gebhart/patrepeval huggingface dataset:
Immune Response to Recombinant Capsid Proteins of Adenovirus in Humans: Antifiber and Anti-Penton Base Antibodies Have a Synergistic Effect on Neutralizing Activity (1998)

Replication-deficient adenovirus used in humans for gene therapy induces a strong immune response to the vector, resulting in transient recombinant protein expression and the blocking of gene transfer upon a second administration. Therefore, in this study we examined in detail the capsid-specific humoral immune response in sera of patients with lung cancer who had been given one dose of a replication-defective adenovirus. We analyzed the immune response to the three major components of the viral capsid, hexon (Hx), penton base (Pb), and fiber (Fi). A longitudinal study of the humoral response assayed on adenovirus particle-coated enzyme-linked immunosorbent assay plates showed that patients had preexisting immunity to adenovirus prior to the administration of adenovirus-beta-gal. The level of the response increased in three patients after adenovirus administration and remained at a maximum after three months. One patient had a strong immune response to adenovirus prior to treatment, and this response was unaffected by adenovirus administration. Sera collected from the patients were assayed for recognition of each individual viral capsid protein to determine more precisely the molecular basis of the humoral immune response. Clear differences existed in the humoral response to the three major components of the viral capsid in serum from humans. Sequential appearance of these antibodies was observed: anti-Fi antibodies appeared first, followed by anti-Pb antibodies and then by anti-Hx antibodies. Moreover, anti-Fi antibodies preferentially recognized the native trimeric form of Fi protein, suggesting that they recognized conformational epitopes. Our results showed that sera with no neutralizing activity contained only anti-Fi antibodies. In contrast, neutralizing activity was only obtained with sera containing anti-Fi and anti-Pb antibodies. More importantly, we showed that anti-native Fi and anti-Pb antibodies had a synergistic effect on neutralization. The application of these conclusions to human gene therapy with recombinant adenovirus should lead to the development of strategies to overcome the formation of such neutralization antibodies, which have been shown to limit the efficacy of gene transfer in humans.
ONLINE CLUSTERING ALGORITHMS (2008)

We introduce a set of clustering algorithms whose performance function is such that the algorithms overcome one of the weaknesses of K-means, its sensitivity to initial conditions which leads it to converge to a local optimum rather than the global optimum. We derive online learning algorithms and illustrate their convergence to optimal solutions which K-means fails to find. We then extend the algorithm by underpinning it with a latent space which enables a topology preserving mapping to be found. We show visualisation results on some standard data sets.
Cloning of a T Cell Growth Factor that Interacts with the β Chain of the Interleukin-2 Receptor (1994)

A cytokine was identified that stimulated the proliferation of T lymphocytes, and a complementary DNA clone encoding this new T cell growth factor was isolated. The cytokine, designated interleukin-15 (IL-15), is produced by a wide variety of cells and tissues and shares many biological properties with IL-2. Monoclonal antibodies to the beta chain of the IL-2 receptor inhibited the biological activity of IL-15, and IL-15 competed for binding with IL-2, indicating that IL-15 uses components of the IL-2 receptor.
Carbon‐flux distribution in the central metabolic pathways of Corynebacterium glutamicum during growth on fructose (1998)

Growth of Corynebacterium glutamicum on fructose was significantly less than that obtained on glucose, despite similar rates of substrate uptake. This was in part due to the production of overflow metabolites (dihydroxyacetone and lactate) but also to the increased production of CO2 during growth on fructose. These differences in carbon-metabolite accumulation are indicative of a different pattern of carbon-flux distribution through the central metabolic pathways. Growth on glucose has been previously shown to involve a high flux (> 50% of total glucose consumption) via the pentose pathway to generate anabolic reducing equivalents. NMR analysis of carbon-isotope distribution patterns of the glutamate pool after growth on 1-13C- or 6-13C-enriched fructose indicates that the contribution of the pentose pathway is significantly diminished during exponential growth on fructose with glycolysis being the predominant pathway (80% of total fructose consumption). The increased flux through glycolysis during growth on fructose is associated with an increased NADH/NAD+ ratio susceptible to inhibit both glyceraldehyde-3-phosphate dehydrogenase and pyruvate dehydrogenase, and provoking the overflow of metabolites derived from the substrates of these two enzymes. The biomass yield observed experimentally is higher than can be estimated from the apparent quantity of NADPH associated with the pentose pathway and the flux through isocitrate dehydrogenase, suggesting an additional reaction yielding NADPH. This may involve a modified tricarboxylic acid cycle involving malic enzyme, expressed to significantly higher levels during growth on fructose than on glucose, and a pyruvate carboxylating anaplerotic enzyme.
Activation of tumoricidal properties in human blood monocytes by liposomes containing lipophilic muramyl tripeptide. (1983)

