gebhart/patrepeval huggingface dataset:
Mechanical and Geometrical Tortuosities: Vanishing and Appearing Tortuosities (2021)

ABSTRACT Tortuosity is one of the critical factors to be considered for complex directional well trajectories, complicated build rates, precise steering in thin reservoirs, and extended reach wells. This paper discusses the pitfalls of estimating tortuosity to quantify borehole quality and answers questions, such as whether the claimed benefits (i.e., enhanced drilling performance, improved hole cleaning, ease of running casing, and superior cement operations) can be fully attributed to reduced borehole tortuosity. Running casing may mask the tortuosity present in the as drilled open hole wellbore section. This vanishing tortuosity alters the apparent "wellbore quality" and the new tortuosity representative of the cased hole path may present new appearing tortuosity. Both vanishing and appearing tortuosity are generally neglected in engineering calculations. Conventional methods to calculate tortuosity are based on the predetermined shape of the trajectory using the minimum curvature method. Wellbore undulation (geometrical tortuosity) is determined using geometrical measurements such as inclination, azimuth, and calculated displacement; however, much of this wellbore undulation vanishes after the casing is run, and thus the cased off wellpath appears smoother. This apparent change in wellbore tortuosity results from the flexural stiffness and rigidity of the casing pipes, and the compression and tension loads along the length of the casing string. Acquiring a subsequent survey along the cased well path yields new inclinations, azimuths, and displacements. This new survey records wellpath undulations resulting from the casings path through the original open hole wellbore geometry and what we call tubular undulation (mechanical tortuosity) which is specific to the path and position of the casing within the wellbore. The smoothing of the wellpath resulting from the casing masking original wellbore tortuosity results in the original geometrical tortuosity vanishing while the new undulations resulting from the mechanical tortuosity of the casing causes additional tortuosity to appear. The comparison between the geometrical and mechanical tortuosity provides a method of quantifying the vanishing and appearing tortuosity.
Toward the implementation of a topic specific dialogue based natural language chatbot as an undergraduate advisor (2013)

In this work, we explain the design of a chat robot that is specifically tailored for providing FAQBot system for university students and with the objective of an undergraduate advisor in student information desk. The chat robot accepts natural language input from users, navigates through the Information Repository and responds with student information in natural language. In this paper, we model the Information Repository by a connected graph where the nodes contain information and links interrelates the information nodes. The design semantics includes AIML (Artificial Intelligence Mark up Language) specification language for authoring the information repository such that chat robot design separates the information repository from the natural language interface component. Correspondingly, in the experiment, we constructed three experimental systems (a pure dialog systems associated with natural language knowledge based entries, a domain knowledge systems engineered with information content and a hybrid system, combining dialog and domain knowledge). Consequently, the information repository can easily be modified and focussed on particular topic without recreating the code design. Experimental parameters and outcome suggests that topic specific dialogue coupled with conversational knowledge yield the maximum dialogue session than the general conversational dialogue.
Advantage of a baculovirus expression system for protein-protein interaction studies. Involvement of posttranslational phosphorylation in the interaction between wt p53 protein and poly(ADP-ribose) polymerase-1. (2005)

We recently observed an interaction between poly(ADP-ribose) polymerase-1 (PARP-1) and the tumor suppressor p53 protein. However, more extensive studies on both proteins, especially those on characterization of their domains involved in the interaction were difficult due to very low expression levels of p53 in mammalian cells. Therefore, we generated recombinant proteins for such studies. To clarify which domains of human PARP-1 and of human wild-type (wt) p53 were involved in this protein-protein interaction, we generated baculoviral constructs encoding full length or distinct functional domains of both proteins. Full length PARP-1 was simultaneously coexpressed in insect cells with full length wt p53 protein or its distinct truncated fragments and vice versa. Reciprocal immunoprecipitation of Sf9 cell lysates revealed that the central and carboxy-terminal fragments of p53 each were sufficient to confer binding to PARP-1, whereas the amino-terminal part harbouring the transactivation functional domain was dispensable. On the other hand, the amino-terminal and central fragments of PARP-1 were both necessary for complex formation with p53 protein. Since the most important features of p53 protein are regulated by phosphorylation, we addressed the question whether its phosphorylation is essential for the binding between the two proteins. Baculovirally expressed wt p53 was post-translationally modified. At least six distinct p53 isomers were resolved by immunoblotting following two-dimensional separation of baculovirally expressed wt p53 protein. Using specific phospho-serine antibodies, we identified phosphorylation of baculovirally expressed p53 protein at five distinct sites. To define the role of p53 phosphorylation, pull-down assays using untreated and dephosphorylated p53 protein were performed. Dephosphorylated p53 failed to bind PARP-1, indicating that complex formation between the two proteins was regulated by phosphorylation of p53. The marked phosphorylation of p53 at Ser392 observed in unstressed cells suggests that the phosphorylated carboxy-terminal part of p53 undergoes complex formation with PARP-1 resulting in masking of the NES and thereby preventing its export.
The future of EPAC-targeted therapies: agonism versus antagonism (2015)

