gebhart/patrepeval huggingface dataset:
Linear presentation of variable side-chain spacing in a highly diverse combinatorial library. (1996)

A synthetic library that presents potential pharmacophores in a linear fashion with variable spacing was designed (alpha, beta, gamma-library). To prove the concept, we synthesized a number of individual compounds as well as a model library. Diamino acids connected by amide bonds via their alpha- or side-chain amino groups were used to form the backbone (scaffold) of this library. The remaining amino group of the diamino acids were acylated by a variety of carboxylic acids, generating an appreciable diversity of compounds in this library. The compositions of compounds in the library were identified by reading a peptide tag synthesized concurrently with the library structures. This code contained the information regarding the carboxylic acid coupled, and the diamino acid and amino group to which the acid was coupled.
Time-Domain Analysis of Frequency Stability Using Nonzero Dead-Time Counter Techniques (1985)

This paper evaluates the impact of nonzero, dead time when implementing classical, numerical, frequency measurement algorithms and computes observables such as the 2-pair (Allan) variance. The extended 2-pair variance algorithms which permit increasing the effective averaging terms by computational methods is investigated. This methodology permits straightforward use of Fourier techniques and the derivation of a countertransfer function.
Synthesis of a Porphyrin with Fused Five- and Seven-membered Exocyclic Rings from a Cross-conjugated Tetracyclic Dipyrrole (1994)

1-Aza-7-pyrrolylmethyl-1,4,5,6-tetrahydroazulene 1 was cyclized with 3.5% HBr-AcOH to give a cross-conjugated dipyrrole 3 in good yield; hydrogenation of the double bond gave the tetracyclic dipyrrole 5 and subsequent hydrogenolysis of the benzyl esters, followed by acid catalyzed condensation with diformyldipyrrylmethane 7 gave a porphyrin 8 bearing two fused exocyclic rings.
Mx proteins in blood leukocytes for monitoring interferon beta-1b therapy in patients with MS (2000)

Mx levels in lysed blood cells may represent a useful surrogate marker for IFNbeta-1b activity corresponding to the clinical response during treatment of MS.
Impaired Resistance and Enhanced Pathology During Infection with a Noninvasive, Attaching-Effacing Enteric Bacterial Pathogen, Citrobacter rodentium , in Mice Lacking IL-12 or IFN-γ (2002)

Mice infected with Citrobacter rodentium represent an excellent model in which to examine immune defenses against an attaching-effacing enteric bacterial pathogen. Colonic tissue from mice infected with C. rodentium harbors increased transcripts for IL-12 and IFN-gamma and displays mucosal pathology compared with uninfected controls. In this study, the role of IL-12 and IFN-gamma in host defense and mucosal injury during C. rodentium infection was examined using gene knockout mice. IL-12p40(-/-) and IFN-gamma(-/-) mice were significantly more susceptible to mucosal and gut-derived systemic C. rodentium infection. In particular, a proportion of IL-12p40(-/-) mice died during infection. Analysis of the gut mucosa of IL-12p40(-/-) mice revealed an influx of CD4(+) T cells and a local IFN-gamma response. Infected IL-12p40(-/-) and IFN-gamma(-/-) mice also mounted anti-Citrobacter serum and gut-associated IgA responses and strongly expressed inducible NO synthase (iNOS) in mucosal tissue, despite diminished serum nitrite/nitrate levels. However, iNOS does not detectably contribute to host defense against C. rodentium, as iNOS(-/-) mice were not more susceptible to infection. However, C57BL/6 mice infected with C. rodentium up-regulated expression of the mouse beta-defensin (mBD)-1 and mBD-3 in colonic tissue. In contrast, expression of mBD-3, but not mBD-1, was significantly attenuated during infection of IL-12- and IFN-gamma-deficient mice, suggesting mBD-3 may contribute to host defense. These studies are among the first to examine mechanisms of host resistance to an attaching-effacing pathogen and show an important role for IL-12 and IFN-gamma in limiting bacterial infection of the colonic epithelium.
Rapid Thermal Processing of High Efficiency N-Type Silicon Solar Cells with Al Back Junction (2006)

