gebhart/patrepeval huggingface dataset:
A Comprehensive Set of In Vitro Transcribed RNAs as Controls for Leukemia Molecular Diagnostics. (2005)

Abstract Introduction: Leukemia is one of several cancers in which genetic sub-types are differentially responsive to specific chemotherapeutic agents, with success rates being directly proportional to early detection and treatment. Detection of specific fusion transcripts from chromosomal translocations (sub-typing) is required for rapid differential diagnosis and initiation of treatment strategies. Since leukemia assays are often performed in small test runs in many facilities, a pooled control that minimizes kit usage and cost by supplying multiple markers in a convenient single-tube format is optimal. As a means to better assess the accuracy and robustness of leukemia assays, we have developed a simple yet flexible external control comprised of in vitro transcribed RNA fusion transcripts of leukemia-associated chromosome translocations. These transcripts include b2a2, b3a2, e1a2, E2A/PBX1, TEL/AML1, AML1/ETO, PML/RARa (Long and Short forms), MLL/AF4 (e10e4 and e9e5) and inv16 (A and D types). To accompany this positive control is translocation-negative, HL-60 cell-line RNA. It serves as a negative control to assess assay background levels. Materials and Methods: The RNA fusion transcripts include about 150 nucleotides flanking each side of the transcript fusion point. Additionally, we fused an MS2 bacteriophage operator to the 3′ end of the transcript sequences to provide a binding site for MS2 coat protein dimers for eventual conversion into Armored RNA Quant™, a stable synthetic quantitative standard that can be utilized upstream in the workflow to run alongside patient samples at the collection and RNA extraction steps. Once all the sequences have been verified for their accuracy, the transcripts were manufactured individually and formulated into a mixture with HL-60 total RNA to mimic leukemic cell extract conditions. The HL-60 total RNA was also tested as an external negative control. Results: We demonstrated that these controls can be used with the Signature LTx assay for simultaneous detection of twelve leukemia-related fusion transcript targets in a single well. We anticipate that these control transcripts will be compatible with current conventional RT-PCR or real-time PCR platforms as well. Conclusion: The twelve transcripts in a single-tube pooled positive control plus the accompanying negative control will provide clinical laboratories with an invaluable tool for tracking day-to-day performance for both multiplex and simplex leukemia molecular diagnostic assays.
Phytochemical And Antimicrobial Effects Of <i>Chrozophora senegalensis</i> (2008)

The in vitro antimicrobial activities of the whole plant extract (ethanolic-CEE) of Chrozophora senegalensis and its fractions (ethyl acetate-EAA, n-butanol-NBE, aqueous-AQE) were assayed using the agar plate diffusion and nutrient broth dilution methods. Test microorganisms were Bacillus subtilis (NCTC 8326 B76), Escherichia coli (ATCC 11775), Pseudomonas aeruginosa (ATCC 10145), Staphylococcus aureus (ATCC 021001). Aspergillus flavus, Aspergillus niger, Candida albicans and Salmonella typhi--laboratory isolates. CEE, EAA and NBE inhibited all the test bacterial organisms and a fungus--Aspergillus flavus. AQE inhibited only Salmonella typhi and Bacillus subtilis. None of the extracts had activity on other 3 fungal organisms tested. CEE and EAA showed minimum inhibition concentration (MIC) of 0.390 and 3.125 mg/ml against S. typhi and E. coli, while NBE and AQE had MIC of 3.125 and 1.563 mg/ml against S. typhi respectively. NBE had an MIC of 12.500 mg/ml against E. coli. The minimum bactericidal concentration (MBC) of CEE and EAA was found to be <0.098 against S. typhi. The MBC of AQE was 12.5 mg/ml against E. coli and S. aureus, and 6.25 mg/ml towards P. aeruginosa. CEE and EAA exhibited similar antibacterial activities, followed by AQE. The extracts revealed the presence of carbohydrates, tannins, saponins, sterols determined by utilizing standard methods of analysis. This study has justified the traditional use of the plant for treating diarrhea, boils and syphilis.
Sound insulating partitions and acoustical doors (1987)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Edwin N. Naslund; Sound insulating partitions and acoustical doors. J. Acoust. Soc. Am. 1 August 1987; 82 (2): 724. https://doi.org/10.1121/1.395402 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Differential Effect of Dietary Methionine on the Biopotency of Selenomethionine and Selenite in Cancer Chemoprevention1 (1988)

