gebhart/patrepeval huggingface dataset:
Presence of Wilms' tumor gene (wt1) transcripts and the WT1 nuclear protein in the majority of human acute leukemias. (1995)

The wt1 gene is located on chromosome 11p13 and encodes a zinc finger motif-containing transcription factor involved in regulation of growth and differentiation. Its expression was shown during embryonic development in various tissues as well as in a few human malignancies including acute leukemias. Using RT-PCR, we found wt1 gene expression in blast cells of the majority of 150 acute leukemia patients. Particularly, the wt1 transcript was detected in 12 of 14 (86%) pre-pre-B-ALL patients, in 33 of 41 (80%) cALL patients, in 23 of 31 (74%) T-ALL patients, and in 53 of 57 (93%) AML patients. Additionally, mononuclear cells from CML patients expressed the wt1 gene only when diagnosed with blast crisis. In contrast to acute human leukemias, mononuclear cells from reactive bone marrow (n = 4), and peripheral blood of healthy volunteers (n = 20), as well as normal peripheral CD34+ hematopoietic progenitors (n = 6) did not express the wt1 gene at detectable levels. Using the anti-WT1 MoAb 6F-H2 in an immunofluorescence assay on single cell level, we found the translated WT1 protein only in nuclei of leukemia blast cells but not in nuclei of normal CD34+ hematopoietic progenitor cells. Blast cells of 12 of 20 leukemia patients (60%) all tested positive for the wt1 gene expression by RT-PCR displayed a strong nuclear immunofluorescence. Its expression in the majority of human acute leukemias but not in normal mononuclear blood cells and normal CD34+ hematopoietic progenitors qualifies the wt1 gene transcript as a 'pan-acute leukemic' marker probably useful in monitoring minimal residual disease after chemotherapy and in detecting leukemic blast cells in purged or unpurged hematopoietic stem cell preparations intended to be used for autologous bone marrow transplantation.
Fast contact evolution for piecewise smooth surfaces (2009)

Dynamics simulation of smooth bodies in contact is a critical problem in physically based animation and interactive virtual environments. We describe a technique which uses reduced coordinates to evolve a single continuous contact between Loop subdivision surfaces. The incorporation of both slip and no-slip friction into our algorithm is straightforward. The dynamics equations, though slightly more complex due to the reduced coordinate formulation, can be integrated easily using explicit integrators without the need for constraint stabilization. The use of reduced coordinates also confines integration errors to lie within the constraint manifold which is preferable for visualization. Our algorithm is suitable for piecewise parametric or parameterizable surfaces with polygonal domain boundaries. Because a contact will not always remain in the same patch, we demonstrate how a contact can be evolved across patch boundaries. We also address the issue of non-regular parameterizations occurring in Loop subdivision surfaces through surface replacement with n sided S-patch surfaces. Three simulations show our results. We partially verify our technique first with a frictionless system and then with a blob sliding and rolling inside a bowl. Our third simulation shows that our formulation correctly predicts the spin reversal of a rattleback top. We also present timings of the various components of the algorithm.
Self-assembling amphiphilic poly(propargyl methacrylate) grafted DNA copolymers into multi-strand helices (2015)

DNA was covalently grafted onto poly(propargyl methacrylate) (PPMA) via "click" chemistry to synthesize the amphiphilic polymer brush. The PPMA-g-DNA brush could assemble into a primary structure of a nanofiber, which can be compactly spun into a multiple-strand helix in micron-length. The brush could also self-assemble with DNA labelled gold nanoparticles.
Comparison of Next-Generation Sequencing Systems (2012)

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.
A Unified Coding Method of Image and Text Data Using Discrete Orthogonal Transform (1990)

Abstract A unified coding method of image and text data is proposed in this paper. This scheme enables us to embed a text into an image by using some redundant region in the frequency space. Our results show that a text of about 4 k to 8 kbytes can be embedded into the image of 256 × 256 pixels and it retains an S/N ratio of about 30 to 40 dB.
Stochastic models, estimation and control, Volume 1 (1979)

This volume builds upon the foundations set in Volumes 1 and 2. Chapter 13 introduces the basic concepts of stochastic control and dynamic programming as the fundamental means of synthesizing optimal stochastic control laws.Author: Maybeck, Peter S. Publisher: Academic Press Illustration: N Language: ENG Title: Stochastic Models, Estimation, and Control: Volume 3 Pages: 00291 (Encrypted PDF) On Sale: 1982-07-28 SKU-13/ISBN: 9780124807037 Category: Mathematics : Probability & Statistics General Category: Mathematics : Mathematical Analysis Category: Mathematics : General
15-Lipoxygenase and Its Inhibition: A Novel Therapeutic Target for Vascular Disease (1999)

