gebhart/patrepeval huggingface dataset:
Activators of Protein Kinase C Enhance Accumulation of Interferon-β mRNA in Murine Cell Lines (1989)

Murine C127 fibroblasts carrying an expression vector for a human interferon gene (HuIFN-beta, under the control of a constitutive promoter) can be induced to produce murine (Mu) IFN by double-stranded (ds) RNA or virus infection. Fibroblasts treated with the protein kinase C activators 1-oleyl-2-acetylglycerol (OAG) or phorbol-12-myristate-13-acetate (PMA) secrete greater amounts of MuIFN than untreated cells, but the same amount of HuIFN-beta. Accordingly, the level of MuIFN-beta mRNA increases in the presence of protein kinase C activators whereas that of HuIFN-beta mRNA is unchanged. In time course experiments after induction with dsRNA, accumulation of MuIFN-beta mRNA is observed within 30 min in the presence of OAG, when this mRNA cannot be detected in control cells. The protein kinase C activators increase accumulation of MuIFN-beta mRNA, even in the presence of the inhibitor of protein synthesis cycloheximide. A similar increase in MuIFN-beta mRNA is observed in C243 fibroblasts treated with phorbol-12-myristate-13-acetate, but not in parental C127 cells. These findings suggest that protein kinase C does not promote synthesis of regulatory factors controlling transcription of IFN mRNA, but that it may be directly or indirectly involved in activation of such factors in some murine cell lines.
Electrochemical proton gradient across the cell membrane of Halobacterium halobium: effect of N,N'-dicyclohexylcarbodiimide, relation to intracellular adenosine triphosphate, adenosine diphosphate, and phosphate concentration, and influence of the potassium gradient (1980)

The proton motive force across the cell membrane of halobacterial cells has been estimated and compared to intracellular values of ATP, ADP, and inorganic phosphate concentrations with respect to the chemiosmotic hypothesis. The accumulation of 14C-labeled indicator substances, triphenylmethylphosphonium for the membrane potential and 5,5-dimethyloxazolidine-2,4-dione for the pH difference between the cell interior and the medium, has been measured in the cells. Values up to 270 mV for the proton motive force have been found in cells pretreated with N,N'-dicyclohexylcarbodiimide (DCCD, 10(-4) M, 30 degrees C, 12 h). Upon illumination a high membrane potential is generated, which is then gradually replaced by a large pH difference. Cells treated with lower DCCD concentrations show only an enhancement of membrane potential upon illumination; the pH difference remains at a low level. Under anaerobic dark conditions, untreated cells maintain a proton motive force of 120-140 mV, which is equilibrated with the intracellular levels of ATP, ADP, and inorganic phosphate. The pH gradient is 1 unit at pH 6 but 0 at pH 8. The membrane potential is low (60-80 mV) at pH 6 and high (120-130 mV) at pH 8. We propose that the proton translocating ATPase compensates for the lowered pH difference at high external pH values by enhancing the membrane potential. The concentration difference of the potassium ions influences the proton motive force and the intracellular ATP levels, apparently via its action on the membrane potential. When the difference of the chemical potential of the potassium ion, expressed in millivolts, exceeds the preexisting membrane potential, the intracellular ATP level is enhanced. When the difference of the chemical potential of the potassium ion (millivolts) is smaller than the membrane potential, the ATP level is decreased.
Sonic Hedgehog Opposes Epithelial Cell Cycle Arrest (1999)

Stratified epithelium displays an equilibrium between proliferation and cell cycle arrest, a balance that is disrupted in basal cell carcinoma (BCC). Sonic hedgehog (Shh) pathway activation appears sufficient to induce BCC, however, the way it does so is unknown. Shh-induced epidermal hyperplasia is accompanied by continued cell proliferation in normally growth arrested suprabasal cells in vivo. Shh-expressing cells fail to exit S and G2/M phases in response to calcium-induced differentiation and also resist exhaustion of replicative growth capacity. In addition, Shh blocks p21(CIP1/WAF1)-induced growth arrest. These data indicate that Shh promotes neoplasia by opposing normal stimuli for epithelial cell cycle arrest.
On the synthesis of 3,4-dihydroxyprolines. I. cis -Glycolation of 3,4-dehydroproline derivatives (1968)

