gebhart/patrepeval huggingface dataset:
Characterization of a new simian virus 40 mutant, tsA3900, isolated from deletion mutant tsA1499 (1985)

The simian virus 40 (SV40) mutant tsA1499 contains an 81-base-pair deletion in the region of A gene encoding the C-terminal portion of the large T antigen. This mutant is particularly interesting, since it is a temperature-sensitive mutant that is apparently able to separate the lytic growth and transforming functions of the SV40 large T antigen at 38.5 degrees C. We report the isolation of a tsA1499 revertant (tsA1499-Rev) which is no longer temperature sensitive for lytic growth but still contains the 81-base-pair deletion of tsA1499. Marker rescue experiments with tsA1499-Rev or wild-type strain 830 (wt830) DNAs revealed that the original tsA1499 mutant contained a second mutation within the HindIII-Fnu4HI restriction fragment between 0.425 and 0.484 map units. Sequencing of this DNA fragment from the tsA1499, tsA1499-Rev, and wt830 viruses revealed that tsA1499 contained a single-base transversion (C to G) at 0.455 map units (nucleotide 4261). This transversion resulted in the creation of a new RsaI cleavage site in the tsA1499 DNA and predicts an arginine-to-threonine substitution at amino acid position 186 in the mutant large T antigen. The DNA sequence of the tsA1499-Rev HindIII-Fnu4HI fragment was identical to that of wt830. To determine whether tsA1499 was temperature sensitive for lytic growth solely as a result of the newly discovered point mutation or because of a combination of the point and deletion mutations, a series of viruses were constructed which contained the point mutation, the deletion mutation, both mutations, or neither. This was done by ligating the PstI A and B DNA fragments from either tsA1499 or wt830 and transfecting the ligated DNA into BSC-1H monkey kidney cells. This experiment revealed that all viruses containing the point mutation (the tsA1499 PstI A DNA fragment) were temperature sensitive for lytic growth, regardless of the presence of the 81-base-pair deletion (the tsA1499 PstI B DNA fragment). This newly discovered point mutation, at nucleotide 4261, is therefore unique, since to our knowledge it is the first tsA mutation to be described in the 0.455-map-unit region of the SV40 genome. We then tested the effect of this unique mutation on the ability of the SV40 virus to transform cultured rat cells to anchorage independence.(ABSTRACT TRUNCATED AT 400 WORDS)
In Vivo Endoscopic Optical Biopsy with Optical Coherence Tomography (1997)

Current medical imaging technologies allow visualization of tissue anatomy in the human body at resolutions ranging from 100 micrometers to 1 millimeter. These technologies are generally not sensitive enough to detect early-stage tissue abnormalities associated with diseases such as cancer and atherosclerosis, which require micrometer-scale resolution. Here, optical coherence tomography was adapted to allow high-speed visualization of tissue in a living animal with a catheter-endoscope 1 millimeter in diameter. This method, referred to as "optical biopsy," was used to obtain cross-sectional images of the rabbit gastrointestinal and respiratory tracts at 10-micrometer resolution.
LIBLINEAR: A Library for Large Linear Classification (2008)

LIBLINEAR is an open source library for large-scale linear classification. It supports logistic regres-sion and linear support vector machines. We provide easy-to-use command-line tools and library calls for users and developers. Comprehensive documents are available for both beginners and advanced users. Experiments demonstrate that LIBLINEAR is very efficient on large sparse data sets.
Bias compensation recursive algorithm for dual‐rate rational models (2018)

In dual‐rate rational systems, some output data are missing (unmeasurable) to make the traditional recursive least squares (RLS) parameter estimation algorithms invalid. In order to overcome this difficulty, this study develops a bias compensation RLS algorithm for estimating the missing outputs and then the model parameters. The algorithm based on auxiliary model and particle filter has four steps: (i) to establish an auxiliary model to estimate unmeasurable outputs, (ii) to compensate bias induced by correlated noise, (iii) to add a filter to improve estimation accuracy of the unmeasurable outputs and (iv) to obtain an unbiased parameter estimation. Three examples are selected for simulation demonstrations to give further guarantees on the usefulness of the proposed algorithms. The comparative studies show that the bias compensation RLS is more effective for such systems with dual‐rate input and output data.
Inside Family Viewing: Ethnographic Research on Television’s Audiences (1993)