In this paper we report on the design, fabrication and modeling of 49 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , 200-mum thick, 1-5 Omega-cm, n- and p-type lang111rang and lang100rang screen-printed silicon solar cells. A simple process involving RTP front surface phosphorus diffusion, low frequency PECVD silicon nitride deposition, screen-printing of Al metal and Ag front grid followed by co-firing of front and back contacts produced cell efficiencies of 15.4% on n-type lang111rang Si, 15.1% on n-type lang100rang Si, 15.8% on p-type lang111rang Si and 16.1% on p-type lang100rang Si. Open circuit voltage was comparable for n and p type cells and was also independent of wafer orientation. High fill factor values (0.771-0.783) for all the devices ruled out appreciable shunting which has been a problem for the development of co-fired n-type lang100rang silicon solar cells with Al back junction. Model calculations were performed using PC1D to support the experimental results and provide guidelines for achieving >17% n-type silicon solar cells by rapid firing of Al back junction
Interleukin-1&beta; inhibitors for the treatment of cryopyrin-associated periodic syndrome (2011)

Cryopyrin-associated periodic syndrome (CAPS) comprises a group of rare, but severe, inherited autoinflammatory disorders associated with aberrant secretion of interleukin (IL)-1. These distinct conditions of autoinflammatory origin include Muckle-Wells syndrome, familial cold autoinflammatory syndrome, and neonatal-onset multisystem inflammatory disease (NOMID), which is also referred to as chronic infantile neurologic cutaneous and articular syndrome. Recently, this group of diseases has been associated with mutations in the NLRP3 gene that encodes for the protein cryopyrin, a component of the inflammasome complex that regulates the maturation and secretion of inflammatory cytokine IL-1β. Immune cells from patients with NOMID secrete higher levels of active IL-1β compared with monocytes from healthy subjects. Overproduction of IL-1 is believed to promote aberrant inflammatory response in CAPS patients. Evidence supporting the clinical value of IL-1β in CAPS has been provided from the complete response of patients after treatment with IL-1 blocking agents.
Effect of Nanoscale Morphology on the Conductivity of Polymerized Ionic Liquid Block Copolymers (2011)

Polymerized ionic liquid (POIL) block copolymers represent a unique class of materials for fundamental studies of single ion conduction as a function of morphology in microphase-separated polymer electrolytes for energy storage and conversion applications. We describe the synthesis of a series of poly(styrene-b-4-vinylbenzylalkylimidazolium bis(trifluoromethanesulfonyl)imide) (PS-b-PVBn(alkyl)ImTFSI; alkyl = CH3 (Me), n-C4H9 (Bu), n-C6H13 (Hex)) diblock copolymers (2.7–17.0 mol % POIL) via exhaustive functionalization and ion exchange of relatively narrow molecular weight dispersity poly(styrene-b-4-vinylbenzyl chloride) precursors derived from nitroxide-mediated block copolymerizations. The solid-state morphology of these PS-b-PVBn(alkyl)ImTFSI copolymers were studied using a combination of temperature-dependent synchrotron small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). From electrochemical impedance spectroscopy measurements, we observe that lamellar samples having similar compositions exhibit comparable values of conductivity (0.1 mS cm–1 at 150 °C) regardless of imidazolium alkyl substituent. The ionic conductivity of a compositionally varied series of PS-b-PVBnHexImTFSI diblocks depends nonlinearly on POIL composition (0.01 mS cm–1 for 8.6 mol % POIL and 0.1 mS cm–1 for 17.0 mol % POIL at 150 °C), thus highlighting the influence of morphology on the observed ionic conductivity of POIL block copolymers for the first time. By using different polymer processing strategies, we further demonstrate that the ionic conductivity of a single sample (8.6 mol % POIL) may vary by more than one order of magnitude depending on the long-range ordering of the microphase separated morphology. These studies indicate that macroscopic connectivity and morphological defects strongly affect the observed conductivity in these materials.
Low-Molecular-Weight Heparin and Cancer (2000)

Heparin is a familiar anticoagulant drug with properties that may impede tumor growth; it modifies properties of cells that contribute to malignant dissemination such as angiogenesis, growth factor and protease activity, immune function, proliferation, and gene expression. Heparin has antitumor effects in animal models of malignancy, and studies in human malignancy show improved cancer outcome with heparin treatment. Meta-analyses comparing unfractionated heparin (UFH) and low-molecular-weight heparin (LMWH) for treatment of deep-vein thrombosis have shown apparent substantial improvement in cancer outcome in the subset of patients with malignancy who were randomly assigned to receive LMWH. This experience, together with the favorable pharmacokinetic properties of LMWH, provides a rationale for prospective clinical trials of LMWH in patients with cancer. Such trials should provide (a) definitive data on possible antitumor effects of this treatment, (b) insight into possible heterogeneous responses to heparin treatment among different histological types and stages of malignancy, and (c) a setting for exploring mechanisms of antineoplastic effect in human malignancy.
Induction of Lysosomal Enzyme Secretion by Alveolar Macrophages in Response to the Purified Complement Fragments C5a and C5a des-arg (1979)

