gebhart/patrepeval huggingface dataset:
Strategies targeting tumor necrosis factor in Crohn's disease. (2001)

Tumor necrosis factor plays an important role in mediating the inflammation of Crohn's disease. Strategies aimed at reducing tumor necrosis factor in patients with Crohn's disease include the mouse/human chimeric monoclonal antibody infliximab, the humanized monoclonal antibody CDP571, the human recombinant tumor necrosis factor receptor fusion protein etanercept, and the small molecule thalidomide. Infliximab is effective for treating active Crohn's disease, maintaining remission, and closing fistulas. Side effects occurring in patients treated with infliximab include human anti-chimeric antibodies, infusion reactions, formation of autoantibodies, and rarely drug induced lupus. CDP571 is effective for treating active Crohn's disease, steroid sparing, and possibly for closing fistulas and maintaining remission. Side effects occurring in patients treated with CDP571 include anti-idiotype antibodies, infusion reactions, and formation of autoantibodies. Pilot studies have suggested that etanercept and thalidomide may also be beneficial. Anti-tumor necrosis factor therapies are effective for the treatment for Crohn's disease.
Human embryonic stem cells differentiate into a homogeneous population of natural killer cells with potent in vivo antitumor activity (2009)

Natural killer (NK) cells serve as important effectors for antitumor immunity, and CD56+CD45+ NK cells can be routinely derived from human embryonic stem cells (hESCs). However, little is know about the ability of hESC-derived NK cells to mediate an effective in vivo antitumor response. Using bioluminescent imaging, we now demonstrate that H9 line hESC-derived NK cells mediate effective clearance of human tumor cells in vivo. In addition to increased in vitro killing of diverse tumor targets, the in vivo tumor clearance by H9 hESC-derived NK cells was more effective compared with NK cells derived from umbilical cord blood (UCB). Phenotypic analysis demonstrates the hESC-derived NK cells are uniformly CD94+CD117(low/-), an NK-cell population characterized by potent cytolytic activity and thus more competent to mediate tumor clearance. These studies demonstrate that hESCs provide an important model to study human lymphocyte development and may serve as a novel source for antitumor immunotherapy.
Effect of peroxisome proliiferators on intrachromosomal and interchromosomal recombination in yeast (1990)

Peroxisome proliferators are a class of non-mutagenic hepatocarcinogens, which induce a similar pleiotropic response such as hepatomegaly, proliferation of the peroxisomes in hepatocytes and hepatocarcinogenesis. Peroxisome proliferators are not detectable by the Ames assay and various other short-term tests. Recently a system for intrachromosomal recombination in yeast (DEL) has been shown to be inducible by a variety of non-mutagenic carcinogens. These include many carcinogens that are not detectable by the Ames assay or by various other short-term tests. In the present study the peroxisome proliferators [4-chloro-6-(2,3-xylidino)-2-pyrimidinyl-thio]acetic acid (Wy-14,643); methyl-2-[4-(p-chlorophenyl)phenoxy]2-methyl propionate (methyl clofenopate); 2-methyl-2[p-(1,2,3,4-tetrahydro-1- naphthyl)phenoxy]-propionic acid (nafenopin); 2-[4-(2,2-dichlorocyclopropyl)phenoxy]2-methyl-propionic acid (ciprofibrate); [4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio(N-beta-hydroxyethyl)-acetam ide] (BR-931); and ethyl alpha-p-chlorophenoxyisobutyrate (clofibrate) have been tested for their potential to induce DEL as well as interchromosomal recombination in yeast. No evidence for induction of either system has been found in the presence or the absence of the supernatant (S9) from rat liver homogenate. The data support the notion that peroxisome proliferators are truly non-mutagenic carcinogens.
Sugar Modified Oligonucleotides (1991)

Abstract The synthesis and enzymatic stability of oligonucleotides with 1-(2, 3-dideoxy-β-D-erythro-hexopyranosyl) thymine and (S)-9-(3,4-dihydroxybutyl)adenine as monomeric units are described.
A multicenter evaluation of assays for detection of SV40 DNA and results in masked mesothelioma specimens. (2001)