Against a backdrop of growing unease with traditional quantitative empirical research methods and an equal unease with abstract psychoanalytical models, ethnography is increasingly seen as one of the few empirical methods which is not completely undercut by contemporary theoretical work. Indeed, it is only recently that ethnography has begun to show its power to construct and explain in media studies. James Lull's work in this area has proved an influential model, and in this collection he covers writing on social uses, the case study of television use in the family, and ethnographic theory and method.
Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering (2013)

Single-molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, nonfluorescent single-molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.
Prebiotics in Infant Formulas (2004)

The data obtained indicate that the prebiotic mixture under study is able to stimulate the development of a microbial flora similar to that of breast-fed infants. Several biota, whose growth is enhanced by this prebiotic mixture, represent important factors in the postnatal development of the immune system. On this evidence it can be suggested that prebiotics may play a role as modulators of the postnatal development of the immune system.
Novel Heteroarotinoids as Potential Antagonists of Mycobacterium bovis BCG (2004)

A series of 15 heteroarotinoids has been prepared and evaluated for activity against Mycobacterium bovis BCG with the thiourea-containing isoxyl (7) (0.5 microg/mL) as the standard. 2,2,4-Trimethyl-2H-chromen-7-yl 4-(methoxycarbonyl)benzoate (8) displayed the most significant activity (2.0-4.0 microg/mL) in terms of the lowest concentration (microg/mL) (MIC, minimum inhibitory concentration) required to produce a 99% reduction in the number of colonies on a plate as compared to that system free of the agent at the same dilution of the culture suspension. Ethyl 4-[[N-(2,2,4,4-tetramethylchroman-6-yl)thiocarbamoyl]amino]benzoate (9) and [[(1E,3Z,5E)-1-aza-4-methyl-6-(1,2,2,4-tetramethyl(1,2-dihydroquinolyl))hexa-1,3,5-trienyl]amino]aminomethane-1-thione (10) exhibited activity at 5.0-10.0 and 10.0-20.0 microg/mL, respectively, while the other examples had MIC values of 20 microg/mL or greater. The inhibitory ability of 8 may occur via the inhibition of mycolic acid synthesis in a like manner as found with 7, but this requires further study. The heteroarotinoids are the first examples to exhibit inhibitory ability against the growth of Mycobacterium bovis BCB.
Hepatocyte growth factor/scatter factor (HGF/SF) is produced by human bone marrow stromal cells and promotes proliferation, adhesion and survival of human hematopoietic progenitor cells (CD34+). (1998)

The fate of hematopoietic progenitor cells (HPCs) in the bone marrow (BM) microenvironment is determined by two different interactions: 1) they adhere (via integrins) to both extracellular matrix molecules and BM stromal cells; and 2) stromal cells produce cytokines that influence their survival, proliferation, differentiation, and mobilization. The ligands for the protein tyrosine kinase receptors c-KIT and FLT3/FLK2, stem cell factor (SCF), and FL are produced by BM stromal cells and are known to affect several facets of hematopoiesis. We studied another protein tyrosine kinase receptor, c-MET, and its ligand hepatocyte growth factor (HGF), also known as scatter factor (SF), which play a similar role in hematopoiesis. c-MET mRNA is expressed in immature human BM HPCs (CD34+CD33- or CD34+CD38-), but not in more mature HPCs (CD34+CD33+ or CD34+CD38+). The ligand HGF/SF is predominantly produced by BM stromal cells at both the mRNA and protein levels. We confirmed functionally that HGF/SF alone has no effect on proliferation of HPCs, but that when combined with granulocyte/macrophage colony-stimulating factor (GM-CSF) or interleukin-3 it acts as a synergistic proliferative factor, although not as potently as kit-ligand or FLT-3/FLK-2 ligand. Furthermore, HGF/SF promotes adhesion of HPCs to immobilized fibronectin. HGF/SF-induced adhesion to fibronectin is probably caused by activation of the integrins alpha4beta1 and alpha5beta1, insofar as we were able to block this interaction by using monoclonal blocking antibodies directed against these integrin subunits. Addition of the tyrosine-phosphorylation inhibitor genistein inhibited HGF/SF-induced adhesion, supporting the idea that HGF/SF-induced effects are the result of signaling via the receptor c-MET after ligand binding. The enhanced adhesion of HGF/SF to fibronectin proved to be beneficial for the maintenance of the colony-forming potential of HPCs. HGF/SF alone and especially in combination with fibronectin prolongs survival of GM colony-forming cells in liquid culture. Our data indicate that HGF/SF is a polyfunctional cytokine in the BM microenvironment. It is produced by human BM stromal cells and directly or indirectly promotes proliferation, adhesion, and survival of human HPCs.
Dramatic performance enhancements for the FASTER optimization algorithm (2006)