The disease process known as atherosclerosis is the leading cause of morbidity and mortality in the Western world. Current therapies have focused on treating the major risk factors identified to date including plasma lipid derangements, hypertension, clotting disorders, and diabetes. However, a significant number of individuals will be diagnosed with this malady in the apparent absence of known risk factors. Recent attention has turned toward treating the disease at the level of the vessel wall. In this review, we assess the relevancy of the oxygenating enzyme 15-lipoxygenase (15-LO) as a therapeutic target. In vitro studies suggest that this enzyme may be involved in processes that modify native LDL in such a way as to be avidly taken up by tissue macrophages. In support of this contention are reports demonstrating the colocalization of 15-LO with macrophage-rich arterial lesions and epitopes of modified LDL. Investigations using transgenic animals also suggest that the site of 15-LO expression may be an important factor in the development of the disease. The alteration of important cellular fatty acids may also generate intracellular signals that promote a pro-atherogenic phenotype in the absence of measurable changes in bulk lipid peroxidation. A limited number of studies have examined 15-LO inhibitors and those structural determinants necessary for inhibition of the enzyme. These include natural products and synthetic analogs. Structure activity relationships have been defined for a number of compounds including caffeic acid derivatives, propargyl ethers, and catechols. A novel, potent, specific inhibitor of 15-LO that lacks significant antioxidant activity was tested for its ability to inhibit atherosclerotic lesion formation in vivo. This benzothiopyranoindole virtually eliminated lesion formation in two animal models in the absence of significant changes in plasma lipids. Further, it prevented the progression of pre-established lesions in another study. Collectively, these data provide a strong scientific rationale for exploring the inhibition of 15-LO as a therapeutic strategy.
Software prefetching for mark-sweep garbage collection (2004)

Tracing garbage collectors traverse references from live program variables, transitively tracing out the closure of live objects. Memory accesses incurred during tracing are essentially random: a given object may contain references to any other object. Since application heaps are typically much larger than hardware caches, tracing results in many cache misses. Technology trends will make cache misses more important, so tracing is a prime target for prefetching.Simulation of Java benchmarks running with the Boehm-De-mers-Weiser mark-sweep garbage collector for a projected hardware platform reveal high tracing overhead (up to 65% of elapsed time), and that cache misses are a problem. Applying Boehm's default prefetching strategy yields improvements in execution time (16% on average with incremental/generational collection for GC-intensive benchmarks), but analysis shows that his strategy suffers from significant timing problems: prefetches that occur too early or too late relative to their matching loads. This analysis drives development of a new prefetching strategy that yields up to three times the performance improvement of Boehm's strategy for GC-intensive benchmark (27% average speedup), and achieves performance close to that of perfect timing ie , few misses for tracing accesses) on some benchmarks. Validating these simulation results with live runs on current hardware produces average speedup of 6% for the new strategy on GC-intensive benchmarks with a GC configuration that tightly controls heap growth. In contrast, Boehm's default prefetching strategy is ineffective on this platform.
Numerical framework for the modeling of electrokinetic flows (1998)

This paper presents a numerical framework for design-based analyses of electrokinetic flow in interconnects. Electrokinetic effects, which can be broadly divided into electrophoresis and electroosmosis, are of importance in providing a transport mechanism in microfluidic devices for both pumping and separation. Models for the electrokinetic effects can be derived and coupled to the fluid dynamic equations through appropriate source terms. In the design of practical microdevices, however, accurate coupling of the electrokinetic effects requires the knowledge of several material and physical parameters, such as the diffusivity and the mobility of the solute in the solvent. Additionally wall-based effects such as chemical binding sites might exist that affect the flow patterns. In this paper, we address some of these issues by describing a synergistic numerical/experimental process to extract the parameters required. Experiments were conducted to provide the numerical simulations with a mechanism to extract these parameters based on quantitative comparisons with each other. These parameters were then applied in predicting further experiments to validate the process. As part of this research, we have created NetFlow, a tool for micro-fluid analyses. The tool can be validated and applied in existing technologies by first creating test structures to extract representations of the physical phenomena in the device, and then applying them in the design analyses to predict correct behavior.
Strongly-Typed Recurrent Neural Networks (2016)

Recurrent neural networks are increasing popular models for sequential learning. Unfortunately, although the most effective RNN architectures are perhaps excessively complicated, extensive searches have not found simpler alternatives. This paper imports ideas from physics and functional programming into RNN design to provide guiding principles. From physics, we introduce type constraints, analogous to the constraints that forbids adding meters to seconds. From functional programming, we require that strongly-typed architectures factorize into stateless learnware and state-dependent firmware, reducing the impact of side-effects. The features learned by strongly-typed nets have a simple semantic interpretation via dynamic average-pooling on one-dimensional convolutions. We also show that strongly-typed gradients are better behaved than in classical architectures, and characterize the representational power of strongly-typed nets. Finally, experiments show that, despite being more constrained, strongly-typed architectures achieve lower training and comparable generalization error to classical architectures.
Effects of vitamin E treatment on peroxisome proliferator‐activated receptor‐α expression and insulin resistance in patients with non‐alcoholic steatohepatitis: results of a pilot study (2007)

