gebhart/patrepeval huggingface dataset:
A glial-specific, repressible, adenovirus vector for brain tumor gene therapy. (1998)

The principle hurdles for gene therapy are selectivity and efficacy. Toward that end, we constructed an adenovirus gene delivery system to enable robust, glial-specific, and repressible ectopic expression. A replication-incompetent (E1-deleted) adenovirus 5 vector was modified by the addition of three tandem repeats of a 300-bp fragment enhancer region of the glial fibrillary acidic protein gene coupled to a minimal promoter sequence from human cytomegalovirus to drive a tetracycline-controlled transactivator. Using beta-galactosidase as a reporter gene, we demonstrated high level expression in cells of glial origin (including cell lines derived from glioblastoma multiforme) but no detectable expression in nonglial cells (neuroblastoma or fibroblasts). Furthermore, expression was tightly regulated by anhydrous tetracycline. To our knowledge, this is the first gene therapy delivery system that is glial specific and which also allows for repression of ectopic gene expression.
Modeling the Initiation and Progression of Human Acute Leukemia in Mice (2007)

Our understanding of leukemia development and progression has been hampered by the lack of in vivo models in which disease is initiated from primary human hematopoietic cells. We showed that upon transplantation into immunodeficient mice, primitive human hematopoietic cells expressing a mixed-lineage leukemia (MLL) fusion gene generated myeloid or lymphoid acute leukemias, with features that recapitulated human diseases. Analysis of serially transplanted mice revealed that the disease is sustained by leukemia-initiating cells (L-ICs) that have evolved over time from a primitive cell type with a germline immunoglobulin heavy chain (IgH) gene configuration to a cell type containing rearranged IgH genes. The L-ICs retained both myeloid and lymphoid lineage potential and remained responsive to microenvironmental cues. The properties of these cells provide a biological basis for several clinical hallmarks of MLL leukemias.
Inhibition of Clostridium perfringens by a Novel Strain of Bacillus subtilis Isolated from the Gastrointestinal Tracts of Healthy Chickens (2005)

The objectives of this study were to isolate beneficial strains of microorganisms from the gastrointestinal tracts of healthy chickens and to screen them against Clostridium perfringens, a causative agent of necrotic enteritis in poultry. One of the bacteria isolated, a strain of Bacillus subtilis, was found to possess an anticlostridial factor that could inhibit the C. perfringens ATCC 13124 used in this study. The anticlostridial factor produced by B. subtilis PB6 was found to be fully or partially inactivated in the presence of pronase, trypsin, and pepsin. In contrast, the antimicrobial activity of the anticlostridial factor was not affected by treatment at 100 or 121 degrees C or by treatment with any of the organic solvents used in the study. The optimum growth temperature and optimum pH for production of the anticlostridial factor were 37 degrees C and 6.20, respectively. Using the mass spectroscopy-mass spectroscopy technique, the apparent molecular mass of the anticlostridial factor was estimated to be in the range from 960 to 983 Da. In terms of the antimicrobial spectrum, the anticlostridial factor was inhibitory toward various strains of C. perfringens implicated in necrotic enteritis in poultry, Clostridium difficile, Streptococcus pneumoniae, Campylobacter jejuni, and Campylobacter coli.
Design, Synthesis, and Characterization of Conifer‐Shaped Dendritic Architectures (2006)

An elongated structural design leading to more conical-shaped dendritic architectures by using a combination of 1-->3, 1-->(2+1), and 1-->(2+1 Me) C-branched monomers is presented. Synthesis of the conifer-shaped macromolecule was achieved by reaction between isocyanate 20 and amine 26 in dry CH2Cl2. A resultant extended focal adamantane-modified dendron was deprotected to generate the water-soluble product, which was subsequently complexed with beta-cyclodextrin in D2O to create the desired tree-like product. Host-guest interactions of the adamantane moiety with the beta-cyclodextrin cavity were monitored by 1H NMR spectroscopy. All monomers, key intermediates, and final products were fully characterized by 1H and 13C NMR spectroscopy, ESI or MALDI-TOF mass spectrometry, and IR spectroscopy.
An Experimental Evaluation to Determine the Effect of an Organometallic Fuel Additive on Particulate Trap Regeneration (1990)

