gebhart/patrepeval huggingface dataset:
Biotin-Avidin Microplate Assay for the Quantitative Analysis of Enzymatic Methylation of DNA by DNA Methyltransferases (2000)

An assay is described to measure methylation of biotinylated oligonucleotide substrates by DNA methyltransferases using [methyl-3H]-AdoMet. After the methylation reaction the oligonucleotides are immobilized on an avidin-coated microplate. The incorporation of [3H] into the DNA is quenched by addition of unlabeled AdoMet to the binding buffer. Unreacted AdoMet and enzyme are removed by washing. To release the radioactivity incorporated into the DNA, the wells are incubated with a non-specific endonuclease and the radioactivity determined by liquid scintillation counting. As an example, we have studied methylation of DNA by the EcoRV DNA methyltransferase. The reaction progress curves measured with this assay are linear with respect to time. Methylation rates linearly increase with enzyme concentration. The rates are comparable to results obtained with the same enzyme using a different assay. The biotin-avidin assay is inexpensive, convenient, quantitative, fast and well suited to process many samples in parallel. The accuracy of the assay is high, allowing to reproduce results within +/- 10%. The assay is very sensitive as demonstrated by the detection of incorporation of 0.8 fmol methyl groups into the DNA. Under the experimental conditions, this corresponds to methylation of only 0.03% of all target sites of the substrate. Using this assay, the DNA methylation activity of some M.EcoRV variants could be detected that was not visible by other in vitro methylation assays.
Non-Resonant Multiphoton Photoacoustic Spectroscopy for Noninvasive Subsurface Chemical Diagnostics (2004)

This paper describes the development and validation of a novel noninvasive spectroscopic subsurface chemical detection technique, non-resonant multiphoton photoacoustic spectroscopy (NMPPAS). In this technique, non-resonant multiphoton excitation is used to provide subsurface excitation of chemical constituents in a sample followed by the subsequent detection of an acoustic signal using a piezoelectric transducer. Because NMPPAS relies on non-radiative relaxation of the absorbing species, it is capable of monitoring both fluorescent and non-fluorescent species. Moreover, since the majority of the energy imparted to most molecules upon the absorption of light is released through non-radiative pathways, sensitive measurements of even fluorescent molecules can be performed. In this paper, demonstration of proof-of-principle of this novel technique has been shown using test samples of common fluorescent dyes and biomarkers including rhodamine 6G, tryptophan, and NADH in solution and gelatin tissue phantoms. From these studies, it was found that detection limits of these chromophores are in the subnanomolar concentration regime. In addition, preliminary results on excised tumor and healthy tissue samples have demonstrated significant differences between the tumorous and non-tumorous tissues at 740 nm and 950 nm wavelengths. From this work, it was found that NMPPAS has a great deal of potential for subsurface chemical diagnostics in the field of biomedical research.
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value (2008)

Our method is implemented in the freely available R package 'MAclinical' which can be downloaded from http://www.stat.uni-muenchen.de/~socher/MAclinical
Replicating vectors for cancer therapy: a question of strategy. (1994)

Direct gene transfer to tumor cells in vivo may have considerable therapeutic potential, provided that a high enough efficiency of gene delivery can be achieved. All other things being equal (e.g. dose, route of administration), a replicating vector should give a higher efficiency of gene transfer than a nonreplicating vector due to local spread from the initially transduced cells. Almost any virus could provide the basis for a replicating gene transfer vector but, for the treatment of human cancer, the choice is greatly constrained by issues of public safety and potential efficacy. Public safety considerations point to viruses of low pathogenicity which are already prevalent in the human population whilst efficacy considerations point to viruses which replicate efficiently in the tumor cells to be targeted. Additional factors influencing the suitability of individual viruses as a basis for replicating vectors include the availability of an infectious molecular clone, the capacity for foreign gene insertion, genomic stability, potential for targeting by coat protein engineering or promoter engineering, cell-cycle dependence and availability of an effective vaccine.
Zidovudine-resistant human immunodeficiency virus selected by passage in cell culture (1991)