The influence of a low methionine intake on the chemopreventive efficacy of selenomethionine versus selenite was compared in the 7,12-dimethylbenz[a]anthracene-induced mammary tumor model in rats. Animals were fed from weaning a purified 20% casein diet with or without 0.3% methionine supplementation. Selenomethionine or selenite, at a final concentration of 3 ppm of selenium (Se), was added to the diet starting 5 days after DMBA administration. Control rats continued to receive the basal diets which contained 0.1 ppm of Se. Results of the carcinogenesis experiment indicated that suboptimal dietary methionine significantly reduced the protective effect of selenomethionine in cancer prevention. In contrast, the efficacy of selenite was not affected. In rats given 3 ppm of selenomethionine, tissue Se was actually higher in those fed a diet with a suboptimal amount of methionine than in those with an adequate intake of methionine. On the other hand, dietary methionine did not influence the level of tissue Se in animals given selenite. An increase of dietary methionine to 0.6% did not enhance the efficacy of selenomethionine in cancer protection but would allow the use of a higher level of selenite without the accompanying adverse effects. The biological significance of Se utilization under suboptimal or adequate methionine intake was also assessed using the glutathione peroxidase assay in the liver of Se-deficient rats given graded levels of Se as either selenite or selenomethionine. The enzyme study demonstrated that low dietary methionine decreased the nutritional biopotency of selenomethionine in restoring glutathione peroxidase activity but not that of selenite. These experiments suggest that adequate methionine intake is required for the utilization of selenomethionine for nutritional and anticarcinogenic purposes.
AND-OR tree analysis of distributed LT codes (2009)

In this contribution, we consider design of distributed LT codes, i.e., independent rateless encodings of multiple sources which communicate to a common relay, where relay is able to combine incoming packets from the sources and forwards them to receivers. We provide density evolution formulae for distributed LT codes, which allow us to formulate distributed LT code design problem and prove the equivalence of performance of distributed LT codes and LT codes with related parameters in the asymptotic regime. Furthermore, we demonstrate that allowing LT coding apparatus at both the sources and the relay may prove advantageous to coding only at the sources and coding only at the relay.
Mechanical Analysis of Single Myocyte Contraction in a 3-D Elastic Matrix (2013)

Our mechanical analyses provide analytic solutions that readily lend themselves to parametric studies. The resulting 3-D mapping of the strain and stress states serve to analyze and interpret ongoing cell-in-gel experiments, and the mathematical model provides an essential tool to decipher and quantify mechanotransduction mechanisms in cardiac myocytes.
I<sub>5</sub>S Miktoarm Star Block Copolymers:  Packing Constraints on Morphology and Discontinuous Chevron Tilt Grain Boundaries (2001)

A morphological study of three I5S six-arm miktoarm star block copolymers is presented. These miktoarm stars are comprised of five arms of polyisoprene (PI) and one arm of polystyrene (PS) joined together at a single junction point. The strong segregation limit theory for the morphological behavior of miktoarm stars predicts that these materials should form spherical morphologies, but only lamellar and cylindrical morphologies were observed by TEM and SAXS. These results are similar to previously reported discrepancies between experimentally observed morphological behaviors of miktoarm stars and the predictions of the theory. Previous work has attributed the discrepancies to the neglect of the effect of the multifunctional junction points on calculated free energies. The current results suggest that, in addition to this, geometrical packing constraints prevent the formation of morphologies such as spheres and cylinders in highly asymmetric miktoarm stars in which the minor volume fraction component would need to occupy the matrix phase. Finally, unusual broken chevron tilt grain boundary morphologies were observed in a lamellar I5S material. We attribute these new structures to the asymmetric energy penalties for interfacial bending which result from the molecular asymmetry of the miktoarm stars.
Do Dopamine Receptors Mediate Part of MAC? (2006)

These data, plus data from studies by others about D1 dopamine receptors, indicate that dopamine receptors do not mediate the immobility produced by inhaled anesthetics.
Sarcoidosis (2011)

