gebhart/patrepeval huggingface dataset:
Cloning and characterization of a histone deacetylase, HDAC9 (2001)

Histone deacetylase (HDAC) catalyzes the removal of the acetyl group from the lysine residues in the N-terminal tails of nucleosomal core histones. Eight human HDACs have been identified so far. Here, we report the identification of a ninth member of the HDAC family, designated HDAC9. HDAC9 is a class II HDAC and its gene resides on human chromosome 7. HDAC9 has several alternatively spliced isoforms. One of these isoforms is histone deacetylase-related protein or myocyte enhancer-binding factor 2-interacting transcriptional repressor that we and others have previously reported and which does not possess an HDAC catalytic domain. The longest of the HDAC9 isoforms contains 1,011 aa. The isoform, designated HDAC9a, is 132 aa shorter at the C terminus than HDAC9. Also, we have identified isoforms of HDAC9 that lack the nuclear localization signal. Similar to histone deacetylase-related protein, HDAC9 transcripts are expressed at high levels in brain and skeletal muscle. The ratio of HDAC9 and HDAC9a transcripts differs among the tissues examined. HDAC9 and HDAC9a contain the HDAC catalytic domain, and Flag-tagged HDAC9 and HDAC9a possess deacetylase activity. HDAC9 and HDAC9a also repress myocyte enhancer-binding factor 2-mediated transcription. In the present study, we have identified HDAC9 and a number of alternatively spliced isoforms of HDAC9 with potentially different biological activities.
Inverse global illumination (1999)

In this paper we present a method for recovering the reflectance properties of all surfaces in a real scene from a sparse set of photographs, taking into account both direct and indirect illumination. The result is a lighting-independent model of the scene's geometry and reflectance properties, which can be rendered with arbitrary modifications to structure and lighting via traditional rendering methods. Our technique models reflectance with a lowparameter reflectance model, and allows diffuse albedo to vary arbitrarily over surfaces while assuming that non-diffuse characteristics remain constant across particular regions. The method's input is a geometric model of the scene and a set of calibrated high dynamic range photographs taken with known direct illumination. The algorithm hierarchically partitions the scene into a polygonal mesh, and uses image-based rendering to construct estimates of both the radiance and irradiance of each patch from the photographic data. The algorithm computes the expected location of specular highlights, and then analyzes the highlight areas in the images by running a novel iterative optimization procedure to recover the diffuse and specular reflectance parameters for each region. Lastly, these parameters are used in constructing high-resolution diffuse albedo maps for each surface.
Studies on Starches of High Amylose Content. Part 17. A Review of Current Concepts (1974)

Abstract This review deals with the starches of high amylose‐content from genotypes of pea, maize and barley. These starches are distinguished by abnormal granular forms and by the presence of unusual starch material. A critical review of our work in this field is presented, and we emphasize that each starch‐type is unique. Current and future problems are discussed.
Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells (2008)

Here, we report on the discovery of a locus in the human genome, which evolved by gene duplication followed by an internal DNA inversion. This locus exhibits high sequence similarity to the gene for the inducible isoform of NOS protein (NOS2A) and is transcribed into a noncoding RNA containing a region of significant antisense homology with the NOS2A mRNA. We show that this antisense transcript (anti-NOS2A RNA) is expressed in different types of brain tumors, including meningiomas and glioblastomas. More importantly, we demonstrate that the expression profiles of the anti-NOS2A RNA and the NOS2A mRNA exhibit concurrent reciprocal changes in undifferentiated human embryonic stem cells (hESCs) and in hESCs induced to differentiate into neurogenic precursors such as neurospheres. As NOS2A has a role in neurogenesis, our results suggest that the anti-NOS2A RNA is involved in the regulation of neuronal differentiation of hESCs through the modulation of NOS2A gene expression.
Targeting Wnt Signaling: Can We Safely Eradicate Cancer Stem Cells? (2010)