Variants of human immunodeficiency virus (HIV) with reduced sensitivity to zidovudine (3'-azido-3'-deoxythymidine) have been selected by passage of virus in cell culture in the presence of drug. Wild-type, sensitive virus became partially resistant to zidovudine by passage 12 (50% inhibitory dose values measured in HeLa CD4+ cells increased from 0.014 to 0.2 microM), and genetic analysis using the polymerase chain reaction revealed that mutations in the reverse transcriptase coding region identical to those seen in clinical isolates from treated individuals had occurred. The order of appearance of these resistance mutations in passaged virus was also similar to that in clinical isolates. The partially resistant strain, HIVRTMC/F, became highly zidovudine resistant by passage 12 (50% inhibitory dose values increased from 0.4 to 2.5 microM during passages 7 to 11). Nucleotide sequence analysis of the reverse transcriptase from this variant revealed a novel amino acid substitution (Lys----Glu) at codon 219. A different substitution at this codon (Lys----Gln) had been seen previously in clinical isolates. When this mutation was created in HIVRTMC/F by site-directed mutagenesis, the resulting partially resistant virus became highly resistant, thus confirming the significance of this change. In view of the possibility that this mutation might occur in HIV isolates during treatment of patients, we adapted our selective polymerase chain reaction procedure to enable screening for this change in clinical samples. The virus passage procedure described here may be useful for gaining further insight into the mutational events occurring during the development of resistance to zidovudine and other HIV inhibitors.
What Is the Point? How Point-of-Care Sexually Transmitted Infection Tests Can Impact Infected Patients (2010)

Point-of-care (POC) tests are an important strategy to address the epidemic of sexually transmitted infections (STIs) among both adolescents and young adults. While access to care and confidentiality are major barriers to STI care, POC tests allow the clinician to provide immediate and confidential test results and treatment. In addition, POC test results constitute a "teachable moment"; that is, an opportunity to provide immediate feedback to the patient that may impact his/her risk behaviors. This paper reviews published data and manufacturer's product literature describing current point-of-care STI tests, including studies of test performance as well as impact on treatment intervals and disease spread. It presents theoretical and proposed pitfalls and solutions of implementing POC tests in clinical settings, non-traditional settings, and home care venues. We reviewed the available STI tests according to the World Health Organization (WHO) criteria for judging POC tests: the "ASSURRED" criteria (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, Delivered).
Infection in sickle cell disease: A review (2009)

Infection is a significant contributor to morbidity and mortality in sickle cell disease (SCD). The sickle gene confers an increased susceptibility to infection, especially to certain bacterial pathogens, and at the same time infection provokes a cascade of SCD-specific pathophysiological changes. Historically, infection is a major cause of mortality in SCD, particularly in children, and it was implicated in 20-50% of deaths in prospective cohort studies over the last 20 years. Worldwide, it remains the leading cause of death, particularly in less developed nations. In developed countries, measures to prevent and effectively treat infection have made a substantial contribution to improvements in survival and quality of life, and are continually being developed and extended. However, progress continues to lag in less developed countries where the patterns of morbidity and mortality are less well defined and implementation of preventive care is poor. This review provides an overview of how SCD increases susceptibility to infections, the underlying mechanisms for susceptibility to specific pathogens, and how infection modifies the outcome of SCD. It also highlights the challenges in reducing the global burden of mortality in SCD.
Genetic characterization of the secretory mutant MS‐1 of Tetrahymena thermophila: Vacuolarization and block in secretion of lysosomal hydrolases are caused by a single gene mutation (1992)

The genetics and phenotypic features (light and electron microscopy) of a secretory mutant, MS-1 of Tetrahymena thermophila blocked in secretion of lysosomal acid hydrolases have been analyzed. Although blocked constitutively in secretion, MS-1 contains active lysosomal hydrolases in amounts equivalent to the wild type. The 3:1 segregation in F-2 in sib crosses and the 1:1 segregation in test crosses indicate that the block in secretion of lysosomal hydrolases is controlled by a recessive single gene locus termed sec. The sec allele of MS-1 proved also to be responsible for the highly vacuolarized phenotype the mutant developed when it was transferred from nutrient medium into buffers of low ionic strength. Deletion mapping by crossing MS-1 with nullisomic strains, all secreting lysosomal hydrolases at wild-type rates, was performed. The sec phenotype was expressed in monosomic-4 progeny only, indicating that the sec allele is located on chromosome 4 of T. thermophila.
When there is no single best biological agent: psoriasis and psoriatic arthritis in the same patient responding to two different biological agents (2008)

