperature of the reference electrode on the calibration of the pH electrode could be avoided if the reference electrode was placed in a potassium chloride (KCl) solution outside the body and connected to the subcutaneous tissues with a salt bridge. The second set of experiments, which were conducted in vivo in dogs, demonstrated that MpH measurements made with the reference electrode in the limb were not affected by ischemic electrocardiographic changes. This system was then used successfully in 10 patients undergoing coronary artery bypass surgery. Reliable, reproducible, and uniform changes were observed. Baseline MpH prior to revascularization was 6.81 +/- 0.07. Myocardial protection with cold K+ cardioplegia resulted in a significant rise in MpH to 7.45 +/- 0.06. Throughout the period of cross-clamping, MpH remained high. After revascularization and discontinuation of cardiopulmonary bypass, MpH stabilized at 6.93 +/- 0.04.(ABSTRACT TRUNCATED AT 250 WORDS)
Analysis of virulence and growth of a purine auxotrophic mutant ofXanthomonas oryzaepathovaroryzae (2007)

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice. A random insertional mutant library of Xoo KACC10331 was constructed using a Tn5-derived transposon, and the virulence of the mutants against the susceptible rice cultivar IR24 was assayed. After the virulence assay, the M793 (purD::Tn5) mutant that had reduced virulence against the rice plants was isolated. Thermal asymmetric interlaced-PCR and sequence analysis revealed that the transposon was inserted into the purD gene (encodes a phosphoribosylamine-glycine ligase) of the M793 mutant. The reverse transcriptase-PCR assay revealed that the mutation of the purD gene did not affect the expression of other purine biosynthesis genes. However, the M793 mutant required exogenous purines and thiamine for growth in minimal media. These results indicate that the purD gene plays a crucial role in the growth and virulence of Xoo.
Wilms' Tumor (WT1) Gene Mutations Occur Mainly in Acute Myeloid Leukemia and May Confer Drug Resistance (1998)

In a previous study of acute leukemia, we have shown that WT1 gene mutations occur in both myeloid and biphenotypic subtypes, where they are associated with refractoriness to standard induction chemotherapy. We have now extended this study to a total of 67 cases (34 acute myeloid leukemia [AML], 23 acute lymphoblastic leukemia [ALL], 10 acute undifferentiated leukemia [AUL]/biphenotypic) and find that WT1 mutations occur in 14% of AML and 20% of biphenotypic leukemia, but are rare in ALL (one case). In contrast to the findings in Wilms' tumor, where mutations in the WT1 gene usually behave according to Knudson's two hit model for tumor suppressor genes, seven of eight leukemia-associated WT1 mutations are heterozygous, implying a dominant or dominant-negative mode of action in hematopoietic cells. In AML, the presence of a WT1 mutation is associated with failure to achieve complete remission and a lower survival rate. These data (1) confirm that WT1 mutations underlie a similar proportion of cases of AML to that seen in Wilms' tumors and (2) show for the first time that WT1 mutations can contribute to leukemogenesis of lymphoid as well as myeloid origin, suggesting that its normal role in hematopoiesis lies at a very early progenitor stage. The relationship of WT1 mutation to chemoresistance merits further investigation.
RTPrimerDB: the Real-Time PCR primer and probe database (2003)

The real-time polymerase chain reaction (PCR) methodology has become increasingly popular for nucleic acids detection and/or quantification. As primer/probe design and experimental evaluation is time-consuming, we developed a public database application for the storage and retrieval of validated real-time PCR primer and probe sequence records. The integrity and accuracy of the data are maintained by linking to and querying other reference databases. RTPrimerDB provides free public access through the Web to perform queries and submit user based information. Primer/probe records can be searched for by official gene symbol, nucleotide sequence, type of application, detection chemistry, LocusLink or Single Nucleotide Polymorphism (SNP) identifier, and submitter's name. Each record is directly linked to LocusLink, dbSNP and/or PubMed to retrieve additional information on the gene/SNP for which the primers/probes are designed. Currently, the database contains primer/probe records for human, mouse, rat, fruit fly and zebrafish, and all current detection chemistries such as intercalating dyes (SYBR Green I), hydrolysis probes (Taqman), adjacent hybridizations probes and molecular beacons. Real-time PCR primer/probe records are available at http://www.realtimeprimerdatabase.ht.st.
Graphoepitaxy of Self-Assembled Block Copolymers on Two-Dimensional Periodic Patterned Templates (2008)

