gebhart/patrepeval huggingface dataset:
I-SceIII an intron-encoded DNA endonuclease from yeast mitochondria. Asymmetrical DNA binding properties and cleavage reaction (1993)

We have previously discovered the new intron-encoded endonuclease I-Sce III by expressing, in E. coli, the ORF contained in the third intron of the yeast mitochondrial COX I gene. In this work, we analyzed the in vitro properties of partially purified I-Sce III and found that it is a very specific DNA endonuclease, tolerating relatively few base changes in its 20 base pair long target site. I-Sce III should be a useful molecular tool to analyze the structure of large genomes. Interestingly, I-Sce III is the first P1-P2 DNA endonuclease for which DNA binding properties could be analyzed by band-shift experiments. Clearly, the cleavage products corresponding to the upstream A3 exon and to the downstream A4 exon could compete with the substrate A3-A4 in forming a DNA-protein complex. However, the A3 exon competes more efficiently than the downstream A4 product. The cleavage of the two DNA strands is also asymmetric the top strand (non-transcribed strand) is cleaved faster than the bottom strand, a property found under various experimental conditions. These findings suggest that this intron-encoded DNA endonuclease may have role in the RNA splicing process of the intron.
A three-dimensional microelectrode array for chronic neural recording (1994)

This paper describes a 3-D microelectrode array for the chronic recording of single-unit activity in the central nervous system. The array is formed by a microassembly of planar silicon multishank microprobes, which are precisely positioned in a micromachined platform that resides on the surface of the cortex. Interconnects between the probes and the platform are formed using electroplated nickel lead transfers, implemented using automated computer control. All dimensions are controlled to +/- 1 micron and sank/probe separations as small as 100 microns are possible. Four-probe 16-shank prototype arrays have been tested chronically in guinea pig cortex. After three months in vivo, no significant tissue reaction has been observed surrounding these structures when they remain free to move with the brain, with normal appearing tissue between shanks spaced at 150 microns to 200 microns intervals. The array structure is compatible with the use of signal processing circuitry both on the probes and on the platform. A platform-based signal processing system has been designed to interface with several active probes, providing direct analog access to the recording sites, performing on-chip analog-to-digital conversion of neural activity, and providing simple binary-output recognition of single-unit spike events using a user-input threshold voltage.
Genotype at a promoter polymorphism of the interleukin-6 gene is associated with baseline levels of plasma C-reactive protein (2002)

Baseline plasma CRP is a significantly heritable cardiovascular risk factor. Levels are associated with genotype at the -174G/C polymorphism of the IL-6 gene.
A Novel Peptide Isolated from a Phage Display Peptide Library with Trastuzumab Can Mimic Antigen Epitope of HER-2 (2004)

Trastuzumab, a humanized antibody to HER-2, has been shown to be effective in the treatment of breast cancer in which HER-2 overexpression and metastasis occurs. In our search for an effective mimic epitope of HER-2 binding with trastuzumab and to develop HER-2 peptide vaccine, we screened a phage display 12-mer peptide library with trastuzumab as the target. A mimetic peptide (mimotope) H98 (LLGPYELWELSH) that could specifically recognize trastuzumab was isolated. The DNA encoding peptide H98 was cloned and expressed as the fusion protein GST-H98 in Escherichia coli BL21. The purified GST-H98 could specifically bind to trastuzumab and block the binding of trastuzumab to HER-2 protein. Moreover, H98 could significantly block the function of trastuzumab inhibiting the growth of cancer cells. Mice that were immunized with GST-H98 made specific antibody to H98 as well as to HER-2. In addition, T-cell proliferation occurred in mice immunized with GST-H98. Although no sequence homology was found between H98 and HER-2, through the use of structure analysis we were able to determine that peptide H98 contributed to a conformational epitope of HER-2. Furthermore, we determined that the last two amino acids at the C terminus, and the third together with the fourth amino acid at the N terminus of peptide H98 are critical to the binding of H98 to trastuzumab. As a result, we conclude that peptide H98 has potential for being developed as a HER-2 vaccine for biotherapy of cancer with HER-2 overexpression.
Coordinate expression of membrane type-matrix metalloproteinases-2 and 3 (MT2-MMP and MT3-MMP) and matrix metalloproteinase-2 (MMP-2) in primary and metastatic melanoma cells. (2001)

