gebhart/patrepeval huggingface dataset:
Enumeration of T lymphocyte subsets by monoclonal antibodies in young and aged humans. (1981)

The percentage and absolute number of peripheral blood mononuclear cells reactive with monoclonal antibodies identifying mature thymocytes and T cells (T3+), helper/inducer cells (T4+), and suppressor/cytotoxic cells (T8+) was determined in 19 young (mean age 35 yr) and 31 elderly (mean age 72 yr) individuals. The percent representation but not the absolute number of T cells (T3+) declined significantly (p less than 0.001) in the elderly, and the decline was attributable to both an absolute and relative decrease in the representation of the subpopulation of cytotoxic/suppressor (T8+) cells. The percentage and number of helper/inducer (T4+) T cells was comparable in both age groups.
Epitope Structure of the Carbohydrate Recognition Domain of Asialoglycoprotein Receptor to a Monoclonal Antibody Revealed by High-Resolution Proteolytic Excision Mass Spectrometry (2011)

Recent studies suggest that the H1 subunit of the carbohydrate recognition domain (H1CRD) of the asialoglycoprotein receptor is used as an entry site into hepatocytes by hepatitis A and B viruses and Marburg virus. Thus, molecules binding specifically to the CRD might exert inhibition towards these diseases by blocking the virus entry site. We report here the identification of the epitope structure of H1CRD to a monoclonal antibody by proteolytic epitope excision of the immune complex and high-resolution MALDI-FTICR mass spectrometry. As a prerequisite of the epitope determination, the primary structure of the H1CRD antigen was characterised by ESI-FTICR-MS of the intact protein and by LC-MS/MS of tryptic digest mixtures. Molecular mass determination and proteolytic fragments provided the identification of two intramolecular disulfide bridges (seven Cys residues), and a Cys-mercaptoethanol adduct formed by treatment with β-mercaptoethanol during protein extraction. The H1CRD antigen binds to the monoclonal antibody in both native and Cys-alkylated form. For identification of the epitope, the antibody was immobilized on N-hydroxysuccinimide (NHS)-activated Sepharose. Epitope excision and epitope extraction with trypsin and FTICR-MS of affinity-bound peptides provided the identification of two specific epitope peptides (5-16) and (17-23) that showed high affinity to the antibody. Affinity studies of the synthetic epitope peptides revealed independent binding of each peptide to the antibody.
Buying and selling computational power over the network (2002)

Powerful processors and high-bandwidth communications which are available provide a very large amount of cycles at supercomputer speeds. This can serve emerging data-intensive applications which require extremely high data rates. Workstations equipped with such processors are often utilized for a fraction of the time and sit idle otherwise. It may become possible to sell and buy computational power over the network in the same way that electrical power is sold and bought by utilities over the power grid today. Potential buyers are users in need of more cycles than those provided by their own workstations. A request made by a potential buyer can be directed to any of the sellers and a best match of buyer and seller (trading) has to be made. For scalability, traders use an extended version of the adaptive partitioning algorithm which may be applicable whenever mutual interest is clearly defined, i.e. a seller is interested in finding a buyer and vice versa. It is shown that server or client selection for buying or selling computation power over the network using adaptive partitioning is simple and efficient.
ATP activation of DNA polymerase III holoenzyme from Escherichia coli. II. Initiation complex: stoichiometry and reactivity. (1982)

DNA polymerase III holoenzyme (holenzyme) has an ATPase activity elicited only by a primed DNA template. Reaction of preformed ATP.holoenzyme complex with a primed template results in hydrolysis of the ATP bound to the holoenzyme, release of ADP and Pi, and formation of an initiation complex between holoenzyme and the primed template. Approximately two ATP molecules are hydrolyzed for each initiation complex formed, a value in keeping with the number bound in the ATP.holoenzyme complex. The possibility that the latter and the initiation complex contain two holoenzyme molecules is supported by the presence of two beta monomers in the initiation complex. Holoenzyme action in the absence of ATP resembles that of pol III (the holoenzyme core) or DNA polymerase III (holoenzyme lacking the beta subunit), with or without ATP, in sensitivity to salt and in processivity of elongation. The initiation complex formed by ATP-activated holoenzyme resists a level of KCl (150 mM) that completely inhibits nonactivated holoenzyme and the incomplete forms of the holoenzyme, and displays a processivity at least 20 times greater. Upon completing replication of available template, holoenzyme can dissociate and form an initiation complex with another primed template, provided ATP is available to reactivate the holoenzyme. By inference, no essential subunits are lost in the cycle of initiation, elongation and dissociation.
Three-dimensional medical imaging (1991)