The Wnt signaling pathways have been conserved throughout evolution and regulate cell proliferation, morphology, motility, and fate during embryonic development. These pathways also play important roles throughout adult life to maintain homeostasis of tissues including skin, blood, intestine, and brain by regulating somatic stem cells and their niches. Aberrant regulation of the Wnt pathway leads to neoplastic proliferation in these same tissues. It has been suggested that Wnt signaling is also involved in the regulation of cancer stem cells (CSC), because there are many similarities in the signaling pathways that regulate normal adult stem cells and CSC. In this Perspective, we have focused on the Wnt/beta-catenin signaling pathway, which is the most intensively studied and best characterized Wnt signaling pathway. We provide an overview on the function of the Wnt/beta-catenin signaling pathway in CSC, and the possibility of the development of novel therapeutics to target this pathway.
The myosin-I-binding protein Acan125 binds the SH3 domain and belongs to the superfamily of leucine-rich repeat proteins (1997)

The SH3 domains of src and other nonreceptor tyrosine kinases have been shown to associate with the motif PXXP, where P and X stand for proline and an unspecified amino acid, but a motif that binds to the SH3 domain of myosin has thus far not been characterized. We previously showed that the SH3 domain of Acanthamoeba myosin-IC interacts with the protein Acan125. We now report that the Acan125 protein sequence contains two tandem consensus PXXP motifs near the C terminus. To test for binding, we expressed a polypeptide, AD3p, which includes 344 residues of native C-terminal sequence and a mutant polypeptide, AD3delta977-994p, which lacks the sequence RPKPVPPPRGAKPAPPPR containing both PXXP motifs. The SH3 domain of Acanthamoeba myosin-IC bound AD3p and not AD3delta977-994p, showing that the PXXP motifs are required for SH3 binding. The sequence of Acan125 is related overall to a protein of unknown function coded by Caenorhabditis elegans gene K07G5.1. The K07G5.1 gene product contains a proline-rich segment similar to the SH3 binding motif found in Acan125. The aligned sequences show considerable conservation of leucines and other hydrophobic residues, including the spacing of these residues, which matches a motif for leucine-rich repeats (LRRs). LRR domains have been demonstrated to be sites for ligand binding. Having an LRR domain and an SH3-binding domain, Acan125 and the C. elegans homologue define a novel family of bifunctional binding proteins.
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method (2007)

The C2H2 zinc finger is the most commonly utilized framework for engineering DNA-binding domains with novel specificities. Many different selection strategies have been developed to identify individual fingers that possess a particular DNA-binding specificity from a randomized library. In these experiments, each finger is selected in the context of a constant finger framework that ensures the identification of clones with a desired specificity by properly positioning the randomized finger on the DNA template. Following a successful selection, multiple zinc-finger clones are typically recovered that share similarities in the sequences of their DNA-recognition helices. In principle, each of the clones isolated from a selection is a candidate for assembly into a larger multi-finger protein, but to date a high-throughput method for identifying the most specific candidates for incorporation into a final multi-finger protein has not been available. Here we describe the development of a specificity profiling system that facilitates rapid and inexpensive characterization of engineered zinc-finger modules. Moreover, we demonstrate that specificity data collected using this system can be employed to rationally design zinc fingers with improved DNA-binding specificities.
Posterior C1-C2 Transarticular Screw Fixation for Atlantoaxial Arthrodesis (1998)

Rigidly fixating C1-C2 instability with transarticular screws was associated with a significantly higher fusion rate than that achieved using wired grafts alone. The risk of screw malpositioning and catastrophic vascular or neural injury is small and can be minimized by assessing the position of the foramen transversaria on preoperative computed tomographic scans and by using intraoperative fluoroscopy and frameless stereotaxy to guide the screw trajectory.
Hapten may play an important role in food allergen-related intestinal immune inflammation (2011)

There has been a significant increase in the prevalence of allergic diseases especially over the past 2 to 3 decades. However, the etiology and pathogenesis of food allergy are not fully understood. In recent years, with the huge increase in atopic disease, there has also been an increase in dietary hapten exposure. Allergic reactions to chemical haptens occur, in the overwhelming majority of cases, as an inflammatory reaction in the skin to direct contact with haptens. While reactions to haptens on other epithelial surfaces have only rarely been investigated; it is still not clear whether haptens can combine the food antigens and play a role in the induction of food allergen-related inflammation in the intestine. Further research is needed to reveal the underlying mechanism.
Expression of the c- fos Gene and of an fos -Related Gene Is Stimulated by Platelet-Derived Growth Factor (1984)