Pharmaceutical manipulation of cAMP levels exerts beneficial effects through the regulation of the exchange protein activated by cAMP (EPAC) and protein kinase A (PKA) signalling routes. Recent attention has turned to the specific regulation of EPAC isoforms (EPAC1 and EPAC2) as a more targeted approach to cAMP-based therapies. For example, EPAC2-selective agonists could promote insulin secretion from pancreatic β cells, whereas EPAC1-selective agonists may be useful in the treatment of vascular inflammation. By contrast, EPAC1 and EPAC2 antagonists could both be useful in the treatment of heart failure. Here we discuss whether the best way forward is to design EPAC-selective agonists or antagonists and the current strategies being used to develop isoform-selective, small-molecule regulators of EPAC1 and EPAC2 activity.
Magnetic characterization of isolated candidate vertebrate magnetoreceptor cells (2012)

Over the past 50 y, behavioral experiments have produced a large body of evidence for the existence of a magnetic sense in a wide range of animals. However, the underlying sensory physiology remains poorly understood due to the elusiveness of the magnetosensory structures. Here we present an effective method for isolating and characterizing potential magnetite-based magnetoreceptor cells. In essence, a rotating magnetic field is employed to visually identify, within a dissociated tissue preparation, cells that contain magnetic material by their rotational behavior. As a tissue of choice, we selected trout olfactory epithelium that has been previously suggested to host candidate magnetoreceptor cells. We were able to reproducibly detect magnetic cells and to determine their magnetic dipole moment. The obtained values (4 to 100 fAm(2)) greatly exceed previous estimates (0.5 fAm(2)). The magnetism of the cells is due to a μm-sized intracellular structure of iron-rich crystals, most likely single-domain magnetite. In confocal reflectance imaging, these produce bright reflective spots close to the cell membrane. The magnetic inclusions are found to be firmly coupled to the cell membrane, enabling a direct transduction of mechanical stress produced by magnetic torque acting on the cellular dipole in situ. Our results show that the magnetically identified cells clearly meet the physical requirements for a magnetoreceptor capable of rapidly detecting small changes in the external magnetic field. This would also explain interference of ac powerline magnetic fields with magnetoreception, as reported in cattle.
Inhibition of organ invasion by the matrix metalloproteinase inhibitor batimastat (BB-94) in two human colon carcinoma metastasis models. (1995)

The effect of the matrix metalloproteinase inhibitor batimastat was evaluated in two human colorectal cancer metastasis models involving: (a) the liver-invasive tumor C170HM2 and (b) the lung-invasive tumor AP5LV, both of which have been shown to express the M(r) 72,000 type IV collagenase. Batimastat at concentrations between 0.01 and 3.0 micrograms/ml had no direct cytotoxic effects on the in vitro growth of the cell lines. In the liver-invasive tumor model, batimastat administered i.p. from day 10 to termination of the therapy (day 39) at 40 mg/kg reduced both the mean number of liver tumors (35% of vehicle-treated control; P < 0.05) and the cross-sectional area of the tumors (43% of vehicle-treated control; P < 0.05). In the lung-invasive tumor model, batimastat administered daily (40 mg/kg i.p.) significantly reduced tumor weight within the lung (72% of vehicle-treated control; P < 0.05) but did not significantly affect nodule number. In the latter model, in which the take rate was unaffected, tumor cells were introduced into the lateral tail vein, and lung localization may have been a physical phenomenon not involving invasion. In the former model, tumor cells were introduced directly into the peritoneal cavity, and from there the cells adhered to and invaded the liver capsule. Because the take rate is significantly reduced, it may be that the matrix metalloproteinases are involved in this process. Batimastat may be a therapeutic modality for the treatment of colorectal cancer metastasis.
Antiplaque properties of sustained release SnF<sub>2</sub>: pilot studies (1984)

