gebhart/patrepeval huggingface dataset:
Support Vector Machine Classification of Microarray from Gene Expression Data (1999)

We introduce a new method of functionally classifying genes using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). We describe SVMs that use different similarity metrics including a simple dot product of gene expression vectors, polynomial versions of the dot product, and a radial basis function. The radial basis function SVM appear to provide superior performance in classifying functional classes of genes when compared to the other SVM similarity metrics. In addition, SVM performance is compared to four standard machine learning algorithms. SVMs have many features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. Work done while visiting UCSC. 1 1 Introduction The advent of DNA mi...
Adeno Associated Virus 9–Based Gene Therapy Delivers a Functional Monocarboxylate Transporter 8, Improving Thyroid Hormone Availability to the Brain of Mct8-Deficient Mice (2016)

These results indicate that MCT8 delivery to brain barriers by IV but not ICV injection is crucial for its proper function. MCT8 has no constitutive activity but acts through an increase in T3 entering the brain tissue. Increasing MCT8 expression in brain cell membranes, including neurons, is insufficient to produce an effect without an increase in brain T3 content. The correct hMCT8 isoform along with an optimized delivery method are critical for an effective gene therapy to provide functional MCT8 in the brain of patients with MCT8 mutations.
A hybrid fractal transform (1993)

A generalization of fractal coding of images is presented in which image blocks are represented by mappings derived from least squares approximations using fractal functions. Previously known matching techniques used in fractal transforms are subjects of this generalized method, which is called the Bath fractal transform (BFT). By introducing searching for the best image region for application of the BFT, a hybrid of known methods is achieved. Their fidelity is evaluated by a root-mean-square error measure for a number of polynomial instances of the BFT, over a range of searching levels using a standard test image. It is shown that the fidelity of the fractal transform increases with both search level and order of the polynomial approximation. The method readily extends to data of higher or lower dimensions, including time as an image sequences.< <ETX>&gt;</ETX>
Alginate graft copolymers and alginate–co-excipient physical mixture in oral drug delivery (2011)

The value of alginate graft copolymers as the potential alternative to alginate-co-excipient physical mixture in oral drug delivery cannot be entirely defined by past and present research. Such an issue is complicated by the lack of green chemistry graft copolymer synthesis approach, high grafting process cost, complications and hazards, and the formed graft copolymers having unknown toxicity. Future research will need to address these matters to achieve a widespread commercialization and industrial application of alginate graft copolymers in oral drug delivery.
Anti-Neutrophil-Elastase Defenses of the Lower Respiratory Tract in α1-Antitrypsin Deficiency Directly Augmented with an Aerosol of α1-Antitrypsin (1989)

Short-term aerosol administration of human plasma alpha 1-antitrypsin to patients with alpha 1-antitrypsin deficiency is safe and feasible, resulting in a return to normal of anti-neutrophil-elastase defenses in the lower respiratory tract. The aerosol approach, therefore, merits serious long-term evaluation as an alternative to other parenteral forms of administering therapeutic proteins.
Magnetic Particle Imaging with Advanced Tomographic Reconstruction Methods (2014)

Magnetic Particle Imaging (MPI) is an emerging imaging modality with potential clinical applications in rapid angiography, cell therapy tracking, cancer imaging, and inflammation imaging. While still in its infancy, MPI already has excellent contrast, safety, depth penetration, and sensitivity without the serious health risks posed by current modalities such as ionizing radiation and iodinated contrast agents.With any tracer imaging modality, high sensitivity is necessary to improve safety and enable new clinical applications. The first Magnetic Computed Tomography (MCT) system and experimental images were created in this work with the goal of improving sensitivity in MPI. MCT uses projection reconstruction algorithms similar to those in X-ray computed tomography to reconstruct 3D images from a projection MPI sytem. Analytical derivation and experimental evidence demonstrate that MCT has an order-of-magnitude higher SNR than previous 3D MPI methods for the same scan time as well as a 40% resolution improvement. The MCT experimental system acquisition speed was improved from initial work to acquire images twenty-fold faster at less than two minutes per 3D image.Critical to any medical imaging technology is the reliability and accuracy of image reconstruction. Unfortunately, prior approaches to x-space MPI reconstruction suffer from image artifacts such as banding and haze. In this work, a priori knowledge of image continuity and non-negativity are introduced into a new optimization formulation to reduce these non-physical artifacts in 2D and 3D reconstructions.
Analysis of 148 kb of Genomic DNA Around thewnt1Locus ofFugu rubripes (1999)

