gebhart/patrepeval huggingface dataset:
NonviableBurkholderia malleiInduces a Mixed Th1- and Th2-Like Cytokine Response in BALB/c Mice (2002)

Nonviable cell preparations of Burkholderia mallei, the causative agent of glanders, were evaluated as potential vaccine candidates in a BALB/c murine model. Three different B. mallei cell preparations plus Alhydrogel were evaluated: a heat-killed preparation, an irradiation-inactivated preparation, and a preparation of a capsule-negative mutant strain which had been irradiation inactivated. BALB/c mice were vaccinated twice with the different B. mallei preparations, and spleens and sera were collected to determine their cellular and humoral immune responses. All three bacterial cell preparations had essentially the same results in two cellular immune response assays. In a splenocyte proliferation assay, the amount of cell proliferation in response to the homologous immunogen, concanavalin A, or lipopolysaccharide was similar for all the cell preparations. Also, splenocytes from the inoculated mice expressed interleukin 2 (IL-2), gamma interferon, and small amounts of IL-4 and IL-5, and more IL-10 cytokine in the presence of the homologous antigen. When the immunoglobulin subclasses from these mice were examined, they all produced higher levels of IgG1 than IgG2a subclasses. The higher ratio of IgG1 to IgG2a was not due to the amount of the immunogen or the adjuvant (Alhydrogel) used in the BALB/c mice. The cell preparations did not protect the vaccinated mice from a live challenge (>300 50% lethal doses). Our results suggest that in BALB/c mice, a mixed T-helper-cell-like response to nonviable B. mallei is obtained, as demonstrated by a Th1- and Th2-like cytokine response and a Th2-like subclass immunoglobulin response. This may be the reason for the inability of the B. mallei cells that were examined as candidate vaccines to protect the mice from a live challenge.
A microplate enzyme-immunoassay for toxoplasma antibody. (1976)

A new test for the detection and measurement of toxoplasma antibody is described. Test sera are reacted with antigen-sensitized wells in micro-haemagglutination plates. Any attached antibody is shown by the addition of an enzyme-labelled antiglobulin followed by assay of the enzyme reaction with its substrate. The test is easy to carry out on a large scale, and there is a positive correlation between the results and dye test and haemagglutination test titres.
Testing finite state machines (1991)

Article Testing finite state machines Share on Author: Mihalis Yannakakis AT&T Bell Labs., Murray Hill, NJ AT&T Bell Labs., Murray Hill, NJView Profile , Editor: David Lee AT&T Bell Labs., Murray Hill, NJ AT&T Bell Labs., Murray Hill, NJView Profile Authors Info & Claims STOC '91: Proceedings of the twenty-third annual ACM symposium on Theory of ComputingJanuary 1991 Pages 476–485https://doi.org/10.1145/103418.103468Online:03 January 1991Publication History 37citation1,310DownloadsMetricsTotal Citations37Total Downloads1,310Last 12 Months13Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Emergence of a Stable Cortical Map for Neuroprosthetic Control (2009)

Cortical control of neuroprosthetic devices is known to require neuronal adaptations. It remains unclear whether a stable cortical representation for prosthetic function can be stored and recalled in a manner that mimics our natural recall of motor skills. Especially in light of the mixed evidence for a stationary neuron-behavior relationship in cortical motor areas, understanding this relationship during long-term neuroprosthetic control can elucidate principles of neural plasticity as well as improve prosthetic function. Here, we paired stable recordings from ensembles of primary motor cortex neurons in macaque monkeys with a constant decoder that transforms neural activity to prosthetic movements. Proficient control was closely linked to the emergence of a surprisingly stable pattern of ensemble activity, indicating that the motor cortex can consolidate a neural representation for prosthetic control in the presence of a constant decoder. The importance of such a cortical map was evident in that small perturbations to either the size of the neural ensemble or to the decoder could reversibly disrupt function. Moreover, once a cortical map became consolidated, a second map could be learned and stored. Thus, long-term use of a neuroprosthetic device is associated with the formation of a cortical map for prosthetic function that is stable across time, readily recalled, resistant to interference, and resembles a putative memory engram.
Preparation of Substituted Imidazolidinones and Hydantoins by Ring-Expansion of Aziridinones (1997)