Guidelines and treatment strategies for the new biological agents have been developed, but dermatologists continue to face difficulties in adopting these guidelines into their daily practices. We report a patient with psoriasis and psoriatic arthritis whose skin lesions responded only to efalizumab, and the arthritis to etanercept. This case shows that different biological agents may achieve different success rates even in the same patient. Each biological agent offers different advantages and disadvantages, which sometimes make it difficult to choose the single best agent for a patient. Psoriasis often becomes one of the most difficult diseases to treat and does not respond to any single antipsoriatic agent. Perhaps in the future, rotational or combination treatment with different biological treatments will be used.
Intramolecular coupling of active sites in the pyruvate dehydrogenase multienzyme complex of Escherichia coli (1978)

The intramolecular passage of substrate between the component enzymes of the pyruvate dehydrogenase multienzyme complex of Escherichia coli was examined. A series of partly reassembled complexes, varying only in their E1 (pyruvate decarboxylase, EC 1.2.4.1) content, was incubated with pyruvate in the absence of CoA, conditions under which the lipoic acid residues covalently bound to the E2 (lipoate acetyltransferase, EC2.3.1.12) chains of the complex become reductively acetylated, and the reaction then ceases. The fraction of E2 chains thus acetylated was estimated by specific reaction of the thiol groups in the acetyl-lipoic acid moieties with N-ethyl[2,3-14C]maleimide. The simplest interpretation of the results was that a single E1 dimer is capable of catalysing the rapid acetylation of 8-12 E2 chains, in good agreement with the results of Bates, Danson, Hale, Hooper & Perham [(1977) Nature (London) 268, 313-316]. This novel functional connexion of active sites must be brought about by transacetylation reactions between lipoic acid residues of neighbouring E2 chains in the enzyme complex. There was also a slow transacylation process between the rapidly acetylated lipoic acid residues and those that did not react in the initial, faster phase. This interaction was not investigated in detail, since it is too slow to be of kinetic significance in the normal enzymic reaction.
The Management of Cerebral Edema in Pediatric Practice (1976)

Cerebral edema is one of the most dreaded complications associated with many central nervous system (CNS) disorders. The condition adds significantly to the morbidity from such diverse conditions as neonatal hypoxia and hypernatremia, water intoxication, meningitis, encephalitis, birth trauma, lead poisoning, and radiation therapy of the brain, as well as brain tumors and abscesses. Cerebral edema increases the volume of the intracranial contents and, thus, may precipitate the intracranial translocation syndromes of uncal and tonsillar herniation which often result in death. Indeed, the mass effect due to edema of the CNS tissue (brain, cord) is often more harmful than is that of the underlying blood clot, tumor, or other pathologic process (Fig. 1). Diffuse and widespread cerebral edema can produce massive increases in intracranial pressure. The successful treatment of cerebral edema, therefore, remains a matter of paramount importance and may have a critical effect upon the patient's prognosis. Two types of therapeutic measures must be considered: (1) those that diminish the volume of intracranial contents in a nonspecific manner, and (2) those that reduce cerebral edema per se. An understanding of their correct use is essential.1,2 Prevention of cerebral edema is, of course, preferable to treating it. In infants and children undergoing neurosurgical operations, preoperative prophylactic measures can be instituted to reduce the magnitude of postoperative cerebral edema. In most situations, however, therapy cannot be initiated before the edema-producing insult occurs. Nevertheless, steps to minimize the development of cerebral edema often may be taken, and these will be discussed. Cerebral edema has been defined as the abnormal accumulation of fluid in cerebral tissue.
Effects of Eplerenone, Enalapril, and Eplerenone/Enalapril in Patients With Essential Hypertension and Left Ventricular Hypertrophy (2003)

Eplerenone was as effective as enalapril in LVH regression and blood pressure control. The combination of eplerenone and enalapril was more effective in reducing LV mass and systolic blood pressure than eplerenone alone.
Preparation of Newcastle Disease Virus Hemagglutination-Inhibition Test Antigen (1975)

