gebhart/patrepeval huggingface dataset:
Phage Wrapping with Cationic Polymers Eliminates Nonspecific Binding between M13 Phage and High pI Target Proteins (2009)

M13 phage have provided scaffolds for nanostructure synthesis based upon self-assembled inorganic and hard materials interacting with phage-displayed peptides. Additionally, phage display has been used to identify binders to plastic, TiO(2), and other surfaces. However, synthesis of phage-based materials through the hybridization of soft materials with the phage surface remains unexplored. Here, we present an efficient "phage wrapping" strategy for the facile synthesis of phage coated with soluble, cationic polymers. Polymers bearing high positive charge densities demonstrated the most effective phage wrapping, as shown by assays for blocking nonspecific binding of the anionic phage coat to a high pI target protein. The results establish the functional group requirements for hybridizing phage with soft materials and solve a major problem in phage display-nonspecific binding by the phage to high pI target proteins.
Housing related challenges for culturally and linguistically diverse communities (2018)

'Kim' was 61 years old when she first became homeless. She moved to Australia from Vietnam (speaking Cantonese) with her new husband who was 20 years her senior. Kim's husband was abusive, controlling and isolating; she did not have anyone to ask for help. She had distant relatives in Australia, but they didn't provide any support due to concern their lives would be 'contaminated' by her hardship. Kim did not speak any English.
INTEGRATION OF LASER SCANNING AND PHOTOGRAMMETRY (2007)

Commission III/3, III/4, V/3, VIII/11 ABSTRACT: The term integration can be defined as the fusion of two separate entities, resulting in a new entity. Integrating laser scanning with photogrammetry allows us to compensate for the individual weaknesses of each method alone, thus providing more accurate modelling, interpretation and classification of the surroundings. Laser scanners produce data that can vary in terms of point density, field of view, amount of noise, incident angle, and distribution method. Similarly, the accuracy requirements or level of automation may also vary. Therefore, no single registration method overcomes others. The most suitable method is usually case-specific. This paper presents a short overview of current registration approaches and proposes four levels of integration: object-level integration, photogrammetry aided by laser scanning, laser scanning aided by photogrammetry, and tightly integrated laser scanning and optical images. In addition, some examples are presented of integrated laser scanning and photogrammetric data.
Visualizing the dynamics of T cell activation: Intracellular adhesion molecule 1 migrates rapidly to the T cell/B cell interface and acts to sustain calcium levels (1998)

T cell recognition typically involves both the engagement of a specific T cell receptor with a peptide/major histocompatibility complex (MHC) and a number of accessory interactions. One of the most important interactions is between the integrin lymphocyte function-associated antigen 1 (LFA-1) on the T cell and intracellular adhesion molecule 1 (ICAM-1) on an antigen-presenting cell. By using fluorescence video microscopy and an ICAM-1 fused to a green fluorescent protein, we find that the elevation of intracellular calcium in the T cell that is characteristic of activation is followed almost immediately by the rapid accumulation of ICAM-1 on a B cell at a tight interface between the two cells. This increased density of ICAM-1 correlates with the sustained elevation of intracellular calcium in the T cell, known to be critical for activation. The use of peptide/MHC complexes and ICAM-1 on a supported lipid bilayer to stimulate T cells also indicates a major role for ICAM-1/LFA-1 in T cell activation but, surprisingly, not for adhesion, as even in the absence of ICAM-1 the morphological changes and adhesive characteristics of an activated T cell are seen in this system. We suggest that T cell antigen receptor-mediated recognition of a very small number of MHC/peptide complexes could trigger LFA-1/ICAM-1 clustering and avidity regulation, thus amplifying and stabilizing the production of second messengers.
Stimulation of Neural Cells by Lateral Currents in Conductive Layer‐by‐Layer Films of Single‐Walled Carbon Nanotubes (2006)

The first example of neural stimulation through a SWNT material assembled by layer-by-layer deposition is described (see figure). Excitation by lateral currents in the nanotube coating results in the opening of voltage-dependent Na+ ion channels. The experimental observations indicate the possibility of engineering of implantable biomedical devices from SWNT/polymer multilayers to be used for neuron prosthesis, pain management, and muscle stimulation.
Addendum to Response of Man to Infection with Vibrio cholerae (1974)

