gebhart/patrepeval huggingface dataset:
Brain cDNA clone for human cholinesterase. (1987)

A cDNA library from human basal ganglia was screened with oligonucleotide probes corresponding to portions of the amino acid sequence of human serum cholinesterase (EC 3.1.1.8). Five overlapping clones, representing 2.4 kilobases, were isolated. The sequenced cDNA contained 207 base pairs of coding sequence 5' to the amino terminus of the mature protein in which there were four ATG translation start sites in the same reading frame as the protein. Only the ATG coding for Met-(-28) lay within a favorable consensus sequence for functional initiators. There were 1722 base pairs of coding sequence corresponding to the protein found circulating in human serum. The amino acid sequence deduced from the cDNA exactly matched the 574 amino acid sequence of human serum cholinesterase, as previously determined by Edman degradation. Therefore, our clones represented cholinesterase (EC 3.1.1.8) rather than acetylcholinesterase (EC 3.1.1.7). It was concluded that the amino acid sequences of cholinesterase from two different tissues, human brain and human serum, were identical. Hybridization of genomic DNA blots suggested that a single gene, or very few genes, coded for cholinesterase.
Vertical electrochemical transistor based on poly(3-hexylthiophene) and cyanoethylpullulan (2004)

We have fabricated an all-solid state and vertical electrochemical transistor, which employs poly(3-hexylthiophene) and cyanoethylpullulan as the semiconducting layer and solid electrolyte, respectively. The device has the same structure as a vertical field effect transistor, but can function using a different mechanism of operation in which the doping and dedoping to polythiophene are controlled by the gate voltage and the source–drain current is modulated by the doping–dedoping process. The transistor behaves like p-channel accumulation-mode devices and has a switching speed of 50Hz in vacuum.
The American Cancer Society guidelines for breast screening with magnetic resonance imaging (2008)

The ACS guidelines for breast MRI screening may systematically exclude MRI screening for many women who have a substantial risk for BRCA mutation. The current results demonstrated a need for greater awareness of breast cancer risk factors in the screening mammography population, so that high-risk women can be identified and given access to genetic testing and counseling regarding all risk-reducing interventions.
Characterization and Subcellular Targeting of GCaMP-Type Genetically-Encoded Calcium Indicators (2008)

Genetically-encoded calcium indicators (GECIs) hold the promise of monitoring [Ca(2+)] in selected populations of neurons and in specific cellular compartments. Relating GECI fluorescence to neuronal activity requires quantitative characterization. We have characterized a promising new genetically-encoded calcium indicator-GCaMP2-in mammalian pyramidal neurons. Fluorescence changes in response to single action potentials (17+/-10% DeltaF/F [mean+/-SD]) could be detected in some, but not all, neurons. Trains of high-frequency action potentials yielded robust responses (302+/-50% for trains of 40 action potentials at 83 Hz). Responses were similar in acute brain slices from in utero electroporated mice, indicating that long-term expression did not interfere with GCaMP2 function. Membrane-targeted versions of GCaMP2 did not yield larger signals than their non-targeted counterparts. We further targeted GCaMP2 to dendritic spines to monitor Ca(2+) accumulations evoked by activation of synaptic NMDA receptors. We observed robust DeltaF/F responses (range: 37%-264%) to single spine uncaging stimuli that were correlated with NMDA receptor currents measured through a somatic patch pipette. One major drawback of GCaMP2 was its low baseline fluorescence. Our results show that GCaMP2 is improved from the previous versions of GCaMP and may be suited to detect bursts of high-frequency action potentials and synaptic currents in vivo.
Hardware transactional memory for GPU architectures (2011)

