gebhart/patrepeval huggingface dataset:
MSRE-PCR for analysis of gene-specific DNA methylation (2005)

Abnormal DNA methylation is observed in certain promoters of neoplastic cells, although the likelihood of methylation for each individual promoter varies. Simultaneous analysis of many promoters in the same sample can allow use of statistical methods for identification of neoplasia. Here we describe an assay for such analysis, based on digestion of genomic DNA with methylation-sensitive restriction enzyme and multiplexed PCR with gene-specific primers (MSRE-PCR). MSRE-PCR includes extensive digestion of genomic DNA (uncut fragments cannot be identified by PCR), can be applied to dilute samples (<1 pg/microl), requires limited amount of starting material (42 pg or genomic equivalent of seven cells) and can identify methylation in a heterogeneous mix containing <2% of cells with methylated fragments. When applied to 53 promoters of breast cancer cell lines MCF-7, MDA-MB-231 and T47D, MSRE-PCR correctly identified the methylation status of genes analyzed by other techniques. For selected genes results of MSRE-PCR were confirmed by methylation-specific PCR and bisulfite sequencing. The assay can be configured for any number of desired targets in any user-defined set of genes.
A digital MAC decoder for the display of a 16/9 aspect ratio picture on a conventional TV receiver (1988)

The compatibility of the MAC (multiplex analog component) decoder, intended for eventual use with HDTV (high-definition television) pictures of 16/9 aspect ratio, with current 4/3 TV pictures is considered. A system is described that will be included in a conventional MAC decoder to provide aspect ratio adaptation at the receiver side. The hardware structure of the MAC decoder, which will allow two ways of displaying the picture when the program is broadcast in 16/9, is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multi-view image and ToF sensor fusion for dense 3D reconstruction (2009)

Multi-view stereo methods frequently fail to properly reconstruct 3D scene geometry if visible texture is sparse or the scene exhibits difficult self-occlusions. Time-of-Flight (ToF) depth sensors can provide 3D information regardless of texture but with only limited resolution and accuracy. To find an optimal reconstruction, we propose an integrated multi-view sensor fusion approach that combines information from multiple color cameras and multiple ToF depth sensors. First, multi-view ToF sensor measurements are combined to obtain a coarse but complete model. Then, the initial model is refined by means of a probabilistic multi-view fusion framework, optimizing over an energy function that aggregates ToF depth sensor information with multi-view stereo and silhouette constraints. We obtain high quality dense and detailed 3D models of scenes challenging for stereo alone, while simultaneously reducing complex noise of ToF sensors.
&lt;title&gt;Highly automated nonparametric statistical learning for autonomous target recognition&lt;/title&gt; (1992)

Image pattern recognition is presented as three sequential tasks: feature extraction, object plausibility estimation (determining class likelihoods), and decision processing. Several data- driven techniques yield discriminant functions to produce object plausibility estimates from image features, including traditional statistical methods and neural network approaches. A statistical learning algorithm which integrates multiple-regression algorithms, functional networking strategies, and a statistical modeling criterion is presented. It provides a non- parametric learning algorithm for the synthesis of discriminant functions. Image understanding tasks such as object plausibility estimation require robust modeling techniques to deal with the uncertainty prevalent in real-world data. Specifically, these complex tasks require robust and cost-effective techniques to successfully integrate multi-source information. AbTech and others have shown that implementation of the statistical learning concepts discussed provide a modeling approach ideal for information fusion tasks such as autonomous object recognition for tactical targets and space-based assets. The results of using this approach to develop a prototype aircraft recognition system is presented.
Fiber based organic photovoltaic devices (2008)