FASTER is a combinatorial optimization algorithm useful for finding low-energy side-chain configurations in side-chain placement and protein design calculations. We present two simple enhancements to FASTER that together improve the computational efficiency of these calculations by as much as two orders of magnitude with no loss of accuracy. Our results highlight the importance of choosing appropriate initial configurations, and show that efficiency can be improved by stringently limiting the number of positions that are allowed to relax in response to a perturbation. The changes we describe improve the quality of solutions found for large-scale designs, and allow them to be found in hours rather than days. The improved FASTER algorithm finds low-energy solutions more efficiently than common optimization schemes based on the dead-end elimination theorem and Monte Carlo. These advances have prompted investigations into new methods for force field parameterization and multiple state design.
The latent collagenase and gelatinase of human polymorphonuclear neutrophil leucocytes (1980)

Two metallo-proteinases of human neutrophil leucocytes, collagenase and gelatinase, were studied. Collagenase specifically cleaved native collagen into the TCA and TCB fragments, whereas gelatinase degraded denatured collagen, i.e. gelatin, and the TCA fragments produced by collagenase. On subcellular fractionation by zonal sedimentation, collagenase was found to be localized in the specific granules, separate from gelatinase, which was recovered in smaller subcellular organelles known as C-particles. Neither enzyme was present in the azurophil granules, which contain the two major serine proteinases of neutrophils, elastase and cathepsin G. Collagenase and gelatinase were separated by gel filtration from extracts of partially purified granules. Both enzymes were found to occur in latent forms and were activated either by trypsin or by 4-aminophenylmercuric acetate. Gelatinase was also activated by cathepsin G, which, however, destroyed collagenase. Both enzymes were destroyed by neutrophil elastase. Activation resulted in a decrease by 25 000 in the apparent mol. wt. of both latent metallo-proteinases.
Human CASK/LIN-2 Binds Syndecan-2 and Protein 4.1 and Localizes to the Basolateral Membrane of Epithelial Cells (1998)

In Caenorhabditis elegans, mutations in the lin-2 gene inactivate the LET-23 receptor tyrosine kinase/Ras/MAP kinase pathway required for vulval cell differentiation. One function of LIN-2 is to localize LET-23 to the basal membrane domain of vulval precursor cells. LIN-2 belongs to the membrane-associated guanylate kinase family of proteins. We have cloned and characterized the human homolog of LIN-2, termed hCASK, and Northern and Western blot analyses reveal that it is ubiquitously expressed. Indirect immunofluorescence localizes CASK to distinct lateral and/or basal plasma membrane domains in different epithelial cell types. We detect in a yeast two-hybrid screen that the PDZ domain of hCASK binds to the heparan sulfate proteoglycan syndecan-2. This interaction is confirmed using in vitro binding assays and immunofluorescent colocalization. Furthermore, we demonstrate that hCASK binds the actin-binding protein 4.1. Syndecans are known to bind extracellular matrix, and to form coreceptor complexes with receptor tyrosine kinases. We speculate that CASK mediates a link between the extracellular matrix and the actin cytoskeleton via its interaction with syndecan and with protein 4.1. Like other membrane-associated guanylate kinases, its multidomain structure enables it to act as a scaffold at the membrane, potentially recruiting multiple proteins and coordinating signal transduction.
A high performance factoring machine (1984)

Factoring, primality testing, and other problems of current interest [1, 2, 3, 4, 5, for example] in experimental number theory require machines with different architectures from those for any other application. Algorithms for such problems are small, but their execution requires high-speed arithmetic on very long integers interspersed with shorter precision computing that can conveniently be done by several processors acting in parallel. In this paper, we describe the preliminary design of a processor specifically for computational number theoretic problems. The primary component is a 256-bit ALU which is dynamically reconfigurable to provide for parallel independent operations on groups of 32-bit subwords within the 256-bit word.
EGFR-TKIs resistance via EGFR-independent signaling pathways (2018)