&lt;div class="htmlview paragraph"&gt;The regenerative characteristics of a diesel particulate filter have been experimentally examined. The effect of particulate accumulation on system backpressure was of primary interest. To improve particulate regeneration, a copper compound was added to the fuel. The test results demonstrate that copper-containing fuel additives improve the regeneration characteristics of the filter, maintaining system backpressure at an acceptable level. Improved regeneration performance is expected to extend the operating range and life of the filter system. A model describing regeneration characteristics was developed to indicate the benefits of fuel copper concentration in controlling system backpressure.&lt;/div&gt;
Symbiotic Bacteria Direct Expression of an Intestinal Bactericidal Lectin (2006)

The mammalian intestine harbors complex societies of beneficial bacteria that are maintained in the lumen with minimal penetration of mucosal surfaces. Microbial colonization of germ-free mice triggers epithelial expression of RegIIIgamma, a secreted C-type lectin. RegIIIgamma binds intestinal bacteria but lacks the complement recruitment domains present in other microbe-binding mammalian C-type lectins. We show that RegIIIgamma and its human counterpart, HIP/PAP, are directly antimicrobial proteins that bind their bacterial targets via interactions with peptidoglycan carbohydrate. We propose that these proteins represent an evolutionarily primitive form of lectin-mediated innate immunity, and that they reveal intestinal strategies for maintaining symbiotic host-microbial relationships.
Fluid-phase connectivity and translational diffusion in a eutectic, two-component, two-phase phosphatidylcholine bilayer (1991)

In recent work [Vaz, W.L.C., Melo, E.C.C., & Thompson, T.E. (1989) Biophys. J. 56, 869-876] we have shown that translational diffusion studies using fluorescence recovery after photobleaching (FRAP) provide information concerning domain structures and fluid-phase connectivity in lipid bilayers in which solid and fluid phases coexist. In the present paper, translational diffusion of the fluid-phase-soluble, solid-phase-insoluble fluorescent lipid derivative N-(7-nitrobenzoxa-2,3-diazol-4-yl) dilauroyl-phosphatidylethanolamine and the fluid-phase connectivity are examined in lipid bilayers prepared from binary mixtures of 1-docosanoyl-2-dodecanoylphosphatidylcholine (C22:0C12:0PC) and 1,2-diheptadecanoylphosphatidylcholine (di-C17:0PC) by using FRAP. The phosphatidylcholine mixture used provides a eutectic system with a eutectic point at a composition of about 0.4 mole fraction of di-C17:0PC and a temperature of about 37 degrees C [Sisk, R.B., Wang, Z.Q., Lin, H.N., & Huang, C.H. (1990) Biophys. J. 58, 777-783]. Two regions in temperature and composition, respectively below and above 0.4 mole fraction of di-C17:0PC, where fluid and solid phases coexist in the same lipid bilayer, are available for examination of fluid-phase connectivity. In mixtures containing less than 0.4 mole fraction of di-C17:0PC the fluid phase coexists with a mixed interdigitated Lc gel phase composed mostly of C22:0C12:0PC, whereas in mixtures containing greater than 0.4 mole fraction of di-C17:0PC the fluid phase coexists with a P beta' gel phase mostly composed of di-C17:0PC. When the solid phase is a P beta' gel phase, the temperature of fluid-phase connectivity for the mixtures lies close to the fluidus, which means that a small (approximately 20%) mass fraction of solid phase can divide the large bulk of the bilayer that is fluid into nonconnected domains.(ABSTRACT TRUNCATED AT 250 WORDS)
Nicotine and Cotinine Adducts of a Melanin Intermediate Demonstrated by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (2001)

Pigmentation is a major factor in the incorporation of many drugs into hair. In an attempt to elucidate potential mechanisms of drug-melanin interaction, melanin was synthesized in vitro in the presence of nicotine, which we have shown to have a substantial interaction with melanin, and cotinine, a primary nicotine metabolite. L-DOPA, a precursor of eumelanin, was oxidized and oligomerized with tyrosinase. Nicotine, cotinine, and/or their deuterated analogues were added to the oligomerization reaction mixture in a 10:1 L-DOPA:drug ratio. A black precipitate formed within 60 min. Aliquots were removed from the incubation mixture at 60, 120, and 360 min. MALDI-TOF MS determinations were carried out on each sample to provide a mean and standard error for the masses of interest. Internal calibration allowed accurate mass measurement of the products. A careful comparison of the spectra of samples prepared both with and without drug indicated the presence of masses corresponding to the protonated drug, melanin oligomers, and nicotine or continine adducts of the monomeric melanin intermediate dopaquinone (DOPAQ). Additional support for the presence of drug-melanin adducts was provided by employing deuterated analogues of nicotine and L-DOPA in the reaction and observing that the masses shifted accordingly. Structures of the adducts were further confirmed by select ion gating and postsource decay analysis.
Pathogenesis and cellular immunity in experimental murine brucellosis. (1984)