Reaction of 1,3-di-tert-butylaziridinone and other di-tert-alkylaziridinones with cyanamides produces an imidazolidinone (3 or 6) bearing the tert-alkyl substituents at positions 1 and 5 only, by selective cleavage of the acyl-nitrogen bond. Treatment of the product from the unsubstituted cyanamide (3) with HNO2 furnishes the corresponding hydantoin (5), whereas treatment with alkyl halides and base affords another imidazolidinone (7).
Selective disruption of lymphotoxin ligands reveals a novel set of mucosal lymph nodes and unique effects on lymph node cellular organization (1997)

Lymphotoxin (LT) provides a critical signal for the genesis of lymph nodes (LN) in mice. Here we show that mice treated in utero with LT beta-R-Ig, which binds to the membrane LT alpha 1 beta 2 heterotrimer, lacked most LN, yet retained a set of mucosal surface draining LN. Since mice genetically deficient in LT alpha lack all LN, including the mucosal set, we hypothesize that a novel LT alpha-dependent pathway controls their genesis. This novel set of mucosal LN cannot be discriminated on the basis of addressin expression. The discovery of LN in mice treated with LT beta-R-Ig fusion protein in utero allowed us to compare the roles of membrane LT alpha beta or soluble LT alpha/tumor necrosis factor (TNF) in the development of cellular organization in LN and spleen. Our results indicate that both membrane LT alpha beta and soluble LT alpha/TNF mediate T-B cell segregation and the organization of B cell follicles in spleen and LN. Interestingly, while antagonism of membrane LT alpha beta or soluble LT alpha/TNF prevented germinal center (GC) formation in spleen, antagonism of soluble LT alpha/TNF had no effect on LN formation. The data suggest that multiple LT/TNF ligands control B cell follicle organization in the spleen and LN of adult mice, and that the requirements for LT/TNF ligands in GC formation are distinct in the different lymphoid organs.
Comparison of Real-Time PCR, Conventional PCR, and Galactomannan Antigen Detection by Enzyme-Linked Immunosorbent Assay Using Bronchoalveolar Lavage Fluid Samples from Hematology Patients for Diagnosis of Invasive Pulmonary Aspergillosis (2003)

An iCycler iQ real-time PCR assay targeting 18S rRNA Aspergillus-specific sequences was developed for the diagnosis of invasive pulmonary aspergillosis (IPA). Positive findings were obtained for 18 of 20 (90%) bronchoalveolar lavage (BAL) fluid specimens from patients with probable or confirmed IPA and were obtained for none of the 24 BAL samples from patients with no clinical evidence of aspergillosis. These results were concordant with those of a nested PCR assay, which detected 90% of the patients with IPA, while galactomannan ELISA revealed positivity for 100% of these patients, suggesting that combined use of methods might improve the diagnosis of IPA.
Neurotrophic Factors, Cytokines and Stress Increase Expression of Basic Fibroblast Growth Factor in Retinal Pigmented Epithelial Cells (1997)

Basic fibroblast growth factor (bFGF) and FGF receptors have been localized to photoreceptors and retinal pigmented epithelium (RPE), but the function of bFGF in adult retina and RPE is unknown. Exogenous bFGF has a neuroprotective effect in retina and brain and its expression is increased in some neurons in response to cytokines or stress. In this study, we investigated the effect of light, other types of stress, neurotrophic factors, and cytokines on bFGF levels in cultured human RPE. Some agents that protect photoreceptors from the damaging effects of constant light, including brainderived neurotrophic factor (BDNF), ciliary neurotrophic factor, and interleukin-1 beta, increase bFGF mRNA levels in RPE cells. Intense light and exposure to oxidizing agents also increase bFGF mRNA levels in RPE cells and cycloheximide blocks the increase. An increase in bFGF protein levels was demonstrated by ELISA in RPE cell supernatants after incubation with BDNF or exposure to intense light or oxidizing agents. These data indicate that bFGF is modulated in RPE cells by stress and by agents that provide protection from stress and support the hypothesis that bFGF functions as a survival factor in the outer retina.
Recent progress in ankylosing spondylitis treatment (2003)