Peripheral blood monocytes were isolated from normal human donors by separation on a continuous Percoll gradient and adherence to yield preparations of blood monocytes with a high degree of purity (greater than 99%). The monocytes were incubated in vitro with medium alone or with multilamellar liposomes that contained either a lipophilic derivative of muramyl dipeptide, muramyl tripeptide (MTP-PE), or medium. The cytotoxic properties of the monocytes were assessed by an in vitro radioisotope release assay against various allogeneic targets. Monocytes that have phagocytosed liposomes containing MTP-PE were rendered tumoricidal. These monocytes lysed cells of three different tumorigenic lines but not cells of two nontumorigenic lines. The ability of MTP-PE-activated human blood monocytes to recognize and selectively lyse neoplastic cells was also demonstrated under cocultivation conditions. We conclude that human blood monocytes can be rendered tumoricidal after interaction with liposomes containing MTP-PE.
Indirect tolerability comparison of Deutetrabenazine and Tetrabenazine for Huntington disease (2017)

ClinicalTrials.gov NCT01795859 and NCT00219804.
17β-Estradiol Decreases Endothelin-1 Levels in the Coronary Circulation of Postmenopausal Women With Coronary Artery Disease (2000)

Short-term intracoronary 17beta-estradiol administration decreases coronary endothelin-1 levels. There was no enhancement of vasomotor responses to SP after the administration of estrogen, suggesting that the effects of estrogen on coronary acetylcholine responses may be a specific and not a generalized effect on coronary vasoreactivity.
Functional human transcobalamin II isoproteins are secreted by insect cells using the baculovirus expression system (1993)

Transcobalamin II (TCII) is a cobalamin (Cbl, vitamin B12)-binding protein in mammalian plasma that facilitates the cellular uptake of the vitamin. To obtain human TCII in sufficient quantity for analytical studies, the complementary DNA (cDNA) encoding TCII was inserted into the plasmid PVL 1393, and the baculovirus expressing TCII was obtained by homologous recombination in Spodoptera frugiperda (SF9) insect cells by cotransfection with the wildtype virus. Under optimized conditions, SF9 cells infected with the recombinant virus secreted 2 to 4 micrograms of TCII per milliliter of culture medium. TCII did not accumulate in the SF9 cells and seemed to be constitutively secreted as observed previously in cultured human endothelial cells. The purified recombinant TCII has the same molecular weight by SDS-PAGE as purified human TCII. The recombinant TCII cross-reacts with an antiserum to native human TCII, binds Cbl and facilitates the uptake of Cbl in eukaryotic cells by binding to the receptor for TCII-Cbl on the plasma membrane of K562 cells. Amino acid sequence analysis of the purified recombinant TCII identified two polypeptides, one identical to the amino acid sequence deduced from the cDNA and a second lacking the first and second N-terminal residues. These sequences are identical to two TCII polypeptides purified from Cohn fraction III of pooled human plasma. The two forms of recombinant TCII have the same isoelectric points as the two predominant isoprotein forms of TCII in human serum. Since the baculovirus construct contains a single cDNA that can encode only one amino acid sequence, the two isoproteins in recombinant TCII must be generated by a mechanism other than allele specific expression. A plausible mechanism for generating isoproteins of nonglycosylated peptides, such as TCII, may be by splicing of the leader peptide at alternative sites.
A High-Plex PCR Approach for Massively Parallel Sequencing (2013)