Graphics processor units (GPUs) are designed to efficiently exploit thread level parallelism (TLP), multiplexing execution of 1000s of concurrent threads on a relatively smaller set of single-instruction, multiple-thread (SIMT) cores to hide various long latency operations. While threads within a CUDA block/OpenCL workgroup can communicate efficiently through an intra-core scratchpad memory, threads in different blocks can only communicate via global memory accesses. Programmers wishing to exploit such communication have to consider data-races that may occur when multiple threads modify the same memory location. Recent GPUs provide a form of inter-block communication through atomic operations for single 32-bit/64-bit words. Although fine-grained locks can be constructed from these atomic operations, synchronization using locks is prone to deadlock. In this paper, we propose to solve these problems by extending GPUs to support transactional memory (TM). Major challenges include supporting 1000s of concurrent transactions and committing non-conflicting transactions in parallel. We propose KILO TM, a novel hardware TM design for GPUs that scales to 1000s of concurrent transactions. Without cache coherency hardware to depend on, it uses word-level, value-based conflict detection to avoid broadcast communication and reduce on-chip storage overhead. It employs speculative validation using a novel bloom filter organization to increase transaction commit parallelism. For a set of TM-enhanced GPU applications, KILO TM captures 59% of the performance of fine-grained locking, and is on average 128x faster than executing all transactions serially, for an estimated hardware area overhead of 0.5% of a commercial GPU.
Reconstruction and Quantification of the Carotid Artery Bifurcation From 3-D Ultrasound Images (2004)

Three-dimensional (3-D) ultrasound is a relatively new technique, which is well suited to imaging superficial blood vessels, and potentially provides a useful, noninvasive method for generating anatomically realistic 3-D models of the peripheral vasculature. Such models are essential for accurate simulation of blood flow using computational fluid dynamics (CFD), but may also be used to quantify atherosclerotic plaque more comprehensively than routine clinical methods. In this paper, we present a spline-based method for reconstructing the normal and diseased carotid artery bifurcation from images acquired using a freehand 3-D ultrasound system. The vessel wall (intima-media interface) and lumen surfaces are represented by a geometric model defined using smoothing splines. Using this coupled wall-lumen model, we demonstrate how plaque may be analyzed automatically to provide a comprehensive set of quantitative measures of size and shape, including established clinical measures, such as degree of (diameter) stenosis. The geometric accuracy of 3-D ultrasound reconstruction is assessed using pulsatile phantoms of the carotid bifurcation, and we conclude by demonstrating the in vivo application of the algorithms outlined to 3-D ultrasound scans from a series of patient carotid arteries.
Histograms of Oriented Gradients for Human Detection (2005)

We study the question of feature sets for robust visual object recognition; adopting linear SVM based human detection as a test case. After reviewing existing edge and gradient based descriptors, we show experimentally that grids of histograms of oriented gradient (HOG) descriptors significantly outperform existing feature sets for human detection. We study the influence of each stage of the computation on performance, concluding that fine-scale gradients, fine orientation binning, relatively coarse spatial binning, and high-quality local contrast normalization in overlapping descriptor blocks are all important for good results. The new approach gives near-perfect separation on the original MIT pedestrian database, so we introduce a more challenging dataset containing over 1800 annotated human images with a large range of pose variations and backgrounds.
Amyloid β‐abrogated TrkA ubiquitination in PC12 cells analogous to Alzheimer's disease (2015)

Amyloid beta (Aβ) protein is the primary proteinaceous deposit found in the brains of patients with Alzheimer's disease (AD). Evidence suggests that Aβ plays a central role in the development of AD pathology. Here, we show in PC12 cells, Aβ impairs tropomyosin receptor kinase A (TrkA) ubiquitination, phosphorylation, and its association with p75(NTR), p62, and TRAF6 induced by nerve growth factor. The ubiquitination and tyrosine phosphorylation of TrkA was also found to be impaired in postmortem human AD hippocampus compared to control. Interestingly, the nitrotyrosylation of TrkA was increased in AD hippocampus and this explains why the phosphotyrosylation and ubiquitination of TrkA was impaired. In AD brain, the production of matrix metalloproteinase-7 (MMP-7), which cleaves proNGF, was reduced, thereby leading to the accumulation of pro-NGF and a decrease in the level of active NGF. TrkA signaling events, including Ras/MAPK and phosphatidylinositol 3-kinase (PI3K)/Akt pathways, are deactivated with Aβ and in the human AD hippocampus. Findings show that Aβ blocks the TrkA ubiquitination and downstream signaling similar to AD hippocampus. Cell survival and differentiation are essential for living organisms. We propose that under normal conditions, nerve growth factor (NGF) leads to Tropomyosin receptor kinase A (TrkA) phosphorylation, ubiquitination and its association with p75(NTR), p62 and TRAF6, thereby promoting cell survival and differentiation. In diseased conditions such as Alzheimer's, proNGF leads to nitrotyrosylation of TrkA, thereby impairing its ubiquitination and downstream signaling which results in apoptosis. TRAF6 = tumor necrosis factor receptor-associated factor 6; Ub = ubiquitin.
Context query in information retrieval (2003)

