gebhart/patrepeval huggingface dataset:
A 165-Base Pair Sequence Between the Dihydrofolate Reductase Gene and the Divergently Transcribed Upstream Gene Is Sufficient for Bidirectional Transcriptional Activity (1989)

The dihydrofolate reductase gene encodes a key enzyme of one-carbon metabolism and is constitutively expressed in all cells. Recently, transcripts initiated at 89 base pairs upstream from the transcriptional initiation site of the dihydrofolate reductase gene and transcribed from the opposite strand have been identified and shown to encode for a protein with homology to a bacterial DNA mismatch repair enzyme (Fujii, H., and Shimada, T. (1989) J. Biol. Chem. 264, 10057-10064). Therefore, the two genes are organized in a head-to-head configuration separated by an 89-base pair segment. The promoter activities of this short spacer sequence were studied in a transient assay using the chloramphenicol acetyltransferase and the guanine phosphoribosyltransferase genes as reporters. A 165-base pair fragment from -111 to +54 relative to the dihydrofolate reductase initiation site was shown to be sufficient for transcriptional activity in either direction, suggesting that expression of the two divergent genes is regulated by a bidirectional promoter that may use common regulatory elements.
Conserved Mechanism of tRNA Splicing in Eukaryotes (1991)

The ligation steps of tRNA splicing in yeast and vertebrate cells have been thought to proceed by fundamentally different mechanisms. Ligation in yeast cells occurs by incorporation of an exogenous phosphate from ATP into the splice junction, with concomitant formation of a 2' phosphate at the 5' junction nucleotide. This phosphate is removed in a subsequent step which, in vitro, is catalyzed by an NAD-dependent dephosphorylating activity. In contrast, tRNA ligation in vertebrates has been reported to occur without incorporation of exogenous phosphate or formation of a 2' phosphate. We demonstrate in this study the existence of a yeast tRNA ligase-like activity in HeLa cells. Furthermore, in extracts from these cells, the entire yeastlike tRNA splicing machinery is intact, including that for cleavage, ligation, and removal of the 2' phosphate in an NAD-dependent fashion to give mature tRNA. These results argue that the mechanism of tRNA splicing is conserved among eukaryotes.
A New Process (VAPEX) For Recovering Heavy Oils Using Hot Water And Hydrocarbon Vapour (1991)

Abstract There are extensive deposits of heavy oils in Saskatchewan and Alberta which can only be recovered with low efficiency by conventional methods. Thermal recovery processes using steam, although effective, are uneconomic in many of the Lloydminster type reservoirs because the deposits are relatively thin and heat loses to the overburden and under burden are excessive. A new idea is to use a solvent, such as propane, in the vapour phase which can form a vapour-filled chamber within the reservoir. Vapour dissolves in the oil around the chamber and the resulting solution drains, driven by gravity, to a horizontal production well placed low in the formation. The solvent vapour, at or near its dew paint, is injected simultaneously with hot water from a horizontal well located at the top of the reservoir. The temperature and flow rate of the water are chosen so that the reservoir temperature is raised to the range of only 40 °C to 80 °C. As the diluted bitumen drains toward the production well, it interacts with hot water and some propane re-distils upward to dilute further bitumen. There is, thus, a transport of heat from low down in the reservoir to the upper reaches by the evaporation of propane near the bottom and its condensation (dissolution) at the top. This mechanism causes the heat in the water to be distributed through the reservoir, in particular, laterally away from the point of injection. Results are presented that show the gas/oil and water/oil ratios and the additional oil recovery from a vertical, two-dimensional scaled reservoir model due to propane injection near the end of a hot water flood. The essential feature of the recovery mechanism and the process conditions are discussed. Introduction There are extensive deposits of heavy oils in Saskatchewan and Alberta which can only be recovered with a low recovery efficiency by conventional methods. Primary recovery in the best of these heavy oil reservoirs can yield about 6% of the original-oil-in-place. Waterflooding can improve the recovery but only to an extent of 1% to 2% because of the adverse mobility ratio. The recovery concept, which is described here, is closely related to the steam-assisted gravity drainage (SAGD) Process which has been discussed in the literature(1–8). In the SAGD process, a growing steam chamber forms as steam is injected into the reservoir and steam flows continuously to the perimeter of the chamber where it condenses and heats the surrounding oil. The heated oil drains, driven by gravity, to a horizontal well located at the base of the reservoir. This process is effective and can be economic if the heat (steam) requirements are not too high. The heat requirements can become excessive, however, in thin reservoirs where the vertical heat losses above and below the reservoir tend to be high and also in low-permeability carbonates where the reservoir heat capacity per unit volume of contained oil is high. One potential means for overcoming the problem of heat loss is to use solvents in place of heat to mobilize the oil.
CD8+ T Cells Provide an Immunologic Signature of Tuberculosis in Young Children (2011)