The analysis of the sequence of approximately 150 kb of a genomic region corresponding to the wnt1 gene of the Japanese pufferfish Fugu rubripes confirms the compact structure of the genome. Fifteen genes were found in this region, and 26.6% of the analyzed sequence is coding sequence. With an average intergenic distance of <5 kb, this gene density is comparable to that of Caenorhabditis elegans. The compactness of this region corresponds to the reduction of the overall size of the genome, consistent with the conclusion that the gene number in Fugu and human genomes is approximately the same. Eight of the genes have been mapped in the human genome and all of them are found in the chromosomal band 12q13, indicating a high degree of synteny in both species, Fugu and human. Comparative sequence analysis allows us to identify potential regulatory elements for wnt1 and ARF3, which are common to fish and mammals.
Ritonavir blocks AKT signaling, activates apoptosis and inhibits migration and invasion in ovarian cancer cells (2009)

Our results demonstrate a potential use of ritonavir for ovarian cancer with additive effects in conjunction with conventional chemotherapeutic regimens. Since ritonavir is clinically approved for human use for HIV, drug repositioning for ovarian cancer could accelerate the process of traditional drug development. This would reduce risks, limit the costs and decrease the time needed to bring the drug from bench to bedside.
Progress in the development of an HIV vaccine (2003)

Despite the remarkable advances that have been made in the last 20 years regarding the molecular virology, pathogenesis and epidemiology of HIV, the development of an effective HIV vaccine remains an elusive goal. The major reason for this is that we have not determined a correlate of immunity. The various explantations for this include integration of the virus into the host cell genome, infection of long-lived immune cells, HIV genetic diversity (especially in its envelope), persistent high viral replication releasing up to 10 billion viral particles per day and/or production of immunosuppressive products or proteins. However, there is evidence that the host can be protected: some highly exposed persons have remained uninfected; the relatively low incidence of mother to child (fetus) transmission; the initial effective immune response that significantly, if temporally, reduces viral loads; some infected persons are long-term non-progressors; experimental vaccines and passive immunisation have proven effective in experimental animals; and finally, successful vaccine development against other viral infections. At this time, the experimental vaccine pipeline is quite robust and ranges from HIV proteins (although the first such vaccine, recombinant gp120 made on Chinese hamster ovary cells, failed to protect volunteer men having sex with men [MSM]) to DNA vaccines and various novel delivery strategies. Perhaps the greatest impediment is the requirement to test these experimental vaccines in resource-poor developing countries that, at present, lack the necessary infrastructure for performing large, long-term, scientifically valid studies.
Arf induces p53-dependent and -independent antiproliferative genes. (2003)

The tumor suppressor p19(Arf) (p14(ARF) in humans), encoded by the Ink4a/Arf locus, is mutated, deleted, or silenced in many forms of cancer. p19(Arf) induces growth arrest by antagonizing the activity of the p53-negative regulator, Mdm2, thereby inducing a p53 transcriptional response. p19(Arf) can also inhibit cell cycle progression of mouse embryo fibroblasts lacking Cip1 or lacking both Mdm2 and p53, although in the absence of p53, arrest occurs more slowly. Profiling with high-density oligonucleotide GeneChips and cDNA microarrays was used to interrogate mouse genes, the expression of which was induced or suppressed by a conditionally regulated Arf gene. Cluster analysis of temporal gene expression patterns and validation of the results by RNA analysis identified Arf-responsive genes whose induction was both p53-dependent and -independent. The latter included four members of the B-cell translocation gene family (Btg1, Btg2, Btg3, and Tob1) that were demonstrated to inhibit cell proliferation in primary mouse embryo fibroblasts expressing or lacking functional p53. Together, the results indicate that p19(Arf) induces a broad spectrum of proteins that likely act in concert to arrest cell proliferation.
Operating and maintenance features of container handling systems (1987)

