gebhart/patrepeval huggingface dataset:
Axotomy- and Autotomy-Induced Changes in the Excitability of Rat Dorsal Root Ganglion Neurons (2001)

The spontaneous, ectopic activity in sensory nerves that is induced by peripheral nerve injury is thought to contribute to the generation of "neuropathic" pain in humans. To examine the cellular mechanisms that underlie this activity, neurons in rat L(4)-L(5) dorsal root ganglion (DRG) were first grouped as "large," "medium," or "small" on the basis of their size (input capacitance) and action potential (AP) shape. A fourth group of cells that exhibited a pronounced afterdepolarization (ADP) were defined as AD-cells. Whole cell recording was used to compare the properties of control neurons with those dissociated from rats in which the sciatic nerve had been sectioned ("axotomy" group) and with neurons from rats that exhibited self-mutilatory behavior in response to sciatic nerve section ("autotomy" group). Increases in excitability in all types of DRG neuron were seen within 2-7 wk of axotomy. Resting membrane potential (RMP) and the amplitude and duration of the afterhyperpolarization (AHP) that followed the AP were unaffected. Effects of axotomy were greatest in the small, putative nociceptive cells and least in the large cells. Moderate changes were seen in the medium and AD-cells. Compared to control neurons, axotomized neurons exhibited a higher frequency of evoked AP discharge in response to 500-ms depolarizing current injections; i.e., "gain" was increased and accommodation was decreased. The minimum current required to discharge an AP (rheobase) was reduced. There were significant increases in spike width in small cells and significant increases in spike height in small, medium, and AD-cells. The electrophysiological changes promoted by axotomy were intensified in animals that exhibited autotomy; spike height, and spike width were significantly greater than control for all cell types. Under our experimental conditions, spontaneous activity was never encountered in neurons dissociated from animals that exhibited autotomy. Thus changes in the electrical properties of cell bodies alone may not entirely account for injury-induced spontaneous activity in sensory nerves. The onset of autotomy coincided with alterations in the excitability of large, putative nonnociceptive, neurons. Thus large cells from the autotomy group were much more excitable than those from the axotomy group, whereas small cells from the autotomy group were only slightly more excitable. This is consistent with the hypothesis that the onset of autotomy is associated with changes in the properties of myelinated fibers. Changes in Ca2+ and K+ channel conductances that contribute to axotomy- and autotomy-induced changes in excitability are addressed in the accompanying paper.
Cell Penetrating Agents Based on a Polyproline Helix Scaffold (2005)

Cell penetrating agents were designed and synthesized that introduce cationic and hydrophobic moieties along the backbone of a polyproline helix (PPII) in an amphiphilic manner. The CD profile has the features that are expected for a PPII helix, demonstrating that the addition of these groups had little effect on the backbone structure. Dramatic increases in uptake were found with MCF-7 cells when up to six guanidinium groups were positioned on the polyproline helix, whereas only modest increases in cellular uptake were observed with the amine-containing polyproline compounds as compared to their flexible counterparts. Amphiphilicity played a key role in the enhanced cell translocation, as scrambled versions of the designed agents, with hydrophobic and cationic groups on all faces of the helix, were only as effective as their flexible peptide counterparts. Interestingly, the most potent agent, P11LRR, demonstrated almost an order of magnitude more efficient cellular uptake as compared to that of the well-studied Tat peptide, with minimal cytotoxicity.
A transposon insertion in thegumGhomologue ofXanthomonas oryzaepv.oryzaecauses loss of extracellular polysaccharide production and virulence (1999)

Xanthomonas oryzae pv. oryzae causes a serious disease of rice called bacterial leaf blight. It produces copious amounts of extracellular polysaccharide (EPS). An EPS- and virulence-deficient mutant of X. oryzae pv. oryzae was isolated by Tn5 mutagenesis. The mutant allele in this strain was cloned by transposon tagging in the Escherichia coli vector pBluescript and the DNA sequences flanking the transposon insertion site were determined. Computer-based similarity searches in the DNA database using the BLAST algorithm showed these sequences to be 78% identical at the nucleotide level to a gene, gumG, in the gum cluster, which is required for EPS biosynthesis in Xanthomonas campestris pv. campestris. A 36-kb X. oryzae pv. oryzae genomic clone containing the putative EPS biosynthetic gene cluster of X. oryzae pv. oryzae restored both EPS production and virulence proficiency to the gumGXo::Tn5 mutant. The results suggest that EPS is an important virulence factor of X. oryzae pv. oryzae.
Construction and Characterization of Single-Chain Variable Fragment Antibodies Directed against the Bordetella pertussis Surface Adhesins Filamentous Hemagglutinin and Pertactin (2007)