Sarcoidosis is a multisystem granulomatous disorder that most often affects the lungs and may cause significant morbidity. Sarcoidosis can manifest as neurological disease, uveitis, blindness, end-stage pulmonary fibrosis, pulmonary hypertension, dysrhythmias, cardiomyopathy, hypercalcemia, and renal failure. Sarcoidosis persists as chronic disease in approximately one-third of those affected. Clinical pitfalls and misconceptions about the course of disease place this population at risk for delayed or inadequate care. While noncaseating granulomas are the histopathological hallmark of sarcoidosis, they also are nonspecific. No pathognomonic diagnostic test exists for sarcoidosis, so the diagnosis remains one of exclusion. While the etiology of sarcoidosis is still unknown, recent insights into its immunopathogenesis have moved investigators closer to finding more effective treatments. Corticosteroids remain the standard of care when treatment is indicated, despite their adverse effect profile. Clinical investigations of novel drugs and biological agents targeting mechanisms involving CD4 type 1 helper T cells may provide more effective, better tolerated therapies.
Describing Mobile Devices as RESTful Services for the End-Users (2016)

This paper presents an end-user oriented approach of describing mobile devices as RESTful services. The mobile services are provided to the end-users through a centralized server. To enable plugging of devices, they provide a machine-processable device description with detailed specification of their RESTful API. The device description is used to generate required user interface as well as generating the RESTful invocations. We provide general guidelines on how to design a REST API for a mobile device and a device description for machine-to-machine interactions. The approach is demonstrated by building a centralized marketplace to promote and use available mobile services. The central marketplace acts as a broker for the dynamic mobile services. In addition, we use two case study applications to demonstrate the service registration, provisioning, and usage.
Fully automated capillary isotachophoresis of proteins (1989)

An apparatus for fully automated capillary isotachophoresis was constructed. A commercial apparatus (Shimadzu IP-2A) was modified in the electrolyte pumping system and the flow lines were simplified. An automatic sampler was used for sequential sampling. The equipment, pumps, the sampler, a high-voltage DC power supply, and a recorder, were controlled by a system controller which comprises a microcomputer and a BASIC program for time-control of the equipments. The apparatus was successfully used for the automated sequential analysis of human serum proteins. Forty serum samples were analyzed within 17 h without manual operation and for each sample the serum proteins were resolved into about twenty UV peaks or shoulders.
Merging hardware and software: intellectual property cores for Internet applications (2002)

The Internet continuous growth and its widespread applications require different router architectures where flexibility and reconfigurability are the paradigms. In this scenario system engineers and designers ask for adequate and flexible solutions suitable both for prototypes and advanced products. This paper presents hard and soft Intellectual Property (IP) cores, parameterized and programmable for design reuse purposes, that can be efficiently used in address lookup units to forward Internet packet streams. The soft macro, IPCAM, is an innovative IP implementing a ternary Content Addressable Memory (CAM), which is capable of solving both exact and longest match operations; it is composed of a hardware module for fast search and a software module for search table configuration. The hard macro is a configurable and physical ternary CAM. Both are suitable for implementing a broad range of lookup functions. Moreover, the efficiency of the proposed cores have been proved on silicon and through a hardware emulation platform.
N-glycoside of nicotine derivative: N-(5-(N'-methyl-2'-pyrrolidinyl)-2-pyridon)-.BETA.-D-glucopyranoside. (1982)

effect of nicotine (1) on the autonomic nervous system has long been examined concerning with tobacco smorking, but 1 has been recognized to have less value as a medicine for clinical use. Whereas recently the other action of it particularly on the central nervous system comes to be interested in psycophysiological field.1>2) Hence such a nicotine compound that affects
Rapid characterization of emulsions by pulsed field gradient nuclear magnetic resonance (2013)

A method for rapid characterization of emulsions is presented. From the proposed setup we are able to measure the droplet size distribution of brine or water droplets confined by an oil phase, even though there is complete overlap in relaxation times and/or molecular mobility between the water and the oil phases. A PFG-NMR sequence is presented that applies the spoiler recovery method for significant reduction in acquisition time, and the method is used for rapid characterization of emulsions.
Deterministic reshaping of single-photon spectra using cross-phase modulation (2016)