Journal Article Addendum to Response of Man to Infection with Vibrio cholerae Get access Richard A. Cash, M.D. Richard A. Cash, M.D. Division of Infectious Diseases School of Medicine University of Maryland, Baltimore, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 129, Issue 4, April 1974, Page 477, https://doi.org/10.1093/infdis/129.4.477 Published: 01 April 1974
Modulating the immune response to genetic immunization (1998)

Genetic immunization, also known as DNA or polynucleotide immunization, is a novel strategy for vaccine development in which plasmid DNA encoding either individual or a collection of antigens is directly administered to a host. Such immunization leads to host expression of the delivered foreign gene, resulting in the induction of a specific immune response against the in vivo produced antigen. DNA immunization has been shown to induce protective immune responses in several infectious disease and cancer experimental model systems. Furthermore, DNA vaccines have recently entered the clinic for analysis as both prophylactic and therapeutic agents. Although the mechanisms of immunity to DNA have not yet been fully elucidated, it has become apparent that the immune response achieved by DNA vaccination is quite malleable, and can be manipulated by altering the conditions under which the vaccine is administered. Either through changing the method or location of immunization, altering the number of immunostimulatory sequences in the plasmid, altering the immunization regimen, or coadministering genes for cytokines or costimulatory molecules, one can modulate both the magnitude and orientation of the subsequent immune response. Through maximization of this feature of DNA immunization, we will likely be able to design vaccines and immunotherapeutic agents that are tailored to the correlates of protection for a particular disease, resulting in a new generation of more focused and effective immune stimulating agents.
Synthesis of Some Fused 2-Arylimidazoles and their Derivatives (1979)

Department of Chemistry, Berhampur University, Berhampur 760007, Orissa, India. <em>Manuscript received 20 October 1978, revised 2 January 1979, accepted 27 April 1979</em> The synthesis of several fused 2-arylimidazoles, 1-hydroxy-2-arylimidazole-3-oxides, 1-hydroxy-2-arylimidazoles starting from 2-arylimino-3-aryl-1, 3-thiazolidine-4, 5-diones(I) 4H-thiazolo (2 1-b) imidazole-2, 3-dione (II) 1,4-henzothiazin-2, 3-dione(III), phanquone (IV), aceoaphthenequinone. furil, phenanthraquinone have been described. Few imidazoies gave coloured dimeric products (VIII, IX &amp; X) on oxidation with hexacyanoferrate. Their structures have been confirmed by elemental analysis and IR spectra.
Involvement of BAFF and APRIL in the resistance to apoptosis of B-CLL through an autocrine pathway (2003)

Tumor necrosis factor (TNF) superfamily members BAFF, or B-cell activation factor of the TNF family, and APRIL, a proliferation-inducing ligand, are involved in normal B-cell survival and differentiation. They interact with 3 receptors: BAFF-R, specific to BAFF; and TACI and BCMA, which are shared by BAFF and APRIL. We tested the potential role of these proteins in B-cell chronic lymphocytic leukemia (B-CLL) resistance to apoptosis. TACI and BAFF-R mRNAs were found in leukemic B cells. BAFF and APRIL mRNAs and proteins were detected in B-CLL leukemic cells and normal blood or tonsil-derived B lymphocytes. Yet, in contrast to normal B lymphocytes, BAFF and APRIL were expressed at the membranes of leukemic cells. Adding soluble BAFF or APRIL protected B-CLL cells against spontaneous and drug-induced apoptosis and stimulated NF-kappaB activation. Conversely, adding soluble BCMA-Fc or anti-BAFF and anti-APRIL antibodies enhanced B-CLL apoptosis. Moreover, a soluble form of BAFF was detected using surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry (SELDI-TOF MS) in the sera of B-CLL patients but not of healthy donors. Taken together, our results indicate that B-CLL cells can be rescued from apoptosis through an autocrine process involving BAFF, APRIL, and their receptors. Inhibiting BAFF and APRIL pathways may be of therapeutic value for B-CLL treatment.
Ambient Mass Spectrometry (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Different Training Procedures Recruit Either One or Two Critical Periods for Contextual Memory Consolidation, Each of Which Requires Protein Synthesis and PKA (1998)