Infection of mice with Brucella abortus strain 19 provides a most useful and interesting model in which to study chronic infection with intracellular bacteria. Most strains of mice develop a chronic infection. However, certain strains are better able to handle their infection. Long term bone marrow chimeras showed this to be due to bone marrow derived cells, rather than host physiology, although whether it is due T or B lymphocytes, macrophages or polymorphs is yet to be determined. In vitro treatment of lymphocytes from infected donors showed that the subpopulations transferring protection to naive mice was Thy 1+ 2+ Ia-. i.e. the same T cell which induces cell mediated immunity to Listeria. In vivo injection of an optimal regime of anti Ly1 monoclonal antibody exacerbated infection and removed the population of cells transferring immunity. Sub-optimal amounts of anti-Ly-1 abrogated IgG Brucella agglutinating antibody without affecting bacterial numbers, thus confirming the T dependence of IgG antibody and suggesting that it is not important in recovery from infection. Marked splenomegaly occurred about 3 weeks after infection of the mice. It was transferred by T lymphocytes and involved marked influx of macrophages, increased haemopoiesis, fibrin deposition and fluid in the spleen. Although the macrophages were immunosuppressive in vitro they did not appear to account for chronicity of infection. In seeking to account for this chronicity we have compared a number of aspects of the immune response in chronically infected mice and in mice which were able to control their infection. Although we have ruled out a number of possibilities, we have not yet established the basis of chronicity.
On-demand node-disjoint multipath routing in wireless ad hoc networks (2004)

An on-demand node-disjoint multipath routing protocol is proposed to overcome the shortcomings of on-demand unipath routing protocols like AODV and DSR. The protocol has two novel aspects compared to the other on-demand multipath protocols: it reduces routing overhead dramatically and achieves multiple node-disjoint routing paths. Simulation results show that the proposed protocol achieves lower data delay and control overhead as well as higher packet delivery ratio.
NQO1 and NQO2 Regulation of Humoral Immunity and Autoimmunity (2006)

NAD(P)H:quinone oxidoreductase 1 (NQO1) and NRH:quinone oxidoreductase 2 (NQO2) are cytosolic enzymes that catalyze metabolic reduction of quinones and derivatives. NQO1-null and NQO2-null mice were generated that showed decreased lymphocytes in peripheral blood, myeloid hyperplasia, and increased sensitivity to skin carcinogenesis. In this report, we investigated the in vivo role of NQO1 and NQO2 in immune response and autoimmunity. Both NQO1-null and NQO2-null mice showed decreased B-cells in blood, lower germinal center response, altered B cell homing, and impaired primary and secondary immune responses. NQO1-null and NQO2-null mice also showed susceptibility to autoimmune disease as revealed by decreased apoptosis in thymocytes and pre-disposition to collagen-induced arthritis. Further experiments showed accumulation of NADH and NRH, cofactors for NQO1 and NQO2, indicating altered intracellular redox status. The studies also demonstrated decreased expression and lack of activation of immune-related factor NF-kappaB. Microarray analysis showed altered chemokines and chemokine receptors. These results suggest that the loss of NQO1 and NQO2 leads to altered intracellular redox status, decreased expression and activation of NF-kappaB, and altered chemokines. The results led to the conclusion that NQO1 and NQO2 are endogenous factors in the regulation of immune response and autoimmunity.
Different mechanisms for resistance to trastuzumab versus lapatinib in HER2- positive breast cancers - role of estrogen receptor and HER2 reactivation (2011)

