gebhart/patrepeval huggingface dataset:
Pure Culture Fermentation of Brined Cucumbers (1964)

The relative abilities of Pediococcus cerevisiae, Lactobacillus plantarum, L. brevis, and several other species of lactic acid bacteria to grow and produce acid in brined cucumbers were evaluated in pure culture fermentations. Such fermentations were made possibly by the use of two techniques, gamma radiation (0.83 to 1.00 Mrad) and hot-water blanching (66 to 80 C for 5 min), designed first to rid the cucumbers of naturally occurring, interfering, and competitive microbial groups prior to brining, followed by inoculation with the desired lactic acid bacteria. Of the nine species tested, strains of the three common to cucumber fermentations, P. cerevisiae, L. plantarum, and L. brevis, grew to the highest populations, and produced the highest levels of brine acidity and the lowest pH values in fermentations at 5.4 to 5.6% NaCl by weight; also, their sequence of active development in fermentations, with the use of a three-species mixture for inoculation, was in the species order just named. This sequence of occurrence was similar to that estimated by others for natural fermentations. The rates of growth and acid production in fermentations with a mixture of P. cerevisiae, L. plantarum, and L. brevis increased as the incubation temperature was increased from 21 to 27 to 32 C; however, the maximal populations and acidities attained were essentially the same for fermentations at each temperature. Further, these same three species were found to be the most salt tolerant of those tested; their upper limit for appreciable growth and measurable acid production was about 8% salt, whereas thermophilic species such as L. thermophilus, L. lactis, L. helveticus, L. fermenti, and L. delbrueckii exhibited a much lower salt tolerance, ranging from about 2.5 to 4.0%. However, certain strains of L. delbrueckii grew very rapidly in cucumbers brined at 2.5 to 3.0% salt, and produced sufficient acid in about 30 hr at 48 C to reduce the brine pH from above 7.0 to below 4.0. An inexpensive, pure culture fermentor which was suitable for gamma radiation, resistant to salt and acid, and which permitted repeated aseptic sampling of the fermenting brine, is illustrated and the specifications are given.
V.—The Geology of the Dolgelley Gold-belt, North Wales (1910)

Bryn-y-groes Lode .—About 500 yards east of the Clogau lode, there is a parallel lode which has been worked for copper. Striking 50° east of north, its outcrop may be traced for about 1½ miles; its width is very variable. Chalcopyrite and pyrites and a little gold are present in the quartz. The lode is confined to the Vigra Beds, and running with the beds, it is associated throughout its length with greenstone sills.
Maskless Projection Lithography for the Fast and Flexible Generation of Grayscale Protein Patterns (2012)

Protein patterns of different shapes and densities are useful tools for studies of cell behavior and to create biomaterials that induce specific cellular responses. Up to now the dominant techniques for creating protein patterns are mostly based on serial writing processes or require templates such as photomasks or elastomer stamps. Only a few of these techniques permit the creation of grayscale patterns. Herein, the development of a lithography system using a digital mirror device which allows fast patterning of proteins by immobilizing fluorescently labeled molecules via photobleaching is reported. Grayscale patterns of biotin with pixel sizes in the range of 2.5 μm are generated within 10 s of exposure on an area of about 5 mm(2) . This maskless projection lithography method permits the rapid and inexpensive generation of protein patterns definable by any user-defined grayscale digital image on substrate areas in the mm(2) to cm(2) range.
The dragon processor (1987)

The Xerox PARC Dragon is a VLSI research computer that uses several techniques to achieve dense code and fast procedure calls in a system that can support multiple processors on a central high bandwidth memory bus.
An approximate timing analysis method for datapath circuits (1996)

We present a novel timing analysis method ACD that computes an approximate value for the delay of datapath circuits. Based on the conditional delay matrix (CDM) formalism we introduced earlier, the ACD method exploits the fact that most datapath signals are directed by a small set of control inputs. The signal propagation conditions are restricted to a set of predefined control inputs, which results in significant reductions in the size of the conditions as well as computation time. We have implemented ACD and experimented with reverse-engineered high-level versions of the ISCAS-85 benchmarks. Our results demonstrate up to three orders of magnitude speedup in computation time over exact methods, with little or no loss in accuracy.
The clinically used PARP inhibitor olaparib improves organ function, suppresses inflammatory responses and accelerates wound healing in a murine model of third‐degree burn injury (2017)