The interaction of OsO4 and protected derivatives of 3,4-dehydro-DL-proline gives high yields of 2,3- trans -3,4- cis -3,4-dihydroxy-DL-proline derivatives, with only traces of the 2,3- cis -3,4- cis diastereoisomers. Corresponding a-glycolation with KMnO4 gives mixtures of the 2,3- trans -3,4- cis and 2,3-cis-3,4- cis isomers in the ratio 1 : 1. Separation of the components of such mixtures is extremely difficult. The free amino acids in these two families of the 3,4-dihydroxy-DL-prolines have been characterized. Epimerization at C2 of 2,3- cis derivatives occurs readily. O-Tosylation of the 2,3- cis series occurs more readily than for other hydroxyprolines. Esters of N,O,O-tritosyl-2,3- trans -3,4- cis -3,4-dihydroxyproline are converted very rapidly by mild alkali into the equivalent esters of X-tosylpyrrole-2-carboxylic acid. For the corresponding N,O,O-tritosyl carboxylic acid, decarboxylation also takes place during aromatization, to yield N-tosylpyrrole.
Dendritic cells and the intestinal bacterial flora: a role for localized mucosal immune responses (2003)

Mammals coexist in an overall symbiotic relationship with a complex array of commensal bacterial flora that colonizes the gastrointestinal tract. These intestinal bacteria interface with cells of the mucosal immune system, including DCs. Here we discuss mechanisms of interaction between intestinal bacteria and DCs and the role of localized gastrointestinal immune responses.
High-level expression of enzymatically active human Cu/Zn superoxide dismutase in Escherichia coli. (1986)

Expression of human Cu/Zn superoxide dismutase (SOD) with activity comparable to the human erythrocyte enzyme was achieved in Escherichia coli by using a vector containing a thermoinducible lambda PL promoter and a beta-lactamase-derived ribosomal binding site. The recombinant human SOD was found in the cytosol of disrupted bacteria and represented greater than 10% of the total bacterial protein. The enzyme was purified to homogeneity by salt precipitation, gel filtration chromatography, and ion exchange chromatography. The active enzyme was obtained in high yield only when 1 mol of copper and 1 mol of zinc were incorporated into each mol of subunit during bacterial growth or by reconstitution of the apoenzyme. Human Cu/Zn SOD produced in bacteria has an apparent subunit molecular mass of 19 kDa on NaDodSO4/polyacrylamide gels. The native enzyme behaves as a dimer of 32 kDa as determined by gel filtration. Sequence analysis of the NH2 terminus revealed that the first 14 amino acids corresponded to authentic human SOD except that the NH2-terminal alanine was not acetylated. Thus, the bacterial processing system readily removes the NH2-terminal methionine residue from recombinant human SOD.
Oxidative and nitrative DNA damage in animals and patients with inflammatory diseases in relation to inflammation-related carcinogenesis (2006)

Infection and chronic inflammation are proposed to contribute to carcinogenesis through inflammation-related mechanisms. Infection with hepatitis C virus, Helicobacter pylori and the liver fluke, Opisthorchis viverrini (OV), are important risk factors for hepatocellular carcinoma (HCC), gastric cancer and cholangiocarcinoma, respectively. Inflammatory bowel diseases (IBDs) and oral diseases, such as oral lichen planus (OLP) and leukoplakia, are associated with colon carcinogenesis and oral squamous cell carcinoma (OSCC), respectively. We performed a double immunofluorescence labeling study and found that nitrative and oxidative DNA lesion products, 8-nitroguanine and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), were formed and inducible nitric oxide synthase (iNOS) was expressed in epithelial cells and inflammatory cells at the site of carcinogenesis in humans and animal models. Antibacterial, antiviral and antiparasitic drugs dramatically diminished the formation of these DNA lesion markers and iNOS expression. These results suggest that oxidative and nitrative DNA damage occurs at the sites of carcinogenesis, regardless of etiology. Therefore, it is considered that excessive amounts of reactive nitrogen species produced via iNOS during chronic inflammation may play a key role in carcinogenesis by causing DNA damage. On the basis of our results, we propose that 8-nitroguanine is a promising biomarker to evaluate the potential risk of inflammation-mediated carcinogenesis.
DEVELOPMENT ON REINFORCED MORTAR BY FLY ASH FIBER AND APPLICATION TO OUTER-SHELL PRECAST CONCRETE MEMBERS : Studies on utilization of coal ash for coment products (1999)