Self-assembling materials are the building blocks of bottom-up nanofabrication processes, but they need to be templated to impose long-range order and eliminate defects. In this work, the self-assembly of a thin film of a spherical-morphology block copolymer is templated using an array of nanoscale topographical elements that act as surrogates for the minority domains of the block copolymer. The orientation and periodicity of the resulting array of spherical microdomains are governed by the commensurability between the block copolymer period and the template period and is accurately described by a free-energy model. This method, which forms high-spatial-frequency arrays using a lower-spatial-frequency template, will be useful in nanolithography applications such as the formation of high-density microelectronic structures.
Enzyme-Replacement Therapy in Life-Threatening Hypophosphatasia (2012)

ENB-0040, an enzyme-replacement therapy, was associated with improved findings on skeletal radiographs and improved pulmonary and physical function in infants and young children with life-threatening hypophosphatasia. (Funded by Enobia Pharma and Shriners Hospitals for Children; ClinicalTrials.gov number, NCT00744042.).
RNA binding determinant in some class I tRNA synthetases identified by alignment-guided mutagenesis. (1992)

The N-terminal nucleotide binding folds of all 10 class I tRNA synthetases (RSs) contain characteristic conserved sequence motifs that define this class of synthetases. Sequences of C-terminal domains, which in some cases are known to interact with anticodons, are divergent. In the 676-amino acid Escherichia coli methionyl-tRNA synthetase (MetRS), interactions with the methionine tRNA anticodon are sensitive to substitutions at a specific location on the surface of the C-terminal domain of this protein of known three-dimensional structure. Although four class I synthetases of heterogeneous lengths and unknown structures are believed to be historically related to MetRS, pair-wise sequence similarities in the region of this RNA binding determinant are obscure. A multiple alignment of all sequences of three of these synthetases with all MetRS sequences suggested a location for the functional analog of the anticodon-binding site in these enzymes. We chose a member of this set for alignment-guided mutagenesis, combined with a functional analysis of mutant proteins. Substitutions within two amino acids of the site fixed by the multiple sequence alignment severely affected interactions with tRNA but not with ATP or amino acid. Multiple individual replacements at this location do not disrupt enzyme stability, indicating this segment is on the surface, as in the MetRS structure. The results suggest the location of an RNA binding determinant in each of these three synthetases of unknown structure.
Trellis coded quantization of memoryless and Gauss-Markov sources (1990)

Trellis-coded quantization (TCQ) is developed and applied to the encoding of memoryless and Gauss-Markov sources. The theoretical justification for the approach is alphabet-constrained rate distortion theory, which is a dual to the channel capacity argument that motivates trellis-coded modulation (TCM). The authors adopt the notions of signal set expansion, set partitioning, and branch labeling of TCM, but modify the techniques to account for the source distribution, to design TCQ coders of low complexity with excellent mean-squared-error (MSE) performance. For a memoryless uniform source, TCQ provides an MSE within 0.21 dB of the distortion-rate bound at all positive (integral) rates. The performance is superior to that promised by the coefficient of quantization for all of the best lattices known in dimensions 24 or less. For a memoryless Gaussian source, the TCQ performance at rates of 0.5, 1, and 2 b/sample is superior to all previous results the authors found in the literature. The encoding complexity of TCQ is very modest. TCQ is incorporated into a predictive coding structure for the encoding of Gauss-Markov sources. Simulation results for first-, second-, and third-order Gauss-Markov sources are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Cloning and Characterization of anN-Acetylglucosamine-6-O-sulfotransferase (1998)