Among young children, M. tuberculosis-specific CD8(+) T cells develop in response to high bacillary loads, as occurs during tuberculosis, and are unlikely to be found after M. tuberculosis exposure. T-cell responses measured in peripheral blood mononuclear cells are generated after M. tuberculosis exposure alone, and thus cannot distinguish exposure from disease. In young children, IFN-γ-producing M. tuberculosis-specific CD8(+) T cells provide an immunologic signature of primary M. tuberculosis infection resulting in disease.
Neural Stem Cells for CNS Transplantation (1993)

Neurodegenerative disorders such as Parkinson's, Alzheimer's, and Huntington's disease are becoming ever more prominent in our society. A direct approach towards therapeutic treatment of these diseases is through replacement therapy where normal tissue is transplanted back to the nervous system. Recently, significant progress has been achieved with transplants in Parkinson's disease, but the process is heavily dependent on an unstable and problematic source of fetal tissue. Neural stem cells may become the tissue/cell source necessary for developing the therapeutic potential of neural transplantation. Stem cells are self-renewing, multipotent and could provide a well-characterized and clean source of transplantable material. A number of new in vitro approaches have led to the development of continuously propagated stem cells that are potential candidates for nervous system transplantation. These include oncogene-induced immortalization and growth-factor stimulation of naturally occurring central and peripheral nervous system stem cells. The nature of these cells and their suitability for transplantation into the CNS will be evaluated.
The brown midrib3 (bm3) mutation in maize occurs in the gene encoding caffeic acid O-methyltransferase. (1995)

The brown midrib mutations are among the earliest described in maize. Plants containing a brown midrib mutation exhibit a reddish brown pigmentation of the leaf midrib starting when there are four to six leaves. These mutations are known to alter lignin composition and digestibility of plants and therefore constitute prime candidates in the breeding of silage maize. Here, we show that two independent brown midrib3 (bm3) mutations have resulted from structural changes in the COMT gene, which encodes the enzyme O-methyltransferase (COMT; EC 2.1.1.6), involved in lignin biosynthesis. Our results indicate that the bm3-1 allele (the reference mutant allele) has arisen from an insertional event producing a COMT mRNA altered in both size and amount. By sequencing a COMT cDNA clone obtained from bm3-1 maize, a retrotransposon with homology to the B5 element has been found to be inserted near the junction of the 3' coding region of the COMT gene intron. The second bm3 allele, bm3-2, has resulted from a deletion of part of the COMT gene. These alterations of the COMT gene were confirmed by DNA gel blot and polymerase chain reaction amplification analyses. These results clearly demonstrate that mutations at the COMT gene give a brown midrib3 phenotype. Thus, the gene genetically recognized as bm3 is the same as the one coding for COMT.
Isolation of six cysteine proteinase inhibitors from human urine. Their physicochemical and enzyme kinetic properties and concentrations in biological fluids. (1986)