Purified C5a and its "inactive" form, C5a des-arg, were shown to induce secretion of acid hydrolases from rabbit alveolar macrophages (AM) in a concentration-dependent manner. Secretion increased with time to 5 times above controls by 72 hr. Concentrations of these enzymes in the cell lysates did not decrease during the incubation, suggesting that synthesis of new enzyme was occurring. The lysosomal enzyme secretion was accompanied by increased pinocytosis and release of proteolytic enzymes from the macrophages. At no time was significant lactic dehydrogenase liberated, indicating that secretion was selective and not due to cell death. Data presented also suggest that C5a des-arg induced secretion from the macrophages of a chemotactic factor for neutrophils. It was concluded that C5a and C5a des-arg may play a role in lung injury by interactions with AM, inducing the secretion of acid hydrolases and proteolytic enzymes that can cause tissue damage, and by regulating the influx of other inflammatory cells into the interstitium and air spaces.
Expression in Escherichia coli of a cloned crystal protein gene of Bacillus thuringiensis subsp. israelensis (1987)

A ca. 10-kilobase (kb) HindIII fragment of plasmid DNA from Bacillus thuringiensis subsp. israelensis was cloned into plasmid pUC9 and transformed into Escherichia coli. Extracts of the recombinant strain contained a 27-kilodalton (kDa) peptide that reacted with antibodies to a 27-kDa peptide isolated from crystals produced by B. thuringiensis subsp. israelensis. Extracts of the recombinant strain were hemolytic and toxic to Aedes aegypti larvae. Full expression of the 27-kDa peptide required the presence of a ca. 0.8-kb region of DNA located 4 kb upstream from the structural gene; the 0.8-kb region could be present in cis or trans relative to the gene and apparently acted post-transcriptionally. Analysis of maxicells showed that the 10-kb insert also coded for peptides of 67, 20, and 16 kDa; data obtained with different subclones suggest that the 20-kDa peptide is encoded in the 0.8-kb DNA region.
Endogenous 24(S),25-Epoxycholesterol Fine-tunes Acute Control of Cellular Cholesterol Homeostasis (2007)

Certain oxysterols, when added to cultured cells, are potent regulators of cholesterol homeostasis, decreasing cholesterol synthesis and uptake and increasing cholesterol efflux. However, very little is known about whether or not endogenous oxysterol(s) plays a significant role in cholesterol homeostasis. 24(S),25-Epoxycholesterol (24,25EC) is unique among oxysterols in that it is produced in a shunt of the mevalonate pathway which also produces cholesterol. We investigated the role of endogenously produced 24,25EC using a novel strategy of overexpressing the enzyme 2,3-oxidosqualene cyclase in Chinese hamster ovary cells to selectively inhibit the synthesis of this oxysterol. First, loss of 24,25EC decreased expression of the LXR target gene, ABCA1, substantiating its role as an endogenous ligand for LXR. Second, loss of 24,25EC increased acute cholesterol synthesis, which was rationalized by a concomitant increase in HMG-CoA reductase gene expression at the level of SREBP-2 processing. Therefore, in the absence of 24,25EC, fine-tuning of the acute regulation of cholesterol homeostasis is lost, supporting the hypothesis that 24,25EC functions to protect the cell against the accumulation of newly synthesized cholesterol.
Zingiberaceae extracts for pain: a systematic review and meta-analysis (2015)

Our findings indicated that Zingiberaceae extracts are clinically effective hypoalgesic agents and the available data show a better safety profile than non-steroidal anti-inflammatory drugs. However, both non-steroidal anti-inflammatory drugs and Zingiberaceae have been associated with a heightened bleeding risk, and there have been no comparator trials of this risk. Further clinical studies are recommended to identify the most effective type of Zingiberaceae extract and rigorously compare safety, including bleeding risk.
T Helper Cell Type 2 Cytokine–Mediated Comitogenic Responses and Ccr3 Expression during Differentiation of Human Mast Cells in Vitro (1999)

