gebhart/patrepeval huggingface dataset:
Localization of the decoding region on the 30S Escherichia coli ribosomal subunit by affinity immunoelectron microscopy. (1979)

The decoding region of the Escherichia coli ribosome has been localized by affinity immunoelectron microscopy. Valyl-tRNA1Val, derivatized at the alpha-amino end with the dinitrophenyl group, was bound to the ribosomal P site of 70S ribosomes and crosslinked specifically to 16S RNA by 310- to 325-nm irradiation. Previous work has shown that crosslink occurs between the 5' anticodon base of the tRNA and a pyrimidine in the 3' one-third of the 16S RNA. By reaction of the dinitrophenyl group with antibody, dimers of the 30S tRNA covalent complexes were prepared containing one covalently attached tRNA per 30S subunit. Electron microscopic visualization of the antibody attached to the dinitrophenyl group located the position of the 3' end of the tRNA. Several sites, with a strong preference for the large protrusion or cleft region in the upper one-third of the subunit, were found. The multiplicity of sites is likely due to the freedom of orientation of the 3' end of the tRNA which is approximately 80 A from the site of crosslinking. By extrapolating this distance from each of the antigenic sites, we concluded that the anticodon of tRNA when in the P site is probably located in the cleft region of the 30S subunit.
How soccer players would do stream joins (2011)

In spite of the omnipresence of parallel (multi-core) systems, the predominant strategy to evaluate window-based stream joins is still strictly sequential, mostly just straightforward along the definition of the operation semantics.
[The role of oligophosphate and nucleoside fragments upon the interaction of a nucleotide with RecA protein]. (1993)

Pyrophosphate and 1-pyrophospho-5-phosphoribose displace the nucleotide from the complex with RecA protein (in the absence of DNA). Adenosine, AMP, inorganic phosphate riboso-5-phosphate have no effect. Pyrophosphate causes the dissociation of RecA-ssDNA-complex in the same manner as ADP, circular hexaphosphate has no effect. In the complex with RecA protein the dissociation constant for pyrophosphate is 1.6 mM and 710 mM for adenosine. It is proposed that the oligophosphate is the main binding group in the RecA-nucleotide interaction. Two vicinal "closed" -O and one terminal "open" oxygenous =O-groups of oligophosphate take part in the binding. The nucleoside fragment alone cannot provide the firm binding of the nucleotide with the protein, but probably is responsible for the specificity of the nucleotide to protein binding.
Interactions of Cyclodextrins with Dipalmitoyl, Distearoyl, and Dimyristoyl Phosphatidyl Choline Liposomes. A Study by Leakage of Carboxyfluorescein in Inner Aqueous Phase of Unilamellar Liposomes. (2000)

The interaction of cyclodextrins (CDs) with L-alpha-dipalmitoyl phopsatidyl choline (DPPC), L-alpha-distearoyl phosphatidyl choline (DSPC), and L-alpha-dimyristoyl phosphatidyl choline (DMPC) unilamellar liposomes was investigated by the leakage of carboxylfluorescein (CF) entrapped in the inner aqueous phase of liposomes, at 25 degrees C (DPPC and DSPC liposomes) and at 5 degrees C (DMPC liposomes). The efficiency of CDs for CF leakage was remarkable in the order of heptakis (2,6-di-O-methyl)-beta-CD (DOM-beta-CD) > alpha-CD > heptakis (2,3,6-tri-O-methy)-beta-CD (TOM-beta-CD) from DPPC liposomes, in the order of DOM-beta-CD > TOM-beta-CD > alpha-CD from DSPC liposomes and in the order of alpha-CD > DOM-beta-CD > TOM-beta-CD from DMPC liposomes. The other CDs used in the present studies, beta-CD, 2-hydroxylpropyl beta-CD, and gamma-CD scarcely induced the CF leakage from above the three liposomes. From the profiles of % CF leakage, together with measurements of differential scanning calorimetry, it was found that hydrophobic DOM-beta-CD penetrates the matrix of the liposomes to interact with them as well as TOM-beta-CD, and that less hydrophobic alpha-CD exists at the surface of the membrane to interact with the liposomes. Further, it was found that the interaction of CDs with liposomes changes depending not only on the length of fatty acid chain of phospholipid (condensation force and hydrophobicity) but also the hydrophobicity and the cavity size of CD.
Measurement of the critical DNA lesions produced by antibody-directed enzyme prodrug therapy (ADEPT) in vitro, in vivo and in clinical material (2001)