Combined L + T treatment provides a more complete and stable inhibition of the HER network. With sustained HER2 inhibition, ER functions as a key escape/survival pathway in ER-positive/HER2-positive cells. Complete blockade of the HER network, together with ER inhibition, may provide optimal therapy in selected patients.
Workflow Comparison for Label-Free, Quantitative Secretome Proteomics for Cancer Biomarker Discovery: Method Evaluation, Differential Analysis, and Verification in Serum (2010)

The cancer cell secretome has emerged as an attractive subproteome for discovery of candidate blood-based biomarkers. To choose the best performing workflow, we assessed the performance of three first-dimension separation strategies prior to nanoLC-MS/MS analysis: (1) 1D gel electrophoresis (1DGE), (2) peptide SCX chromatography, and (3) tC2 protein reversed phase chromatography. 1DGE using 4-12% gradient gels outperformed the SCX and tC2 methods with respect to number of identified proteins (1092 vs 979 and 580, respectively), reproducibility of protein identification (80% vs 70% and 72%, respectively, assessed in biological N = 3). Reproducibility of protein quantitation based on spectral counting was similar for all 3 methods (CV: 26% vs 24% and 24%, respectively). As a proof-of-concept of secretome proteomics for blood-based biomarker discovery, the gradient 1DGE workflow was subsequently applied to identify IGF1R-signaling related proteins in the secretome of mouse embryonic fibroblasts transformed with human IGF1R (MEF/Toff/IGF1R). VEGF and osteopontin were differentially detected by LC-MS/MS and verified in secretomes by ELISA. Follow-up in serum of mice bearing MEF/Toff/IGF1R-induced tumors showed an increase of osteopontin levels paralleling tumor growth, and reduction in the serum of mice in which IGF1R expression was shut off and tumor regressed.
Heparin’s anti-inflammatory effects require glucosamine 6-O-sulfation and are mediated by blockade of L- and P-selectins (2002)

Heparin has been used clinically as an anticoagulant and antithrombotic agent for over 60 years. Here we show that the potent anti-inflammatory property of heparin results primarily from blockade of P-selectin and L-selectin. Unfractionated heparin and chemically modified analogs were tested as inhibitors of selectin binding to immobilized sialyl LewisX and of cell adhesion to immobilized selectins or thrombin-activated endothelial cells. Compared with unfractionated heparin, the modified heparinoids had inhibitory activity in this general order: over–O-sulfated heparin > heparin > 2-O,3-O-desulfated ≥ N-desulfated/N-acetylated heparin ≥ carboxyl-reduced heparin ≥ N-,2-O,3-O-desulfated heparin >> 6-O-desulfated heparin. The heparinoids also showed similar differences in their ability to inhibit thioglycollate-induced peritonitis and oxazolone-induced delayed-type hypersensitivity. Mice deficient in P- or L-selectins showed impaired inflammation, which could be further reduced by heparin. However, heparin had no additional effect in mice deficient in both P- and L-selectins. We conclude that (a) heparin’s anti-inflammatory effects are mainly mediated by blocking P- and L-selectin–initiated cell adhesion; (b) the sulfate groups at C6 on the glucosamine residues play a critical role in selectin inhibition; and (c) some non-anticoagulant forms of heparin retain anti-inflammatory activity. Such analogs may prove useful as therapeutically effective inhibitors of inflammation.
Tau cleavage and tau aggregation in neurodegenerative disease (2010)

Deposition of highly phosphorylated tau in the brain is the most significant neuropathological and biochemical characteristic of the group of neurodegenerative disorders termed the tauopathies. The discovery of tau fragments in these diseases suggests that tau cleavage and tau phosphorylation, both of which induce conformational changes in tau, could each have roles in disease pathogenesis. The identities of the proteases responsible for degrading tau, resulting in the appearance of truncated tau species in physiological and pathological conditions, are not known. Several fragments of tau are reported to have pro-aggregation properties, but the lack of disease-relevant cell models of tau aggregation has hampered investigation of the effects of tau aggregation on normal cellular functioning. In the present paper, we describe our findings of N-terminally truncated tau in the brain in a subgroup of the tauopathies in which tau isoforms containing four microtubule-binding domains predominate. We also discuss the evidence for the involvement of proteases in the generation of tau pathology in neurodegenerative disease, since these enzymes warrant further investigation as potential therapeutic targets in the tauopathies.
Adiabatic, shock, and plastic work heating of solids and exploding metal cylinders (2002)