The frequency conversion of light has proved to be a crucial technology for communication, spectroscopy, imaging, and signal processing. In the quantum regime, it also offers great potential for realizing quantum networks incorporating disparate physical systems and quantum-enhanced information processing over a large computational space. The frequency conversion of quantum light, such as single photons, has been extensively investigated for the last two decades using all-optical frequency mixing, with the ultimate goal of realizing lossless and noiseless conversion. I demonstrate another route to this target using frequency conversion induced by cross-phase modulation in a dispersion-managed photonic crystal fiber. Owing to the deterministic and all-optical nature of the process, the lossless and low-noise spectral reshaping of a single-photon wave packet in the telecommunication band has been readily achieved with a modulation bandwidth as large as 0.4 THz. I further demonstrate that the scheme is applicable to manipulations of a nonclassical frequency correlation, wave packet interference, and entanglement between two photons. This approach presents a new coherent frequency interface for photons for quantum information processing.
3D Manipulation of 2D Materials Using Microdome Polymer (2020)

We demonstrate 3D mechanical manipulations, such as sliding, rotating, folding, flipping, and exfoliating, of 2D materials using a microdome polymer (MDP) via in situ real-time observation with an optical microscope. A dimethylpolysiloxane (PDMS)-based MDP is covered with a poly(vinyl chloride) (PVC) adhesion layer. This PVC-MDP structure enables us to achieve small and adjustable contact areas between the PVC-MDP and a 2D-material flake, which is typically between ∼10 and ∼100 μm in diameter. The adhesion between the PVC polymer and 2D materials is fully tunable with temperature: Strong adhesion at ∼70 °C allows pick-up of the 2D material, and release occurs at ∼130 °C when the adhesion is weak. Thus the PVC-MDP functions as a point-of-contact manipulator for 2D materials, permitting the 3D manipulation of 2D-material flakes. Our method could facilitate the expansion of van der Waals heterostructure fabrication technology and the development of preparation techniques for more complex 3D structures.
Real-Time Estimation of Urban Street Segment Travel Time Using Buses as Speed Probes (2009)

Using transit buses as probes to detect general vehicle traffic conditions could be a real-time traffic monitoring mechanism in an urban advanced traveler information system. The feasibility of such an application depends primarily on the existence of quantifiable relationships between bus traffic and general vehicle traffic and infrequent bus travel observations (constrained by the scheduled bus headway and route configuration) that are sufficiently sensitive to infer real-time general vehicle traffic conditions. Considering that urban bus probe studies have focused only on the first criterion, this study is designed to examine real-time sensitivity between buses and cars. A generic framework of real-time urban travel time estimation is proposed, followed by a field study in which real-time bus travel information is available and a simulation study that examines the impact of passenger demand on performance of the proposed framework. The study findings provide insights into the feasibility of a real bus probe application in an urban traffic environment. Future studies are desired to explore bus probe performance in nonrecurrent traffic congestion.
IPF1/PDX1 Deficiency and β-Cell Dysfunction in <i>Psammomys obesus,</i> an Animal With Type 2 Diabetes (2001)

The homeodomain transcription factor IPF1/PDX1 is required in beta-cells for efficient expression of insulin, glucose transporter 2, and prohormone convertases 1/3 and 2. Psammomys obesus, a model of diet-responsive type 2 diabetes, shows markedly depleted insulin stores when given a high-energy (HE) diet. Despite hyperglycemia, insulin mRNA levels initially remained unchanged and then decreased gradually to 15% of the basal level by 3 weeks. Moreover, insulin gene expression was not increased when isolated P. obesus islets were exposed to elevated glucose concentrations. Consistent with these observations, no functional Ipf1/Pdx1 gene product was detected in islets of newborn or adult P. obesus using immunostaining, Western blot, DNA binding, and reverse transcriptase-polymerase chain reaction analyses. Other beta-cell transcription factors (e.g., ISL-1, Nkx2.2, and Nkx6.1) were expressed in P. obesus islets, and the DNA binding activity of the insulin transcription factors RIPE3b1-Act and IEF1 was intact. Ipf1/Pdx1 gene transfer to isolated P. obesus islets normalized the defect in glucose-stimulated insulin gene expression and prevented the rapid depletion of insulin content after exposure to high glucose. Taken together, these results suggest that the inability of P. obesus islets to adapt to dietary overload, with depletion of insulin content as a consequence, results from IPF1/PDX1 deficiency. However, because not all animals become hyperglycemic on HE diet, additional factors may be important for the development of diabetes in this animal model.
Identification of putative ligand-binding sites of the integrin <i>α</i>4<i>β</i>1 (VLA-4, CD49d/CD29) (1995)