A fiber-shaped organic photovoltaic cell is demonstrated, utilizing concentric thin films of small molecular organic compounds. Illuminated at normal incidence to the fiber axis through a thin metal electrode, the cell exhibits 0.5% power conversion efficiency, compared to 0.76% for a planar control device. The fiber device efficiency is nearly independent of illumination angle, increasing its power generation over the planar counterpart for diffuse illumination. Losses due to partial shading of the fiber surface are minimal, while the coated fiber length is limited only by the experimental deposition chamber geometry—factors favoring scale-up to woven energy harvesting textiles.
Strategies for ocular siRNA delivery: Potential and limitations of non-viral nanocarriers (2012)

Controlling gene expression via small interfering RNA (siRNA) has opened the doors to a plethora of therapeutic possibilities, with many currently in the pipelines of drug development for various ocular diseases. Despite the potential of siRNA technologies, barriers to intracellular delivery significantly limit their clinical efficacy. However, recent progress in the field of drug delivery strongly suggests that targeted manipulation of gene expression via siRNA delivered through nanocarriers can have an enormous impact on improving therapeutic outcomes for ophthalmic applications. Particularly, synthetic nanocarriers have demonstrated their suitability as a customizable multifunctional platform for the targeted intracellular delivery of siRNA and other hydrophilic and hydrophobic drugs in ocular applications. We predict that synthetic nanocarriers will simultaneously increase drug bioavailability, while reducing side effects and the need for repeated intraocular injections. This review will discuss the recent advances in ocular siRNA delivery via non-viral nanocarriers and the potential and limitations of various strategies for the development of a 'universal' siRNA delivery system for clinical applications.
Supercritical fluid mixing: preparation of thermally sensitive polymer composites containing bioactive materials (2001)

We report the use of supercritical carbon dioxide (scCO2) to create a diverse range of polymeric composites incorporating thermal and solvent labile guest materials such as proteins; no additional co-solvents are required; the entire process can be carried out at near ambient conditions; polymer morphology is controllable; high loadings of guest species can be achieved and the protein function is retained.
Nucleotide sequence and expression in <i>Escherichia coli</i> of the gene coding for sphingomyelinase of <i>Bacillus cereus</i> (1988)

Bacillus cereus secretes phospholipases C, which hydrolyze phosphatidylcholine, sphingomyelin and phosphatidylinositol. A 7.5-kb HindIII fragment of B. cereus DNA cloned into Escherichia coli, with pUC18 as a vector, directed the synthesis of the sphingomyelin-hydrolyzing phospholipase C, sphingomyelinase. Nucleotide sequence analysis of the subfragment revealed that it contained two open reading frames in tandem. The upstream truncated open reading frame corresponds to the carboxy-terminal portion of the phosphatidylcholine-hydrolyzing phospholipase C, and the downstream open reading frame to the entire translational portion of the sphingomyelinase. The two phospholipase C genes form a gene cluster. As inferred from the DNA sequence, the B. cereus sphingomyelinase has a signal peptide of 27 amino acid residues and the mature enzyme comprises 306 amino acid residues, with a molecular mass of 34233 Da. The signal peptide of the enzyme was found to be functional in protein transport across the membrane of E. coli. The enzymatic properties of the sphingomyelinase synthesized in E. coli resemble those of the donor strain sphingomyelinase. The enzymatic activity toward sphingomyelin was enhanced 20-30-fold in the presence of MgCl2, and the adsorption of the enzyme onto erythrocyte membranes was accelerated in the presence of CaCl2.
Ocular manifestations of autoimmune disease. (2002)

