gebhart/patrepeval huggingface dataset:
Error-bounded sampling for analytics on big sparse data (2014)

Aggregation queries are at the core of business intelligence and data analytics. In the big data era, many scalable shared-nothing systems have been developed to process aggregation queries over massive amount of data. Microsoft's SCOPE is a well-known instance in this category. Nevertheless, aggregation queries are still expensive, because query processing needs to consume the entire data set, which is often hundreds of terabytes. Data sampling is a technique that samples a small portion of data to process and returns an approximate result with an error bound, thereby reducing the query's execution time. While similar problems were studied in the database literature, we encountered new challenges that disable most of prior efforts: (1) error bounds are dictated by end users and cannot be compromised, (2) data is sparse , meaning data has a limited population but a wide range. For such cases, conventional uniform sampling often yield high sampling rates and thus deliver limited or no performance gains. In this paper, we propose error-bounded stratified sampling to reduce sample size. The technique relies on the insight that we may only reduce the sampling rate with the knowledge of data distributions. The technique has been implemented into Microsoft internal search query platform. Results show that the proposed approach can reduce up to 99% sample size comparing with uniform sampling, and its performance is robust against data volume and other key performance metrics.
Formation of a multilayer cellular lining on a polyurethane vascular graft following endothelial cell sodding (1992)

Small-diameter (less than 6 mm) clinically available vascular grafts often fail due in part to the inherent thrombogenicity of artificial polymers. Transplantation of endothelial cells onto the lumen of these vascular grafts has been suggested as one method to overcome this thrombogenicity. We have developed a compliant polyurethaneurea (PEUU) 4-mm graft with a luminal surface modified by a glow discharge gas plasma. Autologous microvessel endothelial cells were isolated from canine falciform ligament fat, were transplanted onto the luminal surface of the grafts using an intraoperative isolation and sodding technique, and both endothelial-cell-treated and non-cell-treated grafts were placed as bilateral carotid interposition grafts in a canine model. After 5 weeks of implantation, explanted control (non-cell-treated) grafts exhibited a deposition of platelets, white cells and fibrin characteristic of a thrombogenic surface. MVEC sodded grafts exhibited a multicellular lining within but distinct from the lumen of the PEUU graft. The blood-contacting surface of this lining exhibited an antithrombogenic endothelial cell monolayer. We suggest that the PEUU graft supported the initial deposition of MVEC and development of and endothelial cell lining. During the 5 weeks of implantation this lining continued to proliferate and detached from the PEUU graft substratum. The final neocellular lining exhibited a luminal diameter and histological features similar to a native artery.
Observing presenters' use of visual aids to inform the design of classroom presentation software (2008)

Large classrooms have traditionally provided multiple blackboards on which an entire lecture could be visible. In recent decades, classrooms were augmented with a data projector and screen, allowing computer-generated slides to replace hand-written blackboard presentations and overhead transparencies as the medium of choice. Many lecture halls and conference rooms will soon be equipped with multiple projectors that provide large, high-resolution displays of comparable size to an old fashioned array of blackboards. The predominant presentation software, however, is still designed for a single medium-resolution projector. With the ultimate goal of designing rich presentation tools that take full advantage of increased screen resolution and real estate, we conducted an observational study to examine current practice with both traditional whiteboards and blackboards, and computer-generated slides. We identify several categories of observed usage, and highlight differences between traditional media and computer slides. We then present design guidelines for presentation software that capture the advantages of the old and the new and describe a working prototype based on those guidelines that more fully utilizes the capabilities of multiple displays.
Regulation of mammalian nucleotide metabolism and biosynthesis (2015)