Expression of MMP-2 in melanoma cells has been demonstrated to be involved in the degradation of extracellular matrix during melanoma growth and to correlate with later melanoma metastasis. MMP-2 is considered to be activated by membrane-associated matrix metalloproteinases (MT-MMPs). To know whether MT-MMPs are involved in the activation of MMP-2 in melanoma cells, immunohistochemical studies were performed in primary and metastatic melanoma by use of the antibodies for MT1-MMP, MT2-MMP and MT3-MMP. Expression of MT1-MMP, MT2-MMP, MT3-MMP and MMP-2 in nevocellular nevus (n = 5), dysplastic nevus (n = 2) and juvenile melanoma (n = 3) was undetectable or detected in only a few cells. Superficial spreading melanoma (SSM) (n = 3) and acral lentiginous melanoma (ALM) (n = 3) showed a moderate expression of MT1 approximately 3-MMP. In nodular melanoma (NM) (n = 2) and metastatic melanoma (n = 3), MT1 approximately 3-MMP was more intensely expressed. Double immunofluorescence demonstrated a consistent colocalization of MT2-MMP/MMP-2 and MT3-MMP/MMP-2 in the NM and metastatic melanoma cells. The colocalization of MT2,3-MMP and MMP-2 in nodular and metastatic melanoma cells suggests that MT-MMPs and MMP-2 co-operate in the invasive and metastatic process of melanoma cells.
Intravesical Bacillus Calmette-Guérin therapy for murine bladder tumors: initiation of the response by fibronectin-mediated attachment of Bacillus Calmette-Guérin. (1987)

Intravesical Bacillus Calmette-Guérin (BCG) is considered to be one of the most effective treatments for superficial bladder cancer. Although the mechanisms by which BCG inhibits tumor growth are not known, previous studies have shown that systemic immunization to BCG and the local expression of the immune response in the bladder are associated with a favorable response to BCG therapy. We have investigated the conditions required for the initiation of an immunological response after the intravesical instillation of BCG. Initial histological studies showed that BCG attached to the bladder wall only in areas where the urothelium was damaged by electrocautery and suggested that attachment was associated with the fibrin clot. Quantitative studies verified the histological observations. Minimal BCG attachment (mean less than 10(2) colony forming units) was observed in normal bladders in contrast with a mean of 1.42 X 10(4) colony forming units/bladder in bladders damaged by electrocautery (10 separate experiments). BCG attachment to the bladder wall was durable since organisms were observed in bladders 48 h after instillation. To investigate the proteins to which BCG attached, we tested the binding of BCG to extracellular matrix and inflammatory proteins which comprise a significant portion of the fibrin clot. BCG bound in vitro to coverslips coated in vivo with extracellular matrix proteins but did not bind to control albumin-coated coverslips. BCG also bound to coverslips coated with purified plasma fibronectin but not to coverslips coated with other purified extracellular matrix proteins including laminin, fibrinogen, and type IV collagen. BCG attachment to coverslips coated with either extracellular matrix proteins or purified fibronectin was inhibited by antibodies specific for fibronectin. Moreover, BCG attachment to cauterized bladders in vivo was inhibited by antifibronectin antibodies. These results demonstrate that fibronectin mediates the attachment of BCG to surfaces and suggest that it is the primary component mediating attachment within the bladder. Moreover, the data suggest that the BCG-fibronectin interaction may be a requisite first step for the initiation of the antitumor activity in intravesical BCG for bladder cancer.
Integrin targeted drug and gene delivery (2010)