This report describes test results on the mechanical properties of fly ash fiber reinforced mortar, and application of permanent precast forms to concrete members. As the test results, it was confirmed that the fly ash fiber reinforced mortar maintained excellent workability, high flexural strength and thermal resistance. Therefore, as the fly ash reinforced mortar precast form is thin and light, treatment in the site of construction is very easy. And the results of measurement of the strain at surfaces of the precast form, the fly ash fiber reinforced precast form possesses the full safety for lateral pressure due to ready mixed concrete.
Cellular Localization and Function of the Antiviral Protein, Ovine Mx1 (oMx1): II. The oMx1 Protein Is a Regulator of Secretion in an Ovine Glandular Epithelial Cell Line (2006)

We showed that oMx1 protein is secreted by oGE cells and that reduction in oMx1 protein levels by siRNA reduced secretion of ISG15, but not beta2MG. Results support the hypothesis that oMx1 is a regulator of secretion through unconventional secretory pathway(s).
Off-Axis Paths in Spherical Mirror Interferometers (1964)

When a spherical mirror interferometer is illuminated by an off-axis ray of light, the repeated reflections cause the ray to trace a path which lies on the surface of a hyperboloid, with the points of reflection on the mirrors on ellipses. Under special conditions, these ellipses may become circles, with the points of reflection displaced by an angle 2θ after every round trip. When 2νθ = 2μπ, ν and μ being integers, the rays retrace their paths. These ray paths give rise to additional resonances which were observed. Pictures of the points of reflection are reproduced. The theory is in good agreement with the experimental observations. In laser amplifiers these ray paths enable one to obtain long effective path lengths in the active medium which may be contained in a thin annular cylindrical or hyperboloidal shell.
Dose-Dependent Kinetics of Probenecid in Rhesus Monkeys -Intravenous Bolus Studies (1981)

14 bolus studies with probenecid in a dose range of 8.2--164 mg/kg were carried out in 3 monkeys. The protein binding of probenecid in the plasma was studied by an ultracentrifugation method. Plasma clearances of both total and unbound probenecid decreased with increasing doses, while the volume of distribution and fraction of metabolites excreted in the urine remained constant. The urinary excretion rates of probenecid and it metabolites were measured in a bladder-catheterized monkey and were found to be urine flow dependent. Since the rate-limiting step for the excretion of the metabolites did not depend on the formation rate only, biliary recycling was speculated.
Comparison of Traditional and Plethysmographic Methods for Measuring Pulsus Paradoxus (2004)

Measurement of PP using the pulse oximeter-pulse plethysmographic waveform offers a simple and noninvasive method for evaluating patients with airway obstruction.
Arterial Baroreflex Control of the Peripheral Vasculature in Humans (2008)

Arterial baroreceptors originating in the carotid arteries and aorta play a pivotal role in the rapid reflex adjustments that accompany acute cardiovascular stressors. There is now ample evidence to indicate that the arterial baroreflex remains functional during exercise by resetting in direct relation to the intensity of exercise from rest to maximum. Moreover, there is convincing evidence that a properly functioning arterial baroreflex is requisite for an appropriate neural cardiovascular response to exercise. Importantly, an understanding of the underlying means by which the baroreflex responds to changes in blood pressure has been elucidated. In this regard, both at rest and during exercise, alterations in stroke volume do not appear to contribute to the maintenance of arterial blood pressure (ABP) by the carotid baroreceptors (CBR), and therefore, any reflex-induced changes in cardiac output are the result of CBR-mediated changes in heart rate (HR). More importantly, it appears that CBR-induced changes in ABP are primarily mediated by alterations in vascular conductance with only minimal contributions from cardiac output. Therefore, the capacity of the CBR to regulate ABP depends critically on its ability to alter vascular tone both at rest and during exercise. Indeed, studies have clearly indicated that active and inactive skeletal muscle vascular beds contribute to mediating CBR-induced changes in ABP. The purpose of this review is to describe the mechanisms by which the CBR responds to alterations in ABP both at rest and during exercise in humans with a particular emphasis on the importance of baroreflex-mediated vascular responses.
A method for sequencing restriction fragments with dideoxynucleoside triphosphates (1978)