We have used a combined genetic and pharmacological approach to define the time course of the requirement for protein kinase A (PKA) and protein synthesis in long-term memory for contextual fear conditioning in mice. The time course of amnesia in transgenic mice that express R(AB) and have genetically reduced PKA activity in the hippocampus parallels that observed both in mice treated with inhibitors of PKA and mice treated with inhibitors of protein synthesis. This PKA- and protein synthesis-dependent memory develops between 1 hr and 3 hr after training. By injecting the protein synthesis inhibitor anisomycin or the PKA inhibitor Rp-cAMPs at various times after training, we find that depending on the nature of training, contextual memory has either one or two brief consolidation periods requiring synthesis of new proteins, and each of these also requires PKA. Weak training shows two time periods of sensitivity to inhibitors of protein synthesis and PKA, whereas stronger training exhibits only one. These studies underscore the parallel dependence of long-term contextual memory on protein synthesis and PKA and suggest that different training protocols may recruit a common signaling pathway in distinct ways.
Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals (2012)

Imaging the activities of individual neurons with genetically encoded Ca(2+) indicators (GECIs) is a promising method for understanding neuronal network functions. Here, we report GECIs with improved neuronal Ca(2+) signal detectability, termed G-CaMP6 and G-CaMP8. Compared to a series of existing G-CaMPs, G-CaMP6 showed fairly high sensitivity and rapid kinetics, both of which are suitable properties for detecting subtle and fast neuronal activities. G-CaMP8 showed a greater signal (F(max)/F(min) = 38) than G-CaMP6 and demonstrated kinetics similar to those of G-CaMP6. Both GECIs could detect individual spikes from pyramidal neurons of cultured hippocampal slices or acute cortical slices with 100% detection rates, demonstrating their superior performance to existing GECIs. Because G-CaMP6 showed a higher sensitivity and brighter baseline fluorescence than G-CaMP8 in a cellular environment, we applied G-CaMP6 for Ca(2+) imaging of dendritic spines, the putative postsynaptic sites. By expressing a G-CaMP6-actin fusion protein for the spines in hippocampal CA3 pyramidal neurons and electrically stimulating the granule cells of the dentate gyrus, which innervate CA3 pyramidal neurons, we found that sub-threshold stimulation triggered small Ca(2+) responses in a limited number of spines with a low response rate in active spines, whereas supra-threshold stimulation triggered large fluorescence responses in virtually all of the spines with a 100% activity rate.
Nanosilicon‐Coated Graphene Granules as Anodes for Li‐Ion Batteries (2011)

Uniform deposition of Si and C layers on high surface area graphene produces granules with specific surface area of ∼5 m2·g−1. The anode composed of the nanocomposite particles exhibited specific capacity in excess of 2000 mAh·g−1 at a current density of 140 mA·g−1 and excellent stability for 150 cycles. The low surface area of the composite resulted in an average Coulombic efficiency in excess of 99%.
Chloride secretion in a morphologically differentiated human colonic cell line that expresses the epithelial Na+ channel (2003)

Cell line models of colonic electrolyte transport have been extensively used despite lacking some of the characteristics of native tissue. While native colonic crypts absorb or secrete NaCl, immortalized cell lines only retain the secretory phenotype. In the present study we have characterized functionally and molecularly, vectorial fluid and electrolyte transport in the morphologically differentiated human colonic cell line LIM1863. LIM1863 cells form morphologically differentiated organoids resembling native human colonic crypts, which secrete fluid and electrolytes across the apical membrane into a centrally located lumen. Net fluid secretion was evaluated by means of morphometric measurement of lumens formed in LIM organoids in response to known secretagogues. Pharmacological profiling of the channels and transporters involved in fluid and electrolyte transport showed that net fluid transport requires Cl- uptake across the basolateral membrane through a Na(+)-K(+)-2Cl- cotransporter (NKCC1) and its subsequent exit across an apical cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel. Similar to the native colon, net Cl- secretion in the LIM1863 cell line is activated by cAMP-mediated agonists. Carbachol, a Ca(2+)-mediated agonist, does not induce net Cl- secretion but modulates the cAMP-activated response. Expression of chloride channels (CFTR and the Ca(2+)-dependent Cl- channel, ClCa1), potassium channels (KCNN4 and KCNQ1), epithelial Na+ channel (ENaC) alpha, beta and gamma subunits and ion transporters (NKCC1; anion exchanger, AE2; Na+/H+ exchangers, NHE1-3) was detected by RT-PCR and Western blot in the case of ENaC. Based on this evidence we propose that LIM1863 cells provide a unique model for studying CFTR-dependent Cl- secretion in a morphologically differentiated human colonic crypt cell line that also expresses ENaC.
Cell migration through defined, synthetic extracellular matrix analogues (2002)