A single-chain variable fragment (scFv) antibody library against Bordetella pertussis was constructed using M13 phage display. The library was enriched for phages surface displaying functional scFv by biopanning against B. pertussis immobilized on polystyrene plates. Two hundred eighty-eight individual clones from the enriched library were screened for binding to B. pertussis cells, filamentous hemagglutinin (FHA), and pertactin (PRN) in enzyme-linked immunosorbent assays (ELISAs). Based on the binding ability, the clones were put into eight groups. The scFv DNA inserts from the 288 clones were digested with BstOI, and 18 unique restriction patterns, named types 1 to 18, were found. Eight clones (types 1 to 7 and 18) were selected for further testing against FHA, PRN, and B. pertussis by ELISA. The results showed that types 1, 5, 7, and 18 bound strongly to B. pertussis cells as well as FHA and PRN. Type 3 bound strongly to the cells and FHA but weakly to PRN. Types 4 and 6 bound FHA only, and type 2 did not bind to the cells or antigens. The ability of the eight clones to inhibit B. pertussis from binding to HEp-2 cells was assayed. Types 1, 5, and 7, but not the remaining clones, inhibited the adherence of B. pertussis to HEp-2 cells. The scFvs were sequenced, and the deduced amino acid sequence showed that the scFvs were different antibodies. Maltose-binding protein (MBP) fusion proteins composed of three different regions of FHA (heparin-binding domain, carbohydrate recognition domain, and the RGD triplet motif) were constructed. The three fusion proteins and Mal85 (MBP-FHA type I domain) were used to map the binding sites for scFvs of types 1, 5, and 7 by ELISA. The results showed that all three scFvs bound to the heparin-binding domain fusion protein but not the other fusion proteins. BALB/c mice who received recombinant phage-treated B. pertussis had reduced bacterial counts in the nasal cavity, trachea, and lungs compared to the control groups.
Molecular cloning and characterization of the 15-kilodalton major immunogen of Treponema pallidum (1989)

Pathogen-specific membrane immunogens of Treponema pallidum subsp. pallidum (T. pallidum) have been identified previously by phase partitioning with the nonionic detergent Triton X-114. One of these antigens, a 15-kilodalton (kDa) polypeptide, is expressed in relatively small quantities in T. pallidum but is highly immunogenic in both human and experimental syphilis. The native T. pallidum antigen was purified to homogeneity from the mixture of Triton X-114 detergent-phase proteins by chromatofocusing. Recombinant Escherichia coli clones were selected from a T. pallidum genomic DNA library by using monoclonal antibodies specific to the 15-kDa antigen; immunoblotting and minicell analyses confirmed expression of the 15-kDa protein in the transformants. Southern hybridization with a 1.1-kilobase fragment of DNA encoding the 15-kDa-antigen gene indicated that the gene is probably present in a single copy within the genomes of both T. pallidum and T. pallidum subsp. pertenue (the agent of yaws), while it is absent from the genome of the nonpathogenic Treponema phagedenis biotype Reiter. Cell fractionation studies with Triton X-114 demonstrated that the recombinant polypeptide possesses hydrophobic properties similar to those of the native antigen and localized the cloned 15-kDa antigen to the inner membrane of E. coli. Protein processing experiments in minicells revealed that a precursor appears to be processed to the mature 15-kDa polypeptide.
Identification of TRAF6, a Novel Tumor Necrosis Factor Receptor-associated Factor Protein That Mediates Signaling from an Amino-terminal Domain of the CD40 Cytoplasmic Region (1996)