Ankylosing spondylitis (AS) is a systemic inflammatory rheumatic disease responsible for back pain, stiffness and loss of functional capacity. The therapeutic management of AS includes regular physical exercise together with the use of NSAIDs. Second-line treatments, such as sulfasalazine, are required in cases of NSAID-refractory AS. Some patients have severe and inadequately controlled disease, explaining the need for the development of new treatments. This therapeutic development in AS involves the assessment of new NSAIDs, namely COX2 selective agents and new second-line treatments, such as methotrexate (MTX), pamidronate and anti-TNFα agents. Controlled studies are lacking for MTX. Pamidronate showed to be effective in NSAID refractory AS patients in open and controlled trials. Anti-TNFα agents (infliximab and etanercept) gave promising results with dramatic improvement of AS symptoms in open and preliminary controlled trials, but further studies are required to evaluate the real long-term effects and tolerability of these drugs.
Vectors for gene expression and amplification in the yeastYarrowia lipolytica (2001)

New vector systems were developed for gene expression in Y. lipolytica. These plasmids contain: (a) as integration target sequences, either a rDNA region or the long terminal repeat zeta of the Y. lipolytica retrotransposon Ylt1; (b) the YlURA3 gene as selection marker for Y. lipolytica, either as the non-defective ura3d1 allele for single integration or the promotor truncated ura3d4 allele for multiple integration; (c) the inducible ICL1 or XPR2 promoters for gene expression; and (d) unique restriction sites for gene insertion. Multiple plasmid integration occurred as inserted tandem-repeats, which are present at 3-39 copies per cell. A correlation between gene copy number and the expressed enzyme activity was demonstrated with Escherichia coli lacZ as reporter gene under the control of the regulated ICL1 promoter. Increases in copy numbers from 5 to 13 for the lacZ expression cassettes resulted in an up to 10-11-fold linear increase of the beta-galactosidase activity in multicopy transformants during their growth on ethanol or glucose, compared with the low-copy replicative plasmid transformants (1.6 plasmid copies). These new tools will enhance the interest in Y. lipolytica as an alternative host for heterologous protein production.
Policy based networking in the integration effort of 4G networks and services (2005)

We present system integration requirements and provide a new framework to support the integration of 4G networks and services. This framework uses a policy based networking concept in order to provide the unified control in the oncoming 4G networks and services. We also provide an analysis of the candidate signaling protocols in this framework. Two approaches are described: i) the unified QoS, mobility, and security signaling and ii) the heterogeneous QoS, mobility, and security signaling. In addition, we introduce user, terminal, network and service profiles and management in order to provide a user centric approach and consider different user, terminal, network, and service constraints in order to better adapt the user service as well as the network configuration to these constraints. Finally, we give a short estimation on the composition of exchanged signaling data with respect to the aspired level of integration.
Design and evaluation of algorithms for image retrieval by spatial similarity (1995)