This nine-laboratory multicenter investigation was designed to assess the sensitivity, specificity, and reproducibility of previously described assays for detection of SV40 DNA with three goals, i.e., (a) to compare methods for testing human tissues, (b) to examine the ability of these methods to detect SV40 in human mesotheliomas, and (c) to uncover assay differences that could explain conflicting findings in some past investigations. Each laboratory received, in a masked fashion, paired replicate DNA samples extracted from 25 fresh frozen mesotheliomas (50 samples) and one from each of 25 normal human lungs. Interspersed were masked positive (titrations of the SV40 genome) and negative control samples. Preliminary studies confirmed the adequacy of the samples for testing high molecular weight double-stranded linear DNA targets. All 15 PCR-based assays detected 5,000 copies or less of the SV40 genome spiked into 2 microg of WI-38 DNA. A high level of specificity and reproducibility was found among the PCR assays performed in most laboratories. However, none of the selected normal human lung tissue or the 25 mesothelioma tumor specimens obtained from archival samples at a single center was reproducibly positive for the presence of SV40 DNA. Further studies are needed to reconcile these results with previous reports of detection of SV40 DNA in tumor specimens.
A Critical Evaluation of New Agents for the Treatment of Sepsis (1991)

OBJECTIVE - To evaluate new treatments directed against endotoxin, tumor necrosis factor alpha, and interleukin 1 for use in sepsis and related disorders (sepsis syndrome and septic shock). DATA SOURCES - Investigations of these treatments in animal models, healthy human volunteers, and patients with sepsis and related disorders. STUDY SELECTION - Particular attention was paid to studies of patients with sepsis and related disorders, especially randomized, double-blind, controlled trials. DATA EXTRACTION - Animal studies and investigations with human volunteers were judged by how closely the experimental model replicated the clinical disorder (sepsis). Patient trials were assessed by sample size and design. Results of all studies were used to evaluate the likelihood that a given treatment would reduce mortality. DATA SYNTHESIS - Direct comparison of E5 and HA-1A antibody studies is difficult because of differences in their design, definitions of shock, and methods of subgroup analysis. However, both antibodies improve outcome in some subgroups: E5 benefits patients with gram-negative infection (bacteremic or focal) who do not have refractory shock, and HA-1A benefits those with gram-negative bacteremia (regardless of whether shock is present) but not those with focal gram-negative infection. Two agents that may be beneficial in gram-positive and gram-negative infection are monoclonal antibodies to tumor necrosis factor alpha and receptor antagonists to interleukin 1. Preliminary results with both are reviewed. CONCLUSIONS - All three types of treatment may improve outcome in sepsis. The best results will probably be obtained with combination therapy that interrupts multiple points of the inflammatory cascade underlying sepsis.
Autologous Fibrin Gel (1991)

Fibrin glue is an effective hemostatic agent in a variety of clinical situations; its utility is limited by potential transmission of viral infection. We studied the bactericidal properties of fibrin gel (FG) in a murine contaminated hepatic injury model and in vitro by agar plate culture method. Intra-abdominal abscess formation and adhesion rate were assessed following controlled liver injury in association with abdominal contamination with 10(7) Bacteroides fragilis and hepatorrhaphy (H, n = 15) or FG (n = 12). Animals treated by hepatorrhaphy had a significantly greater intra-abdominal abscess rate (15/15 vs. 4/12, p less than 0.05) and adhesion rate (14/15 vs. 6/12, p less than 0.05) than animals treated with FG. Fibrin gel is bactericidal to Bacteroides fragilis, Enterobacter faecium, Escherichia coli, and Staphylococcus aureus but has no effect against Klebsiella pneumoniae or Pseudomonas aeruginosa; the plasma component appears active. Fibrin gel demonstrates significant improvement in adhesion formation and intra-abdominal abscess rate when compared with suture hepatorrhaphy. Fibrin gel appears protective in contaminated hepatic injury.
Application of HIV-1-green fluorescent protein (GFP) reporter viruses in neutralizing antibody assays. (2001)

We made reporter HIV-1 DNA constructs carrying green fluorescent protein (GFP) gene and exchangeable env of subtype E. The recombinant constructs were used to produce infectious reporter viruses, which induced infected cells to emit green fluorescent light and rendered them easily detectable at single cell level. Because the env in this construct can be easily exchanged, viruses with different antigenic epitopes can be made. We used these reporter viruses to set up a neutralizing antibody assay based on fluorescence reduction by flow cytometric measurement. The result of this new assay correlated with the standard infectivity reduction assay using primary isolates. Because this new assay is faster and much less costly than the standard assay using a p24 endpoint and can be performed in peripheral blood mononuclear cells (PBMC), it provides a useful tool for analysis of HIV-1 immune responses.
Alpha‐generation as basic response‐signature to transcranial magnetic stimulation (TMS) targeting the human resting motor cortex: A TMS/EEG co‐registration study (2011)