Complementary DNA clones of genes induced by platelet-derived growth factor (PDGF) in BALB/c-3T3 cells were isolated; one such clone contains a domain having nucleotide sequence homology with the third exon of c-fos. This nucleotide sequence homology is reflected in the predicted amino acid sequences of the gene products. Under low stringency conditions, the mouse v-fos gene cross-hybridizes with the PDGF-inducible complementary DNA clone. However, the messenger RNA transcripts of mouse c-fos and the new fos-related gene can be distinguished by gel electrophoresis and by S1 nuclease analysis. Expression of the authentic c-fos gene is induced by PDGF and superinduced by the combination of PDGF and cycloheximide.
Dielectrophoretic separation of Bacillus subtilis spores from environmental diesel particles (2006)

Isolation of pathogenic bacteria from non-biological material of similar size is a vital sample preparation step in the identification of such organisms, particularly in the context of detecting bio-terrorist attacks. However, many detection methods are impeded by particulate contamination from the environment such as those from engine exhausts. In this paper we use dielectrophoresis--the induced motion of particles in non-uniform fields--to successfully remove over 99% of diesel particulates acquired from environmental samples, whilst letting bacterial spores of B. subtilis pass through the chamber largely unimpeded. We believe that such a device has tremendous potential as a precursor to a range of detection methods, improving the signal-to-noise ratio and ultimately improving detection rates.
AutoAugment: Learning Augmentation Policies from Data (2018)

Data augmentation is an effective technique for improving the accuracy of modern image classifiers. However, current data augmentation implementations are manually designed. In this paper, we describe a simple procedure called AutoAugment to automatically search for improved data augmentation policies. In our implementation, we have designed a search space where a policy consists of many sub-policies, one of which is randomly chosen for each image in each mini-batch. A sub-policy consists of two operations, each operation being an image processing function such as translation, rotation, or shearing, and the probabilities and magnitudes with which the functions are applied. We use a search algorithm to find the best policy such that the neural network yields the highest validation accuracy on a target dataset. Our method achieves state-of-the-art accuracy on CIFAR-10, CIFAR-100, SVHN, and ImageNet (without additional data). On ImageNet, we attain a Top-1 accuracy of 83.5% which is 0.4% better than the previous record of 83.1%. On CIFAR-10, we achieve an error rate of 1.5%, which is 0.6% better than the previous state-of-the-art. Augmentation policies we find are transferable between datasets. The policy learned on ImageNet transfers well to achieve significant improvements on other datasets, such as Oxford Flowers, Caltech-101, Oxford-IIT Pets, FGVC Aircraft, and Stanford Cars.
New enzyme-linked immunosorbent assay for glycocalicin in plasma. (1991)

A new sandwich-type enzyme-linked immunosorbent assay for quantifying glycocalicin, a proteolytic fragment of platelet membrane glycoprotein Ib, is described. The assay is based on the use of two monoclonal antibodies raised against glycoprotein Ib and involves the avidin-biotin technique. The detection limit is 7 micrograms/L and the range of glycocalicin determined in plasma is 0.01 to 1 mg/L. Assay time is 2 h. The intra-assay CV ranged from 3.6% to 5.2%, the interassay CV from 5.4% to 8.0%. Analytical recovery of purified glycocalicin added to a plasma pool averaged 96%. In 36 healthy subjects, the mean glycocalicin concentration in plasma was 0.36 (SD 0.07) mg/L (2.7 nmol/L). We conclude that this assay is suitable for measuring glycocalicin in plasma and is also more sensitive and precise than the previously published immunoassays based on competitive binding assay.
Determination of Disulfide Bond Assignments andN-Glycosylation Sites of the Human Gastrointestinal Carcinoma Antigen GA733-2 (CO17-1A, EGP, KS1-4, KSA, and Ep-CAM) (2001)