This training manual deals with the main operating and maintenance features of container-handling equipment. They have been developed for World Bank staff involved in the preparation and appraisal of port projects which include investment in container-handling systems. The materials will also be valuable to those senior policy makers and managers in the governments and port authorities of developing countries who are involved in the selection of equipment and the preparation and appraisal of projects submitted to the World Bank and other international lending agencies. The desired outcomes of the training are a more informed and productive communication between the principals involved in port container investment projects and an improvement in the equipment selection process. The materials will also focus attention on the equipment management function and assist port authorities and terminal operators to select the most appropriate equipment for the operating conditions and maintenance capabilities of their ports.
Nucleolin is one component of the B cell-specific transcription factor and switch region binding protein, LR1 (1997)

LR1 is a B cell-specific, sequence-specific DNA binding activity that regulates transcription in activated B cells. LR1 also binds Ig heavy chain switch region sequences and may function in class switch recombination. LR1 contains two polypeptides, of 106 kDa and 45 kDa, and here we report that the 106-kDa component of LR1 is nucleolin. This identification, initially made by microsequence analysis, was verified by showing that (i) LR1-DNA binding activity increased in B cells transfected with a nucleolin cDNA expression construct; (ii) LR1-DNA binding activity was recognized by antibodies raised against recombinant human nucleolin; and (iii) in B cells transfected with epitope-tagged nucleolin expression constructs, the LR1-DNA complex was recognized by the anti-tag antibody. Nucleolin is an abundant nucleolar protein which is believed to play a role in rDNA transcription or organization, or rRNA processing. Homology between nucleolin and histone H1 suggests that nucleolin may alter DNA organization in response to cell cycle controls, and the nucleolin component of LR1 may therefore function to organize switch regions before, during, or after switch recombination. The demonstration that nucleolin is a component of a B cell-specific complex that binds switch region sequences suggests that the G-rich switch regions may have evolved from rDNA.
Proton Abstraction Reaction, Steady-State Kinetics, and Oxidation−Reduction Potential of Human Glutaryl-CoA Dehydrogenase (2000)

Glutaryl-CoA dehydrogenase catalyzes the oxidation of glutaryl-CoA to crotonyl-CoA and CO(2) in the mitochondrial degradation of lysine, hydroxylysine, and tryptophan. We have characterized the human enzyme that was expressed in Escherichia coli. Anaerobic reduction of the enzyme with sodium dithionite or substrate yields no detectable semiquinone; however, like other acyl-CoA dehydrogenases, the human enzyme stabilizes an anionic semiquinone upon reduction of the complex between the enzyme and 2,3-enoyl-CoA product. The flavin potential of the free enzyme determined by the xanthine-xanthine oxidase method is -0.132 V at pH 7.0, slightly more negative than that of related flavoprotein dehydrogenases. A single equivalent of substrate reduces 26% of the dehydrogenase flavin, suggesting that the redox equilibrium on the enzyme between substrate and product and oxidized and reduced flavin is not as favorable as that observed with other acyl-CoA dehydrogenases. This equilibrium is, however, similar to that observed in isovaleryl-CoA dehydrogenase. Comparison of steady-state kinetic constants of glutaryl-CoA dehydrogenase with glutaryl-CoA and the alternative substrates, pentanoyl-CoA and hexanoyl-CoA, suggests that the gamma-carboxyl group of glutaryl-CoA stabilizes the enzyme-substrate complex by at least 5.7 kJ/mol, perhaps by interaction with Arg94 or Ser98. Glu370 is positioned to function as the catalytic base, and previous studies indicate that the conjugate acid of Glu370 also protonates the transient crotonyl-CoA anion following decarboxylation [Gomes, B., Fendrich, G. , and Abeles, R. H. (1981) Biochemistry 20, 3154-3160]. Glu370Asp and Glu370Gln mutants of glutaryl-CoA dehydrogenase exhibit 7% and 0. 04% residual activity, respectively, with human electron-transfer flavoprotein; these mutations do not grossly affect the flavin redox potentials of the mutant enzymes. The reduced catalytic activities of these mutants can be attributed to reduced extent and rate of substrate deprotonation based on experiments with the nonoxidizable substrate analogue, 3-thiaglutaryl-CoA, and kinetic experiments. Determination of these fundamental properties of the human enzyme will serve as the basis for future studies of the decarboxylation reaction which is unique among the acyl-CoA dehydrogenases.
Connectivity reveals relationship of brain areas for reward-guided learning and decision making in human and monkey frontal cortex (2015)