An antibody-directed enzyme prodrug therapy (ADEPT) system against CEA-positive tumours is currently in phase I clinical trials. It consists of a prodrug, 4-[N,N-bis(2-iodoethyl) amino] phenoxycarbonyl L -glutamic acid (ZD2767P) and a conjugate of the F(ab')(2) anti-CEA antibody A5B7 and the bacterial enzyme carboxypeptidase G2 (CPG2). ZD2767P is converted by antibody-targeted CPG2 into an active bifunctional alkylating drug (ZD2767) at the tumour site. The IC(50) value of the prodrug against the human colorectal tumour LS174T cell line was 55 +/- 9 microM following a 1 h exposure. In contrast, co-incubation of ZD2767P with CPG2 resulted in 229-fold increase in activity. Using a modified comet assay, DNA interstrand cross links (ISC) were detected within 1 h of ZD2767P + CPG2 treatment and were repaired by 24 h. A clear dose-response was seen between the level of ISC, growth inhibition and ZD2767 concentration. Administration of a therapeutic dose of ZD2767P 72 h after the F(ab')(2) A5B7 conjugate to mice bearing LS147T xenografts resulted in extensive ISC in the tumour after 1 h; repair was seen at 24 h. Tumour biopsies and peripheral lymphocytes were studied in 5 patients on the ADEPT phase I clinical trial. In 4 patients no ISC were detected. These patients also demonstrated poor localization of conjugate and no tumour response was seen. However a significant level of ISC was detected in one tumour biopsy, which also showed evidence of conjugate localization and clinical response. These studies demonstrate the application of the comet assay in the measurement of ISC in vitro and in clinical material and confirm that activation of ZD2767P results in the formation of DNA crosslinks.
Treatment with oral 3,4 diaminopyridine improves leg strength in multiple sclerosis patients (1996)

To examine the efficacy and toxicity of oral 3,4 diaminopyridine (DAP) in dosages up to 100 mg/day, 36 patients with multiple sclerosis (MS) enrolled in a randomized, double-blind, placebo-controlled, crossover trial. The primary outcome measure was improvement of a prospectively defined neurologic deficit, which was leg weakness in 34 patients. Secondary outcome measures included the patient's subjective response, scored manual motor testing (MMT) of leg strength, scored leg strength from videotaped motor testing (VMT), quadriceps and hamstrings strength (QMT) measured by isometric dynamometry, neuropsychological testing (NPT), ambulation index (AI), and Expanded Disability Status Scale (EDSS) score. Paresthesias and abdominal pain were common and were dose limiting in eight patients. Three patients had episodes of confusion, and one patient had a seizure while on DAP. Eight patients withdrew from the study, leaving 28 evaluable patients for the efficacy analysis. The prospectively defined neurologic deficit improved in 24 patients-22 on DAP and 2 on placebo (p = 0.0005). All improvements were in leg weakness. Subjective response and measures of leg strength and function (MMT, VMT, QMT, and AI) improved on DAP compared with placebo. Neither NPT nor EDSS scores improved. DAP treatment can induce improvements in leg strength in MS patients, but toxicity is limiting in many patients.
Airway remodeling in asthma (1999)

Asthma is estimated to affect 15 million people in the United States. After declining in the 1970s, its prevalence, morbidity, and mortality have increased since the 1980s. It now affects 1 in 7 children in the United Kingdom, and is the most frequent reason for preventable childhood hospitalizations in the United States. In 1990, total asthma-related health care costs were estimated at 6.2 billion dollars in the United States. This figure exceeded 10 billion dollars by 1995.
Increased Activity of Nuclear Factor-κB Participates in Cardiovascular Remodeling Induced by Chronic Inhibition of Nitric Oxide Synthesis in Rats (2000)

The NF-kappaB system participates importantly in the development of early vascular inflammation and subsequent medial thickening but not in fibrogenesis in this model. The present study may provide a new aspect of how endothelium-derived NO contributes to anti-inflammatory and/or antiarteriosclerotic properties of the vascular endothelium in vivo.
Measurement of Thin Film Parameters with a Prism Coupler (1973)

The prism coupler, known from experiments on integrated optics, can be used to determine the refractive index and the thickness of a light-guiding thin film. Both parameters are obtained simultaneously and with good accuracy by measuring the coupling angles at the prism and fitting them by a theoretical dispersion curve. The fundamentals and limitations. of this method are discussed, its practical use, and mathematical procedures for the evaluation.
Preoperative Assessment of the Carotid Bifurcation (1995)

Three-dimensional TOF MRA is the most accurate noninvasive test. Combined use of MRA and DU results in a marked increase in accuracy to a level that obviates the need for CA in a majority of patients.
Stimulation of Luteinizing Hormone-Releasing Hormone (LHRH) Gene Expression in GT1–7 Cells by Its Metabolite, LHRH-(1–5) (2004)