Although thus far there are still limitations, integrin targeted delivery systems have already shown their potential as important pharmaceuticals in the near future.
Carboxylic Solvents and O-Donor Ligand Effects on CH Activation by Pt(II) (2006)

We report on the design of more efficient C-H activation catalysts based on DFT calculations. The first examples of well-defined, N,O-donor ligated platinum complexes that are competent for fast C-H activation are detailed. These complexes exhibit thermal and protic stability and are efficient catalysts for H/D exchange reactions with benzene. The C-H activation is shown to benefit from design elements that (A) reduce the barrier for substrate coordination and (B) retain a low barrier for CH cleavage via a novel six-membered transition state involving the carboxylate group of the solvent.
Gastric volume rather than nutrient content inhibits food intake (1996)

To evaluate the separate contributions of distension and nutrient stimulation of the stomach to the inhibition of short-term food intake and, particularly, to reassess previous analyses based on the inflatable gastrointestinal cuff, four experiments were performed. Rats equipped with pyloric cuffs and indwelling gastric catheters consumed a liquid diet ad libitum. Their consumption during short-term (30 min) feeding bout was measured after gastric infusions on cuff-open and cuff-closed trials. Animals taking meals (approximately 5 ml) with cuffs closed immediately after receiving intragastric infusions of 2.5, 5, 7.5, or 10 ml of normal saline exhibited both suppression at the smallest infusion and a dose-dependent reduction across the other volumes (experiment 1). Additionally, when the test diet concentration was varied, animals with their cuffs closed consumed a constant volume, not a constant number of calories (experiment 2). Furthermore, cuff-closed animals exhibited no more suppression to 5-ml intragastric infusions of nutrients (including, on different trials, 50 and 100% Isocal diet; 10, 20, and 40% glucose; and 40% sucrose and 40% fructose) than to the same volume of saline (experiments 3 and 4). In contrast, on cuff-open trials in which gastric contents could empty into the duodenum, these same nutrient loads were more effective (except fructose) than saline in producing suppression of food intake. In summary, although both limited gastric distension with the pylorus occluded and intestinal nutrient stimulation with the cuff open effectively reduced intake, cuff-closed gastric loads of mixed macronutrients or carbohydrate solutions of 2-8 kcal, pH from 5.8 to 6.7, and osmolarities between 117 and 2,294 mosM/kg produced only the distension-based suppression generated by the same volume of saline.
Reaction of Carbon Monoxide and Ozone (1957)

The reaction between ozone and carbon monoxide has been investigated at 35°, 100°, 180°, and 258°C. It could be shown that there is an initial period where the reaction proceeds an order of magnitude faster than after some carbon dioxide is formed. Further oxidation of carbon monoxide by ozone proceeds in the order of magnitude of the thermal decomposition of ozone.
Evolution of Circulating Wild Poliovirus and of Vaccine-Derived Poliovirus in an Immunodeficient Patient: a Unifying Model (2000)

We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.
Nerve growth factor promotes survival of septal cholinergic neurons after fimbrial transections (1986)

Several findings obtained in recent years suggest that NGF, aside from its well-established function as a neurotrophic factor for peripheral sympathetic and sensory neurons, also has trophic influence on the cholinergic neurons of the basal forebrain. The present study assessed whether NGF was able to affect survival of central cholinergic neurons after axonal transections in adult rats. The septo-hippocampal pathway was transected unilaterally by cutting the fimbria, and animals were implanted with a cannula through which NGF or control solutions were injected intraventricularly over 4 weeks. The lesions reduced the number of large cell bodies, as visualized by Nissl staining in the medial septal nucleus and in the vertical limb of the diagonal band of Broca. Furthermore, in the same nuclei, they reduced the number of cell bodies positively stained for AChE after pretreatment with diisopropylfluorophosphate (a method known to result in reliable identification of cholinergic neurons in the septal area). On lesioned sides, the number of cholinergic cells in medial septal nucleus and the vertical limb of the diagonal band was reduced by 50 +/- 4%, as compared to the number on contralateral sides. On lesioned sides of animals chronically treated with NGF, the number of AChE-positive cells in these areas was reduced only by 12 +/- 6%, as compared to control levels. These findings suggest that fimbrial transections resulted in retrograde degeneration of cholinergic septo-hippocampal neurons and that NGF treatment strongly attenuated this lesion-induced degeneration.(ABSTRACT TRUNCATED AT 250 WORDS)
Non-Base Pairing DNA Provides a New Dimension for Controlling Aptamer-Linked Nanoparticles and Sensors (2007)