Current methods for targeted massively parallel sequencing (MPS) have several drawbacks, including limited design flexibility, expense, and protocol complexity, which restrict their application to settings involving modest target size and requiring low cost and high throughput. To address this, we have developed Hi-Plex, a PCR-MPS strategy intended for high-throughput screening of multiple genomic target regions that integrates simple, automated primer design software to control product size. Featuring permissive thermocycling conditions and clamp bias reduction, our protocol is simple, cost- and time-effective, uses readily available reagents, does not require expensive instrumentation, and requires minimal optimization. In a 60-plex assay targeting the breast cancer predisposition genes PALB2 and XRCC2, we applied Hi-Plex to 100 ng LCL-derived DNA, and 100 ng and 25 ng FFPE tumor-derived DNA. Altogether, at least 86.94% of the human genome-mapped reads were on target, and 100% of targeted amplicons were represented within 25-fold of the mean. Using 25 ng FFPE-derived DNA, 95.14% of mapped reads were on-target and relative representation ranged from 10.1-fold lower to 5.8-fold higher than the mean. These results were obtained using only the initial automatically-designed primers present in equal concentration. Hi-Plex represents a powerful new approach for screening panels of genomic target regions.
Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes (1993)

The genes involved in the 2,3-butanediol pathway coding for alpha-acetolactate decarboxylase, alpha-acetolactate synthase (alpha-ALS), and acetoin (diacetyl) reductase were isolated from Klebsiella terrigena and shown to be located in one operon. This operon was also shown to exist in Enterobacter aerogenes. The budA gene, coding for alpha-acetolactate decarboxylase, gives in both organisms a protein of 259 amino acids. The amino acid similarity between these proteins is 87%. The K. terrigena genes budB and budC, coding for alpha-ALS and acetoin reductase, respectively, were sequenced. The 559-amino-acid-long alpha-ALS enzyme shows similarities to the large subunits of the Escherichia coli anabolic alpha-ALS enzymes encoded by the genes ilvB, ilvG, and ilvI. The K. terrigena alpha-ALS is also shown to complement an anabolic alpha-ALS-deficient E. coli strain for valine synthesis. The 243-amino-acid-long acetoin reductase has the consensus amino acid sequence for the insect-type alcohol dehydrogenase/ribitol dehydrogenase family and has extensive similarities with the N-terminal and internal regions of three known dehydrogenases and one oxidoreductase.
Constraint-based LSP setup by message reversing of CR-LDP (2002)

We investigate the problem of constraint-based routing that is one key component of traffic engineering. In constraint-based routing, resource information in addition to topology information is maintained in a database on all participating nodes in the routing domain. Especially the resource information of the links is changed rapidly because the bandwidth availability, for example, is changed whenever new LSPs are established and terminated. Therefore, the information used to compute a constraint-based path may be out-of-date. This means an LSP setup request may be blocked because a link or a node along the selected LSP has insufficient resources. This paper discusses the impact of inaccurate link state information, an LSP setup method coping with the inaccuracies, a new mechanism that allows constraint-based LSP setup and restoration, and gains obtained by our new mechanism.
Flow Equation for Foam Flowing Through Porous Media and Its Application as a Secondary Recovery Fluid (1977)

American Institute of Mining, Metallurgical, and Petroleum Engineers, Inc. Abstract A theoretical and experimental study of the flow of aqueous foam, of homogeneous and fine bubble size, through unconsolidated porous media is described. An equation was developed to describe the flow of non-Newtonian fluids through porous media and is confirmed experimentally using foam. In the light of the equation, the rheological properties of foam are studied experimentally. Externally generated foam, of known quality, was injected continuously into a porous medium. Both flow rate and pressure drop were measured. Foam is shown to behave as a single-body pseudoplastic fluid in unconsolidated porous media, With the help of experimental data, foam's apparent viscosity was calculated and is found to be increasing with the increase of foam quality. Experiments also were conducted to displace oil from unconsolidated linear sand packs using foam of different qualities. Foam's ability to displace oil from porous media was observed and was found to be better as compared with water. High-quality foam displaces oil at a relatively lower rate than low-quality foam. Compared with low-quality foam, less high-quality foam is required to displace the same amount of oil. Introduction In recent years, the aqueous foams have gained popularity in various petroleum operations because of their specific properties. Apart from enjoying application in oil wells as aerated drilling fluid and in workover and remedial well operations, foams, because of their flow-impeding nature, have potential use as a remedial fluid to combat coning and as corrective fluid to improve sweep of fluid injection processes in heterogeneous reservoirs. They also have been suggested as a way of preventing gas leakage through the cap rock of storage reservoirs. Foams have been used as a means of treating wells to reduce water or gas inflow during oil production. They are being used also as fracturing fluid for the stimulation of oil-bearing formation. Consideration of factors that operate to limit the recovery of oil by conventional mechanisms led to the development of secondary or tertiary oil recovery methods. The foamdrive method is one of them. Prompted by the known properties of foam, like its high apparent viscosity, attempts have been made in this study and by others to use foam as a secondary recovery fluid.
Costimulatory signals can selectively modulate cytokine production by subsets of CD4+ T cells. (1995)