Solids subjected to high pressures, shocks, and/or deformation experience an increase in internal energy density and temperature due to adiabatic compression, shock heating, and plastic work heating, respectively. Analytic approximations are derived here for the internal energy and temperature changes that result from these processes based on the analytic constitutive model and Gruneisen equation of state of Steinberg. Although of general use, the utility of the expressions is demonstrated by the detailed example of a cylindrical metal tube filled with high explosives, and detonated on axis at one end. This geometry is often used to determine the detonation properties of high explosives, where it is known as the "cylinder test." The geometry is also of special interest for use as the armature of cylindrical magnetic flux compression pulsed current generators. The results are favorably compared with two dimension numerical simulations of the process using Lawrence Livermore National Laboratory's shock-hydro computer code CALE using the same model for the metal.
The effect of clay amendment on speciation of heavy metals in sewage sludge (1996)

When sewage sludge is used as a soil conditioner, heavy metal contamination can limit its application rates. The potential hazard of heavy metals is, however, dependent on the physico-chemical forms of the metals in the sludge and soil. Bauxite refining residue (red mud) has been used to reduce the mobility and availability of heavy metals in municipal solid waste compost. In the present research a sequential step extraction was employed to investigate metal speciation (into exchangeable, bound to carbonate, to Mn & Fe oxides, to organic matter and in residue phase) and the effect of red mud on metal speciation in sewage sludge for Cd, Cr, Cu, Ni, Pb and Zn. The effect of red mud addition on metal distribution in sewage sludge compost was significant. Red mud addition can effectively reduce the metal mobility and the potential hazard of releasing metals from sludge due to the further breakdown of organic matter. Drying of sludge makes heavy metals more available. Red mud addition will be desirable in such a case. Plant available metals (determined by DTPA extraction) are, however, not as effectively reduced except for Pb and Zn.
Impact of cathepsin B-sensitive triggers and hydrophilic linkers onin vitroefficacy of novel site-specific antibody–drug conjugates (2018)

Herein we describe the synthesis and evaluation of four novel HER2-targeting, cathepsin B-sensitive antibody-drug conjugates bearing a monomethylauristatin E (MMAE) cytotoxic payload, constructed via the conjugation of cleavable linkers to trastuzumab using a site-specific bioconjugation methodology. These linkers vary by both cleavable trigger motif and hydrophilicity, containing one of two cathepsin B sensitive dipeptides (Val-Cit and Val-Ala), and engendered with either hydrophilic or hydrophobic character via application of a PEG<sub>12</sub> spacer. Through evaluation of physical properties, in vitro cytotoxicity, and receptor affinity of the resulting antibody-drug conjugates (ADCs), we have demonstrated that while both dipeptide triggers are effective, the increased hydrophobicity of the Val-Ala pair limits its utility within this type of linker. In addition, while PEGylation augments linker hydrophilicity, this change does not translate to more favourable ADC hydrophilicity or potency. While all described structures demonstrated excellent and similar in vitro cytotoxicity, the ADC with the ValCitPABMMAE linker shows the most promising combination of in vitro potency, structural homogeneity, and hydrophilicity, warranting further evaluation into its therapeutic potential.
OFDM transmission over time-variant multipath channels (1994)

The paper addresses the influence of multipath propagation on the transmission of OFDM (orthogonal frequency division multiplexing) modulated radio signals. The author derives a discrete-time channel model for the WSSUS (wide-sense stationary uncorrelated scattering) channel.
Clock recovery from random binary signals (1975)

A circuit for detecting timing errors between a binary signal and a local clock pulse generator is described. Three binary samples are compared and logical control signals for the clock are derived.
Gene therapy for hemophilia (2015)

Hemophilia is an X-linked inherited bleeding disorder consisting of two classifications, hemophilia A and hemophilia B, depending on the underlying mutation. Although the disease is currently treatable with intravenous delivery of replacement recombinant clotting factor, this approach represents a significant cost both monetarily and in terms of quality of life. Gene therapy is an attractive alternative approach to the treatment of hemophilia that would ideally provide life-long correction of clotting activity with a single injection. In this review, we will discuss the multitude of approaches that have been explored for the treatment of both hemophilia A and B, including both in vivo and ex vivo approaches with viral and nonviral delivery vectors.