Tyrosine kinase inhibitors (TKIs)-treatments bring significant benefit for patients harboring epidermal growth factor receptor (EGFR) mutations, especially for those with lung cancer. Unfortunately, the majority of these patients ultimately develop to the acquired resistance after a period of treatment. Two central mechanisms are involved in the resistant process: EGFR secondary mutations and bypass signaling activations. In an EGFR-dependent manner, acquired mutations, such as T790 M, interferes the interaction between TKIs and the kinase domain of EGFR. While in an EGFR-independent manner, dysregulation of other receptor tyrosine kinases (RTKs) or abnormal activation of downstream compounds both have compensatory functions against the inhibition of EGFR through triggering phosphatidylinositol 3-kinase (PI3K)/Akt and mitogen-activated protein kinase (MAPK) signaling axes. Nowadays, many clinical trials aiming to overcome and prevent TKIs resistance in various cancers are ongoing or completed. EGFR-TKIs in accompany with the targeted agents for resistance-related factors afford a promising first-line strategy to further clinical application.
Staphylococcus aureus but not Staphylococcus epidermidis can acquire iron from transferrin (1995)

Staphylococci grow and cause infection under the iron-restricted conditions found in vivo. They therefore must possess mechanisms to obtain iron for metabolism from this environment. To determine if staphylococci can extract iron bound to human transferrin, we labelled transferrin with 55Fe and performed uptake assays on cells grown in iron-restricted and iron-plentiful conditions. Growing cultures of Staphylococcus aureus NCTC 8532 could take up radioactive iron during mid- to late-exponential phase of growth. This process was iron-regulated and did not require direct contact between the cell and the labelled transferrin. Siderophore production was detected during this phase, but reductase or protease activity was not. S. epidermidis ATCC 14990 could not access 55Fe bound to transferrin, nor did this isolate produce siderophore, reductase or protease. This difference in the ability to acquire iron bound to transferrin may contribute to the increased virulence of S. aureus when compared to S. epidermidis.
Bactericidal activities of cefprozil, penicillin, cefaclor, cefixime, and loracarbef against penicillin-susceptible and -resistant Streptococcus pneumoniae in an in vitro pharmacodynamic infection model (1996)

We examined the bactericidal activities of penicillin, cefprozil, cefixime, cefaclor, and loracarbef against three clinical isolates of Streptococcus pneumoniae which were susceptible, moderately susceptible, and resistant to penicillin. An in vitro two-compartment glass infection model was used to simulate human pharmacokinetics in the presence of bacteria. Also, changes in organism susceptibility and development of resistant subpopulations were evaluated. Simulated pediatric dosage regimens and target peak concentrations in the central compartment were as follows: penicillin V-potassium, 26 mg/kg of body weight every 6 h (q6h) and 14 micrograms/ml; cefaclor, 13.4 mg/kg q8h and 16 micrograms/ml; loracarbef, 15 mg/kg q12h and 19 micrograms/ml; cefprozil, 15 mg/kg q12h and 11 micrograms/ml; and cefixime, 8mg/kg q24h and 4 micrograms/ml. Targeted half-lives of each agent were 1 h for penicillin, cefaclor, and loracarbef; 1.3 h for cefprozil; and 3.5 h for cefixime. Growth controls were performed at two different pump rates, 0.8 and 2.0 ml/min (half-lives = 3.5 and 1 h, respectively). Each isolate demonstrated autolysis at the lower rate which was attributed to a decreased supply of fresh nutrients available to the organisms in the infection compartment. Against the susceptible isolate, the time to 99.9% killing was statistically significant between penicillin V-potassium and both cefaclor and cefixime (P < 0.029). Loracarbef never achieved a 99.9% reduction in the inoculum. At 48 h penicillin, cefprozil, and cefaclor were equivalent in extent of killing. Against the intermediately resistant isolate, cefprozil was superior to all other regimens with respect to rate of killing (P < 0.013) and extent of killing at 24 h (P < 0.0003). At 48 h penicillin, cefprozil, and cefaclor were equivalent in extent of killing. All of the regimens exhibited inferior activity against this penicillin-resistant isolate. A 99.9% kill was never obtained with any of the regimens, nor was there an appreciable decrease in the colony counts. In conclusion, it appears that cefprozil, penicillin, and cefaclor are effective therapies against sensitive and even intermediately sensitive isolates of S. pneumoniae. However, none of the oral therapies appear to be of any benefit against penicillin-resistant isolates. The in vitro model may be an effective tool in evaluating other multiple-dose therapies against this fastidious organism, since the continual supply of fresh medium maintains the viability of S. pneumoniae with minimal stationary-phase autolysis.
Ultrafast Energy-Transfer Dynamics between Block Copolymer and π-Conjugated Polymer Chains in Blended Polymeric Systems (2001)