article Free Access Share on Three-dimensional medical imaging: algorithms and computer systems Authors: M. R. Stytz Air Force Institute of Technology, Wright-Patterson AFB, OH Air Force Institute of Technology, Wright-Patterson AFB, OHView Profile , G. Frieder Syracuse Univ., Syracuse, NY Syracuse Univ., Syracuse, NYView Profile , O. Frieder George Mason Univ., Fairfax, VA George Mason Univ., Fairfax, VAView Profile Authors Info & Claims ACM Computing SurveysVolume 23Issue 4Dec. 1991 pp 421–499https://doi.org/10.1145/125137.125155Published:01 December 1991Publication History 75citation7,320DownloadsMetricsTotal Citations75Total Downloads7,320Last 12 Months106Last 6 weeks41 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 SiteeReaderPDF
Multivalent nanoparticle-based vaccines protect hamsters against SARS-CoV-2 after a single immunization (2021)

The COVID-19 pandemic continues to wreak havoc as worldwide SARS-CoV-2 infection, hospitalization, and death rates climb unabated. Effective vaccines remain the most promising approach to counter SARS-CoV-2. Yet, while promising results are emerging from COVID-19 vaccine trials, the need for multiple doses and the challenges associated with the widespread distribution and administration of vaccines remain concerns. Here, we engineered the coat protein of the MS2 bacteriophage and generated nanoparticles displaying multiple copies of the SARS-CoV-2 spike (S) protein. The use of these nanoparticles as vaccines generated high neutralizing antibody titers and protected Syrian hamsters from a challenge with SARS-CoV-2 after a single immunization with no infectious virus detected in the lungs. This nanoparticle-based vaccine platform thus provides protection after a single immunization and may be broadly applicable for protecting against SARS-CoV-2 and future pathogens with pandemic potential.
Facial Attributes Classification Using Multi-task Representation Learning (2016)

This paper presents a new approach for facial attribute classification using a multi-task learning approach. Unlike other approaches that uses hand engineered features, our model learns a shared feature representation that is wellsuited for multiple attribute classification. Learning a joint feature representation enables interaction between different tasks. For learning this shared feature representation we use a Restricted Boltzmann Machine (RBM) based model, enhanced with a factored multi-task component to become Multi-Task Restricted Boltzmann Machine (MT-RBM). Our approach operates directly on faces and facial landmark points to learn a joint feature representation over all the available attributes. We use an iterative learning approach consisting of a bottom-up/top-down pass to learn the shared representation of our multi-task model and at inference we use a bottom-up pass to predict the different tasks. Our approach is not restricted to any type of attributes, however, for this paper we focus only on facial attributes. We evaluate our approach on three publicly available datasets, the Celebrity Faces (CelebA), the Multi-task Facial Landmarks (MTFL), and the ChaLearn challenge dataset. We show superior classification performance improvement over the state-of-the-art.
Pyruvate: ferredoxin oxidoreductase from Entamoeba histolytica recognized by a monoclonal antibody. (1996)

A mouse monoclonal antibody, Eh208C2-2 MAb, raised against whole cell antigens of Entamoeba histolytica trophozoites of the pathogenic strain HM-1: IMSS and polyclonal antisera (PAb) against membrane antigens of E. histolytica trophozoites of strain HTH-56: MUTM were screened against a cDNA library of the pathogenic strain, SFL3. The monoconal antibody detected many phage plaques expressing an E. histolytica protein. The DNA sequence encoding the protein was approximately 55% identical, over 1,100bp, to Trichomonas vaginalis pyruvate: ferredoxin oxidoreductase (PFOR) and pyruvate: flavodoxin oxidoreductase from Klebsiella pneumoniae, Anabaena variabilis and Enterobacter agglomerans. Two of seven clones detected by mouse polyclonal antisera also encoded this protein. Two others encoded Entamoeba Hsp70, another encoded Entamoeba alkyl-hydroperoxide reductase and the remaining two were unidentified sequences. Entamoeba PFOR is an abundant, antigenic protein which may be a useful target for the development of protective host immune responses against invasive amebiasis.
Association of the Invariant Chain with Major Histocompatibility Complex Class I Molecules Directs Trafficking to Endocytic Compartments (1995)