DNA aptamers have been recently applied as simple and fast colorimetric sensors for a wide range of molecules. A unique feature of these systems is the presence of non-base pairing oligonucleotides in both DNA aptamers and spacers on DNA-functionalized nanoparticles. We report here a systematic investigation on an adenosine aptamer-linked gold nanoparticle system. When the aptamer overhang and the spacer were aligned on the same side, adenosine-responsive disassembly was inhibited. This inhibition effect increased with the length of the spacer, and fully inhibited activity was observed with the spacer containing more than three nucleotides. In contrast to a linear relationship between the spacer length and melting temperature in double-stranded DNA systems without overhangs, the aptamer system displayed a nonlinear relationship, with the melting temperature decreasing exponentially with spacer length. Control experiments suggested that this inhibition effect was due to thermodynamic factors rather than kinetic traps. A comparison with aptamer beacon systems indicated that nanoparticles may play an important role in this inhibition effect, and no specific interactions between the aptamer overhang and spacer were detected. The identity of nucleotides in the spacer did not affect the conclusions. Furthermore, the rate of disassembly or color change was slower at lower temperature or higher ionic strength, but was little affected by pH from 5.2 to 9.2. Therefore, non-base pairing DNA provided another dimension for controlling DNA-linked nanoparticles in addition to pH, temperature, or ionic strength, and this knowledge has resulted in the most optimal construct for sensing applications.
Repression of the Transcription Factor Th-POK by Runx Complexes in Cytotoxic T Cell Development (2008)

Mouse CD4+CD8+ double-positive (DP) thymocytes differentiate into CD4+ helper-lineage cells upon expression of the transcription factor Th-POK but commit to the CD8+ cytotoxic lineage in its absence. We report the redirected differentiation of class I-restricted thymocytes into CD4+CD8- helper-like T cells upon loss of Runx transcription factor complexes. A Runx-binding sequence within the Th-POK locus acts as a transcriptional silencer that is essential for Th-POK repression and for development of CD8+ T cells. Thus, Th-POK expression and genetic programming for T helper cell development are actively inhibited by Runx-dependent silencer activity, allowing for cytotoxic T cell differentiation. Identification of the transcription factors network in CD4 and CD8 lineage choice provides insight into how distinct T cell subsets are developed for regulating the adaptive immune system.
The neural networks of inhibitory control in posttraumatic stress disorder (2008)

The increased inhibitory error and reduced right frontal cortical activation are consistent with compromised inhibitory control in PTSD, while the increased activation of brain regions associated with sensory processing and a greater demand on inhibitory control may reflect enhanced stimulus processing in PTSD, which may undermine cortical control mechanisms.
Homogeneous Enzyme Immunoassay of Acetaminophen in Serum (1984)