A rapid enzymatic approach is described for the sequence analysis of a 5' terminally labelled restriction fragment. It involves limited nicking of the strands of the molecule throughout the sequence by pancreatic DNAase I. The 3' hydroxyl groups exposed by each nick are then used to prime chain extension by DNA polymerase I in four separate reactions. Each reaction uses one of the four chain terminating dideoxynucleoside triphosphates (ddNT-PSs), together with the four deoxynucleoside triphosphates (dNTPs). In a single reaction all the 3' ends are terminated in positions of the same base, which is different for each of the four reactions. When the products of these reactions are resolved by gel electrophoresis according to size, a sequence can be deduced from the pattern of radioactive bands. Sequences can be determined onwards from 10-20 residues from the 5' labelled end. The length of sequence which can be determined is only limited by the resolution of the gel.
Proliferating subventricular zone cells in the adult mammalian forebrain can differentiate into neurons and glia. (1993)

Subventricular zone (SVZ) cells proliferate spontaneously in vivo in the telencephalon of adult mammals. Several studies suggest that SVZ cells do not differentiate after mitosis into neurons or glia but die. In the present work, we show that SVZ cells labeled in the brains of adult mice with [3H]thymidine differentiate directly into neurons and glia in explant cultures. In vitro labeling with [3H]thymidine shows that 98% of the neurons that differentiate from the SVZ explants are derived from precursor cells that underwent their last division in vivo. This report identifies the SVZ cells as neuronal precursors in an adult mammalian brain.
Recurrent Angiotensin-Converting Enzyme Inhibitor—Associated Angioedema (1997)

<h3>Context.</h3> —Angiotensin-converting enzyme (ACE) inhibitors are associated with an increased risk of angioedema, but the risk of recurrent angioedema if treatment is continued is not known. <h3>Objective.</h3> —To test the hypothesis that the association between ACE inhibitor use and angioedema may not be recognized and to determine characteristics of angioedema associated with continued use of ACE inhibitors. <h3>Design.</h3> —Retrospective cohort study. <h3>Setting.</h3> —Tennessee Medicaid program. <h3>Patients.</h3> —Medicaid enrollees aged 15 years or older who used an ACE inhibitor and had a first documented episode of angioedema between 1986 and 1992 were followed up for recurrent episodes through June 1993. <h3>Measurements and Main Results.</h3> —We previously identified 82 patients with a first confirmed diagnosis of angioedema during 51 752 person-years of ACE inhibitor use in this population (1.6 per 1000 person-years). Among these 82 patients, there were 16 outpatient recurrences of angioedema among 13 patients during 189 patient-years of follow-up (8.5 per 100 patient-years). The rate of angioedema was much higher in users of ACE inhibitors with continued exposure (18.7 per 100 patient-years) than in those whose use of the drug was discontinued (1.8 per 100 patient-years) (<i>P</i>=.001). Review of the medical records for patients taking ACE inhibitors who had recurrent angioedema revealed that physicians attributed angioedema to a number of causes not related to ACE inhibitor use, even after multiple recurrences. <h3>Conclusion.</h3> —Continuing use of ACE inhibitors in spite of angioedema results in a markedly increased rate of angioedema recurrence with serious morbidity.
Use of the automatic implantable cardioverter-defibrillator in the treatment of malignant ventricular tachyarrhythmias. (1984)

Since February, 1980 nearly 200 automatic cardioverter - defibrillators have been implanted in patients with malignant ventricular arrhythmias. The currently-employed device weighs 298 grams and occupies a volume of 162 cm3. There are two defibrillation electrodes which also serve as sensors: one, an intravascular catheter placed in the superior vena cava at the level of the right atrium; the other, a flexible rectangular patch placed extrapericardially over the apex of the heart. Additionally, there is a bipolar right ventricular electrode for rate counting and R-wave synchronization which will eventually be used for pacing as well. The unit is powered by lithium batteries with a projected monitoring life of three years, or the capability of discharging approximately 100 times. The arrhythmia detector activates the cardioverter -defibrillator about 15 to 20 seconds after diagnosing a "treatable" arrhythmia, identified on the basis of a striking absence of isoelectric potential segments characteristic of ventricular fibrillation and many ventricular tachycardias. The diagnosis also requires fulfillment of individually-programmed heart rate criteria. If the initial discharge of 25 joules is ineffective, the device will recycle as many as three times with a final pulse of up to 42 joules. Of the twelve nonsurvivors among the initial 52 implantees who underwent implantation through September, 1982, only four deaths were unwitnessed and considered to be sudden and arrhythmic; the other eight deaths were due to heart failure or unrelated causes. Thus, from a predicted mortality of 48% in the same group of patients if the automatic defibrillator had not been implanted, the "sudden death" mortality was reduced to 8.5%.
Architectural Principles for Virtual Computer Systems (1973)