This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
Organic Anion Transporter Family: Current Knowledge (2006)

Organic anion transporters (OATs) play an essential role in the elimination of numerous endogenous and exogenous organic anions from the body. The renal OATs contribute to the excretion of many drugs and their metabolites that are important in clinical medicine. Several families of multispecific organic anion and cation transporters, including OAT family transporters, have recently been identified by molecular cloning. The OAT family consists of six isoforms (OAT1 - 4, URAT1, and rodent Oat5) and they are all expressed in the kidney, while some are also expressed in the liver, brain, and placenta. The OAT family represents mainly the renal secretory and reabsorptive pathway for organic anions and is also involved in the distribution of organic anions in the body, drug-drug interactions, and toxicity of anionic substances such as nephrotoxic drugs and uremic toxins. In this review, current knowledge of and recent progress in the understanding of several aspects of OAT family members are discussed.
Zur Berechnung elektrostatischer Linsen (1955)

Es wird gezeigt, daß sich die Matrizendarstellung, die sehr häufig zur rechnerischen Behandlung von Vierpollinsen angewandt wird, z. B. 1.2 , mit Vorteil auch auf rotationssymmetrische und ebene elektrostatische Felder übertragen läßt. Die Integration der Bahngleichung von geladenen Teilchen in elektrischen Feldern nach der Gans schen Methode wird in Matrizenform geschrieben. Das dabei entstehende Matrizenprodukt, in der richtigen Reihenfolge ausmultipliziert, läßt dann sogleich alle charakteristischen Eigenschaften einer Linse erkennen. Das allgemeine Verhalten mehrerer hintereinandergeschalteter Linsen kann jetzt in übersichtlicher Weise angegeben werden. Außerdem wird gezeigt, wie man den Matrizenkalkül auch zur numerischen Berechnung der charakteristischen Daten eines Linsensystems verwenden kann. Dabei werden insbesondere die Linsensysteme ins Auge gefaßt, die zur ersten Fokussierung in Teilchenbeschleunigern wie Van de Graaff- oder Kaskadengeneratoren dienen.
The Treatment of Thoracic Empyema (1932)

Physician-in-Charge of Out-Patients
HfO[sub 2] Films Grown by ALD Using Cyclopentadienyl-Type Precursors and H[sub 2]O or O[sub 3] as Oxygen Source (2006)

thin films have been deposited onto p-Si(100) substrates by atomic layer deposition (ALD) using or and water or ozone as precursors. The purity of films was better when ozone instead of water was used as oxygen precursor. The use of together with ozone in the ALD window range, viz. 350–400°C, yielded films with less than 0.1 atom % C and H impurities. -processed film contained C and Cl, but again the use of ozone considerably reduced the impurity levels. When using as the metal source, the higher reactivity of ozone as compared to yielded slightly higher growth rate, smoother morphology, higher degree of crystallinity for thicker films, and a close to ideal density. Furthermore, with ozone no inhibition of the growth during initial ALD cycles could be detected. The growth of film on H-terminated Si with the process was retarded and the initial island-like growth took place resulting in rougher surface. With the process, the films showed the best leakage current density characteristics. Slightly higher capacitance equivalent oxide thickness values were calculated for the ozone-processed films.
UPTAKE KINETICS AND INTRACELLULAR LOCALIZATION OF HYPOCRELLIN PHOTOSENSITIZERS FOR PHOTODYNAMIC THERAPY: A CONFOCAL MICROSCOPY STUDY (1995)

Hypocrellins are naturally occurring compounds with photosensitizing properties in biological systems. We have prepared synthetic derivatives of hypocrellin B, which have promise as photosensitizers in the clinical application of photodynamic therapy. The intracellular localization and uptake kinetics of hypocrellin B and several selected hypocrellin congeners were determined semiquantitatively by fluorescence confocal microscopy in monolayer cultures of EMT6/Ed murine tumor cells. Each compound had unique uptake kinetics. Although no compound tested to date has demonstrated nuclear labeling, most could be detected in lysosomes, Golgi, endoplasmic reticulum and, to a minor extent, in cellular membranes. No two compounds gave identical labeling distributions. The differences are assumed to originate in physicochemical properties characteristic of each compound, which may ultimately impact upon the primary modality of phototoxicity.
<title>Effect of atmospheric turbulence on bit-error rate in an on-off-keyed optical wireless system</title> (2002)