Nucleotides are required for a wide variety of biological processes and are constantly synthesized de novo in all cells. When cells proliferate, increased nucleotide synthesis is necessary for DNA replication and for RNA production to support protein synthesis at different stages of the cell cycle, during which these events are regulated at multiple levels. Therefore the synthesis of the precursor nucleotides is also strongly regulated at multiple levels. Nucleotide synthesis is an energy intensive process that uses multiple metabolic pathways across different cell compartments and several sources of carbon and nitrogen. The processes are regulated at the transcription level by a set of master transcription factors but also at the enzyme level by allosteric regulation and feedback inhibition. Here we review the cellular demands of nucleotide biosynthesis, their metabolic pathways and mechanisms of regulation during the cell cycle. The use of stable isotope tracers for delineating the biosynthetic routes of the multiple intersecting pathways and how these are quantitatively controlled under different conditions is also highlighted. Moreover, the importance of nucleotide synthesis for cell viability is discussed and how this may lead to potential new approaches to drug development in diseases such as cancer.
Map-Based Cloning of a Protein Kinase Gene Conferring Disease Resistance in Tomato (1993)

The Pto gene in tomato confers resistance to races of Pseudomonas syringae pv. tomato that carry the avirulence gene avrPto. A yeast artificial chromosome clone that spans the Pto region was identified and used to probe a leaf complementary DNA (cDNA) library. A cDNA clone was isolated that represents a gene family, at least six members of which genetically cosegregate with Pto. When susceptible tomato plants were transformed with a cDNA from this family, they were resistant to the pathogen. Analysis of the amino acid sequence revealed similarity to serine-threonine protein kinases, suggesting a role for Pto in a signal transduction pathway.
Clay-Containing Polysulfone Nanocomposites (2011)

Although there are several definitions of composite materials (Callister, 1994; Chawla, 1987; Hull, 1981; Padilha, 1997; Van Vlack, 1984), composites are artificial multiphase materials in which their constituents are chemically distinct and separated by an easily distinct interface (Moffatt et al., 1964). Some familiar materials are examples of composites: the concrete used in buildings, car tires, the asphalt of our streets. The distinction of artificial materials is necessary due to materials that could be included in this definition, but which occur in a natural way, as, for example, wood (lignine + cellulose fibers), bones (collagen + apathite) in which the combination of different phases results in an enhanced material as compared to the individual phases. Polymer/ clay nanocomposites are a new class of composites with polymer matrixes in which the dispersed phase is the silicate constituted by particles that have at least one of the dimensions in nanometer level. One of the components is the matrix, in which the particles of the second material are dispersed. The most used mineral particles in these nanocomposites are smectitc clays (montmorillonite, saponite and hectorite), having their particles lamellae morphology with sides in micrometer level and thickness around one nanometer (Alexandre & Dubois, 2000; Esteves et al., 2004). The montmorillonite particles are extremely small and, therefore, their structure can only be studied by X-ray diffraction. The unitary layer of the montmorillonite consists in three sheets: one octahedral sheet composed of hydrargilite-brucite included between two tetrahedral sheets composed of silicon and oxygen. These sheets are combined in such a way that the tetrahedral edges of each silica layer form a common layer with one of the hydroxyl layers of the octahedral sheet, with oxygen atoms instead of hydroxyl groups (Papin, 1993). The layers are continuous in the a and b directions and are stacked in the c direction (Fig. 1). Water and other polar molecules can enter the unitary layers causing an expansion in the c direction. The dimension of the c axis of the montmorillonite varies from 9.6 A, when any polar molecule is between the unitary layers, until complete separation in some cases (Brigatti et al., 2006). The interest in the production of polymer nanocomposites comes from the large range of possible applications which involves this type of material. Features such as higher resistances towards high temperatures, UV radiation, high gas impermeability, low expansibility and processing flexibility can be achieved by the production of this type of nanocomposite. Moreover, polymers have a great well-established variety of types of processing as, for example, blending, compression, fusion, mixture and polymerization,
Synthetic far-red light-mediated CRISPR-dCas9 device for inducing functional neuronal differentiation (2018)