Analysis of experimental animal models and human clinical samples has indicated that the selective activation of CD4+ T cell subsets with distinct profiles of cytokine production plays an important role in the pathogenesis of human inflammatory and allergic diseases. The possibility that differential activation of costimulatory pathways is a mechanism for selectively modulating cytokine production by CD4+ T cells was tested. The proliferative response and cytokines secreted by a panel of human CD4+ T cell clones, representative of Th1 or Th2/0 cells, in response to activation of different costimulatory pathways was measured. CD28-mediated costimulatory signals induced proliferation and IFN-gamma secretion by Th1 cells. Although CD28-ligation induced Th2/0 cells to proliferate, it did not trigger IL-4 production. Ligation of LFA-1 and CD45 isoforms also generated costimulatory signals activating cytokine secretion by the different types of T cell clones. Th1 cells secreted the same profile of cytokines, irrespective of which costimulatory pathway was engaged. However, the cytokine secreted by a subset of Th2/0 cells varied, depending upon which costimulatory pathways were activated. These results suggest that the costimulatory pathways activated by APCs can selectively influence cytokine production by CD4+ T cell subsets.
Target structures involved in natural killing (NK): characteristics, distribution, and candidate molecules. (1991)

Natural killer (NK) cells comprise an important immune effector population that has been implicated in surveillance against tumor metastases and virally infected host cells, suppression of the humoral immune response, and regulation of hematopoiesis. These diverse functions require an initial cognate interaction between the NK effector cell and the target cell of interest. This specific interaction triggers the secretion of NK factors (i.e., lymphokines, cytolytic substances) which mediate NK activity. The target structures (TS) that stimulate the NK response remain ill-defined. While apparent TS heterogeneity may contribute to the difficulty in isolating distinct NK-TS, the proposed multifactorial nature of the NK cell-target cell interaction may represent the major complexity in the search for specific TS. Adhesion molecules such as ICAM-1 and LFA-3 may strengthen, while MHC antigens may weaken, the NK cell-target cell interaction. The following article analyzes the molecular interactions currently held to be relevant in target cell recognition by NK cells.
Histidine-rich domain of the knob protein of the human malaria parasite Plasmodium falciparum. (1986)

Membranes of erythrocytes infected with the human malaria parasite Plasmodium falciparum develop protrusions called knobs. These structures are essential for the survival of the parasite in the host, and their induction requires the synthesis of the knob protein by the parasite. We describe the isolation of a cDNA clone encoding the amino-terminal half of the knob protein. A cDNA library was constructed from RNA prepared from ring stages of a P. falciparum isolate that has retained its ability to induce knobs (knob+ phenotype). A synthetic oligonucleotide probe encoding polyhistidine was used to isolate the cDNA clone, which encodes the amino-terminal half of a polypeptide with all the known attributes of the knob protein. The gene is not transcribed in variants that do not synthesize the knob protein and thereby cannot induce knobs (knob- phenotype). The apparent lack of transcription in knob- variants is due to different mechanisms: although the gene is present in one knob- isolate, it has been deleted in a cloned knob- variant. The primary structure of the polypeptide deduced from a partial sequence of the cDNA is distinctly different from other malarial histidine-rich polypeptides. The amino-terminal sequence shows the characteristic features of a signal peptide. This is followed by a histidine-rich domain and a subsequent region which contains one histidine. Peptide map analysis of the knob protein is consistent with the structural features deduced from the sequence analysis of the cDNA.
An overview of research using the one atmosphere uniform glow discharge plasma (OAUGDP) for sterilization of surfaces and materials (2000)