Mast cells (MCs) arise in situ from circulating stem cell factor (SCF)-dependent committed progenitors (PrMCs) and accumulate at sites of allergic mucosal inflammation. We hypothesized that human (h)PrMCs and their mature counterparts might share overlapping patterns of chemokine and cytokine receptor utilization with eosinophils, basophils, and T helper type 2 (Th2) lymphocytes for their homing and allergy-associated hyperplasia. We have characterized committed hPrMCs and fully mature hMCs derived in vitro from cord blood for their functional responses to chemokine and cytokine agonists germane to allergic inflammation and for their maturation-related expression of the corresponding receptors. After 4 wk of culture in the presence of recombinant stem cell factor (SCF), interleukin (IL)-6, and IL-10, the cells were characterized as hPrMCs based upon their uniform surface expression of c-kit and CD13, low-level expression of FcinRIalpha, absence of CD14 and CD16 expression, and immunoreactivity for MC chymase in >80%, and about half were immunoreactive for tryptase and metachromatic with toluidine blue. By week 9, the cells had matured into hMCs, identified by higher levels of c-kit, continued expression of CD13 and low-level FcinRIalpha, uniform toluidine blue metachromasia, and uniform immunoreactivity for both tryptase and chymase. The 4-wk-old hPrMCs expressed four chemokine receptors (CXCR2, CCR3, CXCR4, and CCR5). Each receptor mediated transient rapid calcium fluxes in response to its respective ligand. Both recombinant human eotaxin and stromal cell-derived factor 1alpha elicited chemotaxis of hPrMCs. Only CCR3 was retained on the mature 9-wk-old hMCs from among these chemokine receptors, and hMCs responded to eotaxin with a sustained calcium flux but without chemotaxis. The Th2 cytokines IL-3, IL-5, IL-6, IL-9, and granulocyte/macrophage colony-stimulating factor each augmented the SCF-dependent proliferation of hPrMCs and hMCs. In contrast, the prototypical Th1 cytokine, interferon gamma, suppressed SCF-driven proliferation of both hPrMCs and hMCs. Thus, throughout their development in vitro, hMCs obey SCF-dependent, cytokine-driven mitogenic responses that reflect a Th2-type polarization characteristic of allergy and asthma. Furthermore, committed hPrMCs have a unique profile of chemokine receptor expression from among reported hematopoietic cells, including CCR3, which is shared with the other cells central to allergic inflammation (eosinophils, basophils, and Th2 lymphocytes).
High‐Throughput Real‐Time Quantitative Reverse Transcription PCR (2006)

Extensive detail on the application of the real-time quantitative polymerase chain reaction (QPCR) for the analysis of gene expression is provided in this unit. The protocols are designed for high-throughput, 384-well-format instruments, such as the Applied Biosystems 7900HT, but may be modified to suit any real-time PCR instrument. QPCR primer and probe design and validation are discussed, and three relative quantitation methods are described: the standard curve method, the efficiency-corrected DeltaCt method, and the comparative cycle time, or DeltaDeltaCt method. In addition, a method is provided for absolute quantification of RNA in unknown samples. RNA standards are subjected to RT-PCR in the same manner as the experimental samples, thus accounting for the reaction efficiencies of both procedures. This protocol describes the production and quantitation of synthetic RNA molecules for real-time and non-real-time RT-PCR applications.
Electronic transport through individual ZnO nanowires (2004)

Electronic transport through individual ZnO nanowires has been investigated. The current increases linearly with the bias and the conductance jumps upon ultraviolet illumination. The increase rate upon the illumination is much faster than the decrease rate as the light is off. The decrease rate under vacuum is slower than that in air. These phenomena are related to the surface oxygen species and further confirmed by in situ current–voltage measurements as a function of oxygen pressure at room temperature. Also, the conductance increases greatly as the temperature is raised. These results demonstrate that the surface oxygen species dominate the transport process through individual ZnO nanowires, which indicates their potential application to room temperature gas sensors.
Probability theory for 3-layer remote sensing radiative transfer model: errata (2013)