The ability to control the activity of CRISPR-dCas9 with precise spatiotemporal resolution will enable tight genome regulation of user-defined endogenous genes for studying the dynamics of transcriptional regulation. Optogenetic devices with minimal phototoxicity and the capacity for deep tissue penetration are extremely useful for precise spatiotemporal control of cellular behavior and for future clinic translational research. Therefore, capitalizing on synthetic biology and optogenetic design principles, we engineered a far-red light (FRL)-activated CRISPR-dCas9 effector (FACE) device that induces transcription of exogenous or endogenous genes in the presence of FRL stimulation. This versatile system provides a robust and convenient method for precise spatiotemporal control of endogenous gene expression and also has been demonstrated to mediate targeted epigenetic modulation, which can be utilized to efficiently promote differentiation of induced pluripotent stem cells into functional neurons by up-regulating a single neural transcription factor, <i>NEUROG2</i> This FACE system might facilitate genetic/epigenetic reprogramming in basic biological research and regenerative medicine for future biomedical applications.
Target-to-background enhancement in multispectral endoscopy with background autofluorescence mitigation for quantitative molecular imaging (2014)

Fluorescence molecular imaging with exogenous probes improves specificity for the detection of diseased tissues by targeting unambiguous molecular signatures. Additionally, increased diagnostic sensitivity is expected with the application of multiple molecular probes. We developed a real-time multispectral fluorescence-reflectance scanning fiber endoscope (SFE) for wide-field molecular imaging of fluorescent dye-labeled molecular probes at nanomolar detection levels. Concurrent multichannel imaging with the wide-field SFE also allows for real-time mitigation of the background autofluorescence (AF) signal, especially when fluorescein, a U.S. Food and Drug Administration approved dye, is used as the target fluorophore. Quantitative tissue AF was measured for the ex vivo porcine esophagus and murine brain tissues across the visible and nearinfrared spectra. AF signals were then transferred to the unit of targeted fluorophore concentration to evaluate the SFE detection sensitivity for sodium fluorescein and cyanine. Next, we demonstrated a real-time AF mitigation algorithm on a tissue phantom, which featured molecular probe targeted cells of high-grade dysplasia on a substrate containing AF species. The target-to-background ratio was enhanced by more than one order of magnitude when applying the real-time AF mitigation algorithm. Furthermore, a quantitative estimate of the fluorescein photodegradation (photobleaching) rate was evaluated and shown to be insignificant under the illumination conditions of SFE. In summary, the multichannel laser-based flexible SFE has demonstrated the capability to provide sufficient detection sensitivity, image contrast, and quantitative target intensity information for detecting small precancerous lesions in vivo.
Fabrication of Single-Crystalline Semiconductor CdS Nanobelts by Vapor Transport (2004)

A beltlike single-crystalline CdS nanostructure was successfully synthesized by vapor-phase transport of the desired commercial CdS powder at 850 °C. Its morphology and microstructures were determined by X-ray powder diffraction, scanning electron microscopy, and transmission electron microscopy. The observations reveal that the products consist of a large quantity of beltlike nanostructures with typical lengths in the range of several tens to several hundreds of micrometers. The typical widths of CdS nanobelts range from several tens to several hundreds of nanometers. The as-synthesized semiconductor CdS nanobelts are pure, structurally uniform, and single crystalline. CdS nanobelts, which have a rectangle-like cross section, could be an ideal system for building nanometer-scale optoelectronic devices along individual nanobelts, such as laser light-emitting diodes and optical devices.
Monoclonal Antibody-Based Enzyme Immunoassay for Detection of Botulinum Neurotoxin Type A (2008)