The effects of repetitive transcranial magnetic stimulation (rTMS) on cortical excitability are usually inferred from indirect indexes, such as EMG responses. It has now become possible to directly evaluate rTMS impact by means of concurrent EEG recording. The aim of this study was to examine the modulation induced by high frequency rTMS (20 Hz) over left primary motor cortex on the ongoing oscillatory activity. Thirteen subjects underwent two sham and a real rTMS session while acquiring EEG. Event-related desynchronization/synchronization was calculated for the α and β bands. rTMS induced a dose-dependent increase in synchronization in both bands over central and parietal sites. The strongest effect found for the α band outlasted the end of the stimulation. Considering previous studies, our data suggest that α generation may represent an intrinsic induced response and a basic response signature to TMS targeting the human resting motor cortex.
Filter Paper Disc Modification of the Oxford Cup Penicillin Determination. (1944)

At the present time biological assay methods are the sole means of determining penicillin potency. A number of such methods are in use in various laboratories; however, the Oxford cup method, with several modifications, has continued to be regarded as a procedure in which a commensurate accuracy and speed may be obtained with a minimum of labor. The following filter paper disc modification should reduce the labor and time involved in setting up this test, while the case with which extra replicates may be run should increase the test's accuracy.The principal modification lies in the use of a thick filter paper disc saturated with the penicillin sample, substituted for the sample-containing small cylinder used in the Oxford cup method. These discs may be conveniently set up on the seeded plates at a rate of about 6 per minute, a rate considerably more rapid than that in the original method. Another advantage of the discs is that the test plates may be manipulated freely to facilitate reading. Experience with a large number of tests has indicated that the zones of inhibition obtained with the discs are more consistent and more sensitive to variations in the penicillin content of the sample than the zones obtained with the cup method. This improvement may be due to a more consistent contact of the penicillin solution with the agar and to a more even diffusion from the disc.The test organism, Staphylococcus aureus H (Oxford strain), tends to produce a somewhat granular growth in nutrient broth. With the use of peptone broth as the seeding medium, a more diffuse growth is obtained and this in turn effects a more even seeding of the test plates.
Hepatitis C Virus Glycoproteins Interact with DC-SIGN and DC-SIGNR (2003)

DC-SIGN and DC-SIGNR are two closely related membrane-associated C-type lectins that bind human immunodeficiency virus (HIV) envelope glycoprotein with high affinity. Binding of HIV to cells expressing DC-SIGN or DC-SIGNR can enhance the efficiency of infection of cells coexpressing the specific HIV receptors. DC-SIGN is expressed on some dendritic cells, while DC-SIGNR is localized to certain endothelial cell populations, including hepatic sinusoidal endothelial cells. We found that soluble versions of the hepatitis C virus (HCV) E2 glycoprotein and retrovirus pseudotypes expressing chimeric forms of both HCV E1 and E2 glycoproteins bound efficiently to DC-SIGN and DC-SIGNR expressed on cell lines and primary human endothelial cells but not to other C-type lectins tested. Soluble E2 bound to immature and mature human monocyte-derived dendritic cells (MDDCs). Binding of E2 to immature MDDCs was dependent on DC-SIGN interactions, while binding to mature MDDCs was partly independent of DC-SIGN, suggesting that other cell surface molecules may mediate HCV glycoprotein interactions. HCV interactions with DC-SIGN and DC-SIGNR may contribute to the establishment or persistence of infection both by the capture and delivery of virus to the liver and by modulating dendritic cell function.
In Vitro Experimental Research of Rabbit Condrocytes Biostimulation with Diode Laser Ga-Ai-As: A Preliminary Study (1998)