A method of preparing antigen for Newcastle hemagglutination-inhibition (HI) tests is described; polyethylene glycol precipitation is used for the virus concentration. The virus was inactivated with either formalin or beta-propiolactone. Glycerin was used to stabilize the hemagglutinin activity of the antigen. The stability, uninfectivity, and slow eluting features of the antigen should aid in obtaining accurate HI results without the risks inherent in the use of live virus.
Mast cell expression of gelatinases A and B is regulated by kit ligand and TGF-beta. (1999)

Our prior work shows that cultured BR cells derived from dog mastocytomas secrete the 92-kDa proenzyme form of gelatinase B. We provided a possible link between mast cell activation and metalloproteinase-mediated matrix degradation by demonstrating that alpha-chymase, a serine protease released from secretory granules by degranulating mast cells, converts progelatinase B to an enzymatically active form. The current work shows that these cells also secrete gelatinase A. Furthermore, gelatinases A and B both colocalize to alpha-chymase-expressing cells of canine airway, suggesting that normal mast cells are a source of gelatinases in the lung. In BR cells, gelatinase B and alpha-chymase expression are regulated, whereas gelatinase A expression is constitutive. Progelatinase B mRNA and enzyme expression are strongly induced by the critical mast cell growth factor, kit ligand, which is produced by fibroblasts and other stromal cells. Induction of progelatinase B is blocked by U-73122, Ro31-8220, and thapsigargin, implicating phospholipase C, protein kinase C, and Ca2+, respectively, in the kit ligand effect. The profibrotic cytokine TGF-beta virtually abolishes the gelatinase B mRNA signal and also attenuates kit ligand-mediated induction of gelatinase B expression, suggesting that an excess of TGF-beta in inflamed or injured tissues may alter mast cell expression of gelatinase B, which is implicated in extracellular matrix degradation, angiogenesis, and apoptosis. In summary, these data provide the first evidence that normal mast cells express gelatinases A and B and suggest pathways by which their regulated expression by mast cells can influence matrix remodeling and fibrosis.
[Chitin of mycelial fungi of the genus Penicillium]. (1979)

The effect of the nutrient medium and cultivation conditions on the chitin content in cell walls of mycelial fungi of the Penicillium genus was studied. The chitin accumulation was influenced by the composition and quantity of carbon and nitrogen sources, acidity of the medium, aeration rate and age of the culture. The highest content of chitin in the strains studied was no more than 4--5%. The paper discusses the potential use of the fungi P. digitatum 24 P, P. notatum 1 f, P. terikowskii and P. claviforme as protein producers. It describes the procedure for measuring chitin in cell walls of mycelial fungi.
Endocytotic uptake of small unilamellar liposomes by human trophoblast cells in culture (1997)

We evaluated the mechanism of uptake of carboxyfluorescein-containing small unilamellar liposomes of different surface charge by trophoblast cells in culture. Carboxyfluorescein-encapsulated neutral liposomes were prepared by using equimolar concentrations of lecithin and cholesterol. Anionic and cationic liposomes were prepared by adding dicetylphosphate and stearylamine. Trophoblast cells from human term placenta were cultured and incubated on the first day at 37 degrees C with liposome-encapsulated carboxyfluorescein or 500 nM of free carboxyfluorescein. The mechanism of uptake was determined by pre-treating the cells with metabolic inhibitors: 2 mM of sodium azide and 25 mM of deoxyglucose for 30 min. The uptake of liposomes was also evaluated both qualitatively under fluorescent microscope and quantitatively by measuring carboxyfluorescein fluorometrically. The uptake of free carboxyfluorescein and cationic liposomes was comparable. The anionic liposomes were taken up by the trophoblast cells more avidly than the neutral (13.2 +/- 1.6 versus 9.5 +/- 1.4%; P <0.01), cationic (2.9 +/- 0.4%; P <0.001) and the free carboxyfluorescein (2.1 +/- 0.9%; P <0.01). When cells were pre-treated with metabolic inhibitors, the uptake of anionic (5.9 +/- 1.8%; P <0.001) and neutral liposomes (4.0 +/- 0.8%; P <0.01) was significantly reduced, whereas uptake of cationic and free carboxyfluorescein remained unaltered. This study indicates that small unilamellar liposomes are internalized by the trophoblast cells in culture by an energy-dependent pathway; most probably by endocytosis. The neutral and anionic liposomes are internalized more avidly than cationic liposomes.
Short and Stereoselective Total Synthesis of Furano Lignans (±)-Dihydrosesamin, (±)-Lariciresinol Dimethyl Ether, (±)-Acuminatin Methyl Ether, (±)-Sanshodiol Methyl Ether, (±)-Lariciresinol, (±)-Acuminatin, and (±)-Lariciresinol Monomethyl Ether and Furofuran Lignans (±)-Sesamin, (±)-Eudesmin, (±)-Piperitol Methyl Ether, (±)-Pinoresinol, (±)-Piperitol, and (±)-Pinoresinol Monomethyl Ether by Radical Cyclization of Epoxides Using a Transition-Metal Radical Source (2002)