CD40 signalings play crucial roles in B-cell function. To identify molecules which transduce CD40 signalings, we have utilized the yeast two-hybrid system to clone cDNAs encoding proteins that bind the cytoplasmic tail of CD40. A cDNA encoding a putative signal transducer, designated TRAF6, has been molecularly cloned. TRAF6 has a tumor necrosis factor receptor (TNFR)-associated factor (TRAF) domain in its carboxyl terminus and has a RING finger domain, a cluster of zinc fingers and a coiled-coil domain, which are also present in other TRAF family proteins. TRAF6 does not associate with the cytoplasmic tails of TNFR2, CD30, lymphotoxin-beta receptor, and LMP1 of Epstein-Barr virus. Deletion analysis showed that residues 246-269 of CD40 which are required for its association with TRAF2, TRAF3, and TRAF5 are dispensable for its interaction with TRAF6, whereas residues 230-245 were required. Overexpression of TRAF6 activates transcription factor NFkappaB, and its TRAF-C domain suppresses NFkappaB activation triggered by CD40 lacking residues 246-277. These results suggest that TRAF6 could mediate the CD40 signal that is transduced by the amino-terminal domain (230-245) of the CD40 cytoplasmic region and appears to be independent of other known TRAF family proteins.
Diamond-based field sensor for nEDM experiment (2016)

Ensembles of negatively charged nitrogen vacancy centers in diamonds are investigated as optical sensors for electric and magnetic fields in the interaction region of a neutron electric dipole moment experiment. As a first step towards measuring electric fields, the Stark shift is investigated in the ground electronic state, using optically detected magnetic resonance (ODMR) to measure hyperfine-resolved fine structure transitions. One detection approach is to modulate the electric field and demodulate the ODMR signal at the modulation frequency or its harmonic. Models indicate that the ratio of the amplitudes of these signals provides information about the magnitude of the electric field. Experiments show line shapes consistent with the models. Methods are considered for extending this technique to all-optical measurement of fields. Additionally, progress is reported towards an all-optical, fiberized sensor based on electromagnetically-induced transparency (EIT), which may be suitable for measuring magnetic fields. The design uses total internal reflection to provide a long optical path through the diamond for both the 637 nm EIT laser and a green repump laser.
Rat alpha 2u globulin is encoded by a multigene family. (1981)

The hormonally responsive rat liver protein designated alpha 2u globulin is encoded by a multigene family. Southern blot hybridization analysis, and solution hybridization using a cloned alpha 2u globulin cDNA, indicate the presence of 18-20 alpha 2u globulin genes per haploid genome. In situ hybridization to rat metaphase chromosomes, using 125I-labeled alpha 2u globulin cDNA, indicates that most, and perhaps all, of the alpha 2u globulin genes are clustered on chromosome 5. Several alpha 2u globulin genes have been isolated from a rat library cloned in lambda phage. At least six of these clones appear to contain the entire alpha 2u globulin mRNA coding region. These genes are contained on different-sized restriction fragments, and are surrounded by distinct flanking sequences. Two of the six clones containing the alpha 2u globulin genes were found to have diverged greatly from the other four in the DNA sequence corresponding to the 3' untranslated region of mRNA. The implications for the hormonal control of alpha 2u globulin synthesis are discussed.
Gassing in Li4Ti5O12-based batteries and its remedy (2012)

Destructive gas generation with associated swelling has been a major challenge to the large-scale application of lithium ion batteries (LIBs) made from Li(4)Ti(5)O(12) (LTO) anodes. Here we report root causes of the gassing behavior, and suggest remedy to suppress it. The generated gases mainly contain H(2), CO(2) and CO, which originate from interfacial reactions between LTO and surrounding alkyl carbonate solvents. The reactions occur at the very thin outermost surface of LTO (111) plane, which result in transformation from (111) to (222) plane and formation of (101) plane of anatase TiO(2). A nanoscale carbon coating along with a stable solid electrolyte interface (SEI) film around LTO is seen most effective as a barrier layer in suppressing the interfacial reaction and resulting gassing from the LTO surface. Such an ability to tune the interface nanostructure of electrodes has practical implications in the design of next-generation high power LIBs.
Detection of Nucleic Acid Targets Using Ramified Rolling Circle DNA Amplification: A Single Nucleotide Polymorphism Assay Model (2013)

The methods and results presented here show that a combination of C-probe detection, automated sample processing, and isothermal RAM amplification provide a practical approach for detecting DNA targets in complex mixtures.
A technique for low energy mapping and routing in network-on-chip architectures (2005)