Rheumatoid arthritis, juvenile rheumatoid arthritis, Sjögren's syndrome, the seronegative spondyloarthropathies, systemic lupus erythematosus, multiple sclerosis, giant cell arteritis, and Graves' disease are autoimmune disorders commonly encountered by family physicians. These autoimmune disorders can have devastating systemic and ocular effects. Ocular symptoms may include dry or red eyes, foreign-body sensation, pruritus, photophobia, pain, visual changes, and even complete loss of vision. Because a number of these diseases may initially present with ocular symptoms, physicians should maintain a high index of suspicion to make a timely diagnosis. A thorough ophthalmic examination, including visual acuity, pupillary reaction, ocular motility, confrontation field testing, external inspection, and direct ophthalmoscopy with fluorescein staining, should be completed. In the patient with the complaint of a "dry eye" or a "red eye," simple tools such as the Schirmer's test or the blanching effect of phenylephrine can be useful in diagnosis. In general, managing the systemic effects with nonsteroidal anti-inflammatory drugs, corticosteroids, and immunosuppressive agents controls the ocular symptoms. When visual function is threatened, surgical therapy may be necessary. Early and accurate diagnosis with prompt treatment or referral to an ophthalmologist may prevent systemic and ocular disabilities.
Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan (1992)

The equilibrium binding to the synthetic RNA poly(U) of a series of oligolysines containing one, two, or three tryptophans has been examined as a function of pH, monovalent salt concentration (MX), temperature, and Mg2+. Oligopeptides containing lysine (K) and tryptophan (W) of the type KWKp-NH2 and KWKp-CO2 (p = 1-8), as well as peptides containing additional tryptophans or glycines, were studied by monitoring the quenching of the peptide tryptophan fluorescence upon binding poly(U). Equilibrium association constants, K(obs), and the thermodynamic quantities delta G(o)obs, delta H(o)obs, and delta S(o)obs describing peptide-poly(U) binding were measured as well as their dependences on monovalent salt concentration, temperature, and pH. In all cases, K(obs) decreases significantly with increasing monovalent salt concentration, with (delta log K(obs)/delta log [K+]) = -0.74 (+/- 0.04)z, independent of temperature and salt concentration, where z is the net positive charge on the peptide. The origin of these salt effects is entropic, consistent with the release of counterions from the poly(U) upon formation of the complex. Upon extrapolation to 1 M K+, the value of delta G(o)obs is observed to be near zero for all oligolysines binding to poly(U), supporting the conclusion that these complexes are stabilized at lower salt concentrations due to the increase in entropy accompanying the release of monovalent counterions from the poly(U). Only the net peptide charge appears to influence the thermodynamics of these interactions, since no effects of peptide charge distribution were observed. The binding of poly(U) to the monotryptophan peptides displays interesting behavior as a function of the peptide charge. The extent of tryptophan fluorescence quenching, Qmax, is dependent upon the peptide charge for z less than or equal to +4, and the value of Qmax correlates with z-dependent changes in delta H(o)obs and delta S(o)obs(1 M K+), whereas for z greater than or equal to +4, Qmax, delta H(o)obs, and delta S(o)obs (1 M K+) are constant. The correlation between Qmax and delta H(o)obs and delta S(o)obs(1 M K+) suggests a context (peptide charge)-dependence of the interaction of the peptide tryptophan with poly(U). However the interaction of the peptide tryptophan does not contribute substantially to delta G(o)obs for any of the peptides, independent of z, due to enthalpy-entropy compensations. Each of the tryptophans in multiple Trp-containing peptides appear to bind to poly(U) independently, with delta H(o)Trp = -2.9 +/- 0.7, although delta G(o)Trp is near zero due to enthalpy-entropy compensations.(ABSTRACT TRUNCATED AT 400 WORDS)
&lt;i&gt;SEC31A-ALK&lt;/i&gt; Fusion Gene in Lung Adenocarcinoma (2015)