Intramolecular radical cyclization of suitably substituted epoxy ethers 4a-g using bis(cyclopentadienyl)titanium(III) chloride as the radical source resulted in trisubstituted tetrahydrofurano lignans and 2,6-diaryl-3,7-dioxabicyclo[3.3.0]octane lignans depending on the reaction conditions. The titanium(III) species was prepared in situ from commercially available titanocene dichloride and activated zinc dust in THF. Upon radical cyclization followed by acidic workup, epoxy olefinic ethers 4a-g afforded furano lignans dihydrosesamin 1a, lariciresinol dimethyl ether 1b, acuminatin methyl ether 1e, and sanshodiol methyl ether 1g directly and lariciresinol 1h, acuminatin 1i, and lariciresinol monomethyl ether 1j after removal of the benzyl protecting group by controlled hydrogenolysis of the corresponding cyclized products. The furofuran lignans sesamin 2a, eudesmin 2b, and piperitol methyl ether 2e were also prepared directly by using the same precursors 4a-f on radical cyclization followed by treatment with iodine and pinoresinol 2h, piperitol 2i, and pinoresinol monomethyl ether 2j after controlled hydrogenolysis of the benzyl protecting group of the corresponding cyclized products. Two naturally occurring acyclic lignans, secoisolariciresinol 5h and secoisolariciresinol dimethyl ether 5b, have also been prepared by exhaustive hydrogenolysis of 2h and 2b, respectively.
Neural crest cell migration: requirements for exogenous fibronectin and high cell density. (1983)

Cells of the neural crest participate in a major class of cell migratory events during embryonic development. From indirect evidence, it has been suggested that fibronectin (FN) might be involved in these events. We have directly tested the role of FN in neural crest cell adhesion and migration using several in vitro model systems. Avian trunk neural crest cells adhered readily to purified plasma FN substrates and to extracellular matrices containing cellular FN. Their adhesion was inhibited by antibodies to a cell-binding fragment of FN. In contrast, these cells did not adhere to glass, type I collagen, or to bovine serum albumin in the absence of FN. Neural crest cell adhesion to laminin (LN) was significantly less than to FN; however, culturing of crest cells under conditions producing an epithelioid phenotype resulted in cells that could bind equally as well to LN as to FN. The migration of neural crest cells appeared to depend on both the substrate and the extent of cell interactions. Cells migrated substantially more rapidly on FN than on LN or type I collagen substrates; if provided a choice between stripes of FN and glass or LN, cells migrated preferentially on the FN. Migration was inhibited by antibodies against the cell-binding region of FN, and the inhibition could be reversed by a subsequent addition of exogenous FN. However, the migration on FN was random and displayed little persistence of direction unless cells were at high densities that permitted frequent contacts. The in vitro rate of migration of cells on FN-containing matrices was 50 microns/h, similar to their migration rates along the narrow regions of FN-containing extracellular matrix in migratory pathways in vivo. These results indicate that FN is important for neural crest cell adhesion and migration and that the high cell densities of neural crest cells in the transient, narrow migratory pathways found in the embryo are necessary for effective directional migration.