Atmospheric turbulence produces scintillation at an optical receiver, which leads to fading of the received signal. This fading affects the bit-error-rate (BER) of a digital signal in a way that depends on the depth of the fade, the decision threshold at the receiver, and the average signal-to-noise ratio. The degree of fading can be dramatically reduced by the use of a time-delayed diversity technique, which involves retransmission of the data stream after a short delay, and resynchronization of the received data streams.
Induction and Repression of Pseudomonas aeruginosa Amidase (1964)

The synthesis of an inducible amidase by Pseudomonas aeruginosa 8602/a was studied in cultures growing exponentially in succinate medium. Induction by both the substrate inducer acetamide, and the non-substrate inducer N-acetylacetamide, was repressed by cyanoacetamide. Induction by 10−2mN-acetylacetamide was significantly repressed by 10−4m-cyanoacetamide, but repression of induction by 10−3m-acetamide required a tenfold excess of cyanoacetamide. Amidase synthesis in a medium in which acetamide was the sole carbon + nitrogen source was also repressed by cyanoacetamide, which under these conditions inhibited the growth of non-induced bacteria. Several tricarboxylic acid cycle intermediates, and related compounds, repressed amidase synthesis in exponentially growing organisms. Catabolite repression by propionate in succinate medium was decreased by increasing the concentration of acetamide. These findings are discussed in relation to general theories of regulation of microbial enzyme synthesis.
Oriented Reconstitution of a Membrane Protein in a Giant Unilamellar Vesicle: Experimental Verification with the Potassium Channel KcsA (2011)

We report a method for the successful reconstitution of the KcsA potassium channel with either an outside-out or inside-out orientation in giant unilamellar vesicles, using the droplet-transfer technique. The procedure is rather simple. First, we prepared water-in-oil droplets lined with a lipid monolayer. When solubilized KcsA was encapsulated in the droplet, it accumulated at monolayers of phosphatidylglycerol (PG) and phosphoethanolamine (PE) but not at a monolayer of phosphatidylcholine (PC). The droplet was then transferred through an oil/water interface having a preformed monolayer. The interface monolayer covered the droplet so as to generate a bilayer vesicle. By creating chemically different lipid monolayers at the droplet and oil/water interface, we obtained vesicles with asymmetric lipid compositions in the outer and inner leaflets. KcsA was spontaneously inserted into vesicles from the inside or outside, and this was accelerated in vesicles that contained PE or PG. Integrated insertion into the vesicle membrane and the KcsA orientation were examined by functional assay, exploiting the pH sensitivity of the opening of the KcsA when the pH-sensitive cytoplasmic domain (CPD) faces toward acidic media. KcsA loaded from the inside of the PG-containing vesicles becomes permeable only when the intravesicular pH is acidic, and the KcsA loaded from the outside becomes permeable when the extravesicular pH is acidic. Therefore, the internal or external insertion of KcsA leads to an outside-out or inside-out configuration so as to retain its hydrophilic CPD in the added aqueous side. The CPD-truncated KcsA exhibited a random orientation, supporting the idea that the CPD determines the orientation. Further application of the droplet-transfer method is promising for the reconstitution of other types of membrane proteins with a desired orientation into cell-sized vesicles with a targeted lipid composition of the outer and inner leaflets.
Reciprocal and Complementary Role of <i>MET</i> Amplification and <i>EGFR</i> T790M Mutation in Acquired Resistance to Kinase Inhibitors in Lung Cancer (2010)

These results indicate a reciprocal and complementary relationship between T790M and MET amplification and the necessity of concurrent inhibition of both for further improving patient outcomes.
Comparison of Nd : YAG capsulotomy rates following phacoemulsification with implantation of PMMA, silicone, or acrylic intra-ocular lenses in four European countries (2004)