Reward-guided decision-making depends on a network of brain regions. Among these are the orbitofrontal and the anterior cingulate cortex. However, it is difficult to ascertain if these areas constitute anatomical and functional unities, and how these areas correspond between monkeys and humans. To address these questions we looked at connectivity profiles of these areas using resting-state functional MRI in 38 humans and 25 macaque monkeys. We sought brain regions in the macaque that resembled 10 human areas identified with decision making and brain regions in the human that resembled six macaque areas identified with decision making. We also used diffusion-weighted MRI to delineate key human orbital and medial frontal brain regions. We identified 21 different regions, many of which could be linked to particular aspects of reward-guided learning, valuation, and decision making, and in many cases we identified areas in the macaque with similar coupling profiles.
A behavioural bioassay to identify attractive odours for Glossinidae (1987)

1. A behavioural bioassay, based on antennal movement responses, was developed using Glossina morsitans morsitans Westwood for screening chemical attractancy to tsetse. 2. Chemicals found to be attractive to male tsetse were acetone, formaldehyde, methylethylketone, methylvinylketone, 1-octen-3-ol and pentanal but not acetophenone, hexanal, lactic acid or urea. 3. Female tsetse also responded to all these chemicals in a similar fashion. Overall responses of females were, however, less than those of males. 4. These laboratory bioassay findings agree with field observations on tsetse responses to certain chemical odours. Therefore this behavioural bioassay should be a useful laboratory test procedure for screening attractants.
β3: A New Member of Nicotinic Acetylcholine Receptor Gene Family Is Expressed in Brain (1989)

Abstract Screening of a rat brain cDNA library with a radiolabeled probe made from an alpha 3 cDNA (Boulter, J., Evans, K., Goldman, D., Martin, G., Treco, D., Heinemanns, S., and Patrick, J. (1986) Nature 319, 368-374) resulted in the isolation of a clone whose sequence encodes a protein, beta 3, which is homologous (40-55% amino acid sequence identity) to previously described neuronal nicotinic acetylcholine receptor subunits. The encoded protein has structural features found in other nicotinic acetylcholine receptor (nAChR) subunits. Two cysteine residues that correspond to cysteins 128 and 142 of the Torpedo nAChR alpha subunit are present in beta 3. Absent from beta 3 are 2 adjacent cysteine residues that correspond to cysteines 192 and 193 of the Torpedo subunit. In situ hybridization histochemistry, performed using probes derived from beta 3 cDNAs, demonstrated that the beta 3 gene is expressed in the brain. Thus, beta 3 is the fifth member of the nAChR gene family that is expressed in the brain. The pattern of beta 3 gene expression partially overlaps with that of the neuronal nAChR subunit genes alpha 3, alpha 4, or beta 2. These results lead us to propose that the beta 3 gene encodes a neuronal nAChR subunit.
Dilute acid pretreatment of biomass at high solids concentrations (1986)