Anaplastic lymphoma kinase (ALK) fusion is a common mechanism underlying pathogenesis of non-small cell lung carcinoma (NSCLC) where these rearrangements represent important diagnostic and therapeutic targets. In this study, we found a new ALK fusion gene, SEC31A-ALK, in lung carcinoma from a 53-year-old Korean man. The conjoined region in the fusion transcript was generated by the fusion of SEC31A exon 21 and ALK exon 20 by genomic rearrangement, which contributed to generation of an intact, in-frame open reading frame. SEC31A-ALK encodes a predicted fusion protein of 1,438 amino acids comprising the WD40 domain of SEC31A at the N-terminus and ALK kinase domain at the C-terminus. Fluorescence in situ hybridization studies suggested that SEC31A-ALK was generated by an unbalanced genomic rearrangement associated with loss of the 3'-end of SEC31A. This is the first report of SEC31A-ALK fusion transcript in clinical NSCLC, which could be a novel diagnostic and therapeutic target for patients with NSCLC.
Glycosylation Increases the Thermostability of Human Aquaporin 10 Protein (2011)

Human aquaporin10 (hAQP10) is a transmembrane facilitator of both water and glycerol transport in the small intestine. This aquaglyceroporin is located in the apical membrane of enterocytes and is believed to contribute to the passage of water and glycerol through these intestinal absorptive cells. Here we overproduced hAQP10 in the yeast Pichia pastoris and observed that the protein is glycosylated at Asn-133 in the extracellular loop C. This finding confirms one of three predicted glycosylation sites for hAQP10, and its glycosylation is unique for the human aquaporins overproduced in this host. Nonglycosylated protein was isolated using both glycan affinity chromatography and through mutating asparagine 133 to a glutamine. All three forms of hAQP10 where found to facilitate the transport of water, glycerol, erythritol, and xylitol, and glycosylation had little effect on functionality. In contrast, glycosylated hAQP10 showed increased thermostability of 3-6 °C compared with the nonglycosylated protein, suggesting a stabilizing effect of the N-linked glycan. Because only one third of hAQP10 was glycosylated yet the thermostability titration was mono-modal, we suggest that the presence of at least one glycosylated protein within each tetramer is sufficient to convey an enhanced structural stability to the remaining hAQP10 protomers of the tetramer.
Multimedia image display (1997)

The development of multimedia image review stations offers the cardiologist the ability to review multiple image sets in a single setting rather than moving from one review station to another. To accomplish this goal there are three essential barriers: 1) memory requirements for digital images; 2) standardization of data format; and 3) practical user interfaces. Image compression algorithms can be used to overcome the digital barrier; however, these must be used cautiously so as to not adversely affect image quality. The lack of standardization is being addressed by the implementation of the Digital Communication in Medicine (DICOM) standard, and practical user interfaces are being developed every day with the widespread implementation of World Wide Web technology. These solutions will allow the clinician to review all of a patient's image data in one location, such as in the office, on the nursing unit, or at home.
1.5-µm band quantum-correlated photon pair generation in dispersion-shifted fiber: suppression of noise photons by cooling fiber (2005)

Spontaneous four-wave mixing in a dispersion-shifted fiber (DSF) is a promising approach for generating quantum-correlated photon pairs in the 1.5 microm band. However, it has been reported that noise photons generated by the spontaneous Raman scattering process degrade the quantum correlation of the generated photons. This paper describes the characteristics of quantum-correlated photon pair generation in a DSF cooled by liquid nitrogen. With this technique, the number of noise photons was sufficiently suppressed and the ratio of true coincidence to accidental coincidence was increased to ~30.
Nanotools for Neuroscience and Brain Activity Mapping (2013)

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.
A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules (2010)

Prostate specific membrane antigen (PSMA) is a membrane-bound glutamate carboxypeptidase overexpressed in many forms of prostate cancer. Our laboratory has recently disclosed a class of small molecules, called ARM-Ps (antibody-recruiting molecule targeting prostate cancer) that are capable of enhancing antibody-mediated immune recognition of prostate cancer cells. Interestingly, during the course of these studies, we found ARM-Ps to exhibit extraordinarily high potencies toward PSMA, compared to previously reported inhibitors. Here, we report in-depth biochemical, crystallographic, and computational investigations which elucidate the origin of the observed affinity enhancement. These studies reveal a previously unreported arene-binding site on PSMA, which we believe participates in an aromatic stacking interaction with ARMs. Although this site is composed of only a few amino acid residues, it drastically enhances small molecule binding affinity. These results provide critical insights into the design of PSMA-targeted small molecules for prostate cancer diagnosis and treatment; more broadly, the presence of similar arene-binding sites throughout the proteome could prove widely enabling in the optimization of small molecule-protein interactions.
Genetically manipulated mouse models of lung disease: potential and pitfalls (2011)