Major histocompatibility complex (MHC) class I and class II molecules have been shown to present peptides of different origin to alpha beta T cells. Most peptides presented by class I molecules are derived from endogenously synthesized proteins, whereas most peptides presented by class II molecules are from exogenous sources. This functional dichotomy can largely be achieved by the preferential intracellular association of the invariant chain (Ii) with MHC class II molecules, which may inhibit binding of endogenous peptides to class II molecules and direct them to endocytic compartments where extracellularly derived peptides can be sampled. Here, we show that Ii also can associate with a subset of MHC class I molecules and direct them to endocytic compartments. Ii was coprecipitated with class I molecules after lysis of human lymphocytes in mild detergent such as 3-[(3-cholamidopropyl)dimethylammonio]-1-propane-sulfonic acid or digitonin, and the association was more clearly visualized by the use of dithiobis[succinimidyl-propionate], a homobifunctional chemical cross-linker. The class I.Ii complex was reconstituted in Ii negative cells by transfection of corresponding cDNA clones and was found to be transported through the Golgi to acidic endocytic compartments. These observations may explain how some exogenous antigens can be presented by MHC class I molecules and how MHC class II molecules can bind self peptides derived from MHC class I molecules in endocytic compartments.
Bridging levels: Using a cognitive model to connect brain and behavior in category learning (2006)

Mental localization efforts tend to stress the where more than the what.We argue that the proper targets for localization are well-specified cognitive models.We make this case by relating an existing cognitive model of category learning to a learning circuit involving the hippocampus, perirhinal, and prefrontal cortex.Results from groups varying in function along this circuit (e.g., infants, amnesics, older adults) are successfully simulated by reducing the model's ability to form new clusters in response to surprising events, such as an error in supervised learning or an unfamiliar stimulus in unsupervised learning.Reported task dissociations (e.g., categorization vs. recognition) are explained in terms of cluster recruitment demands.
Localization of perlecan (or a perlecan-related macromolecule) to isolated microglia in vitro and to microglia/macrophages following infusion of beta-amyloid protein into rodent hippocampus (1997)

The origin of the heparan sulfate proteoglycan (PG), perlecan, in beta-amyloid protein (A beta)-containing amyloid deposits in Alzheimer's disease (AD) brain is not known. In the present investigation we used indirect immunofluorescence, SDS-PAGE, and Western blotting with a specific perlecan core protein antibody to identify possible cell candidates of perlecan production in both primary cell cultures and in a rat infusion model. Double and triple-labeled indirect immunofluorescence was performed on dissociated primary rat septal cultures using antibodies for specific identification of cell types and for perlecan core protein. In mixed cultures of both embryonic day 18 (containing neurons and glia) and postnatal day 2-3 (devoid of neurons), microglia identified by labeling with OX-42 or anti-ED1 were the only cell type also double labeled with an affinity-purified polyclonal antibody against perlecan core protein. Similar immunolabeling of microglia with the anti-perlecan antibody was also observed in purified cultures of post-natal rat microglia. Analyses of PGs from cultured postnatal rat microglia by Western blotting using a polyclonal antibody against perlecan core protein revealed an approximately 400 kDa band in cell layer, which was intensified following heparitinase/heparinase digestion, suggestive of perlecan core protein. Other lower Mr bands were also found implicating either degradation of the 400 kDa core protein or the presence of separate and distinct gene products immunologically related to perlecan. Reverse transcription followed by polymerase chain reaction using human perlecan domain I specific primers demonstrated perlecan mRNA in cultured human microglia derived from postmortem normal aged and AD brain. Following a 1-week continuous infusion of A beta (1-40) into rodent hippocampus, immunoperoxidase immunocytochemistry and double-labeled immunofluorescent studies revealed perlecan accumulation primarily localized to microglia/macrophages within the A beta infusion site. These studies have identified microglia/macrophages as one potential source of perlecan (or a perlecan-related macromolecule) which may be important for the ongoing accumulation of both perlecan and A beta in the amyloid deposits of AD.
Real-Time Transport Protocol (RTP) Payload Format and File Storage Format for the Adaptive Multi-Rate (AMR) and Adaptive Multi-Rate Wideband (AMR-WB) Audio Codecs (2002)