he most important new result of the thesis is the model of a process running on a virtual computer system (VCS) and the derivation of design principles from that model. The approach adopted is to consider the introduction of VCS's into the rich, complex architectures likely to be found in 4th generation systems. The model allows us to understand different properties of virtual machines and to interpret a number of proposed implementations of VCS's in terms of the model. Furthermore, the model leads naturally to an implementation of virtual machines, the Hardware Virtualizer (HV) which provides an efficient and simplified mechanism for virtual machines. A number of detailed examples illustrate how the Hardware Vitualizer might operate in an actual 4th generation system.
Transport of Vitamin B 12 in Escherichia coli : Genetic Studies (1973)

The chromosomal location of two genetic loci involved in the transport of cyanocobalamin (B(12)) in Escherichia coli K-12 was determined. One gene, btuA, is believed to code for the transport protein in the cytoplasmic membrane, because a mutant with an alteration in this gene has lost the ability to accumulate B(12) within the cell although normal levels of the surface receptors for B(12) are present. The other locus, btuB, apparently codes for the surface receptor on the outer membrane. These mutants have lost the ability to bind B(12) and have greatly reduced transport activity, although growth experiments have shown that they can utilize B(12) for growth, but with decreased efficiency. This surface receptor for B(12) also appears to function as the receptor for the E colicins, because btuB mutants are resistant to the E colicins, and mutants selected for resistance to colicin E1 are defective in B(12) binding and transport. The gene order was determined by transduction analysis to be cyc-argH-btuA-btuB-rif-purD. In addition, mutations in metH, the gene for the B(12)-dependent homocysteine methylating enzyme, were obtained in this study. This gene was localized between metA and malB.
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection (2015)

Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.
Concentration-dependent increase of murine P388 and B16 population doubling time by the acyclic monoterpene geraniol. (1991)

Geraniol, an acyclic end product of a plant isoprene pathway and a pyrophosphorylated intermediate in plant and animal pathways, caused a concentration-dependent increase in the population doubling time of murine P388 leukemia cells in suspension culture and of B16 melanoma cells in monolayer culture. The suppression of the growth of P388 cells by geraniol (0-0.9 mM) and by mevinolin (0-0.25 microM), a competitive inhibitor of mevalonate biosynthesis, was reversed by the addition of 0.5 mM mevalonolactone to the growth medium. Flow cytometry of asynchronous B16 cells grown with geraniol (0-0.15 mM) revealed a population characterized by larger cells with altered nuclear characteristics. Over the course of four studies, dietary geraniol increased the 50% survival time of mice by 10, 29, 33, and 50% following the i.p. transfer of P388 cells. The results of the latter study showed that, following the i.p. transfer of 1 x 10(5) P388 cells, the control group of female C57BL x DBA/2 F1 mice had a 50% survival time of 24 days and a maximum survival of 27 days. Mice fed a diet containing 0.1% geraniol for 14 days prior to and following the P388 cell transfer had a 50% survival time of 36 days, and 20% of the mice remained free of tumors during the 50-day trial. These studies support the possibility that monoterpenes and other isoprenoid products of plant metabolism are in part responsible for the anticarcinogenic actions of diverse fruits, vegetables, and cereal products.
Image denoising: Can plain neural networks compete with BM3D? (2012)

Image denoising can be described as the problem of mapping from a noisy image to a noise-free image. The best currently available denoising methods approximate this mapping with cleverly engineered algorithms. In this work we attempt to learn this mapping directly with a plain multi layer perceptron (MLP) applied to image patches. While this has been done before, we will show that by training on large image databases we are able to compete with the current state-of-the-art image denoising methods. Furthermore, our approach is easily adapted to less extensively studied types of noise (by merely exchanging the training data), for which we achieve excellent results as well.