We have developed synthetic hydrogel extracellular matrix (ECM) analogues that can be used to study mechanisms involved in cell migration, such as receptor-ligand interactions and proteolysis. The biomimetic hydrogels consist of bioinert polyethylene glycol diacrylate derivatives with proteolytically degradable peptide sequences included in the backbone of the polymer and adhesive peptide sequences grafted to the network. Hydrogels have been developed that degrade as cells secrete proteolytic enzymes. Adhesive peptide sequences grafted to the hydrogel provide ligands that can interact with receptors on the cell surface to mediate adhesion and spreading. In this study, we have characterized the effects of adhesive ligand density on fibroblast migration through collagenase-degradable and plasmin-degradable hydrogels and on smooth muscle cell migration through elastase-degradable hydrogels. In all three cases, we found that cell migration has a biphasic dependence on adhesion ligand concentration, with optimal migration at intermediate ligand levels. Furthermore, both adhesive and proteolytically degradable sequences were required for cell migration to occur. These synthetic ECM analogues may be useful for 3-D mechanistic studies of many aspects of cell migration
Evidence for amelioration of endothelial cell dysfunction by erythropoietin therapy in predialysis patients (1996)

Evidence for the involvement of endothelial cells in the pathogenesis or erythropoietin-induced hypertension, and for endothelial cell damage in patients with chronic renal failure, has emerged and appears to be of major concern. We, therefore, investigated the effect of recombinant human erythropoietin (rHuEPO) therapy on endothelium-derived hormones in predialysis patients with progressive renal anemia. At the entry to the trial, the serum thrombomodulin concentration (Tm) and plasma endothelin-1 concentration (ET-1) in the predialysis patients were significantly higher than those in age- and sex-matched normal subjects. Following a 16 week period of treatment with 6000IU rHuEPO given intravenously once a week, patients' hematocrit increased from 27.1 +/- 2.6% to 34.6 +/- 3.2% (n = 16, P < .001). A positive correlation was found between Tm and serum creatinine concentration (Cr) (r = 0.61, P < .05 (n = 16), but no correlation was found between ET-1 and Cr. Tm and Tm/Cr significantly decreased from 7.9 +/- 2.8 ng/mL to 6.6 +/- 2.4 ng/mL (P < .01, n = 16), and from 2.1 +/- 0.7 (x10(-10) to 1.6 +/- 0.7 (x10(-10), P < .01, n = 16), respectively. However, there was no change in ET-1 as a result of the rHuEPO therapy. Creatinine clearance (Ccr), Cr, total amount of daily Tm excretion, Tm clearance/Ccr, daily urinary protein and albumin excretion, and blood pressure also remained unchanged throughout the trail. The present study indicates that correcting anemia by rHuEPO therapy reduces an abnormally elevated Tm in predialysis patients while blood pressure and renal function remain unchanged, suggesting that rHuEPO has a beneficial effect on endothelial cell dysfunction in chronic renal failure patients. This effect may be mediated via an improved oxygen supply to the endothelial cells due to the amelioration of anemia by rHuEPO.
Hypoxia down-regulates MCP-1 expression: implications for macrophage distribution in tumors (1998)