The GA733-2 antigen is a cell surface glycoprotein highly expressed on most human gastrointestinal carcinoma and at a lower level on most normal epithelia. It is an unusual cell-cell adhesion protein that does not exhibit any obvious relationship to the four known classes of adhesion molecules. In this study, the disulfide-bonding pattern of the GA733-2 antigen was determined using matrix-assisted laser desorption/ionization mass spectrometry and N-terminal sequencing of purified tryptic peptides treated with 2-[2'-nitrophenylsulfonyl]-3-methyl-3-bromoindolenine or partially reduced and alkylated. Numbering GA733-2 cysteines sequentially from the N terminus, the first three disulfide linkages are Cys1-Cys4, Cys2-Cys6, and Cys3-Cys5, which is a novel pattern for a cysteine-rich domain instead of the expected epidermal growth factor-like disulfide structure. The next three disulfide linkages are Cys7-Cys8, Cys9-Cys10, and Cys11-Cys12, consistent with the recently determined disulfide pattern of the thyroglobulin type 1A domain of insulin-like growth factor-binding proteins 1 and 6. Analysis of glycosylation sites showed that GA733-2 antigen contained N-linked carbohydrate but that no O-linked carbohydrate groups were detected. Of the three potential N-linked glycosylation sites, Asn175 was not glycosylated, whereas Asn88 was completely glycosylated, and Asn51 was partially glycosylated. These data show that the extracellular domain of the GA733-2 antigen consists of three distinct domains; a novel cysteine-rich N-terminal domain (GA733 type 1 motif), a cysteine-rich thyroglobulin type 1A domain (GA733 type 2 motif), and a unique nonglycosylated domain without cysteines (GA733 type 3 motif).
SLC4 base (HCO3−, CO32−) transporters: classification, function, structure, genetic diseases, and knockout models (2006)

In prokaryotic and eukaryotic organisms, biochemical and physiological processes are sensitive to changes in H + activity. For these processes to function optimally, a variety of proteins have evolved that transport H + /base equivalents across cell and organelle membranes, thereby maintaining the pH of various intracellular and extracellular compartments within specific limits. The SLC4 family of base (HCO 3 − , CO 3 2 − ) transport proteins plays an essential role in mediating Na + - and/or Cl − -dependent base transport in various tissues and cell types in mammals. In addition to pH regulation, specific members of this family also contribute to vectorial transepithelial base transport in several organ systems including the kidney, pancreas, and eye. The importance of these transporters in mammalian cell biology is highlighted by the phenotypic abnormalities resulting from spontaneous SLC4 mutations in humans and targeted deletions in murine knockout models. This review focuses on recent advances in our understanding of the molecular organization and functional properties of SLC4 transporters and their role in disease.
Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids (2004)

The nucleic acid exchange reaction is a common feature for genetic recombination, DNA replication and transcription. Due to the fact that in the strand-exchange reactions the reactant and product molecules have similar or identical nucleotide sequences, the reaction is undetectable. As a rule, the nucleic acids with radioactive or fluorescence labels are used in such studies. Besides the fact that the labels can perturb the reaction and pose a health risk to the investigators, the assays usually involve extra experimental steps: quenching the reaction, separation, visualization and quantification of the products. Here, we describe a straightforward, direct and precise method to study strand-exchange reaction of unlabeled nucleic acids by real-time measurements of optical absorption. The method takes advantage of the property of some guanine-rich oligonucleotides to adopt monomolecular quadruplex conformation in the presence of certain cations. The conformation is characterized by significant absorption in long-wavelength range of the ultraviolet region where usually other secondary structures are transparent. The 'signal' oligonucleotide is incorporated into reactant duplex by annealing with target sequence. Adding the replacement sequence initiates the release of the 'signal' oligonucleotide into solution, which is accompanied by ultraviolet absorption in long-wavelength range.
Micro‐ and Nanopatterning of Functional Organic Monolayers on Oxide‐Free Silicon by Laser‐Induced Photothermal Desorption (2010)