We isolated a cDNA clone encoding mouse N-acetylglucosamine-6-O-sulfotransferase based on sequence homology to the previously cloned mouse chondroitin 6-sulfotransferase. The cDNA clone contained an open reading frame that predicts a type II transmembrane protein composed of 483 amino acid residues. The expressed enzyme transferred sulfate to the 6 position of nonreducing GlcNAc in GlcNAcbeta1-3Galbeta1-4GlcNAc. Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc and various glycosaminoglycans did not serve as acceptors. Expression of the cDNA in COS-7 cells resulted in production of a cell-surface antigen, the epitope of which was NeuAcalpha2-3Galbeta1-4(SO4-6)GlcNAc; double transfection with fucosyltransferase IV yielded Galbeta1-4(Fucalpha1-3)(SO4-6)GlcNAc antigen. The sulfotransferase mRNA was strongly expressed in the cerebrum, cerebellum, eye, pancreas, and lung of adult mice. In situ hybridization revealed that the mRNA was localized in high endothelial venules of mesenteric lymph nodes. The sulfotransferase was concluded to be involved in biosynthesis of glycoconjugates bearing the 6-sulfo N-acetyllactosamine structure such as 6-sulfo sialyl Lewis X. The products of the sulfotransferase probably include glycoconjugates with intercellular recognition signals; one candidate of such a glycoconjugate is an L-selectin ligand.
Classifying Environmental Sounds with Image Networks (2017)

Context. Environmental Sound Recognition, unlike Speech Recognition, is an area that is still in the developing stages with respect to using Deep Learning methods. Sound can be converted into images by extracting spectrograms and the like. Object Recognition from images using deep Convolutional Neural Networks is a currently developing area holding high promise. The same technique has been studied and applied, but on image representations of sound. Objectives. In this study, investigation is done to determine the best possible accuracy of performing a sound classification task using existing deep Convolutional Neural Networks by comparing the data pre-processing parameters. Also, a novel method of combining different features into a single image is proposed and its effect tested. Lastly, the performance of an existing network that fuses Convolutional and Recurrent Neural architectures is tested on the selected datasets. Methods. In this, experiments were conducted to analyze the effects of data pre-processing parameters on the best possible accuracy with two CNNs. Also, experiment was also conducted to determine whether the proposed method of feature combination is beneficial or not. Finally, an experiment to test the performance of a combined network was conducted. Results. GoogLeNet had the highest classification accuracy of 73% on 50-class dataset and 90-93% on 10-class datasets. The sampling rate and frame length values of the respective datasets which contributed to the high scores are 16kHz, 40ms and 8kHz, 50ms respectively. The proposed combination of features does not improve the classification accuracy. The fused CRNN network could not achieve high accuracy on the selected datasets. Conclusions. It is concluded that deep networks designed for object recognition can be successfully used to classify environmental sounds and the pre-processing parameters’ values determined for achieving best accuracy. The novel method of feature combination does not significantly improve the accuracy when compared to spectrograms alone. The fused network which learns the special and temporal features from spectral images performs poorly in the classification task when compared to the convolutional network alone.
IL-7 Is Essential for Homeostatic Control of T Cell Metabolism In Vivo (2010)

It has become apparent that T cells require growth signals to maintain function and viability necessary to maintain proper immune homeostasis. One means by which cell extrinsic signals may mediate these effects is by sustaining sufficient basal cell metabolism to prevent cell atrophy. The role of metabolism and the specific growth factors essential to maintain metabolism of mature T cells in vivo, however, are poorly defined. As IL-7 is a nonredundant cytokine required for T cell development and survival and can regulate T cell metabolism in vitro, we hypothesized it may be essential to sustain metabolism of resting T cells in vivo. Thus, we generated a model for conditional expression of IL-7R in mature T cells. After IL-7R deletion in a generally normal lymphoid environment, T cells had reduced responses to IL-7, including abrogated signaling and maintenance of antiapoptotic Bcl-2 family expression that corresponded to decreased survival in vitro. T cell survival in vivo was also reduced after loss of the IL-7R in a T cell-intrinsic manner. Additionally, IL-7R deletion resulted in delayed growth and proliferation following stimulation. Importantly, in vivo excision of IL-7R led to T cell atrophy that was characterized by delayed mitogenesis and reduced glycolytic flux. These data are the first to identify an in vivo requirement for a specific cell extrinsic signal to sustain lymphocyte metabolism and suggest that control of glycolysis by IL-7R may contribute to the well-described roles of IL-7 in T cell development, homeostatic proliferation, and survival.