Integrin alpha 4 beta 1 recognizes both fibronectin (CS-1 sequence) and vascular cell adhesion molecule-1 (VCAM-1). To localize the ligand-binding sites of alpha 4, we located the epitopes for function-blocking anti-alpha 4 monoclonal antibodies (mAbs), including those that recognize previously described (but not yet physically localized) functional epitopes (A, B1, B2 and C) using interspecies alpha 4 chimeras expressed in mammalian cells. Epitopes B1 and B2 were associated with ligand binding, and epitopes A and B2 with homotypic cellular aggregation. mAbs P4C2 (epitope B2), 20E4 and PS/2 were mapped within residues 108-182; mAbs HP2/1 (epitope B1), SG/73 and R1-2 within residues 195-268; mAbs HP1/3 (epitope A) and P4G9 within residues 1-52; and B5G10 (epitope C) within residues 269-548. The data suggest that residues 108-268, which do not include bivalent-cation-binding motifs, are related to VCAM-1 and CS-1 binding, and more N-terminal portions of alpha 4 (residues 1 and 52 and 108-182) to homotypic aggregation. Since mAbs PS/2 and HP2/1 block alpha 4 beta 7 binding to mucosal addressin cell adhesion molecule-1 (MAdCAM-1), the MAdCAM-1-binding site is close to, or overlapping with, VCAM-1- and CS-1-binding sites. The role of Asp-130 of beta 1 in the binding to VCAM-1 and CS-1 peptide was examined. Chinese hamster ovary (CHO) cells expressing beta 1 (D130A) (Asp-130 to Ala mutant of beta 1) and alpha 4 showed much less binding to both ligands than CHO cells expressing wild-type beta 1 and alpha 4 [a dominant negative effects of beta 1 (D130A)], suggesting that Asp-130 of beta 1 is critical for binding to both ligands and that the two ligand share common binding mechanisms [corrected].
Development of and Therapeutic Applications for Novel Inhibitors of Deoxycytidine Kinase (2014)

Deoxycytidine kinase (dCK), a rate-limiting enzyme in the deoxyribonucleotide salvage pathway, participates in the production of deoxyribonucleoside triphosphates (dNTPs). dCK is highly expressed in hematopoietic tissues and many cancers. In addition, dCK is responsible for the phosphorylation, and thus activation of several antiviral and anticancer nucleoside analog pro-drugs. Austin, Toy, and colleagues have demonstrated that dCK deficient mice (dCK-/-) have severe developmental defects of the lymphoid and hematopoietic progenitor cells, indicating that dCK is pivotal for their normal development. Further study of the T, B, and erythroid lineages revealed nucleotide pool imbalances resulting in replication stress and cell cycle arrest in the early stages of DNA replication. Dual inactivation of both dCK and thymidine kinase 1 (TK1) in vivo supported our hypothesis that salvage of thymidine by TK1 was responsible for the allosteric block of the de novo pathway enzyme, ribonucleotide reductase, consequentially perturbing the nucleotide pools. These findings and the role of dCK in cancer led to our interest in developing a small molecule inhibitor. Positron Emission Tomography and the dCK-specific substrate, 18F-L-1-(2'-deoxy-2'-F luoroarabinofuranosyl) Cytosine, proved useful in the quick identification of top performing dCK inhibitors in vivo. Following a high throughput screen and a structure-activity relationship study we successfully identified high potency small molecule inhibitors of dCK (dCKi). The combination of the dCKi with pharmacological perturbations of de novo dNTP synthesis, via thymidine, in acute lymphoblastic leukemia cells depletes deoxycytidine triphosphate pools leading to DNA replication stress, cell cycle arrest, and apoptosis in vivo, without detectable toxicity to normal tissues. The results from our studies further our understanding of nucleotide metabolism in normal hematopoiesis and hematological malignancies, and identify dCK as a new therapeutic target in hematological malignancies.