The photothermal laser patterning of functional organic monolayers, prepared on oxide-free hydrogen-terminated silicon, and subsequent backfilling of the laser-written lines with a second organic monolayer that differs in its terminal functionality, is described. Since the thermal monolayer decomposition process is highly nonlinear in the applied laser power density, subwavelength patterning of the organic monolayers is feasible. After photothermal laser patterning of hexadecenyl monolayers, the lines freed up by the laser are backfilled with functional acid fluoride monolayers. Coupling of cysteamine to the acid fluoride groups and subsequent attachment of Au nanoparticles allows easy characterization of the functional lines by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Depending on the laser power and writing speed, functional lines with widths between 1.1 μm and 250 nm can be created. In addition, trifluoroethyl-terminated (TFE) monolayers are also patterned. Subsequently, the decomposed lines are backfilled with a nonfunctional hexadecenyl monolayer, the TFE stripes are converted into thiol stripes, and then finally covered with Au nanoparticles. By reducing the lateral distance between the laser lines, Au-nanoparticle stripes with widths close to 100 nm are obtained. Finally, in view of the great potential of this type of monolayer in the field of biosensing, the ease of fabricating biofunctional patterns is demonstrated by covalent binding of fluorescently labeled oligo-DNA to acid-fluoride-backfilled laser lines, which--as shown by fluorescence microscopy--is accessible for hybridization.
A novel antioxidant alleviates heat hyperalgesia in rats with an experimental painful peripheral neuropathy (1996)

Rats with an experimental painful peripheral neuropathy (the chronic injury (CCI) model) display heatevoked hyperalgesia. There is now considerable evidence that nitric oxide (NO) and nitric oxide synthase are involved in the development of hyperalgesia in acute inflammatory pain states. The mechanisms responsible for hyperalgesia in chronic pain state may involve not only NO itself, but also peroxynitrite, the product of its reaction with superoxide radical, .O2- that can lead to the formation of the free radicals .OH and NO2- Under normal metabolic conditions, the cellular enzyme super oxide dismutase (SOD) provides physiological defence against superoxide radicals. TEMPOL mimics SOD and acts as a catalyst to remove the .O2- radical. The present work shows the efficacy of a stable nitroxide radical, 4-hydroxy-2, 2, 6, 6-tetramethylpiperidine-1-oxyl (TEMPOL), against heat-evoked hyperalgesia.
Cellular Uptake Properties of a 2‵-Amino/2‵-O-Methyl-Modified Chimeric Hammerhead Ribozyme Targeted to the Epidermal Growth Factor Receptor mRNA (1997)

Catalytic RNA or ribozymes have important potential applications as molecular biological tools in the study of gene expression and as therapeutic inhibitors of disease-causing genes. Very little is known, however, about the cellular uptake mechanisms of exogenously delivered synthetic ribozymes. In this study, we have characterized the uptake properties of a synthetic, 2'-O-methyl-modified ribozyme containing U4/U7 amino groups within the catalytic core of the hammerhead motif. The cellular uptake of the internally [32P]-radiolabeled hammerhead ribozyme in U87-MG glioma cells was temperature, energy, and pH dependent and involved an active process that could be competed with cold ribozyme of the same chemistry and sequence, an all 2'-O-methyl-modified ribozyme of the same sequence, antisense PS-ODNs, and a variety of other polyanions (salmon sperm DNA, spermidine, dextran sulfate, and heparin). Subcellular distribution studies of fluorescently labeled ribozymes confirmed an extranuclear, punctate localization similar to that observed for an endosomal marker, dextran. Our study highlights that hammerhead ribozymes, despite exhibiting a defined secondary structure, enter cells by an endocytic mechanism that appears to be similar to that reported for a variety of antisense ODNs. These observations should facilitate the development of more efficient delivery systems.
Evaluation of an Interferon Inducer in Viral Respiratory Disease (1972)

To evaluate the effect of an interferon inducer on respiratory tract virus infection, poly l.poly C was administered intranasally to volunteers for a seven-day period beginning one day prior to inoculation of rhinovirus 13 or type A2 influenza virus/Hong Kong/68. In three separate trials, toxic effects were not detected and there was a small, but definite, reduction in symptoms of upper-respiratory tract illness associated with drug treatment. However, there was a variable effect on the pattern of virus infection. In only one of the two rhinovirus studies was a reduction of virus shedding observed. Treatment did not decrease the shedding of type A2 influenza virus. The minimal amounts of nasal interferon stimulated by the intranasally administered poly l.poly C may have been responsible for the less-than-optimal results obtained.