Gene targeting in mice (transgenic and knockout) has provided investigators with an unparalleled armamentarium in recent decades to dissect the cellular and molecular basis of critical pathophysiological states. Fruitful information has been derived from studies using these genetically engineered mice with significant impact on our understanding, not only of specific biological processes spanning cell proliferation to cell death, but also of critical molecular events involved in the pathogenesis of human disease. This review will focus on the use of gene-targeted mice to study various models of lung disease including airways diseases such as asthma and chronic obstructive pulmonary disease, and parenchymal lung diseases including idiopathic pulmonary fibrosis, pulmonary hypertension, pneumonia, and acute lung injury. We will attempt to review the current technological approaches of generating gene-targeted mice and the enormous dataset derived from these studies, providing a template for lung investigators.
FACL4, a New Gene Encoding Long-Chain Acyl-CoA Synthetase 4, Is Deleted in a Family with Alport Syndrome, Elliptocytosis, and Mental Retardation (1998)

We observed a family in which two boys were diagnosed with Alport syndrome, elliptocytosis, and mental retardation and carried a large deletion of the Xq22.3-q23 region, encompassing the COL4A5 gene. This suggests the possibility of a new contiguous gene syndrome. In an attempt to characterize the genes contributing to this complex phenotype, we have isolated a gene encoding a new long-chain acyl-CoA synthetase (FACL4 or LACS4) from the region deleted in these patients. Among several ESTs identified by searching the human gene map database maintained at the National Center for Biotechnology Information, using the map position as a query, only one was deleted in the patients. RACE products containing the entire ORF were subsequently generated. Northern blot analysis showed a 5-kb mRNA expressed in several tissues except for liver and lung. Brain shows a longer transcript, possibly reflecting the use of a brain-specific upstream ATG start codon. FACL4 encodes a predicted protein product of 670 amino acids (711 in brain), with a remarkable level of conservation compared to the rat acyl-CoA synthetases ACS4 and brain-specific ACS3 protein sequences. We are investigating the possibility that the absence of this enzyme may play a role in the development of mental retardation or other signs associated with Alport syndrome in the family.
High-Speed Spiral-Scan Echo Planar NMR Imaging-I (1986)

An improved echo planar high-speed imaging technique using spiral scan is presented and experimental advantages are discussed. This proposed spiral-scan echo planar imaging (SEPI) technique employs two linearly increasing sinusoidal gradient fields, which results in a spiral trajectory in the spatial frequency domain (k-domain) that covers the entire frequency domain uniformly. The advantages of the method are: 1) circularly symmetric T2 weighting, resulting in a circularly symmetric point spread function in the image domain; 2) elimination of discontinuities in gradient waveforms which in turn will reduce initial transient as well as steady-state distortions; and 3) effective rapid spiral-scan from dc to high frequency in a continuous fashion, which ensures multiple pulsing with interlacing for further resolution improvement without T2 decay image degradation. Some preliminary experimental results will be presented and further possible improvements suggested.
Growth of dark spots by interdiffusion across organic layers in organic electroluminescent devices (1996)

In order to clarify the propagation mechanism of dark spots in an organic multilayered electroluminescent device, in situ electroluminescence microscopy as well as photoluminescence (PL) microscopy and Auger electron spectroscopy of the degraded device was carried out. The difference in local PL spectra between the dark spots and the normal surface area was also observed by using scanning near-field optical/atomic force microscopy. The growing mechanism of the dark spots was proposed from these observations.