Six cysteine proteinase inhibitors were isolated from human urine by affinity chromatography on insolubilized carboxymethylpapain followed by ion-exchange chromatography and immunosorption. Physicochemical and immunochemical measurements identified one as cystatin A, one as cystatin B, one as cystatin C, one as cystatin S, and one as low molecular weight kininogen. The sixth inhibitor displayed immunochemical cross-reactivity with salivary cystatin S but had a different pI (6.85 versus 4.68) and a different (blocked) N-terminal amino acid. This inhibitor was tentatively designated cystatin SU. The isolated inhibitors accounted for nearly all of the cysteine proteinase inhibitory activity of the urinary pool used as starting material. The enzyme inhibitory properties of the inhibitors were investigated by measuring inhibition and rate constants for their interactions with papain and human cathepsin B. Antisera raised against the inhibitors were used in immunochemical determinations of their concentrations in several biological fluids. The combined enzyme kinetic and concentration data showed that several of the inhibitors have the capacity to play physiologically important roles as cysteine proteinase inhibitors in many biological fluids. Cystatin C had the highest molar concentration of the inhibitors in seminal plasma, cerebrospinal fluid, and milk; cystatin S in saliva and tears; and kininogen in blood plasma, synovial fluid, and amniotic fluid.
Evaluation of the Parameters of Strontium Metabolism in the Rat as a Function of Age (1968)

E. A. Gusmano, J. N. Concannon, S. R. Bozzo, S. H. Cohn, Evaluation of the Parameters of Strontium Metabolism in the Rat as a Function of Age, Radiation Research, Vol. 33, No. 3 (Mar., 1968), pp. 540-553
<title>Optical proximity effects and correction strategies for chemical-amplified DUV resists</title> (1996)

Optical proximity effects (OPE) are narrowing the process window in the 0.25micrometers - 0.18micrometers CD range. Hence optical proximity correction (OPC) might be required. These proximity effects and correction strategies are studied in detail in this work. First, an evaluation methodology is derived for the three types of OPE (linewidth differences with pitch, end-of-line effects and corner rounding). Hence, the influence of various parameters on OPE is investigated for negative tone and positive tone resists, since clear differences exist in OPE for dark field and bright field masks. Linewidth differences with pitch are small for negative tone resists, end-of-line effects are less pronounced for positive tone materials. Obviously, optical parameters have an important influence on OPE. Also, loading effects during etch processes deserve attention. Aerial image based proximity correction is evaluated. With respect to CD variations with pitch, important improvements are obtained for some resists, but not for all materials. End-of-line effects and corner rounding are improved by the use of OPC in all our experiments. Superior proximity correction results are expected with the expansion of aerial image based OPC by implementation of resist models.
A scenario for the deployment of interactive multimedia cable television systems in the United States in the 1990s (1994)

This paper discusses the key technologies that are enabling the transition from analog to digital interactive television. Also discussed is a proposed three-phase scenario for the U.S. deployment of interactive multimedia cable television systems during the remainder of the decade of the 1990s and some of the social implications of such networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus (2009)

Fungi are a rich source of bioactive secondary metabolites, and mushroom-forming fungi (Agaricomycetes) are especially known for the synthesis of numerous bioactive and often cytotoxic sesquiterpenoid secondary metabolites. Compared with the large number of sesquiterpene synthases identified in plants, less than a handful of unique sesquiterpene synthases have been described from fungi. Here we describe the functional characterization of six sesquiterpene synthases (Cop1 to Cop6) and two terpene-oxidizing cytochrome P450 monooxygenases (Cox1 and Cox2) from Coprinus cinereus. The genes were cloned and, except for cop5, functionally expressed in Escherichia coli and/or Saccharomyces cerevisiae. Cop1 and Cop2 each synthesize germacrene A as the major product. Cop3 was identified as an alpha-muurolene synthase, an enzyme that has not been described previously, while Cop4 synthesizes delta-cadinene as its major product. Cop6 was originally annotated as a trichodiene synthase homologue but instead was found to catalyse the highly specific synthesis of alpha-cuprenene. Coexpression of cop6 and the two monooxygenase genes next to it yields oxygenated alpha-cuprenene derivatives, including cuparophenol, suggesting that these genes encode the enzymes for the biosynthesis of antimicrobial quinone sesquiterpenoids (known as lagopodins) that were previously isolated from C. cinereus and other Coprinus species.
Expression and Significance of CD44, CD47 and c-met in Ovarian Clear Cell Carcinoma (2015)

Expression of CD44, CD47 and c-met was upregulated in OCCC and pairwise correlation. CD44, CD47 and c-met may have synergistic effects on the development of OCCC and are prognostic factors for ovarian cancer.
Regulation of transport pathways in tumor vessels: Role of tumor type and microenvironment (1998)