community, and requests discussion and suggestions for improvements.
BCL2-mediated tumorigenicity of a human T-lymphoid cell line: synergy with MYC and inhibition by BCL2 antisense. (1990)

A gene-transfer approach was used to explore the function of the BCL2 (B-cell lymphoma/leukemia 2) gene in a human T-cell line, Jurkat. Though stable introduction of a BCL2 expression plasmid into Jurkat T cells was by itself insufficient, the combined transfer of BCL2 and MYC genes markedly enhanced the tumorigenicity of these cells in athymic mice. Moreover, a BCL2 antisense expression plasmid ablated tumor formation by Jurkat cells, providing further evidence that this oncogene contributes to the regulation of the in vivo growth of these human T lymphocytes. In addition to their influence on tumor formation, BCL2 sense and antisense expression plasmids increased and decreased, respectively, the in vitro survival of Jurkat T cells in serum-free medium. These observations extend to T cells the finding of synergy of BCL2 with MYC previously reported for B cells and provide evidence that BCL2 can regulate the growth of human T cells.
Novel compound heterozygous laminina2-chain gene (LAMA2) mutations in congenital muscular dystrophy (1998)

The laminina2-chain gene (LAMA2) encodes a basal lamina protein, laminina2, known to be deficient in one form of congenital muscular dystrophy (CMD). In a laminina2 deficient-CMD patient, we screened the entire LAMA2 cDNA (953bp) by reverse transcriptase polymerase chain reaction combined with single strand conformational polymorphism analysis. Direct sequencing of aberrant conformers in this patient revealed two loss-of-function mutations, consistent with autosomal recessive inheritance. The patient had two novel heterozygous mutations: 1) an exon 4 nonsense mutation caused by a G-->A substitution at cDNA position 547, changing the TGG codon for tryptophan into a TGA stop codon (W166X) in the N-terminus domain VI;ii) an exon 54 frameshift mutation due to a deletion of nucleotide 'C' at cDNA position 7707 (S2553Y), resulting in a premature stop codon (V2587X) in exon 55 in the globular G domain of laminina2 at the C-terminus. These mutations cause a disruption of the open reading frame of LAMA2. The absence of laminina2 observed in the patient's muscle biopsy could result from diminished levels of the LAMA2 transcript. Alternatively, the mutations might lead to translation of a truncated laminina2. By either mechanism the phenotype of congenital muscular dystrophy is believed to be the result of disruption of linkage between the extracellular matrix and the dystrophin glycoprotein complex.
Current small cell lung cancer treatment in China (2015)

The treatment options indicated in our study are in accordance with the international clinical guidelines, which is valuable for the improvement of future guidelines, health care standard, and even the better distribution of health care resources in China.
Time course of the membrane current underlying sensory transduction in salamander olfactory receptor neurones. (1990)