Pilot studies examining the physical and clinical properties of an intracoronal sustained release fluoride delivery system were performed. After testing various percentages of SnF2 incorporated into polycarboxylate, zinc phosphate, and zinc oxide cements, 70% SnF2 polycarboxylate cement was found to have adequate compressive strength while releasing the greatest amount of fluoride in vitro. A 30-day in vivo trial, in which this fluoride cement was used as a temporary intracoronal restoration, produced elevated salivary fluoride levels with only transient elevation in urinary fluoride levels. Plaque scores decreased during the experimental period, suggesting that the released SnF2 affected bacterial growth or attachment. The SnF2-polycarboxylate cement was an adequate temporary restorative material without significant side effects.
P53 and induction of apoptosis as a target for anticancer therapy. (1996)

p53 is the most frequently mutated gone in human cancer cells. Its wild-type gone encodes for a protein with pivotal functions: (i) interaction with key players in the cell cycle leading to cell cycle arrest; (ii) induction of programmed call death, or apoptosis. P53 may be seen as another member of the family of proteins involved in resistance to anticancer therapy, since mutations/deletions involving the p53 gene lead frequently to resistance of radiation/cytotoxic drug treatment. Consequently, patients with p53-mutated tumors may harbor a worse prognosis. On the other hand, reintroducing wild-type P53 may lead to an adequate function of the cellular cell cycle and/or apoptosis program, thus enabling efficient anti-cancer therapy even in the presence of mutated P53. Two options are being discussed: (i) gene therapy approaches; (ii) modulating mutated P53 with yet unknown molecules.
Effects of Ethanol and Methanol on Lipid Metabolism in Bacillus subtilis (1980)

In Bacillus subtilis, the fatty acid moiety of the phospholipids was affected differently during growth in the presence of 1.1 M-methanol or 0.7 M-ethanol, though at these concentrations methanol and ethanol had the same effects on growth rate and completely inhibited sporulation. Synthesis of phosphatidylglycerol was also strongly inhibited and the amount of total cell phospholipids was reduced by 50% by both alcohols. The composition of fatty acids, especially the relative concentration of 12-methyltetradecanoic acid, was modified only by ethanol; in bacteria grown in the presence of methanol, changes in fatty acid composition were negligible. In non-sporulating mutants, synthesis of phosphatidylglycerol was much less affected than in the wild-type and synthesis of phosphatidylethanolamine was increased. In these strains, fatty acid composition was also modified by ethanol but unaffected by methanol.
Tumor-Associated Macrophages Promote Angiogenesis and Melanoma Growth via Adrenomedullin in a Paracrine and Autocrine Manner (2011)

Our study reveals a novel mechanism that TAMs enhance angiogenesis and melanoma growth via ADM and provides potential targets for melanoma therapies.
Fabrication and characterization of nanomaterial-based sensors using dielectrophoresis (2010)

Dielectrophoresis (DEP) is an electrokinetic motion of dielectrically polarized materials in nonuniform electric fields. DEP has been successfully applied to manipulation of nanomaterials including carbon nanotubes (CNTs), metallic nanoparticles, and semiconducting nanowires. Under positive DEP force, which attracts nanomaterials toward the higher field region, nanomaterials are trapped in the electrode gap and automatically establish good electrical connections between them and the external measuring circuit. This feature allows us a fast, simple, and low-cost fabrication of nanomaterial-based sensors based on a bottom-up approach. This paper first presents a theoretical background of DEP phenomena and then reviews recent works of the present author, which were aimed to develop nanomaterial-based sensors, such as a CNT gas sensor and a ZnO nanowire photosensor, using DEP fabrication technique. It is also demonstrated that DEP technique enables self-formation of interfaces between various nanomaterials, which can be also applicable as novel sensing transducers.
pH-dependence and structure–activity relationships in the papain-catalysed hydrolysis of anilides (1971)