Network-on-chip (NoC) has been proposed as a solution for the global communication challenges of System-on-chip (SoC) design in the nanoscale technologies. NoC design with mesh based topologies requires mapping of cores to router ports, and routing of traffic traces such that the bandwidth and latency constraints are satisfied. We present a novel automated design technique that solves the mesh based NoC design problem with an objective of minimizing the communication energy. In contrast to existing research that only take bandwidth constraints as inputs, our technique solves the NoC design problem in the presence of bandwidth as well as latency constraints. We compare our technique with a recent work called NMAP and an optimal MILP based formulation. We prove that the complexity of our technique is lower than that of NMAP. For the latency constrained case, while NMAP fails on most test cases, our technique is able to generate high quality results. In comparison to the MILP formulation, the results produced by our technique are within 14% of the optimal
Receptor Ligand-Facilitated Cationic Liposome Delivery of Anti-HIV-1 Rev-Binding Aptamer and Ribozyme DNAs (1998)

We examined whether HIV-1 gene expression could be inhibited by the anti-HIV Rev-binding aptamer [RBE(apt)], and whether the antiviral effect of the aptamer could be enhanced by a ribozyme directed against the HIV-1 env gene. Since cationic liposomes are relatively safe and non-immunogenic for in vivo gene delivery, we tested the effectiveness of the aptamer and ribozyme DNAs in HeLa cells, using Lipofectin reagent in a transient transfection assay. To increase the transfection efficiency, lipofectin was mixed with transferrin before subsequent addition of DNA. Co-transfection of HeLa cells with the RBE(apt) and the proviral HIV clone, HXBdeltaBgl, resulted in inhibition of virus production. Specific inhibition of viral p24 production following co-transfection of the RBE(apt) and HIV proviral DNAs was observed. These data provide strong support for the use of in vitro evolved ligands as potential anti-HIV agents. The addition of the anti-env ribozyme to the aptamer construct did not further enhance the antiviral activity, suggesting either that we had reached the limits of inhibition in this assay, or that the ribozyme was not able to access its target site with Rev bound to the RBE aptamer. The observed inhibition of p24 production could not be attributed to the non-specific toxicity of the transfection procedure, because no difference in viability was observed between the RBE(apt)- and the vector control-treated cells. All of the aptamer-ribozyme constructs as well as the RBE(apt) were similarly effective.
Immunotherapeutic Implications of Il-6 Blockade for Cytokine Storm (2016)

IL-6 contributes to host defense against infections and tissue injuries. However, exaggerated, excessive synthesis of IL-6 while fighting environmental stress leads to an acute severe systemic inflammatory response known as 'cytokine storm', since high levels of IL-6 can activate the coagulation pathway and vascular endothelial cells but inhibit myocardial function. Remarkable beneficial effects of IL-6 blockade therapy using a humanized anti-IL-6 receptor antibody, tocilizumab were recently observed in patients with cytokine release syndrome complicated by T-cell engaged therapy. In this review we propose the possibility that IL-6 blockade may constitute a novel therapeutic strategy for other types of cytokine storm, such as the systemic inflammatory response syndrome including sepsis, macrophage activation syndrome and hemophagocytic lymphohistiocytosis.
Cloning ofMycoplasma SynoviaeGenes Encoding Specific Antigens and Their Use as Species-Specific DNA Probes (1999)

A genomic library of Mycoplasma synoviae (MS) was generated by using bacteriophage lambda gt11 as a cloning and expression vector. Identification of recombinant clones highly specific to MS was achieved by screening the library for expression of MS proteins with polyclonal antiserum that had been preadsorbed with 6 heterologous avian mycoplasma species antigens. Expression of the recombinant clones in Escherichia coli followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the total cell lysates and immunoblot yielded a predominant reactive fusion protein of 165 kD. Two clones (MS2/28 and MS2/12) that yielded inserts of different size were selected. The 2 MS DNA inserts were subcloned in a plasmid vector, labeled with digoxigenin, and used as probes for the specific recognition of several MS strains. A high degree of conservation was demonstrated for the MS2/12 and MS2/28 genes in tested MS strains. In addition, neither DNA fragment recognized any other avian mycoplasma species (M. gallisepticum, M. meleagridis, M. gallinarum, M. iners, M. anatis, and M. iowae), thus indicating their high specificity to MS. The sensitivity of the slot blot hybridization method using digoxigenin-labeled MS2/12 and MS2/28 probes for direct detection of MS from broth cultures of field isolates was 10(5) colony-forming units/ml. These results demonstrate the effectiveness of adsorbed antisera for the isolation of species-specific mycoplasma DNA and the potential for its use as probes for the specific and direct detection of MS from broth cultures of field isolates.
Intravascular Modalities for Detection of Vulnerable Plaque (2003)