There is an important query requirement missing for search engines. With the wide variation of domain knowledge and user interest, a user would like to retrieve documents in which one query term is discussed in the context of another. Based on existing query mechanisms, what can be specified at most is the co-occurrence of multiple terms in a query. This is insufficient because the co-occurrence of two terms does not necessarily mean that one is discussed in the context of the other. In this paper we propose the context query for Web searching. A new query operator, called the 'in' operator, is used to specify context inclusion between two terms. Heuristic rules to identify context inclusion are suggested and implementation of the 'in' operator in search engines is proposed. Results show that both the precision and ranking relevance of Web searching are improved significantly.
Pulmonary effects of ozone exposure during exercise: dose-response characteristics (1983)

Because minimal data are available regarding the pulmonary effects of ozone (O3) at levels less than 0.27 ppm, six groups of healthy young males were exposed for 2.5 h to one of the following O3 concentrations: 0.0, 0.12, 0.18, 0.24, 0.30, or 0.40 ppm. Fifteen-minute periods of rest and exercise (65 l/min minute ventilation) were alternated during the first 2 h of exposure. Coughing was observed at all levels of O3 exposure. Small changes in forced-expiratory spirometric variables [forced vital capacity (FVC), forced expiratory volume in 1 s, and mean expiratory flow rate between 25 and 75% FVC] were observed at 0.12 and 0.18 ppm O3, and larger changes were found at O3 levels greater than or equal to 0.24 ppm. Changes in tidal volume and respiratory frequency during exercise, specific airway resistance, the presence of pain on deep inspiration, and shortness of breath occurred at O3 levels greater than or equal to 0.24 ppm. In conclusion, pulmonary effects of O3 were observed at levels much lower than that for which these effects have been previously described. Stimulation of airway receptors is probably the mechanism responsible for the majority of observed changes; however, the existence of a second mechanism of action is postulated.
Hormonal regulation of stearoyl coenzyme A desaturase activity and lipogenesis during adipose conversion of 3T3-L1 cells. (1982)

During differentiation of 3T3-Ll cells to adipocytes the desaturation of exogenous ['4C]palmitate and of de novo synthesized fatty acids from exogenous [14C]acetate to monounsaturated fatty acids increased by 5.9and 255-fold, respectively.Under similar conditions, fully differentiated 3T3-Ll adipocytes showed a maximal induction of loo-, 63-, and 50-fold, respectively, in the activities of stearoyl-CoA desaturase, fatty acid synthetase, and malic enzyme.The extent of differentiation into adipocytes and the increase in enzyme activities occurred more slowly when the differentiation was induced by insulin alone than when differentiation was induced by dexamethasone, 1-methyl-3-isobutylxanthine, and insulin.In one experiment a 30-fold induction of overall stearoyl-CoA desaturation was correlated with a 32-fold increase in the activity of terminal component of the desaturase system on differentiation of 3T3-Ll cells.The activities of NADH-ferricyanide reductase, NADH-cytochrome c reductase, and the content of cytochrome b5 increased by 3.4-, 2.3-, and 6.6-fold, respectively, on differentiation of 3T3-Ll cells.However, reconstitution of the stearoyl-CoA desaturation in various preparations of microsomes with excess NADH-cytochrome b5 reductase and cytochrome b6 indicated that the changes in the reductase activity and cytochrome b5 content are not influencing the expression of overall stearoyl-CoA desaturation in microsomes.The induction of stearoyl-CoA desaturation during adipose conversion of 3T3-Ll cells is primarily due to an increase in the activity of A' terminal desaturase.Biotin deficiency in 3T3-Ll adipocytes inhibited de novo fatty acid synthesis from ['%]acetate but did not inhibit phenotypic expression of lipid accumulation as well as activities of stearoyl-CoA desaturase and fatty acid synthetase, suggesting that continued synthesis of saturated fatty acid substrate is not required for the induction of stearoyl-CoA desaturase activity.The induction of stearoyl-CoA desaturase and fatty acid synthetase activities as well as enhanced synthesis of fatty acids and sterols during 3T3-Ll cell differentiation is inhibited by anti-insulin serum, and this inhibition is relieved by the addition of exogenous insulin.These results indicate that insulin supports phenotypic expression as well as the induction of lipogenesis and the activities of stearoyl-CoA desaturase and fatty acid synthetase during adipose conversion of 3T3-Ll cells.
A Peptide Antagonist of CD28 Signaling Attenuates Toxic Shock and Necrotizing Soft-Tissue Infection Induced by Streptococcus pyogenes (2013)