A low incidence of posterior capsular opacification (PCO) and Nd : YAG laser treatment was detected in hydrophobic acrylic IOLs in comparison to three other types of IOLs implanted in a large cohort of persons with age-related cataract. Choice of IOL type may reduce the need for Nd : YAG laser treatment, although further research on the reasons for this is needed.
Immobilized enzyme reaction stability: Attrition of the support material (1974)

Abstract One of the main reasons for immobilizing an enzyme is to enable its reuse, or continuous use, in a reactor. Consequently immobilized enzyme stability is an important factor in enzyme reactor design. The performance of the reactor will decrease if during operation the support material disintegrates into smaller particles that pass out of the reactor system. When β‐galactosidase is immobilized by covalent attachment to AE‐cellulose, the smaller particles have a higher activity. After subjection of the immobilized enxyme to a shear stress the average particle size decreases and the total enzymic activity increases. A loss of small particles from the reactor, although constituting a small weight percent loss of support, will result in a disproportionately large loss in activity. The relevance of these observations to reactor performance is discussed.
DC-Bias-Field-Induced Dielectric Relaxation in Antiferroelectric Phase of TFMHPOBC (1993)

Dielectric properties in TFMHPOBC (4-(1,1,1-trifluoromethyl-heptyloxycarbonyl) phenyl 4'-octyloxybiphenyl-4-carboxylate) have been investigated as functions of temperature and dc bias field. In the antiferroelectric phase under no bias field, relaxation due to the soft mode and molecular rotation around the short axis are observed. Under dc bias field, a new relaxation is observed in chiral smectic C A (Sm C A * ). The dielectric strength of this relaxation depends on the bias field, while the relaxation frequency is not affected by the dc bias field.
Selective increase in the urinary excretion of protein 1 (Clara cell protein) and other low molecular weight proteins during normal pregnancy (1992)

The effect of normal pregnancy on the tubular transport of proteins has been studied by measuring four low molecular weight (Mr) proteins in the urine of pregnant women: protein 1 (a recently discovered urinary protein identical to Clara cell protein), beta 2-microglobulin, retinol-binding protein and alpha 1-microglobulin. The urinary excretion of albumin and beta-N-acetylglucosaminidase was also determined. One hundred and fourteen women with uncomplicated pregnancy were examined: 22 in the first trimester, 42 in the second and 50 in the third trimester. They were compared to 40 age-matched non-pregnant women. The urinary excretion of the four low Mr proteins was significantly increased during the second and third trimester of pregnancy. During the last trimester, the mean relative increases in the urinary excretion of these proteins ranged from 2.8 to 15.6 and prevalences of elevated values from 25 to 46%. This rise in low Mr urinary protein excretion was particularly important in some pregnant women, representing (e.g. for protein 1) more than a 100-fold increase above normal. The urinary excretion of beta-N-acetyl-D-glucosaminidase was also increased during pregnancy but the albuminuria remained stable. These changes in low Mr urinary proteins were reversible after delivery and most likely resulted from a transient decrease in the reabsorptive capacity of the proximal tubule associated with an increase of the filtered load. However, some women excreted high amounts of protein 1 which could not be accounted for by a decreased tubular reabsorption and which might originate from a secretion by the urogenital tract.
Changes in sodium, potassium, and adenosine triphosphate contents of red blood cells in sepsis and septic shock. (1982)

Sepsis and septic shock were induced in fifteen awake rabbits by the infusion of live Escherichia coli. Sodium K+, and adenosine triphosphate (ATP) concentrations in red blood cells (RBC) and plasma were measured during the control, septic, and septic shock periods. The significant elevations of Na+ content in RBC during sepsis appeared to be primarily a function of increased cell membrane permeability. The significantly decreased intracellular K+ concentrations, accompanying the high Na+ levels of RBC later in shock, were consistent with progressive failure of the energy-dependent transport mechanism (Na+-k+ pump). Hyponatremia and hyperkalemia were apparent in the late stages of sepsis, these alterations reached statistically significant levels in the shock period. The electrolyte derangements associated with sepsis and septic shock could not be related to energy depletion. The continuous significant accumulations of ATP, observed in RBC and plasma, were interpreted as a result of decreased energy utilization and attributed to the diminished active ion transport by the impaired Na+-K+ pump.
Chirality in regioregular and soluble polythiophene: An internal probe of conformational changes induced by minute solvation variation (1996)