Novel anti-neoplastic agents such as gene targeting vectors and encapsulated carriers are quite large (approximately 100-300 nm in diameter). An understanding of the functional size and physiological regulation of transvascular pathways is necessary to optimize delivery of these agents. Here we analyze the functional limits of transvascular transport and its modulation by the microenvironment. One human and five murine tumors including mammary and colorectal carcinomas, hepatoma, glioma, and sarcoma were implanted in the dorsal skin-fold chamber or cranial window, and the pore cutoff size, a functional measure of transvascular gap size, was determined. The microenvironment was modulated: (i) spatially, by growing tumors in subcutaneous or cranial locations and (ii) temporally, by inducing vascular regression in hormone-dependent tumors. Tumors grown subcutaneously exhibited a characteristic pore cutoff size ranging from 200 nm to 1.2 microm. This pore cutoff size was reduced in tumors grown in the cranium or in regressing tumors after hormone withdrawal. Vessels induced in basic fibroblast growth factor-containing gels had a pore cutoff size of 200 nm. Albumin permeability was independent of pore cutoff size. These results have three major implications for the delivery of therapeutic agents: (i) delivery may be less efficient in cranial tumors than in subcutaneous tumors, (ii) delivery may be reduced during tumor regression induced by hormonal ablation, and (iii) permeability to a molecule is independent of pore cutoff size as long as the diameter of the molecule is much less than the pore diameter.
The epidermal growth factor receptor/Erb-B/HER family in normal and malignant breast biology (2011)

The EGFR/Erb-B receptor tyrosine kinases each play distinct and complementary roles in normal breast development. The four receptors form both homodimers and heterodimers in response to binding by ligands which show selectivity for one or more of the receptors (except Erb-B2). Together with the additional flexibility generated by the formation of different dimer pairs, these signalling networks play key roles in directing a variety of both autocrine and paracrine cellular responses. Complex two-way interactions between mammary epithelial cells and the surrounding stroma direct proliferation, duct formation, branching and terminal differentiation during puberty, pregnancy and lactation, with each receptor and ligand fulfilling distinct roles. Caricatures of the normal role of EGFR/Erb-B signalling resulting in aberrant cellular responses are seen in breast cancers, where over-expression and/or (less commonly) mutation of one or more of the receptors results in enhanced cell proliferation, motility, release of proteases and angiogenic factors. Given their importance in tumour progression, compared with most normal adult tissues and their links with resistance to chemotherapy and anti-endocrine therapy, Erb-B receptors (most notably Erb-B2) have been exploited as therapeutic targets. Monoclonal antibodies (e.g. trastuzumab, pertuzumab) and small molecule tyrosine kinase inhibitors (e.g. lapatinib, afatinib) have shown significant clinical responses in some breast cancer subtypes. Additional approaches include targeted toxins or drugs, peptide vaccines, immunRNase and chaperone inhibitors to deplete Erb-B2 protein levels. Greater understanding of the full spectrum of Erb-B-mediated signalling pathways and their misregulation in breast cancer will provide additional strategies to control malignant progression.
Use of an enzyme-linked immunosorbent assay for detection of Treponema hyodysenteriae infection in swine (1989)

Discriminate analysis was used to evaluate the enzyme-linked immunosorbent assay (ELISA) for the detection of anti-Treponema hyodysenteriae antibodies in experimentally and naturally infected swine. In trial 1, 26 pigs were randomly divided into three groups (naturally infected, n = 8; experimentally infected, n = 11; and noninfected, n = 7), and samples were collected for 10 weeks. For trial 2, 31 pigs were randomly divided into two groups (naturally infected, n = 22; and noninfected, n = 7), and samples were collected for 20 weeks. Rectal swabs for T. hyodysenteriae isolation were collected daily, and fecal samples for isolation of Salmonella spp. were collected weekly. Serum samples for ELISA evaluation were collected biweekly (trial 1) or weekly (trial 2). Results of discriminate analysis indicated that the ELISA correctly identified 90% or more of the individually infected pigs at prior probabilities of infection ranging from 60 to 90%. The test correctly identified noninfected pigs at a lower rate (61 to 92% range). The mean ELISA titers of naturally infected pigs without clinical signs were not significantly different (P less than 0.05) from the titers of both groups of experimentally infected pigs. Mean ELISA titers of naturally infected pigs without clinical signs were significantly greater than the mean titers of naturally infected pigs with clinical signs. Naturally infected pigs with clinical signs had a mean ELISA titer that was significantly greater than that of noninfected pigs and significantly less than the mean titers of the experimentally infected pigs without clinical signs and the naturally infected pigs without clinical signs.
Effects of Etomidate on Hormonal Responses to Surgical Stress (1984)