Given the central role of the decapeptide LHRH in reproduction and reproductive behavior, it is important to focus on delineating the possible effects of this gene and its products in the regulation of hormone-dependent reproductive processes. In the female, ovulation is preceded by a marked increase in LHRH release; the increase in LHRH release culminates in a preovulatory LH surge, which coincides with a period of sexual receptivity. In contrast to the belief that the proteolytic metabolism of LHRH serves only as a degradative process that removes excess LHRH and attenuates signal transduction through the LHRH receptor, we hypothesized that a metabolite of the decapeptide, LHRH-(1-5), can directly regulate LHRH neuronal function. This study demonstrates the ability of LHRH-(1-5) peptide to regulate LHRH gene expression in the LHRH neuronal cell line, the GT(1-7) cell. The results show that LHRH-(1-5) stimulated LHRH gene expression at the posttranscriptional level. In contrast to the LHRH suppression of its own gene expression, the coadministration of LHRH with the metalloendopeptidase, EC 3.4.24.15, an endopeptidase known to cleave LHRH to form LHRH(1-5), shows a reversal of effect, a stimulation of LHRH gene expression. Finally, the effect of LHRH-(1-5) on LHRH gene expression appears to be mediated by the calcium/calmodulin-dependent protein kinase. The present study supports the hypothesis that the physiological metabolite of LHRH, LHRH-(1-5), is functionally capable of regulating the reproductive neuroendocrine system.
Circadian Periodicity of Intestinal Na+/Glucose Cotransporter 1 mRNA Levels Is Transcriptionally Regulated (1998)

Intestinal expression of the high affinity Na+/glucose cotransporter 1 (SGLT1), which absorbs dietary glucose and galactose, exhibits both circadian periodicity in its activity and induction by dietary carbohydrate. Because the daily variation in SGLT1 activity is established by the feeding schedule (whether ad libitum or imposed) and persists in the absence of food, this variation has been described as anticipatory. To delineate the mechanisms regulating SGLT1, its expression was examined in rats maintained in a 12-h photoperiod with free access to chow. SGLT1 mRNA levels varied significantly, with the maximum abundance occurring near the onset of dark and the minimum near the onset of light. The SGLT1 transcription rate was 7-fold higher in the morning (1000-1100 h) than in the afternoon (1600-1700 h). An element for hepatocyte nuclear factor 1 (HNF-1) was identified in the SGLT1 promoter that formed different complexes with small intestinal nuclear extracts, depending on the time when the source animal was killed. Serological tests indicated that HNF-1alpha was present in complexes throughout the day, while HNF-1beta binding exhibited circadian periodicity. We propose that exchange of HNF-1 dimerization partners contributes to circadian changes in SGLT1 transcription. Because SGLT1 mRNA levels also varied in rhesus monkeys (offset by approximately one-half day from rats), a similar mechanism appears to be present in primates.
Cardiomyocytes induce endothelial cells to trans-differentiate into cardiac muscle: Implications for myocardium regeneration (2001)

The concept of tissue-restricted differentiation of postnatal stem cells has been challenged by recent evidence showing pluripotency for hematopoietic, mesenchymal, and neural stem cells. Furthermore, rare but well documented examples exist of already differentiated cells in developing mammals that change fate and trans-differentiate into another cell type. Here, we report that endothelial cells, either freshly isolated from embryonic vessels or established as homogeneous cells in culture, differentiate into beating cardiomyocytes and express cardiac markers when cocultured with neonatal rat cardiomyocytes or when injected into postischemic adult mouse heart. Human umbilical vein endothelial cells also differentiate into cardiomyocytes under similar experimental conditions and transiently coexpress von Willebrand factor and sarcomeric myosin. In contrast, neural stem cells, which efficiently differentiate into skeletal muscle, differentiate into cardiomyocytes at a low rate. Fibroblast growth factor 2 and bone morphogenetic protein 4, which activate cardiac differentiation in embryonic cells, do not activate cardiogenesis in endothelial cells or stimulate trans-differentiation in coculture, suggesting that different signaling molecules are responsible for cardiac induction during embryogenesis and in successive periods of development. The fact that endothelial cells can generate cardiomyocytes sheds additional light on the plasticity of endothelial cells during development and opens perspectives for cell autologous replacement therapies.
Cross-talk between LPA1 and Epidermal Growth Factor Receptors Mediates Up-regulation of Sphingosine Kinase 1 to Promote Gastric Cancer Cell Motility and Invasion (2008)

Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are lysophospholipid mediators of diverse cellular processes important for cancer progression. S1P is produced by two sphingosine kinases, SphK1 and SphK2. Expression of SphK1 is elevated in many cancers. Here, we report that LPA markedly enhanced SphK1 mRNA and protein in gastric cancer MKN1 cells but had no effect on SphK2. LPA also up-regulated SphK1 expression in other human cancer cells that endogenously express the LPA(1) receptor, such as DLD1 colon cancer cells and MDA-MB-231 breast cancer cells, but not in HT29 colon cancer cells or MDA-MB-453 breast cancer cells, which do not express the LPA(1) receptor. An LPA(1) receptor antagonist or down-regulation of its expression prevented SphK1 and S1P(3) receptor up-regulation by LPA. LPA transactivated the epidermal growth factor receptor (EGFR) in these cells, and the EGFR inhibitor AG1478 attenuated the increased SphK1 and S1P(3) expression induced by LPA. Moreover, down-regulation of SphK1 attenuated LPA-stimulated migration and invasion of MNK1 cells yet had no effect on expression of neovascularizing factors, such as interleukin (IL)-8, IL-6, urokinase-type plasminogen activator (uPA), or uPA receptor induced by LPA. Finally, down-regulation of S1P(3), but not S1P(1), also reduced LPA-stimulated migration and invasion of MKN1 cells. Collectively, our results suggest that SphK1 is a convergence point of multiple cell surface receptors for three different ligands, LPA, EGF, and S1P, which have all been implicated in regulation of motility and invasiveness of cancer cells.
Direct correlation between MUC18 expression and metastatic potential of human melanoma cells (1993)

The expression of the glycoprotein MUC18 in melanoma biopsies has previously been shown to increase with increasing tumour thickness, and thus to correlate with the probability of metastasis development. We have examined the expression of this molecule by nine human melanoma cell lines with known metastatic ability (both spontaneous and experimental) in nude mice. Examination of the expression of both the MUC18 mRNA and of the glycoprotein on the cell surface revealed a statistically significant correlation (P = 0.040) between its expression and the ability to form metastases in vivo. Although MUC18 shows sequence similarity to neural cell adhesion molecules, no correlation was observed between the site of origin of the metastatic lesions (brain, lymph node) and MUC18 expression.
Neonatal Intramuscular Injection with Recombinant Adeno-Associated Virus Results in Prolonged beta-Glucuronidase Expression in Situ and Correction of Liver Pathology in Mucopolysaccharidosis Type VII Mice (1999)

For many metabolic diseases, early correction of the inherited deficiency is required to prevent long-term sequelae. We examined the ability of adeno-associated virus (AAV) to mediate efficient gene transfer during the neonatal period in mice with the lysosomal storage disease mucopolysaccharidosis type VII (MPS VII). Quadriceps of newborn MPS VII mice were injected with an AAV vector containing human beta-glucuronidase (GUSB) cDNA. High-level intramuscular GUSB expression was seen as early as 2 weeks of age, and persisted for at least 16 weeks with no reduction in activity. In addition, GUSB activity was detected in both liver and spleen at later time points. The level of GUSB activity resulted in a significant reduction in lysosomal storage in the liver and a minimal reduction in the spleen at 16 weeks. However, the temporal and spatial pattern of hepatic GUSB activity, coupled with the presence of GUSB cDNA in liver sections, suggests that hematogenous dissemination of virus at the time of injection led to gene transfer to hepatic cells. These results demonstrate that AAV vectors can successfully infect neonatal muscle and persist through the rapid growth phase following birth. However, GUSB secretion from an intramuscular source is inefficient, limiting the therapeutic efficacy of this approach.
Validation of methodologies for quantifying isolated human islets: an islet cell resources study (2009)

Standard counting procedures for enumerating isolated stained human islets is a valid methodology, but computer-assisted digital image analysis assessment of islet mass has the added benefit of providing a permanent record of the isolated islet product being evaluated that improves quality assurance operations of current good manufacturing practice.
1Mb Non-Volatile Random Access Memory Using Oxide Semiconductor (2011)

We propose Non-Volatile Oxide Semiconductor Random Access Memory (NOSRAM) that is a novel memory including a transistor using an oxide semiconductor, In-Ga-Zn Oxide. OS transistors feature extremely low leakage current of about 100-600 yA/μm (1 yA = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-24</sup> A) at 85°C for example, and are applicable to memory elements. Our prototype of a 1Mb NOSRAM has achieved 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> write cycles, no need of erasing operation, low-voltage high-speed write, and the like. The NOSRAM is not theoretically degraded by data write while a flash memory is degraded every time data are written; therefore, our NOSRAM has the possibility to be used as a non-volatile memory superior to a flash memory.
Design, Synthesis and Biological Evaluation of Antagonists of LHRH by Criteria of Potency, Safety and Solubility (1991)