The pH-dependence of the Michaelis-Menten parameters for the papain-catalysed hydrolysis of N-acetyl-l-phenylalanylglycine p-nitroanilide was determined. The equilibrium binding constant, K(s), is independent of pH between 3.7 and 9.3, whereas the acylation constant, k(+2), shows bell-shaped pH-dependence with apparent pK(a) values of 4.2 and 8.2. The effect of substituents in the leaving group on the acylation constant of the papain-catalysed hydrolysis of hippuryl anilides and N-acetyl-l-phenylalanylglycine anilides gives rise in both series to a Hammett rho value of -1.04. This indicates that the enzyme provides electrophilic, probably general-acid, catalysis, as well as the nucleophilic or general-base catalysis previously found. A mechanism involving a tetrahedral intermediate whose formation is general-base-catalysed and whose breakdown is general-acid-catalysed seems most likely. The similarity of the Hammett rho values appears to exclude facilitated proton transfer as a means through which the specificity of papain is expressed.
Radiolabeled Multimeric Cyclic RGD Peptides as Integrin α<sub>v</sub>β<sub>3</sub>Targeted Radiotracers for Tumor Imaging (2006)

Integrin alphavbeta3 plays a significant role in tumor angiogenesis and is a receptor for the extracellular matrix proteins with the exposed arginine-glycine-aspartic (RGD) tripeptide sequence. These include vitronectin, fibronectin, fibrinogen, lamin, collagen, Von Willibrand's factor, osteoponin, and adenovirus particles. Integrin alphavbeta3 is expressed at low levels on epithelial cells and mature endothelial cells, but it is overexpressed on the activated endothelial cells of tumor neovasculature and some tumor cells. The highly restricted expression of integrin alphavbeta3 during tumor growth, invasion, and metastasis presents an interesting molecular target for both early detection and treatment of rapidly growing solid tumors. In the past decade, many radiolabeled linear and cyclic RGD peptide antagonists have been evaluated as the integrin alphavbeta3 targeted radiotracers. Significant progress has been made on their use for imaging tumors of different origin by single photon emission computed tomography (SPECT) or positron emission tomography (PET) in several tumor-bearing animal models. [18F]Galacto-RGD is under clinical investigation as the first integrin alphavbeta3 targeted radiotracer for noninvasive visualization of the activated integrin alphavbeta3 in cancer patients. This review will focus on the radiolabeled multimeric cyclic RGD peptides (dimers and tetramers) useful as radiotracers to image the tumor integrin alphavbeta3 expression by SPECT and PET, and some fundamental aspects for the development of integrin alphavbeta3 targeted radiotracers. These include the choice of radionuclide and bifunctional chelators, selection of targeting biomolecules, and factors influencing the integrin alphavbeta3 binding affinity and tumor uptake, as well as different approaches for modification of radiotracer pharmacokinetics.
<title>Highly Versatile Computer-Controlled Television Detector System</title> (1982)

A computer-controlled intensified television detector, sensitive to Photons between 1μ and 0.05Å, has been built for a wide range of applications, including X-ray astrophysics and observational astronomy. A digitally controlled intensified SIT vidicon camera generates a high resolution image which is digitally processed in real time and integrated in a large, high-speed memory system. The camera electronics can also accommodate CCD arrays or any other raster readout detector or camera. A thin scintillator or phosphor convertor deposited on a fiber optics faceplate is used for X-ray and vacuum ultraviolet applications. Active areas from 4 to 80 mm square and larger can be selected and easily changed. For rates of up to 104 or 105 events/sec the centroid of each event can be computed, while rates of up to 10<sup>12</sup>/sec can be accommodated by continuously digitizing and storing the video signal at each pixel. The camera scan rates and formats and the size and location of the scanned and gated areas of the target are under software control. The data acquisition and processing parameters and operating modes are also under software control. Interactive control and monitoring allow the detector system to be optimally configured for each anplication. Any array size un to 4000x4000 pixels can be selected. The spatial resolution depends on the active area, operating mode, and TV tube resolution, and ranges from 10μ to 200μ. A typical low-cost 25 mm system has a resolution of about 30μ in the photon counting mode and 100μ in the A/D mode. The memory system accommodates up to 16M words of 12 to 24 bits, and can display the integrated image during and after accumulation. Modular construction allows the detector system or any of its subsystems to be easily duplicated at a low cost.
Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1 (1991)