The medical, food processing, and heating, ventilating, and air conditioning industries are searching for improved pasteurization, disinfection, and sterilization technologies. Candidate techniques must deal with and overcome such problems as thermal sensitivity and destruction by heat, formation of toxic by-products, costs, and inefficiency in performance. We report the results of a plasma source, the One Atmosphere Uniform Glow Discharge Plasma (OAUGDP), which operates at atmospheric pressure in air and produces antimicrobial active species at room temperature, OAUGDP exposures have reduced log numbers of Gram negative and Gram positive bacteria, bacterial endospores, yeast, and bacterial viruses on a variety of surfaces. The nature of the surface influenced the degree of lethality, with microorganisms on polypropylene being most sensitive, followed by glass, and cells embedded in agar. Experimental results showed at least a 5 log/sub 10/ CFU reduction in bacteria within a range of 50-90 s of exposure. After 10-25 s of exposure, macromolecular leakage and bacterial fragmentation were observed. Vulnerability of cell membranes to reactive oxygen species (ROC) is hypothesized. Results from several novel OAUGDP configurations are presented, including a remote exposure reactor (RER) which uses transported active species to sterilize material located more than 20 cm from the plasma generation site, and a second planar electrode configuration developed for air filter sterilization. Applications of these technologies to the healthcare industry, the food industry, and decontaminating surfaces compromised by biological warfare agents are discussed.
Amniotic fluid cells and human stem cell research: a new connection. (2002)

Currently it is the hope of both patients and investigators that human progenitor cells and stem cells can be widely used to replace dysfunctional cells within a tissue. It is speculated that such cells may prove to have the potential to treat or cure a myriad of diseases, including Parkinson's and Alzheimer's diseases, heart disease, diabetes, stroke, spinal cord injuries, and burns. A major goal in this area of research is to identify potential new sources for the isolation of progenitor cells or stem cells, without raising the ethical issues involved in embryonic stem cell research. Despite the widespread and well-established use of amniotic fluid cells in routine prenatal genetic testing, current knowledge about the origin and properties of these cells is limited. A wide variety of different origins has been suggested for the mixture of cells within amniotic fluid. Recent observations on cell cultures from amniotic fluid and on amniotic epithelial cells provide evidence that they may represent new sources for the isolation of cells with the potency to differentiate into different cell types. Are these cells suitable for use as primary cell systems for basic research? Do these cells provide a new source for research on stem cell biology? Can amniotic fluid cells be used to develop new approaches in tissue engineering? In this article the authors review the current state of knowledge about these cells, focusing on these questions.
Noninfectious human immunodeficiency virus type 1 mutants deficient in genomic RNA (1990)

All retroviruses contain, in the nucleocapsid domain of the Gag protein, one or two copies of the sequence Cys-X2-Cys-X4-His-X4-Cys. We have generated a series of mutants in the two copies of this motif present in human immunodeficiency virus type 1. These mutants encoded virus particles that were apparently composed of the normal complement of viral proteins but contained only 2 to 20% of the normal level of genomic RNA. No infectivity could be detected in the mutant particles, while 10(5) infectious U were present in an equivalent amount of wild-type particles. Thus, the mutants have another defect in addition to the inefficiency with which they encapsidate genomic RNA. Our results show that both copies of the motif are required for normal RNA packaging and for infectivity. Mutants of this type may have important applications, including nonhazardous materials for research, immunogens in vaccine and immunotherapy studies, and diagnostic reagents.
Complementary dataset to "Nucleus: Finding the sharing limit of heterogeneous cores" (2017)

This dataset supports the article "Nucleus: Finding the sharing limit of heterogeneous cores", accepted for publication at the Transactions on Embedded Computing Systems (TECS) ACM journal