Some analogs of Antide and congeners with higher water solubility have been synthesized by substitutions in positions 1, 5 or 6 with hydrophilic residues. In position 1, D-3-Qal has been incorporated in four peptides and D-3-Pal in one peptide. In positions 5 and 6, D and L-3-Pal, PzAla and (DSer)Lys have been tried. In one peptide, D—(AcDSer)Lys was substituted in position 6. Most of the new analogs had lower AOA (antiovulatory activity) than the parent compounds but three potent analogs were identified. The first one, [N — Ac— D — 3-Qal 1 ,DpClPhe 2 ,D— 3-Pal 3 ,c-PzACAla 5 ,D — PicLys 6 ,ILys 8 ,D — Ala 10 ]— LHRH, had 55% AOA at 0.25 μg and 100% at 0.5 μg. Its ED 50 for in vitro histamine release was 171 ± 17 μg/ml which is an increase from 49±4.8 μg/ml for the parent compound with N—Ac-D-2-Nal [1]. The second analog, [N — Ac— D — 2-Nal 1 ,DpClPhe 2 ,D — 3-Pal 3 ,PicLys 5 ,D — (DSer)Lys 6 ,ILys 8 ,D—Ala 10 ] — LHRH, had 69% AOA at 0.25 μg and 95% at 0.5 μg. This analog released somewhat more histamine than the parent analog featuring D-PicLys 6 , the ED 50 being 18 μg/ml compared to 93 ± 11 for the parent analog. The third analog is: [N — Ac— D— 2-Nal 1 ,DpClPhe 2 ,D— 3-Pal 3 ,c-PzACAla 5 ,D—PzAla 6 ,ILys 8 ,DAla 1 ]— LHRH. The AOA for this analog was 63% at 0.25 μg and the ED 50 for histamine release 88±6.4 μg/ml.
Current understanding of methotrexate pharmacology and efficacy in acute leukemias. Use of newer antifolates in clinical trials. (2001)

Antifolates continue to be an extremely important class of drugs for the treatment of non-neoplastic as well as neoplastic diseases. New inhibitors that target dihydrofolate reductase as well as other folate-dependent enzymes are being evaluated in the clinic, and show promise.
A RANDOMIZED MULTICENTER TRIAL OF THE ANTI-ICAM-1 MONOCLONAL ANTIBODY (ENLIMOMAB) FOR THE PREVENTION OF ACUTE REJECTION AND DELAYED ONSET OF GRAFT FUNCTION IN CADAVERIC RENAL TRANSPLANTATION (1999)

Short term enlimomab induction therapy after renal transplantation did not reduce the rate of acute rejection or DGF.
A-Imilano apoprotein. Isolation and characterization of a cysteine-containing variant of the A-I apoprotein from human high density lipoproteins. (1980)

A recently discovered familial lipoprotein disorder is characterized by reduced plasma levels of high density lipoproteins (HDL) and elevated triglyceride levels. The clinical aspects of this disorder are presented in an accompanying article (Franceschini et al. 1980. J. Clin. Invest. 66: 892-900). The apoprotein content of the HDL isolated from these patients differed markedly from that of normal HDL in that three apoprotein bands not previously described in man were present as major protein components. As determined by sodium dodecyl sulfate (SDS) gel electrophoresis, the relative molecular weights (Mr) of these new apoprotein bands were 55,000, 35,000, and 28,000. Although the Mr 28,000 apoprotein coelectrophoresed with authentic A-I on SDS polyacrylamide gels and showed immunochemical identity with the A-I apoprotein when tested with monospecific apo-A-I antiserum, it contained two amino acid residues, cysteine and isoleucine, which were not present in the amino acid sequence of normal human apo-A-I. This variant form of the A-I apoprotein was designated the A-IMilano apoprotein and denoted A-Icys. By virtue of the presence of cysteine (2 mol/mol A-Icys), the A-Icys apoprotein was capable of forming intermolecular disulfide bonds, and dimer formation of A-Icys produced the Mr 55,000 apoprotein. The Mr 35,000 apoprotein was composed of two different subunits, A-Icys and A-II. By analogy to the apo(E--A-II) complex, which also occurs in human HDL, this mixed disulfide complex was designated as the apo(A-Icys--A-II) complex. The A-IMilano (A-Icys) is the first example of a variation in the primary sequence of a protein of plasma lipoproteins.