A sensitive and specific ELISA was developed to detect BoNT/A in biological fluids. The assay is based on the sandwich format using monoclonal antibodies (MAb) of two distinct specificities. An affinity-purified anti-BoNT/A heavy chain MAb (150-3) is utilized to adsorb BoNT/A from solution; the second anti-BoNT/A heavy chain MAb (44-1A) conjugated with peroxidase is then used to form a sandwich. Peroxidase allows color development and measurement of optical density at 450 nm. Standard curves were linear over the range of 2.5 to 100 ng/mL BoNT/A. The limit of detection was below 5 ng/mL in assay buffer, as well as in a 1:10 dilution of urine or 1:50 dilution of human serum spiked with BoNT/A. The developed BoNT/A assay also showed no cross-reaction to type B neurotoxin (BoNT/B) and type E neurotoxin (BoNT/E).
Two site-specific deletions and t(1;14) translocation restricted to human T-cell acute leukemias disrupt the 5' part of the tal-1 gene. (1991)

Analysis of several cases of t(1:14)(p32;q11) translocation present in 3% of T-cell acute leukemias (T-ALL) has revealed the tal-1 gene. This gene encodes a helix-loop-helix protein. It has been found to be expressed in normal bone marrow and in leukemic T-cell and erythroleukemia cell lines, but not in normal T cells. Recently, a site-specific deletion, tald, renamed tald1 in this paper, has been detected in a high proportion of pediatric T-ALL, which arose by a site-specific DNA recombination between tal-1 and a new locus termed SIL. In this study we searched for structural rearrangements within tal-1 in a panel of 134 non-selected leukemic patients (including 66 with T-ALL). Only 6% of patients with T-ALL harbored the tald1 deletion. A second specific deletion termed tald2 was observed in another 6% of T-ALL patients; it involves another site within tal-1 plus the same site as tald1 in the SIL locus. Similarly to tald1 deletion, tald2 junctions harbor structural characteristics that are reminiscent of aberrant recombinase activity. Moreover, we report a detailed analysis of the tal-1 gene structure. Transcription analysis and in vitro translation data are consistent with the differential expression of several TAL-1 protein species containing the HLH motif but differing in their amino terminus. Taken together, our data indicate that t(1;14) translocations and both tald deletions disrupt the 5' part of the tal-1 gene, placing its entire coding sequences under the control of the regulatory elements of the TCR-delta gene or the SIL gene, both of which are normally expressed in T-cell lineage.
Effects of farnesylcysteine analogs on protein carboxyl methylation and signal transduction. (1991)

Several proteins associated with signal transduction in eukaryotes are carboxyl methylated at COOH-terminal S-farnesylcysteine residues. These include members of the Ras superfamily and gamma-subunits of heterotrimeric G-proteins. The enzymes that catalyze the carboxyl methylation reaction also methylate small molecules such as N-acetyl-S-trans, trans-farnesyl-L-cysteine (AFC). AFC inhibits carboxyl methylation of p21ras and related proteins both in vitro and in vivo. Saturating concentrations of AFC cause a greater than 80% inhibition of chemotactic responses of mouse peritoneal macrophages. Our results suggest that carboxyl methylation may play a role in the regulation of receptor-mediated signal transduction processes in eukaryotic cells.
Antigen-Based Immune Therapeutics for Type 1 Diabetes: Magic Bullets or Ordinary Blanks? (2011)

The ideal drug of modern medicine is the one that achieves its therapeutic target with minimal adverse effects. Immune therapy of Type 1 diabetes (T1D) is no exception, and knowledge of the antigens targeted by pathogenic T cells offers a unique opportunity towards this goal. Different antigen formulations are being considered, such as proteins or peptides, either in their native form or modified ad hoc, DNA plasmids, and cell-based agents. Translation from mouse to human should take into account important differences, particularly in the time scale of autoimmune progression, and intervention. Critical parameters such as administration route, dosing and interval remain largely empirical and need to be further dissected. T1D staging through immune surrogate markers before and after treatment will be key in understanding therapeutic actions and to finally turn ordinary blanks into magic bullets.
Photoreceptor Death, Trophic Factor Expression, Retinal Oxygen Status, and Photoreceptor Function in the P23H Rat (2004)