The hormonal responses to surgical stress were examined in 10 patients scheduled for elective gynecologic laparotomy. Anesthesia was induced with either thiopental, 4 mg/kg, or etomidate, 0.35 mg/kg, and maintained with nitrous oxide and enflurane. Plasma cortisol, aldosterone, ACTH, and catecholamines were measured during the 24 h after the induction of anesthesia. The catecholamine responses of the patients whose anesthesia was induced with either drug were similar. The plasma ACTH concentrations for the etomidate group were greater than baseline values and the concentrations in the thiopental group (P less than 0.05) in the fourth and fifth hours. In the patients receiving thiopental, both cortisol and aldosterone concentrations were greater than the baseline value (P less than 0.05) in the second to fourth hours after induction. In the etomidate group, the plasma concentrations of cortisol were less than baseline values (P less than 0.05) in the first and second hours after induction of anesthesia and both cortisol and aldosterone were lower than those in the thiopental group (P less than 0.05) in the half to fourth hours after induction. These results confirm an earlier report of the suppression of cortisol after etomidate administration and, because aldosterone also was suppressed, suggests that etomidate exerts its effect by inhibiting early stages of steroidogenesis in the adrenal cortex.
TÜRK LİRASI'NDAN SIFIR ATILMASI İŞLEMİNİN TÜKETİCİ DAVRANIŞLARINA ETKİSİ: TRABZON OLAYI (2008)

Ozet: Bu calisma, 2005 yilinda gerceklestirilen TL’den sifir atilmasi isleminin tuketicilerin tutum ve davranislari uzerindeki etkilerini arastirmaktadir. Calisma kapsaminda bir anket calismasi yurutulmustur. Bulgular, fayda-maliyet analizi cercevesinde YTL’ye gecisin yerinde bir uygulama oldugunu ve YTL’ye uyumun kolay saglandigini ortaya koymustur. Ayrica, operasyonla birlikte YTL’nin itibari artmis, diger psikolojik ve ekonomik beklentiler uzerinde ise onemli bir etkisi olmamistir. Operasyonun basarisi paradan sifir atilmasi ihtiyacinin tekrar ortaya cikmamasiyla degerlendirilmelidir. Dolayisiyla, basarinin surdurulebilirligi enflasyonla mucadeledeki etkinlige baglidir. Anahtar Kelimeler: TL’den Sifir Atilmasi, Para Reformu Abstract: This study investigates that the effects on the attitude and behaviour of consumers of the operation the deleting zeros from Turkish Liras in 2005. In this content, a questionnaire was applied. The findings has marked that transition to New Turkish Liras has been a correct application within the framework cost-benefit analysis and has harmonized to New Turkish Liras easily. Also, reputation of New Turkish Liras has increased through this operation but it hasn’t had an important effect on the psychological and economical expectations. The accomplishment of this operation should be assessed according to appearance no need of deleting zero from Turkish Liras again. Accordingly, the sustainability of this accomplisment depend on efficiency of fighting against inflation. Key Words: The Deleting Zeros From Turkish Liras, Currency Reform
Dynamics of self-driven microcantilevers (2002)

The small amplitude thermal vibrations of the microcantilever of an atomic force microscope can be enhanced via a delayed feedback system. This is verified experimentally for a triangular cantilever, and modeled theoretically as a boundary value problem resulting in a second order functional differential equation for the temporal behavior of the cantilever. The eigenvalues of the resulting delay differential equation describing the transverse vibrations of the cantilever are calculated and analyzed. These values are compared with the corresponding resonant frequencies predicted by a point mass model and with the experimentally observed values.