Vitamin E treatment, in addition to its previously shown beneficial effect by suppressing oxidative stress, may also achieve improvement by reducing IR and PPAR-alpha expression in NASH.
Efficient presentation of soluble antigen by cultured human dendritic cells is maintained by granulocyte/macrophage colony-stimulating factor plus interleukin 4 and downregulated by tumor necrosis factor alpha. (1994)

Using granulocyte/macrophage colony-stimulating factor (GM-CSF) and interleukin 4 we have established dendritic cell (DC) lines from blood mononuclear cells that maintain the antigen capturing and processing capacity characteristic of immature dendritic cells in vivo. These cells have typical dendritic morphology, express high levels of major histocompatibility complex (MHC) class I and class II molecules, CD1, Fc gamma RII, CD40, B7, CD44, and ICAM-1, and lack CD14. Cultured DCs are highly stimulatory in mixed leukocyte reaction (MLR) and are also capable of triggering cord blood naive T cells. Most strikingly, these DCs are as efficient as antigen-specific B cells in presenting tetanus toxoid (TT) to specific T cell clones. Their efficiency of antigen presentation can be further enhanced by specific antibodies via FcR-mediated antigen uptake. Incubation of these cultured DCs with tumor necrosis factor alpha (TNF-alpha) or soluble CD40 ligand (CD40L) for 24 h results in an increased surface expression of MHC class I and class II molecules, B7, and ICAM-1 and in the appearance of the CD44 exon 9 splice variant (CD44-v9); by contrast, Fc gamma RII is markedly and sometimes completely downregulated. The functional consequences of the short contact with TNF-alpha are in increased T cell stimulatory capacity in MLR, but a 10-fold decrease in presentation of soluble TT and a 100-fold decrease in presentation of TT-immunoglobulin G complexes.
Efflux pump of the proton antiporter family confers low-level fluoroquinolone resistance in Mycobacterium smegmatis. (1996)

Due to the resurgence of tuberculosis and the emergence of multidrug-resistant strains, fluoroquinolones (FQ) are being used in selected tuberculosis patients, but FQ-resistant strains of Mycobacterium tuberculosis have rapidly begun to appear. The mechanisms involved in FQ resistance need to be elucidated if the effectiveness of this class of antibiotics is to be improved and prolonged. By using the rapid-growing Mycobacterium smegmatis as a model genetic system, a gene was selected that confers low-level FQ resistance when present on a multicopy plasmid. This gene, lfrA, encodes a putative membrane efflux pump of the major facilitator family, which appears to recognize the hydrophilic FQ, ethidium bromide, acridine, and some quaternary ammonium compounds. It is homologous to qacA from Staphylococcus aureus, tcmA, of Streptomyces glaucescens, and actII and mmr, both from Streptomyces coelicoler. Increased expression of lfrA augments the appearance of subsequent mutations to higher-level FQ resistance.
Combined optical tweezers and laser dissector for controlled ablation of functional connections in neural networks (2011)

Regeneration of functional connectivity within a neural network after different degrees of lesion is of utmost clinical importance. To test pharmacological approaches aimed at recovering from a total or partial damage of neuronal connections within a circuit, it is necessary to develop a precise method for controlled ablation of neuronal processes. We combined a UV laser microdissector to ablate neural processes in vitro at single neuron and neural network level with infrared holographic optical tweezers to carry out force spectroscopy measurements. Simultaneous force spectroscopy, down to the sub-pico-Newton range, was performed during laser dissection to quantify the tension release in a partially ablated neurite. Therefore, we could control and measure the damage inflicted to an individual neuronal process. To characterize the effect of the inflicted injury on network level, changes in activity of neural subpopulations were monitored with subcellular resolution and overall network activity with high temporal resolution by concurrent calcium imaging and microelectrode array recording. Neuronal connections have been sequentially ablated and the correlated changes in network activity traced and mapped. With this unique combination of electrophysiological and optical tools, neural activity can be studied and quantified in response to controlled injury at the subcellular, cellular, and network level.
Superparamagnetic Iron Oxide Nanoparticles: Diagnostic Magnetic Resonance Imaging and Potential Therapeutic Applications in Neurooncology and Central Nervous System Inflammatory Pathologies, a Review (2009)