Chirality has been used as an internal probe of structural changes accompanying micro‐aggregation of a soluble regioregular poly(alkylthiophene). First, the synthesis of new polythiophenes having long alkyl chains is described. The UV/vis and circular dichroic spectroscopy are shown to indicate that the transformation of a disordered species in solution into an ordered one in a micro‐aggregated state is a two‐step process. Tentative proposals are made about the nature of the intermediate state, which, however, remains unclear.
Fabrication of Highly Crystalline Corundum-Structured α-(Ga<sub>1-<i>x</i></sub>Fe<sub><i>x</i></sub>)<sub>2</sub>O<sub>3</sub>Alloy Thin Films on Sapphire Substrates (2009)

Highly crystalline corundum-structured α-(Ga1-xFex)2O3 alloy thin films were fabricated on c-plane sapphire substrates by using a mist chemical vapor deposition method. The full-widths at half maximum of X-ray diffraction rocking curves were smaller than 100 arcsec for the entire range of x from 0 to 1. Optical band gaps were artificially tuned to a value between those of α-Ga2O3 and α-Fe2O3, that is, 2.2 and 5.3 eV with changing the Fe content x in the films. Magnetic measurements revealed ferromagnetic properties of a α-(Ga1-xFex)2O3 (x = 0.24) thin film at 110 K.
Cytoskeletal involvement in the modulation of cell-cell junctions by the protein kinase inhibitor H-7 (1994)

The protein kinase inhibitor H-7 has been shown to block junction dissociation induced by low extracellular calcium in Madin Darby canine kidney epithelial cells (S. Citi, J. Cell Biol. (1992) 117, 169-178). To understand the basis of this effect, we have examined how H-7 affects the organization of junctions and the actin cytoskeleton in different types of epithelial cells in culture. Immunofluorescence microscopy showed that H-7 confers Ca2+ independence on cultured epithelial lens cells, which lack tight junctions and desmosomes but have microfilament-associated adherens junctions. In these cells, H-7 did not protect N-cadherin from trypsin digestion at low extracellular calcium, suggesting that H-7 does not stabilize the 'active' cadherin conformation. In cultured Madin Darby canine kidney cells, H-7 partially prevented the fall in transepithelial resistance induced by cytochalasin D, either alone or in conjunction with calcium chelators. Double-immunofluorescence microscopy showed that H-7 inhibits both the fragmentation of labeling for the tight junction protein cingulin and the condensation of actin into cytoplasmic foci induced by cytochalasin D. Taken together, these observations indicate that H-7 inhibits junction dissociation by affecting the contractility of the adherens junction-associated microfilaments following treatment with calcium chelators or cytochalasin D.
Differential Bvg Phase-Dependent Regulation and Combinatorial Role in Pathogenesis of Two <i>Bordetella</i> Paralogs, BipA and BcfA (2007)

To successfully colonize their mammalian hosts, many bacteria produce multiple virulence factors that play essential roles in disease processes and pathogenesis. Some of these molecules are adhesins that allow efficient attachment to host cells, a prerequisite for successful host colonization. Bordetella spp. express a number of proteins which either play a direct role in attachment to the respiratory epithelia or exhibit similarity to known bacterial adhesins. One such recently identified protein is BipA. Despite the similarity of BipA to intimins and invasins, deletion of this protein from B. bronchiseptica did not result in any significant defect in respiratory tract colonization. In this study, we identified an open reading frame in B. bronchiseptica, designated bcfA (encoding BcfA [bordetella colonization factor A]), that is similar to bipA. In contrast to the maximal expression of bipA in the Bvg intermediate (Bvg(i)) phase, bcfA is expressed at high levels in both the Bvg(+) and Bvg(i) phases. We show here that BvgA and phosphorylated BvgA bind differentially to the bcfA promoter region. Utilizing immunoblot assays, we found that BcfA is localized to the outer membrane and that it is expressed during animal infection. While deletion of either bipA or bcfA did not significantly affect respiratory tract colonization, concomitant deletion of both genes resulted in a defect in colonization of the rat trachea. Our results indicate that the two paralogous proteins have a combinatorial role in mediating efficient respiratory tract colonization.