1. Odour elicited currents in freshly isolated olfactory receptor neurones were analysed using the whole-cell patch-clamp technique. Brief pulses (35-50 ms) and steps (100 ms-5 s) of odour solution were delivered by pressure ejection from a nearby micropipette. 2. Pulses of odour solution directed at the cell induced an inward depolarizing current of 50-750 pA leading to the generation of action potentials. The I-V relation for this current was linear over the range -60-(+)20 mV and showed a reversal potential of +5 mV. The magnitude of the current increased with stimulus strength, for a given pulse duration, over approximately one decade of concentration change. 3. Pulses of odour solution focally delivered to the cilia elicited a large response, but those directed toward the soma did not. Conversely pulses of K+ solution at the cilia failed to evoke any response while those directed at the dendrite and soma elicited an inward clamp current. This provides direct evidence that odour sensitivity is localized mainly to the cilia and possibly the distal dendrite. 4. The odour elicited current activated with a long latency of 150-600 ms after the odour solution arrived at the cell. This latency, as well as the time-to-peak and the rise half-time, were relatively independent of stimulus concentration, changing less than 25% over the entire concentration range of stimulus sensitivity. These observations are consistent with the participation of a second messenger system in olfactory transduction. 5. For brief stimulus pulses less than 100 ms, the stimulus diffused away before the odour response current reached its peak value, so that the peak and decay of the odour response occurred in the absence of significant odour stimulus. The time course of the current decay was fitted by a single exponential with a time constant that was concentration dependent, varying from 0.8 to 1.3 s. 6. For longer steps of stimulus presentation, up to 1 s, the magnitude of the response current became a function of the duration of the pulse as well as the stimulus concentration, indicating that the transduction process involved an integrating step. This is consistent with the idea that the odour elicited current is the result of the summation of many smaller unitary events. From responses to weak stimulation an integration period of 700-1000 ms was calculated. 7. During prolonged steps of maintained stimulus presentation (greater than 5 s) the odour elicited current was transient.(ABSTRACT TRUNCATED AT 400 WORDS)
Coinhibitory Pathways in Immunotherapy for Cancer (2016)

The immune system is capable of recognizing tumors and eliminates many early malignant cells. However, tumors evolve to evade immune attack, and the tumor microenvironment is immunosuppressive. Immune responses are regulated by a number of immunological checkpoints that promote protective immunity and maintain tolerance. T cell coinhibitory pathways restrict the strength and duration of immune responses, thereby limiting immune-mediated tissue damage, controlling resolution of inflammation, and maintaining tolerance to prevent autoimmunity. Tumors exploit these coinhibitory pathways to evade immune eradication. Blockade of the PD-1 and CTLA-4 checkpoints is proving to be an effective and durable cancer immunotherapy in a subset of patients with a variety of tumor types, and additional combinations are further improving response rates. In this review we discuss the immunoregulatory functions of coinhibitory pathways and their translation to effective immunotherapies for cancer.
Continuous Measurements of Ground‐Water Seepage Using an Automatic Seepage Meter (1993)

Abstract An automatic seepage meter using a heat pulse method was developed to obtain a continuous measurement of ground‐water seepage rates. According to calibrations of the automatic seepage meter fitted with a 50 cm diameter collection funnel, seepage rates from 2 X 10 ‐5 to 5 X 10 ‐4 cm/sec can be obtained by measuring the time when the temperature as measured by a thermistor peaks after applying a heat pulse. The automatic seepage meter was used to measure continuous seepage rates into Lake Biwa, Japan. The ground‐water seepage rate measured by the automatic seepage meter in Lake Biwa changed by six times within 12 hours. The automatic seepage meter is useful for surface‐/ground‐water studies, because a continuous seepage rate can be obtained without errors caused by the resistance of a collection bag to water flow.
Cell wall monoglycine cross-bridges and methicillin hypersusceptibility in a femAB null mutant of methicillin-resistant Staphylococcus aureus (1997)

The femAB operon is involved in the formation of the characteristic pentaglycine side chain of the staphylococcal peptidoglycan. Allele replacement of the femAB operon with the tetracycline resistance determinant tetK in a methicillin-resistant Staphylococcus aureus strain resulted in impaired growth, methicillin hypersusceptibility, and lysostaphin resistance. The usual pentaglycine cross-bridges were replaced by monoglycine bridges exclusively, and cross-linking of the peptidoglycan strands was drastically reduced. Complementation of the femAB null mutant by either femA or femAB resulted in the extension of the cross-bridges to a triglycine or a pentaglycine, respectively. This finding suggests that FemA is responsible for the formation of glycines 2 and 3, and FemB is responsible for formation of glycines 4 and 5, of the pentaglycine side chain of the peptidoglycan precursor. Moreover, it can be deduced that addition of the first glycine must occur by a femAB-independent mechanism.