The dilute acid pretreatment of biomass (aspen wood and wheat straw) at high solids concentrations (up to 40 weight percent) has been investigated. It produces a concentrated monomeric soluble sugar stream (mainly xylose) with little degradation of the available sugars and a solid residue containing cellulose and lignin. The cellulose remaining in the residue from both aspen and straw pretreated at either 140 degrees or 160 degrees was highly digestible with commercial available enzymes. A somewhat higher acid consumption for wheat straw compared with that for aspen can be alleviated by a cation-removal step.
Ventilation from four-dimensional computed tomography: density versus Jacobian methods (2010)

Two calculation methods to produce ventilation images from four-dimensional computed tomography (4DCT) acquired without added contrast have been reported. We reported a method to obtain ventilation images using deformable image registration (DIR) and the underlying CT density information. A second method performs the ventilation image calculation from the DIR result alone, using the Jacobian determinant of the deformation field to estimate the local volume changes resulting from ventilation. For each of these two approaches, there are variations on their implementation. In this study, two implementations of the Jacobian-based methodology are evaluated, as well as a single density change-based model for calculating the physiologic specific ventilation from 4DCT. In clinical practice, (99m)Tc-labeled aerosol single photon emission computed tomography (SPECT) is the standard method used to obtain ventilation images in patients. In this study, the distributions of ventilation obtained from the CT-based ventilation image calculation methods are compared with those obtained from the clinical standard SPECT ventilation imaging. Seven patients with 4DCT imaging and standard (99m)Tc-labeled aerosol SPECT/CT ventilation imaging obtained on the same day as part of a prospective validation study were selected. The results of this work demonstrate the equivalence of the Jacobian-based methodologies for quantifying the specific ventilation on a voxel scale. Additionally, we found that both Jacobian- and density-change-based methods correlate well with global measurements of the resting tidal volume. Finally, correlation with the clinical SPECT was assessed using the Dice similarity coefficient, which showed statistically higher (p-value < 10(-4)) correlation between density-change-based specific ventilation and the clinical reference than did either Jacobian-based implementation.
Effects of Feeding Spodoptera littoralis on Lima Bean Leaves. II. Continuous Mechanical Wounding Resembling Insect Feeding Is Sufficient to Elicit Herbivory-Related Volatile Emission (2005)

Herbivore feeding elicits defense responses in infested plants, including the emission of volatile organic compounds that can serve as indirect defense signals. Until now, the contribution of plant tissue wounding during the feeding process in the elicitation of defense responses has not been clear. For example, in lima bean (Phaseolus lunatus), the composition of the volatiles induced by both the insect caterpillar Spodoptera littoralis and the snail Cepaea hortensis is very similar. Thus, a mechanical caterpillar, MecWorm, has been designed and used in this study, which very closely resembles the herbivore-caused tissue damage in terms of similar physical appearance and long-lasting wounding period on defined leaf areas. This mode of treatment was sufficient to induce the emission of a volatile organic compound blend qualitatively similar to that as known from real herbivore feeding, although there were significant quantitative differences for a number of compounds. Moreover, both the duration and the area that has been mechanically damaged contribute to the induction of the whole volatile response. Based on those two parameters, time and area, which can replace each other to some extent, a damage level can be defined. That damage level exhibits a close linear relationship with the accumulation of fatty acid-derived volatiles and monoterpenes, while other terpenoid volatiles and methyl salicylate respond in a nonlinear manner. The results strongly suggest that the impact of mechanical wounding on the induction of defense responses during herbivore feeding was until now underestimated. Controlled and reproducible mechanical damage that strongly resembles the insect's feeding process represents a valuable tool for analyzing the role of the various signals involved in the induction of plant defense reactions against herbivory.
Erratum: Sequence Space Localization in the Immune System Response to Vaccination and Disease [Phys. Rev. Lett.91, 068101 (2003) (2003)

Received 21 August 2003DOI:https://doi.org/10.1103/PhysRevLett.91.229902©2003 American Physical Society