Staphylococcus aureus and group A Streptococcus pyogenes (GAS) express superantigen (SAg) exotoxin proteins capable of inducing lethal shock. To induce toxicity, SAgs must bind not only to the major histocompatibility complex II molecule of antigen-presenting cells and the variable β chain of the T-cell receptor but also to the dimer interface of the T-cell costimulatory receptor CD28. Here, we show that the CD28-mimetic peptide AB103 (originally designated "p2TA") protects mice from lethal challenge with streptococcal exotoxin A, as well as from lethal GAS bacterial infection in a murine model of necrotizing soft-tissue infection. Administration of a single dose of AB103 increased survival when given up to 5 hours after infection, reduced inflammatory cytokine expression and bacterial burden at the site of infection, and improved muscle inflammation in a dose-dependent manner, without compromising cellular and humoral immunity. Thus, AB103 merits further investigation as a potential therapeutic in SAg-mediated necrotizing soft-tissue infection.
Electrospinning of ultra‐thin polymer fibers (1998)

Abstract The electrospinning technique was used to spin ultra‐thin fibers from several polymer/solvent systems. The diameter of the electrospun fibers ranged from 16 nm to 2 μm. The morphology of these fibers was investigated with an atomic force microscope (AFM) and an optical microscope. Polyethylene oxide) (PEO) dissolved in water or chloroform was studied in greater detail. PEO fibers spun from aqueous solution show a “beads on a string” morphology. An AFM study showed that the surface of these fibers is highly ordered. The “beads on a string” morphology can be avoided if PEO is spun from solution in chloroform; the resulting fibers show a lamellar morphology. Polyvinylalcohol (PVA) dissolved in water and cellulose acetate dissolved in acetone were additional polymer/solvent systems which were investigated. Furthermore, the electrospinning process was studied: different experimental lay‐outs were tested, electrostatic fields were simulated, and voltage ‐ current characteristics of the electrospinning process were recorded.
ChemInform Abstract: Pharmacological Evaluation of UK‐14,304 Analogues at Cloned Human . alpha.‐Adrenergic Recepors. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Using handheld PCs and peer instruction to improve science teaching and learning in higher education (2006)

Many of the core concepts in earth science systems are complex and counterintuitive, but well illustrated through imagery and/or animation. We have developed a new tool, ImageQuiz, that uses wireless technologies to present images and provide a question requiring a point response. In the study presented here, we use Peer Instruction techniques (Mazur, 1997) in a large geosciences class and deliver ImageQuizes via wireless PocketPC computers. We will discuss development, implementation and learning outcomes.
Cytokines and IgE Regulation (1998)