The blending of polymers has been conventionally employed to increase the quantum efficiencies of polymeric electroluminescence (EL) devices via the energy transfer process, which was interpreted in terms of the Förster-type energy transfer based on dipole−dipole interactions. The detailed analysis of various time-resolved spectroscopic data in the blended polymer between MEH-PPV (poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene]) and DSiPV (poly[1,3-propanedioxy-1,4-phenylene-1,2-ethylene(2,5-bis(trimethylsilyl)-1,4-phenylene)-1,2-ethylene-1,4-phenylene]) provides some evidence that the ultrafast energy-transfer channel via the shortest interchain distance between the adjacent constituent polymer chains should be considered to account for the dynamics of stimulated emission (SE) and photoinduced absorption (PA) in the blended polymeric systems. These interchain interactions are also responsible for the diminishment of SE of the blended polymer in the transient absorption spectra, because PA is enhanced due to the formation of interchain excitons. These results provide new insight into the role of interchain interactions in the improvement of heteropolymeric EL devices.
A real-time electrical impedance tomography system for clinical use-design and preliminary results (1995)

An instrument is described which produces images of the electrical impedance distribution within the body at a rate of 25 frames per second, allowing lung ventilation and lung perfusion to be observed in real time. The instrument makes impedance measurements using an array of 16 electrodes on the surface of the body, and reconstructs the images using a weighted backprojection technique. The design of the data acquisition electronics and the reconstruction and display processor are described. Some preliminary in vitro and in vivo results from the system are presented.
Preparation of Tungsten‐Based Olefin Metathesis Catalysts Supported on Alumina (2011)

Abstract A new tungsten alkylidene complex, W(NAr)(CHCMe 2 Ph)(OHIPT‐NMe 2 )(pyrrolide) {Ar=2,6‐( i‐ Pr) 2 C 6 H 3 ; HIPT‐NMe 2 =2,6‐[2,4,6‐( i‐ Pr) 3 C 6 H 2 ] 2 ‐4‐NMe 2 ‐C 6 H 2 }, has been synthesized and shown to be highly selective for Z homocoupling metathesis of selected terminal olefins in pentane, as is W(NAr)(CH 2 CH 2 CH 2 )(OHIPT)(pyrrolide) ( 5 ). Both 5 and W(NAr)(CHCMe 2 Ph)(OHIPT‐NMe 2 )(pyrrolide) ( 6 ) are adsorbed onto calcined alumina. Control experiments and metathesis homocoupling of four substrates lead to the conclusions that 5 is largely adsorbed in a reaction that liberates HIPTOH, while 6 is adsorbed largely through an interaction between the dimethylamino group and an acidic site on the surface. There is no evidence that any adsorbed catalyst can give rise to Z selectivity of a magnitude equal to that found in a homogeneous reaction involving 5 or 6 .
Kinetics of processes in the Ti–Si1−xGex systems (1996)

The kinetics of processes related to the formation of C49 and C54 Ti(Si1−yGey)2 germanosilicide phases in the two relaxed and strained Ti/Si1−xGex systems (x1=0.35 and x2=0.20) in the temperature range 600–800 °C are considered. These processes have been studied through Auger electron spectroscopy, secondary ion mass spectroscopy, x-ray diffraction, and Raman scattering spectroscopy supported by ion beam etching techniques. Si/Ge ‘‘intergrain’’ alloy has been found between the grains of the C49 or/and C54 phases, with a Ge-rich part Si1−zGez of z=2x–3x in the upper region. At higher temperatures, the Ge concentration in the Ge-rich alloy decreases and its volume increases. The temperature required for obtaining similar changes are higher when x2&amp;lt;x1. A kinetic electron-related model is proposed to explain the observed phenomena.