Similarity-based retrieval of images is an important task in many image database applications. A major class of users' requests requires retrieving those images in the database that are spatially similar to the query image. We propose an algorithm for computing the spatial similarity between two symbolic images. A symbolic image is a logical representation of the original image where the image objects are uniquely labeled with symbolic names. Spatial relationships in a symbolic image are represented as edges in a weighted graph referred to as spatial-orientation graph. Spatial similarity is then quantified in terms of the number of, as well as the extent to which, the edges of the spatial-orientation graph of the database image conform to the corresponding edges of the spatial-orientation graph of the query image. The proposed algorithm is robust in the sense that it can deal with translation, scale, and rotational variances in images. The algorithm has quadratic time complexity in terms of the total number of objects in both the database and query images. We also introduce the idea of quantifying a system's retrieval quality by having an expert specify the expected rank ordering with respect to each query for a set of test queries. This enables us to assess the quality of algorithms comprehensively for retrieval in image databases. The characteristics of the proposed algorithm are compared with those of the previously available algorithms using a testbed of images. The comparison demonstrated that our algorithm is not only more efficient but also provides a rank ordering of images that consistently matches with the expert's expected rank ordering.
The amphipathic alpha-helical repeats of apolipoprotein A-I are responsible for binding of high density lipoproteins to HepG2 cells. (1991)

Nine monoclonal antibodies (mAbs) against apoA-I reacting with distinct but overlapping epitopes covering more than 90% of the sequence have been used to block the interaction of 125I-labeled high density lipoprotein (125I-HDL) with HepG2 cells in order to delineate the cell binding domain of apolipoprotein A-I (apoA-I). While 2 mAbs reacting with epitopes exclusively localized in the N-terminal region (residues 1 to 86) enhanced slightly association of 125I-HDL, all other mAbs, which react with epitopes localized in the regions of amphipathic alpha-helical repeats, inhibited that association by 9 to 15%. Although this inhibition is not significant compared to the effect of an irrelevant mAb, combination of these mAbs could significantly inhibit the association of 125I-HDL (32 to 43%) as could polyclonal antibodies (up to 95%). These results are compatible with the concept of HDL binding to these cells via the nonexclusive interaction of each of the amphipathic alpha-helical repeats of apoA-I. When the same approach was applied to block the association of 3H-cholesteryl ether (CE)-labeled HDL to HepG2 cells, each anti-apoA-I could inhibit by 15 to 25% the cellular association of cholesteryl ether while mAbs in combination or polyclonal antibodies could inhibit this association up to 45% or 60%, respectively. The cholesteryl ether radioactivity that remained associated with the cells (40%) in the presence of polyclonal antibodies could be effectively blocked by addition of an antibody against the receptor binding domain of apoE (1D7). Therefore, the differential cellular association of cholesteryl ether compared to apolipoprotein can be explained by the presence of apoE secreted by HepG2 and apoE or apoB/E receptors. Thus, we conclude that the optimum uptake of both cholesteryl ether and apoA-I of HDL by cells requires the accessibility of the entire apoA-I and the cooperative binding of the amphipathic alpha-helical repeats to HepG2 cell membranes. This type of interaction would explain the competitive binding observed for apoA-I, -A-II, and -A-IV by others.
ClassX: a browsing tool for protein sequence megaclassifications (2002)

The authors have developed an algorithm, HHS, for efficient clustering of very large sequence databases into groups based on sequence similarity. When applied to protein sequence databases, the induced groups objectively define both protein superfamilies and recurring sequence motifs. HHS has been successfully applied to large sequence databases; however, the output is too large and complex to be readily interpreted. The authors report on a software tool called ClassX that was developed to help explore the results of megaclassification runs. They also discuss the problem of automatic annotations, i.e., how to use the classifications produced by the program to label regions of interest in an anonymous protein sequence.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of Hydrodynamic Models Suitable for Air Pollution and Other Mesometerological Studies (1978)