The scope of our study was to verify the effects of a new diode laser device with active material composed of Gallium, Aluminum and Arsenic (Ga-Al-As) configured as MOCVD (780 nm., 3000 mW) for the biostimulation of the cartilage cells in vitro. The condrocytes cells, withdrawn from the cartilage of the medial condyle of the femur of the rabbit, were cultivated, incubated and subject to biostimulation treatment with the laser. The condrocytes cells were placed in 24 Petri dishes at the concentration of 0.25 x 10(5)/ml and divided into 4 groups: 3 group (I, II, III) were treated with the laser and the fourth group (IV) was used as the control group. At the end of the treatment, all four groups, were evaluated with a MTT test and a cell count of the condrocytes cells. Group III (300 J, 1 Watt, 300 Hz, 10' of exposure time with a pulsating emission) provided the best results in terms of cell viability (MTT test) and for the number of cells found in the dishes when compared to the other treated groups and the control group. The results obtained with the use of this new diode laser Ga-Al-As device in the biostimulation of the cartilage tissue, permits us to consider the use of this device clinically.
An extensible genetic algorithm framework for problem solving in a common environment (2000)

The authors describe an object-oriented framework for solving mathematical power system programs using genetic algorithms (GAs). The advantages of this framework are its extensibility, modular design and accessibility to existing programming code. The framework also incorporates a graphical user interface that may be used to build new GAs as well as run GA simulations. Two power system problems are solved by implementing genetic algorithms using the said framework. The first is a continuous optimization problem and the second an integer programming problem. The authors illustrate the flexibility of the framework as well as its other features on their test problems.
Catabolism of the Murine IgGl Molecule: Evidence that Both CH2‐CH3 Domain Interfaces are Required for Persistence of IgGl in the Circulation of Mice (1994)

Site-directed mutagenesis of a recombinant Fc-hinge fragment has previously been used to identify a region of the murine IgG1 molecule that controls catabolism, and this site encompasses amino acid residues at the interface of the CH2 and CH3 domains. In the current study the nature of this 'catabolic site' has been further analysed using recombinant techniques. Fc-hinge, CH2-hinge, CH2 and CH3 fragments have been expressed in Escherichia coli, purified and analysed in pharmacokinetic studies in mice. The CH2-hinge has been analysed as both a monomer and dimer, and the dimer has a longer beta phase half-life (61.6 h) than the monomer (29.1 h). This suggests that two catabolic sites per Fc fragment are required for serum persistence. The need for two functional sites per molecule has been confirmed by the analysis of a hybrid Fc-hinge fragment comprising a heterodimer of one Fc-hinge with the wild type (WT) IgG1 sequence and a mutant Fc-hinge with a defective catabolic site (mutated at His310, Gln311, His433 and Asn434). This hybrid is cleared with a beta phase half-life of 37.9 h and this is significantly shorter than that of the WT Fc-hinge fragment (82.9 h). In contrast to the CH2-hinge dimer, the CH3 domain is cleared rapidly (beta phase half-life of 21.3 h) indicating that the region of this domain (His433 and Asn434) previously identified as being involved in the control of catabolism is not sufficient in the absence of the CH2 domain for the serum persistence of an IgG fragment. The data extend our earlier observations concerning a region of the murine IgG1 molecule that is involved in the control of catabolism and have implications for the design of engineered antibodies for therapy.
A Proprotein Convertase Subtilisin-like/Kexin Type 9 (PCSK9) C-terminal Domain Antibody Antigen-binding Fragment Inhibits PCSK9 Internalization and Restores Low Density Lipoprotein Uptake (2010)

PCSK9 binds to the low density lipoprotein receptor (LDLR) and leads to LDLR degradation and inhibition of plasma LDL cholesterol clearance. Consequently, the role of PCSK9 in modulating circulating LDL makes it a promising therapeutic target for treating hypercholesterolemia and coronary heart disease. Although the C-terminal domain of PCSK9 is not involved in LDLR binding, the location of several naturally occurring mutations within this region suggests that it has an important role for PCSK9 function. Using a phage display library, we identified an anti-PCSK9 Fab (fragment antigen binding), 1G08, with subnanomolar affinity for PCSK9. In an assay measuring LDL uptake in HEK293 and HepG2 cells, 1G08 Fab reduced 50% the PCSK9-dependent inhibitory effects on LDL uptake. Importantly, we found that 1G08 did not affect the PCSK9-LDLR interaction but inhibited the internalization of PCSK9 in these cells. Furthermore, proteolysis and site-directed mutagenesis studies demonstrated that 1G08 Fab binds a region of beta-strands encompassing Arg-549, Arg-580, Arg-582, Glu-607, Lys-609, and Glu-612 in the PCSK9 C-terminal domain. Consistent with these results, 1G08 fails to bind PCSK9DeltaC, a truncated form of PCSK9 lacking the C-terminal domain. Additional studies revealed that lack of the C-terminal domain compromised the ability of PCSK9 to internalize into cells, and to inhibit LDL uptake. Together, the present study demonstrate that the PCSK9 C-terminal domain contribute to its inhibition of LDLR function mainly through its role in the cellular uptake of PCSK9 and LDLR complex. 1G08 Fab represents a useful new tool for delineating the mechanism of PCSK9 uptake and LDLR degradation.
Development of a Novel Thiol Reagent for Probing Ion Channel Structure:  Studies in a Model System (1997)