Deletion mutants of Escherichia coli specific for hydrogenase isoenzyme 1 (HYD1) have been constructed and characterized. The hya operon, which contains genes for the two HYD1 structural subunits and four additional genes, was mapped at 22 min on the E. coli chromosome. The total hydrogenase activities of the HYD1-negative mutant and wild-type strains were similar. However, the formate dehydrogenase activity associated with the formate hydrogen lyase pathway was lower in the mutant. The hya mutant (strain AP1), complemented with only the hydrogenase structural genes (hyaAB), produced antigenically identifiable but inactive HYD1 protein. The first five genes of hya (hyaA to hyaE) were required for the synthesis of active HYD1, but wild-type levels of HYD1 activity were restored only when mutant cells were transformed with all six genes of the operon. When AP1 was complemented with hya carried on a high-copy-number plasmid, the HYD1 structural subunits were overexpressed, but the excess protein was unprocessed and localized in the soluble fraction of the cell. The products of hyaDEF are postulated to be involved in the processing of nascent structural subunits (HYAA and HYAB). This processing takes place only after the subunits are inserted into the cell membrane. It is concluded that the biosynthesis of active HYD1 is a complex biochemical process involving the cellular localization and processing of nascent structural subunits, which are in turn dependent on the insertion of nickel into the nascent HYD1 large subunit.
Reaction of Anion Exchange Resins with 1-Bromo-2-chloroethane (1962)

1-プロム-2-クロルエタンに塩素,臭素およびフッ素形陰イオン交換樹脂AmberliteIRA-400をそれぞれ反応させ,種々のハロゲン原子2個の組み合わぜからなるジハロゲンエタンの生成を試みた。すなわち1-プロム-2-クロルエタン2mlと塩素および臭素形陰イオン交換樹脂2gとを封管中で50°～140℃で種々の時間のもとで反応させた。たとえば140℃,3時間では塩素形陰イオン交換樹脂を使用した場合,1,2-ジクロルエタン13.8×10-3molと1,2-ジブロムエタン2.4×10-3molを得た。臭素形陰イオン交換樹脂の場合は1,2-ジクロルエタン7.5×10-3molと1,2-ジブロムエタン5.1×10-3molを得た。これらの反応は反応前の陰イオン交換樹脂のもつハロゲンの置換によるのみならず,使用した陰イオン交換樹脂(ハロゲン形)の触媒的な働きによるものと考えられる。つぎにフッ素形陰イオン交換樹脂の場合は1-プロム-2-クロルエタン20mlとフッ素形陰イオン交換樹脂20gとを反応させた。その結果,140℃,3時間では3種のフッ素化合物,1,2-ジフルオルエタン16.2,1-クロル-2-フルオルエタン13.3および1-プロム-2-フルオルエタン5.4×10-3mo1を得た。なおフッ素化合物のほかに1,2-ジクロルエタンと1,2-ジブロムエタンを90.0,41.2×10-8得た。このように1,2-ジクロルエタンや1,2-ジブロムエタンが生成されるのはフッ素形陰イオン交換樹脂が塩素または臭素形に一部置換された陰イオン交換樹脂が未反応の1-プロム-2-クロルエタンと反応するためと考えられる。
3‐D in vitro model of early skeletal muscle development (2003)

An understanding of the mechanical and mechano-molecular responses that occur during the differentiation of mouse C2C12 [corrected] myoblasts in 3-D culture is critical for understanding growth, which is important for progress towards producing a tissue-engineered muscle construct. We have established the main differences in force generation between skeletal myoblasts, dermal fibroblasts, and smooth muscle cells in a 3-D culture model in which cells contract a collagen gel construct. This model was developed to provide a reproducible 3-D muscle organoid in which differences in force generation could be measured, as the skeletal myoblasts fused to form myotubes within a collagen gel. Maintenance of the 3-D culture under sustained uni-axial tension, was found to promote fusion of myoblasts to form aligned multi-nucleate myotubes. Gene expression of both Insulin Like Growth Factor (IGF-1 Ea) and an isoform of IGF-1 Ea, Mechano-growth factor (IGF-1 Eb, also termed MGF), was monitored in this differentiating collagen construct over the time course of fusion and maturation (0-7 days). This identified a transient surge in both IGF-1 and MGF expression on day 3 of the developing construct. This peak of IGF-1 and MGF expression, just prior to differentiation, was consistent with the idea that IGF-1 stimulates differentiation through a Myogenin pathway [Florini et al., 1991: Mol. Endocrinol. 5:718-724]. MGF gene expression was increased 77-fold on day 3, compared to a 36-fold increase with IGF-1 on day 3. This indicates an important role for MGF in either differentiation or, more likely, a response to mechanical or tensional cues.