We describe the development of a general, predictive, hydrostatic meteorological model. The model is three-dimensional and is suitable for a wide variety of problems, ranging from the synoptic scale to the small end of the mesoscale. The model contains provisions for variable terrain, a moisture cycle, sensible heat addition at the earth's interface, and high- and low-resolution boundary layer physics. This paper presents the mathematical and numerical formulation used in the various options of the model. First we write the basic equations on a Lambert conformal projection. Then we describe the horizontal and vertical grid structure, the finite-difference equations, and the energetics of the three-dimensional model and its two-dimensional analog. We consider the role of the lateral boundary conditions for limited area forecasts, with emphasis on their effect on the mean motion over the domain. Two options for including the frictional and diabatic effects at the earth's surface are presented. These include a bulk parameterization and a high-resolution model of the planetary boundary layer. Both models use a predictive surface energy equation developed by Blackadar to determine the time-dependent surface heat flux. The water vapor cycle and the parameterization of cumulus convection are summarized. Both stable non-convective (grid-scale relative humidity equal to 100%) and unstable convective (grid-scale relative humidity less than 100%) precipitation are modeled. We present several preliminary simulations with the two-dimensional analog, in order to investigate the sensitivity of the model to the finite-differencing scheme, the treatment of the upper boundary condition, and the effect of the horizontal diffusion on the solutions forced by moderate flow over steep terrain. The model is shown to be energetically consistent to a good approximation, and capable of simulating hydro-static mountain waves realistically. Three-dimensional experiments are discussed in a separate paper by Warner et al. (1978).
Monoclonal antibodies against spore antigens of Bacillus anthracis (1988)

A murine monoclonal antibody produced against heat inactivated spores of Bacillus anthracis Ames, reacted with live or inactivated spores of several anthrax strains in indirect immunofluorescence (IF) tests. The reactive anthrax strain gave only a moderate degree of reaction. No staining of anthrax vegetative cells was observed. The monoclonal did not react with spores of non-anthrax Bacillus strains that gave cross reactions with mouse hyperimmune antiserum raised against Ames spores. The staining of individual spores in B. anthracis preparations was more heterogeneous with the monoclonal antibody than with the hyperimmune serum. Evidence is produced that the epitope for this monoclonal is not stable during long-term storage of inactivated spore preparations, and is not fully available for reaction with antibody until late in spore maturation. The monoclonal did not react by immunoblotting (Western blotting) of spore extracts.
A motion correction system for brain tomography based on biologically motivated models (2008)

A motion correction system for brain tomography is presented, which employs two calibrated video cameras and three vision models (CIECAM'97, RETINA, and BMV). The system is evaluated on the pictures monitoring a subjects head while simulating PET scanning (n=12) and on the face images of subjects with different skin colours (n=31). The results on 2D images with known moving parameters show that motion parameters of rotation and translation along X, Y, and Z directions can be obtained very accurately via the method of facial landmark detection. A feasibility study of the developed algorithms is evaluated by a computer simulation of brain scanning procedures.
The Transmembrane Domain of Influenza Hemagglutinin Exhibits a Stringent Length Requirement to Support the Hemifusion to Fusion Transition (2000)

Glycosylphosphatidylinositol-anchored influenza hemagglutinin (GPI-HA) mediates hemifusion, whereas chimeras with foreign transmembrane (TM) domains mediate full fusion. A possible explanation for these observations is that the TM domain must be a critical length in order for HA to promote full fusion. To test this hypothesis, we analyzed biochemical properties and fusion phenotypes of HA with alterations in its 27-amino acid TM domain. Our mutants included sequential 2-amino acid (Delta2-Delta14) and an 11-amino acid deletion from the COOH-terminal end, deletions of 6 or 8 amino acids from the NH(2)-terminal and middle regions, and a deletion of 12 amino acids from the NH(2)-terminal end of the TM domain. We also made several point mutations in the TM domain. All of the mutants except Delta14 were expressed at the cell surface and displayed biochemical properties virtually identical to wild-type HA. All the mutants that were expressed at the cell surface promoted full fusion, with the notable exception of deletions of >10 amino acids. A mutant in which 11 amino acids were deleted was severely impaired in promoting full fusion. Mutants in which 12 amino acids were deleted (from either end) mediated only hemifusion. Hence, a TM domain of 17 amino acids is needed to efficiently promote full fusion. Addition of either the hydrophilic HA cytoplasmic tail sequence or a single arginine to Delta12 HA, the hemifusion mutant that terminates with 15 (hydrophobic) amino acids of the HA TM domain, restored full fusion activity. Our data support a model in which the TM domain must span the bilayer to promote full fusion.