A new commercially available homogeneous enzyme immunoassay, using the glucose-6-phosphate dehydrogenase (G6PDH) catalyzed conversion of NAD to NADH, has been evaluated and applied to the determination of acetaminophen in serum. Replicate analysis of serum control samples over the range of 10-200 micrograms/mL demonstrated a within-assay coefficient of variation of less than or equal to 4.6% and a between-assay coefficient of variation of less than or equal to 5.8%. Regression analysis of two separate groups of 98 and 47 serum samples by this technic, using different reagent lots, and a HPLC reference method gave equations of y = 0.981x - 0.941 (r = 0.984) and y = 1.06x - 2.21 (r = 0.994), respectively. No interference due to hemolysis or turbidity was noted. Evaluation of samples containing 35 commonly prescribed or over the counter medications demonstrated no significant cross-reactivity. Prepared reagents were stable over a period of at least 2 months when stored at 4 degrees C. Correlations between two reagent lots were excellent (r = 0.998). A single sample can be analyzed expeditiously. The result may help evaluate a potential acetaminophen poisoning. Another way to assess this toxicity, calculation of the elimination half-life, has limitations that depend on the precision of the analysis.
Loss of heterozygosity of the retinoblastoma and adenomatous polyposis susceptibility gene loci and in chromosomes 10p, 10q and 16q in human prostate cancer (1994)

These findings suggest that losses of the RB1 and APC tumour suppressor genes and suspected tumour suppressor genes on 10p, 10q and 16q may be important events in the genesis of prostatic tumours.
Selective submerged productions of three types of glucoamylases by a black-koji mold. (1975)

Aspergillus awamori var. kawachi produced selectively one of the three types of glucoamylases under the following different conditions in the submerged cultures at the controlled pH of 6.5 to 7.0: (1) the raw-starch digestive glucoamylase, type I, by a cultivation in the synthetic medium containing ammonium citrate as a nitrogen source, deficient in zinc and sufficient in phosphate, for a shorter period of 30 hr at 35°C; (2) one of the raw-starch indigestive glucoamylases, type I', showing the same hydrolysis curves for gelatinized starch as the type I, by a cultivation in the synthetic medium containing ammonium acetate as a nitrogen source, sufficient in zinc, for 50 hr at 30°C; (3) the other of the raw-starch indigestive glucoamylases, type II, that was less susceptible for α-1, 6 glucosidic linkages of gelatinized starch, by a cultivation in the synthetic medium containing glucose, casein-peptone and sufficient amount of inorganic elements, especially calcium and zinc, for 96 hr at 25°C.
Granulocyte colony-stimulating factor induces hFc gamma RI (CD64 antigen)-positive neutrophils via an effect on myeloid precursor cells (1993)

In this study we have examined hFc gamma RI expression during myelopoiesis. Normal bone marrow (BM) cells were found to express hFc gamma RI up to the metamyelocyte stage. A different Fc gamma RI expression pattern was observed in an in vitro model of myelopoiesis. Purified CD34-positive BM cells, cultured for 12 to 14 days with granulocyte colony-stimulating factor (G-CSF), differentiate into a population of mature granulocytic cells. In these cultures, in which hFc gamma RI was virtually absent on the initial CD34-positive BM cells, hFc gamma RI was strongly induced by G-CSF after only 5 days. During final maturation the cells remained hFc gamma RI positive. This expression was confirmed functionally by antibody-sensitized erythrocytes (EA)-rosette assays. Moreover, the mature myeloid cells were found to express mRNA encoding for hFc gamma RI, whereas reverse-transcriptase polymerase chain reaction analysis showed that both hFc gamma RIA and hFc gamma RIB genes were expressed. In contrast, on peripheral blood (PB) polymorphonuclear neutrophil leukocytes (PMN) the in vitro effect of G-CSF as to hFc gamma RI induction was limited. Therefore, we conclude that, with respect to hFc gamma RI expression on PMN, G-CSF acts on myeloid precursor cells rather than on mature cells. This conclusion could be strengthened by in vivo administration of a single dose of G-CSF to a healthy volunteer. After a 12-hour lag time, hFc gamma RI expressing PMNs were detected in the peripheral blood. This study shows that hFc gamma RI is an early myeloid differentiation marker that is lost during normal final maturation. However, committed myeloid progenitor cells can be strongly induced by G-CSF to express hFc gamma RI, ultimately resulting in mature granulocytic cells expressing the high-affinity receptor for IgG. This expression may have important consequences for the functional capacity of these cells.