Monocyte chemoattractant protein 1 (MCP-1) is likely to contribute to the macrophage infiltrate in human ovarian carcinomas. Although MCP-1 is predominantly expressed by the tumor parenchyma, macrophages accumulate at highest density in necrotic regions, which are associated with low oxygen tensions. Tumor necrosis factor alpha (TNF-alpha) can stimulate MCP-1 production and is also present within ovarian carcinomas. We have investigated the effect of hypoxia both on MCP-1 expression in ovarian cancer cell lines and monocyte migration. Hypoxia down-regulated TNF-alpha-induced MCP-1 mRNA and protein production by ovarian cancer cells. The effect was mimicked by cobalt chloride and desferrioxamine, consistent with a specific oxygen-sensing mechanism. Unlike antioxidants, hypoxia did not inhibit nuclear factor KB mobilization. Monocyte migration in response to MCP-1 was also diminished under hypoxic conditions. Down-regulation of MCP-1 expression and the inhibition of monocyte migration are independent effects of hypoxia that may contribute to the distribution of macrophages within ovarian tumors.
Ubiquitin-Proteasome Pathway as a New Target for the Prevention of Restenosis (2002)

These proof-of-principle experiments demonstrate that inhibition of the ubiquitin-proteasome system effectively reduces neointima formation in vivo, which corresponds to strong antiproliferative, anti-inflammatory, and proapoptotic effects in vitro and in vivo. Our data suggest the ubiquitin-proteasome system as a new target in the prevention of vascular restenosis.
Efficient Synthesis of Racemic and Enantiomerically Pure 1,2,3,4-Tetrahydroisoquinoline-3-carboxylic Acid and Esters (1992)

Racemic and optically pure 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acids and esters were prepared, via base-catalyzed cyclization of 1,2-bis (halomethyl) benzenes 1 a or b with diethyl 2-(acetylamino)malonate (2), subsequent decarboxylation and amide cleavage. The enantiomer resolution was achieved either by esterification with (-)-menthol followed by column chromatographic separation of the diastereomeric mixture or by diasteromeric salt separation of the benzylic ester with mandelic acid and base- catalyzed saponification of both esters.
The Pleiotropic Functions of Interleukin 15 (2000)

Since its discovery in 1994, IL-15 has been studied in the context of its structural cousin, IL-2 ([1][1]). Early biochemical and in vitro lymphocyte studies revealed many similarities between IL-15 and IL-2: (a) IL-2 and IL-15 constitute the only two members of a family of cytokines containing a
Transductive Learning for Real-Time Twitter Search (2021)

Recency is an important dimension of relevance for real-time Twitter search as users tend to be interested in fresh news and events. By incorporating various sources of evidence, the application of learning to rank (LTR) algorithms to real-time Twitter search has shown beneficial in finding not only relevant, but also recent tweets in response to given queries. However, the potential effectiveness brought by LTR may not have been fully exploited due to the lack of labeled data available for properly learning a ranking model, since human labels are expensive in real-world applications. To this end, this paper proposes a transductive algorithm that incrementally aggregate the labeled tweets through an iterative process. Experimental results on the standard Tweets11 dataset show that our approach is able to outperform strong baselines without the use of human labels.
Degradation of alkanes by bacteria (2009)

Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixture of thousands of compounds. Among them, alkanes constitute the major fraction. Alkanes are saturated hydrocarbons of different sizes and structures. Although they are chemically very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochemical pathways used and on how the expression of pathway genes is regulated and integrated within cell physiology.
Generalized multiprotocol label switching: an overview of routing and management enhancements (2001)

Generalized multiprotocol label switching, also referred to as multiprotocol lambda switching, supports not only devices that perform packet switching, but also those that perform switching in the time, wavelength, and space domains. The development of GMPLS requires modifications to current signaling and routing protocols. It has also triggered the development of new protocols such as the Link Management protocol. We present the traffic engineering enhancements to the Open Shortest Path First Internet routing protocol and ISIS Intradomain Routing Protocol, two popular routing protocols, to support GMPLS. We present the concepts of generalized interfaces, label-switched path hierarchy, and link bundling intended to improve GMPLS scalability. We also discuss the Link Management Protocol which can be used to make the underlying links more manageable.