Several that appeared in [Opt. Express 20, 10004, (2012)] are corrected. ©2013 Optical Society of America OCIS codes: (030.5620) Radiative transfer; (280.4991) Passive remote sensing; (000.5490) Probability theory, stochastic processes, and statistics; (290.6815) Thermal emission; (010.1320) Atmospheric transmittance; (010.1330) Atmospheric turbulence; (300.6340) Spectroscopy, infrared. References and links 1. A. Ben-David and C. E. Davidson, “Probability theory for 3-layer remote sensing radiative transfer model: univariate case,” Opt. Express 20, 10004–10033 (2012), doi:10.1364/OE.20.010004. In Section 3.1.1, 11 line from the bottom of p. 10010, V(x) should be written as 2 2 4 2 2 ) 1 ) ( ]( 1 ) [exp( ) ( + − = − x E k x V T T σ μ . In Section 3.2.3, second full paragraph on p. 10016, distributions of ) ( 1 L B and T Δ omit the effect of the k2 coefficient. It should be written that ) , ( ~ ) ( 2 4 2 2 1 2 1 y y y k k N L B σ μ μ − − − and ) , ( ~ 2 2 4 2 2 1 2 Tc y y Tc y k k N T σ σ μ μ μ + − Δ − − . In Section 5, 4 line from the bottom of p. 10025, “...appear in emission mode...” should be written as “...appear in absorption mode...”. In Appendix A, scaling property of lognormal distributions, 1 line of p. 10029, mean parameter μ + c should be written as μ + c ln . In Appendix C, p. 10032, expression for V(z) should be written as 2 2 ) ( ) ( ) ( z E z E z V − = . #189802 $15.00 USD Received 6 May 2013; published 7 May 2013 (C) 2013 OSA 20 May 2013 | Vol. 21, No. 10 | DOI:10.1364/OE.21.011852 | OPTICS EXPRESS 11852
Efficient prototype filter realizations for cosine-modulated filter banks (1997)

This paper presents efficient realizations of prototype filters for biorthogonal cosine-modulated filter banks with arbitrary overall system delay. The implementation is based on lifting schemes. The lifting coefficients will be approximated such that the filter operations can be realized by a few shift and add operations. Since the lifting scheme is robust against coefficient quantization we do not loose the perfect reconstruction (PR) property of the filter bank when doing this approximation. The original and the approximated prototype filters are compared in terms of complexity and stopband attenuation. 1. INTRODUCTION
Speech recognition using time-warping neural networks (2002)

The author proposes a time-warping neural network (TWNN) for phoneme-based speech recognition. The TWNN is designed to accept phonemes with arbitrary duration, whereas conventional phoneme recognition networks have a fixed-length input window. The purpose of this network is to cope with not only variability of phoneme duration but also time warping in a phoneme. The proposed network is composed of several time-warping units which each have a time-warping function. The TWNN is characterized by time-warping functions embedded between the input layer and the first hidden layer in the network. The proposed network demonstrates higher phoneme recognition accuracy than a baseline recognizer based on conventional feedforward neural networks and linear time alignment. The recognition accuracy is even higher than that achieved with discrete hidden Markov models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
[Mammalian gene-transfer and expression efficiencies of baculovirus bacV-CMV-EGFPA]. (2004)

It has been reported that baculoviruses could serve as a new gene-transfer vehicle for mammalian cells. We have previously constructed recombinant baculovirus BacV-CMV-EGFPA and have proven that mammalian cells could be effectively infected by the recombinant baculovirus. In this report, we studied the efficiency of baculovirus to deliver exogenous gene into twenty mammalian cells, including twelve human cell lines (WI-38, Hela, HepG2, 293, PLC/PRF/5, 143B, MCF-7, BGC-223, DMS 114, CNE, Raji, LCL-cm), seven murine cell lines (BNL 1ME A.7R.1, CHO-K1, L-929, JC, PT67, NIH3T3, P815) and one monkey cell line (CV1). Results showed that most mammalian cell lines could be transduced by the recombinant baculovirus, the transduction efficiencies of the human and monkey cell lines were markedly higher than that of murine cell lines, and the transduction efficiencies in adherent culture cell lines higher than that of suspend culture cell lines, implying that the infection efficiency of the baculovirus may be correlative with the organism used and the growth properties of the cell lines. The plasmid pcDNA3. 1-EGFP, which contains the CMV promoter and EGFP reporter gene, was next transfected by LipofectAMINE into a number of mammalian cells, especially those cells that were low in the baculovirus transfection. Results showed that the CMV promoter could effectively direct the expression of the reporter gene in these mammalian cells. Therefore the gene-expression efficiencies in different mammalian cell lines by the recombinant baculovirus which contains the same CMV promoter were dictated by the ability of the baculovirus to enter the cell lines. This study suggested that the recombinant baculovirus vector is more suitable for gene expression in primate adherent culture cells than in murine cells and suspend culture cells.
Advances in bone marrow purging and processing : fourth international symposium : proceedings of the Fourth International Symposium on Bone Marrow Purging and Processing held in Orlando, Florida, 1993 (1994)

Examines emerging technology in this field, from both the research and clinical arenas. The book describes approaches for utilizing DNA sense and antisense probes, combinations of elutriators and immunomagnetics as well as refinements in the use of mechanical separation. Contributions from more than 400 investigators address topics such as pharmacological purging, marrow processing, clinical studies and tumor cell detection.