Superparamagnetic iron oxide nanoparticles have diverse diagnostic and potential therapeutic applications in the central nervous system (CNS). They are useful as magnetic resonance imaging (MRI) contrast agents to evaluate: areas of blood-brain barrier (BBB) dysfunction related to tumors and other neuroinflammatory pathologies, the cerebrovasculature using perfusion-weighted MRI sequences, and in vivo cellular tracking in CNS disease or injury. Novel, targeted, nanoparticle synthesis strategies will allow for a rapidly expanding range of applications in patients with brain tumors, cerebral ischemia or stroke, carotid atherosclerosis, multiple sclerosis, traumatic brain injury, and epilepsy. These strategies may ultimately improve disease detection, therapeutic monitoring, and treatment efficacy especially in the context of antiangiogenic chemotherapy and antiinflammatory medications. The purpose of this review is to outline the current status of superparamagnetic iron oxide nanoparticles in the context of biomedical nanotechnology as they apply to diagnostic MRI and potential therapeutic applications in neurooncology and other CNS inflammatory conditions.
Trotting gait analysis of a lizard using motion capture (2013)

Research into the gait planning of a walking robot is the underlying development of quadruped robots. Despite the efforts in stable gait planning, many walking robots that have been developed thus far do not have enough ability to adapt to uneven territory. In this paper, we acquired the motion data of the trotting lizards using the motion capture equipment and analyzed the gait systematically. In addition, we applied it to the kinematic model of the lizard and acquired the trajectory of each joint through an inverse kinematic solution. Moreover, we proposed the joint space-based gait of the lizard model by approximating the acquired joint trajectory to a sinusoidal function. We verified through the simulation that the proposed gait faithfully follows actual gait of lizards.
Screening of New HPAM Base Polymers for Applications in High Temperature and High Salinity Carbonate Reservoirs (2018)

Abstract Application of polymer flooding technique under extreme reservoir conditions (~120°C and 167000 ppm) is still of great concern. In high temperature and high salinity (HTHS) reservoirs, the commonly used polymers for improved oil recovery purposes are ineffective due to chemical degradation and poor injectivity. Therefore, the aim of this paper is to screen partially hydrolyzed polyacrylamide (HPAM) base polymers in order to find suitable polymer for a targeted HTHS carbonate reservoirs. Polymer screening study was carried out on three new NVP-HPAM base polymers to identify a potential candidate which can withstand harsh reservoir conditions. Initially, a comprehensive rheological study was conducted at various polymer concentrations (1000-4000 ppm) and brine salinities to investigate the effectiveness of the polymers. Then, thermal stability test was conducted at anaerobic condition and 120°C for three months. Finally, injectivity test was conducted with the best polymer and in the absence of oil at 120°C and formation salinity (167000 ppm). The experiment was done by sequential injection of 3 polymer concentrations (3000, 1500, and 750 ppm). Parameters such as resistance factor, residual resistance factor, insitu rheology, and apparent shear rates were investigated during the experiment. Results from the rheometric studies showed that all three polymers have acceptable initial viscosifying properties at ambient temperature and shear thinning behaviors within shear rate range of 1-100 s-1. The results also indicated that polymer viscosities dropped with increase in temperature and salinity. However, they still showed good resistance up to 167000 ppm and 120°C. The thermal stability test for the potential polymer showed better stability and retained more than 90% of its initial viscosity after the ageing period. Whilst injecting at 3000 ppm, the resistance factor (RF) was between 20-10 (at different flowrates). During 1500 ppm and 750 ppm, the RF were in the range of 14-6.5 and 5-2.7 respectively. At low flowrates (0.05-1.0 cc/min) of polymer injection, shear thinning behavior was observed. Whereas, shear thickening behavior at high flowrates was observed at all concentrations. Finally, the residual resistance factor (RRF) recorded for the injectivity experiment was found to be 6.17. The potential polymer showed promising results for its application in heterogeneous carbonate reservoir with higher temperature and salinity of 120°C and 167,000 ppm respectively. The study also leads to better understanding of polymer flow behavior in high temperature high salinity carbonate reservoirs.
Nucleotide sequence analysis of the L gene of Newcastle disease virus: homologies with Sendai and vesicular stomatitis viruses (1987)

The nucleotide sequence of the L gene of the Beaudette C strain of Newcastle disease virus (NDV) has been determined. The L gene is 6704 nucleotides long and encodes a protein of 2204 amino acids with a calculated molecular weight of 248822. Mung bean nuclease mapping of the 5' terminus of the L gene mRNA indicates that the transcription of the L gene is initiated 11 nucleotides upstream of the translational start site. Comparison with the amino acid sequences of the L genes of Sendai virus and vesicular stomatitis virus (VSV) suggests that there are several regions of homology between the sequences. These data provide further evidence for an evolutionary relationship between the Paramyxoviridae and the Rhabdoviridae. A non-coding sequence of 46 nucleotides downstream of the presumed polyadenylation site of the L gene may be part of a negative strand leader RNA.