We have synthesized a novel thiol reagent, 2-[(methylsulfonyl)thio]ethyl [N-(N,N-dimethylamino)ethyl]carbamate (MTSAC), that contains a carbamate functional group as well as a (positively charged) terminal amino group. The carbamate C-N bond isomerizes on a millisecond time scale and significantly alters the three-dimensional shape of the reagent. The behavior of this reagent was contrasted with that of the commonly used thiol reagent, [(methylsulfonyl)thio]ethylamine MTSEA [Akabas, M. H., & Karlin, A. (1995) Biochemistry 34, 12496-12500], with respect to its effect on single-channel currents passing through modified gramicidin channels. While both reagents decreased single-channel currents, the MTSAC-treated channels also showed a pattern of steps in the current recordings on the time scale of the carbamate bond isomerization. Moreover, the pattern and size of these steps were sensitive to the location of the thiol-reactive site in relation to the channel entrance. Thus, MTSAC may prove useful as a reagent for establishing the proximity to the pore in studies of ion channel proteins of unknown structure.
Insulin-expressing engineered cell lines and primary cells: surrogate β cells from liver, gut, and other sources (2007)

The major challenge associated with insulin gene therapy in non-β cells is to achieve rapid, glucose-responsive secretion, while transdifferentiation approaches require additional characterization of the function and stability of insulin-producing cells. Continued efforts in these areas are warranted, as re-establishment of endogenous insulin production would be a welcome replacement to insulin injections for diabetes treatment.
SUBTRACTION HYBRIDIZATION - AN APPROACH TO THE ISOLATION OF GENES DIFFERENTIALLY EXPRESSED IN CANCER AND OTHER BIOLOGICAL-SYSTEMS (1992)

Subtraction hybridization allows for the isolation and identification of genes which are differentially expressed in different cell types. It allows for such isolation without any a priori knowledge of the sequence or function of the target gene. The only requirement is that there be a difference in the relative abundance of the nucleic acid (mRNA or genomic DNA) in the two cell types being compared. In contrast to differential hybridization, cDNA clones representing mRNAs of very low abundance (0.001% to 0.1%) can be discerned using subtraction hybridization. The concept, applications and techniques of performing subtraction hybridization is discussed.
Role of p53 and p16 gene alterations in determining response to concurrent paclitaxel and radiation in solid tumor. (1999)

Molecular genetic alterations that disturb cell cycle regulation in tumor cells can affect their response to chemotherapeutic agents and radiation. Many genes that regulate the critical cell cycle checkpoint at G1S are altered in human tumors. These genetic changes can result in uncontrolled cellular proliferation, genetic instability, and altered response to radiation and chemotherapy. The p53 tumor suppressor gene serves a critical role at the G1S transition, where it can either block entry into S phase or activate programmed cell death (apoptosis) in response to DNA damage. p53 Gene mutations are common in human tumors and interfere with the activation of apoptosis in response to most chemotherapeutic agents. Paclitaxel is a potent chemotherapeutic agent that interferes with mitotic spindle function to block cells at G2M, the most radiosensitive phase of the cell cycle. Utilization of paclitaxel as a radiation sensitizer in vivo to treat aggressive, locally advanced neoplasms has resulted in high response rates and acceptable toxicity in protocols for non-small cell lung carcinoma, upper gastrointestinal tract carcinoma, and other malignancies. Recent evidence suggests that paclitaxel is unique in its ability to activate apoptosis in tumor cells with p53 mutations in vitro and in vivo. The p16(INK4a) (MTS-1, CDKN2) gene product acts in the same pathway as p53 to inhibit cell cycle progression at G1/S. p16(INK4a) is deleted and/or mutated in a significant fraction of human tumors, including pancreatic carcinoma. The effects of p16(INK4a) alterations in response to paclitaxel/radiation and the risk of systemic relapse are currently being evaluated. Information about molecular genetic alterations in individual tumors ultimately may be a critical factor in choosing between therapeutic options.