Synthesis of allergen-specific immunoglobulin E (IgE) in vivo is a result of multiple interactions among B-cells, T-cells, and professional antigen-presenting cells (APC). B-cell activation is initiated when specific B-cells recognize the allergen by cell surface immunoglobulin (sIg). However, costimulatory molecules expressed by activated T cells in both soluble and membrane-bound forms are necessary for differentiation of B-cells into Ig-secreting plasma cells (1). Activation of T helper (Th) cells requires recognition of an antigenic peptide in the context of major histocompatibility complex (MHC) class II molecules on the plasma membrane of APC, such as monocytes, dendritic cells, Langerhans cells, or primed B-cells. Professional APC can efficiently capture the antigen, and the peptide-MHC class II complexes are formed in a post-Golgi, proteolytic intracellular compartment and subsequently exported to the plasma membrane, where they are recognized by T-cell receptor (TCR) (2). In addition, activated B-cells express CD80 (B7-1) and CD86 (B7-2, B70), which are the counter receptors for CD28 and which provide a costimulatory signal for T-cell activation resulting in T-cell proliferation and cytokine synthesis (3). Since allergen-specific T-cells from atopic individuals generally belong to the Th2-cell subset, activation of these cells also leads to production of interleukin (IL)-4 and IL-13, which, together with membrane-bound costimulatory molecules expressed by activated T-helper cells, direct B-cell differentiation into IgE-secreting plasma cells.
Dlib-ml: A Machine Learning Toolkit (2009)

There are many excellent toolkits which provide support for developing machine learning software in Python, R, Matlab, and similar environments. Dlib-ml is an open source library, targeted at both engineers and research scientists, which aims to provide a similarly rich environment for developing machine learning software in the C++ language. Towards this end, dlib-ml contains an extensible linear algebra toolkit with built in BLAS support. It also houses implementations of algorithms for performing inference in Bayesian networks and kernel-based methods for classification, regression, clustering, anomaly detection, and feature ranking. To enable easy use of these tools, the entire library has been developed with contract programming, which provides complete and precise documentation as well as powerful debugging tools.
Continuous detection of extracellular ATP on living cells by using atomic force microscopy (1999)

Atomic force microscopy is a powerful technique used to investigate the surface of living cells under physiological conditions. The resolution of the instrument is mainly limited by the softness of living cells and the interactions with the scanning tip (cantilever). Atomic force microscopy, in combination with myosin-functionalized cantilevers, was used in the detection of ATP concentrations in solution and on living cells. Functionally active tips were used to scan the surface of cells in culture and to show that the CFTR+ cell line (S9) had a basal surface ATP concentration that could be detected with atomic force microscopy (n = 10). ATP-dependent signals were not detectable in cells scanned with noncoated or heat-inactivated enzyme-coated tips (n = 9). Enzymatically active tips may serve as a model for future development of atomic force microscopy biosensors that can simultaneously detect topographical and biologically important compounds at the surface microenvironment of living cells.
Efficient internalization of the polo-box of polo-like kinase 1 fused to an Antennapedia peptide results in inhibition of cancer cell proliferation. (2002)

Polo-like kinases (Plk) regulate multiple stages in mitosis. Plk1 is overexpressed in tumors. The COOH-terminal regions of Plks contain a conserved domain, termed polo-box, which is required for subcellular localization and for physical interaction with substrates. We linked the polo-box (amino acids 410-429) of Plk1 to an Antennapedia peptide and studied its impact on tumor cells. Whereas the wild-type polo-box inhibited the proliferation of tumor cells associated with induction of apoptosis, a mutated derivative was much less effective. The treatment caused mitotic arrest, misaligned chromosomes, and multiple centrosomes. Taken together, membrane-permeable polo-box peptides inhibit cancer cell proliferation efficiently.
Atorvastatin increases human serum levels of proprotein convertase subtilisin/kexin type 9 (2007)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) has gained attention as a key regulator of serum low density lipoprotein cholesterol (LDL-C) levels. This novel protease causes the degradation of hepatic low density lipoprotein receptors. In humans, gain-of-function mutations in PCSK9 cause a form of familial hypercholesterolemia, whereas loss-of-function mutations result in significantly decreased LDL-C levels and cardiovascular risk. Previous studies have demonstrated that statins upregulate PCSK9 mRNA expression in cultured cells and animal models. In light of these observations, we studied the effect of atorvastatin on circulating PCSK9 protein levels in humans using a sandwich ELISA to quantitate serum PCSK9 levels in patients treated with atorvastatin or placebo for 16 weeks. We observed that atorvastatin (40 mg/day) significantly increased circulating PCSK9 levels by 34% compared with baseline and placebo and decreased LDL-C levels by 42%. These results suggest that the addition of a PCSK9 inhibitor to statin therapy may result in even further LDL-C decreases.