Excess photoreceptor degeneration in the P23H-3 retina begins just after eye opening, peaks in early postnatal life, and then slows, but persists into adulthood. In the adult retina, surviving photoreceptors operate in an environment that is chronically hyperoxic (and therefore toxic) and in which protective factors (CNTF, FGF-2) are chronically upregulated. The net result, slow degeneration and degraded function in an environment that is both toxic and protective, may be representative of adult photoreceptor status in a number of human retinal degenerations. Hyperoxia-induced photoreceptor death may be a self-reinforcing factor that increases oxidative stress in surviving photoreceptors.
Coating of commercially available materials with a new heparinizable material (1991)

Different commercial materials, such as polyurethane (PU), plasticized PVC (PVC), glass, Gore-tex, and Dacron, were coated with a well-characterized biomaterial (PUPA) based on polyurethane and poly(amido-amine) components. Two different classes of coating were obtained due to the different characteristics of the substrates. In the case of PVC and polyurethane which are soluble in the solvent of the PUPA-coating solution, there was penetration and blending of the coating and underlying materials. In the case of glass, Gore-tex, and Dacron, which are insoluble in the solvent of the coating solution, only a superficial layer of PUPA could be obtained. The coating stability was investigated and the interaction between coating and underlying material studied by FT-IR. All the stable coatings showed the ability to bind as much heparin as PUPA material by itself.
Restless Legs Syndrome: From Pathophysiology to Clinical Diagnosis and Management (2017)

Restless legs syndrome (RLS), a common neurological sensorimotor disorder in western countries, has gained more and more attention in Asian countries. The prevalence of RLS is higher in older people and females. RLS is most commonly related to iron deficiency, pregnancy and uremia. The RLS symptoms show a significant circadian rhythm and a close relationship to periodic limb movements (PLMs) in clinical observations, while the pathophysiological pathways are still unknown. The diagnostic criteria have been revised in 2012 to improve the validity of RLS diagnosis. Recent studies have suggested an important role of iron decrease of brain in RLS pathophysiology. Dopaminergic (DA) system dysfunction in A11 cell groups has been recognized long ago from clinical treatment and autopsy. Nowadays, it is believed that iron dysfunction can affect DA system from different pathways and opioids have a protective effect on DA system. Several susceptible single nucleotide polymorphisms such as BTBD9 and MEIS1, which are thought to be involved in embryonic neuronal development, have been reported to be associated with RLS. Several pharmacological and non-pharmacological treatment are discussed in this review. First-line treatments of RLS include DA agents and α2δ agonists. Augmentation is very common in long-term treatment of RLS which makes prevention and management of augmentation very important for RLS patients. A combination of different types of medication is effective in preventing and treating augmentation. The knowledge on RLS is still limited, the pathophysiology and better management of RLS remain to be discovered.
[Treatment of Jessner-Kanof disease with thalidomide]. (1983)

Five patients present a Jessner-Kanof's lymphocytic infiltration of the skin with 6-year duration for 4 of them. The skin lesions are numerous on the face and the back and characteristic of this disease. Histologic examination shows a lymphocytic infiltrate in the dermis without any modification of epidermis. Direct immunofluorescent study is negative in all cases. In 3 cases, response to chloroquine had been inconsistent or negative. The 5 cases have a excellent result with 100 mg/day of Thalidomide. In 4 cases the skin lesions reappear when treatment is stopped. With a continuous treatment of 25-50 mg/day for more than 2 years, 3 of 5 patients have normal skin. Thalidomide appears to be the best treatment of Jessner-Kanof's disease.
A MAPOS version 1 Extension - Node Switch Protocol (1997)

This document describes a MAPOS extension, Node Switch Protocol, for automatic node address assignment. MAPOS is a multiple access protocol for transmission of network-protocol datagrams, encapsulated in High-Level Data Link Control (HDLC) frames, over SONET/SDH. NSP automates the HDLC address configuration of each node. Using NSP, a node retrieves its HDLC address from the switch to which it is connected.