Progress in the diagnosis, treatment, and prevention of atherosclerotic coronary artery disease is dependent on a greater understanding of the mechanisms of coronary plaque progression. Autopsy studies have characterized a subgroup of high-risk, or vulnerable, plaques that result in acute coronary syndromes or sudden cardiac death. These angiographically modest plaques share certain pathologic characteristics: a thin, fibrous cap, lipid-rich core, and macrophage activity. Diagnostic techniques for vulnerable-plaque detection, including serologic markers and noninvasive and invasive techniques, are needed. Recent advances in intravascular imaging have significantly improved the ability to detect high-risk, or vulnerable, plaque in vivo by using various features of plaque vulnerability as methods of identification. The characteristic anatomy of a thin, fibrous cap overlying a lipid pool has promoted high-resolution imaging, such as intravascular ultrasound, optical coherence tomography, and intracoronary magnetic resonance. The lipid-rich core is identifiable by angioscopically detected color changes on the plaque surface or by its unique absorption of energy, or "Raman shift," of its cholesterol core, driving coronary spectroscopy. Finally, temperature heterogeneity arising at foci of plaque inflammation has prompted the development of intracoronary thermography. In this review, we will discuss these techniques, their relative advantages and limitations, and their potential clinical application.
Graphical User Interface Programming (2004)

This paper is revised from an earlier version that appeared as: Brad A. Myers. &amp;quot;User Interface Software Tools,&amp;quot; ACM Transactions on Computer-Human Interaction. vol. 2, no. 1, March, 1995. pp. 64-103. Draft of: January 27, 2003 To appear in: CRC HANDBOOK OF COMPUTER SCIENCE AND ENGINEERING -- 2 nd Edition, 2003. Allen B. Tucker, Editor-in-chief 51.1.
Sensitive and Specific Detection of the Non-Human Sialic Acid N-Glycolylneuraminic Acid In Human Tissues and Biotherapeutic Products (2009)

We report a reliable antibody-based method for highly sensitive and specific detection of the non-human sialic acid Neu5Gc in human tissues and biotherapeutic products that has not been previously described.
Electrolyte Additive in Support of 5 V Li Ion Chemistry (2011)

An electrolyte additive based on highly fluorinated phosphate ester structure was identified as being able to stabilize carbonate-based electrolytes on class cathode surfaces. The synthesis and structural analysis of the additive are described, and preliminary yet encouraging results from electrochemical characterization showed that this additive participates in forming a protective interphasial chemistry not only on transition metal oxide cathode at high voltage ( vs Li) but also on graphitic graphite at low voltage ( vs Li), making it possible to formulate an electrolyte supporting reversible -intercalation chemistry in the coveted region.
An “External” RNA Removable from Mammalian Cells by Mild Proteolysis (1974)

Brief exposure of Chinese hamster ovary cell monolayers prelabeled with [(32)P]phosphate and [(3)H]leucine to 1 mug/ml of trypsin under conditions in which cells remain fully viable causes the release of macromolecular (32)P and (3)H. Whereas ribonuclease treatment was found to affect markedly both the (32)P and (3)H radioactivity, Pronase treatment had little effect on the macromolecular (32)P. Treatment of cells prelabeled with [(3)H]glucosamine and [(32)P]phosphate with insolubilized papain also revealed a parallel release of macromolecular glucosamine together with ribonuclease-susceptible macromolecular phosphate. Lactoperoxidase-mediated radioiodination of surface components in cells prelabeled with [(32)P]phosphate revealed electrophoretic comigration between the (125)I and the (32)P that are removed from the cells by mild proteolysis. Growth of the cells in Bt(2)cAMP-testosterone altered the kinetics of release and nature of the macromolecular (32)P liberated by proteolysis.