gebhart/patrepeval huggingface dataset:
Correcting for Wettability and Capillary Pressure Effects on Formation Tester Measurements (2000)

Abstract Conventional formation tester interpretation techniques have long assumed that the measured tester pressure is identical to the pressure of the continuos phase in the virgin zone of the formation. As such, a series of pressure measurements at different depths would be expected to consistently yield a pressure gradient corresponding to the density of the formation fluid. Recent work by the authors of this papers as well as by others has shown that the formation testers will actually measure the pressure of the continuos phase present in the invaded region, typically the drilling fluid filtrate. The measured tester pressure is, thus, different from formation pressure by the amount of capillary pressure. This capillary pressure has been shown to be a strong a function of the wetting phase saturation. The effects of the rock wettability and capillary pressure on wireline formation tester measurements are manifested as pressure gradient changes and/or fluid contact level changes on many logs, particularly those recorded with oil-based mud in the borehole. This paper summarizes the effects of wettability and capillary on wireline formation measurements and investigates in detail the possible techniques for recognition and estimation of and correction for those effects. The older techniques rely on the use of core capillary pressure data log-computed flushed zone saturations, but they can often yield inconsistent results. Amongst the more innovative techniques suggested in this paper is the use of NMR measurements to estimate the magnitude of capillary pressure effects and hence correct the measured tester pressure. Also discussed in the use of the pump-out capability of the Modular Dynamics Tester (MDTTM) to estimate the capillary pressure effect by making measurements before and after the removal of drilling mud filtrate. This allows accurate correction for capillary pressure effects, or better still, the elimination of the need for the correction altogether.
A calculated response: control of inflammation by the innate immune system (2008)

Inflammation is a rapid yet coordinated response that can lead to the destruction of microbes and host tissue. Triggers capable of inducing an inflammatory response include tissue damage and infection by pathogenic and nonpathogenic microbes. Each of these triggers represents a qualitatively distinct stress to the host immune system, yet our understanding of whether they are interpreted as such remains poor. Accumulating evidence suggests that recognition of these distinct stimuli converges on many of the same receptors of the innate immune system. Here I provide an overview of these innate receptors and suggest that the innate immune system can interpret the context of an inflammatory trigger and direct inflammation accordingly.
Connective tissue cells, cell proliferation and synthesis of extracellular matrix — a review (1975)

The ubiquitous connective tissues contain a wide range of cells including fibroblasts, osteoblasts and chondroblasts. Recently it has been demonstrated that another principal cell of the connective tissue is the smooth muscle cell in several organ systems. These have been shown to be responsible for the synthesis of the connective tissue matrix components of the uterine myometrium and of the arterial system, including collagen, both elastic fibre proteins and glycosaminoglycan. Microtubule inhibitors such as colchicine and vinblastine, and iron chelators such as alpha,alpha -dipyridyl have been used to study their morphologic and chemical effects on collagen synthesis and secretion. Colchicine produces an increase in large Golgi-associated vacuoles, which sometimes contain material reminiscent of aggregates of collagen macromolecules. Vinblastine produces alterations in the endoplasmic reticulum cisternae similar to alterations seen in ascorbic acid deficiency, and alpha,alpha-dipyridyl increases the frequency of regions in cells, interpretable as potential sites of communication of rough endoplasmic reticulum cisternae with the cell surface. Ferritin conjugated anti-procallagen sera were used to localize procollagen in cells and demonstrated procollagen not only in the cisternae of rough endoplasmic reticulum but in all of the elements of the Golgi complex as well. The studies reported in this review have shown that in cell culture arterial smooth muscle will produce not only the microfibrillar protein of the elastic fibre but soluble and/or insoluble elastin as well. Recent studies on serum factors responsible for the proliferation of connective tissue cells have demonstrated that at least one of the principal factors responsible for fibroblast and/or smooth muscle cell proliferation in culture is derived from thrombocytes. Medium containing serum derived from cell-free plasma lacks most of this proliferative effect which can be reinstated when platelets are present during recalcification to form serum. This effect is due to the platelet release reaction as shown by combining supernatant factors derived from platelets exposed to purified thrombin to cell-free, plasma derived serum. Studies with macrophages have also suggested that phagocytic macrophages release factor(s) into a cell culture medium that may also participate in stimulating fibroblasts to proliferate in vitro. The means by which these factors stimulate fibroblast proliferation and connective tissue synthesis remains to be elucidated.
Ethoxyresorufin-O-deethylase (EROD) Activity in Fish as a Biomarker of Chemical Exposure (2000)

This review compiles and evaluates existing scientific information on the use, limitations, and procedural considerations for EROD activity (a catalytic measurement of cytochrome P4501A induction) as a biomarker in fish. A multitude of chemicals induce EROD activity in a variety of fish species, the most potent inducers being structural analogs of 2,3,7,8-tetracholordibenzo-p-dioxin. Although certain chemicals may inhibit EROD induction/activity, this interference is generally not a drawback to the use of EROD induction as a biomarker. The various methods of EROD analysis currently in use yield comparable results, particularly when data are expressed as relative rates of EROD activity. EROD induction in fish is well characterized, the most important modifying factors being fish species, reproductive status and age, all of which can be controlled through proper study design. Good candidate species for biomonitoring should have a wide range between basal and induced EROD activity (e.g., common carp, channel catfish, and mummichog). EROD activity has proven value as a biomarker in a number of field investigations of bleached kraft mill and industrial effluents, contaminated sediments, and chemical spills. Research on mechanisms of CYP1A-induced toxicity suggests that EROD activity may not only indicate chemical exposure, but also may also precede effects at various levels of biological organization. A current research need is the development of chemical exposure-response relationships for EROD activity in fish. In addition, routine reporting in the literature of EROD activity in standard positive and negative control material will enhance confidence in comparing results from different studies using this biomarker.
Movable cameras enhance social telepresence in media spaces (2009)

Media space is a promising but still immature technology to connect distributed sites. We developed a simple additional function that moved a remote camera forward when a local user approached a display so that the approach was amplified by a remote person's expanding image accompanied by motion parallax. We conducted an experiment in which we observed that a movable camera enhanced social telepresence, which is the feeling of facing a remote person in the same room. Despite the camera's movement, subjects believed that the camera did not move and a zoom-in function expanded the image. Surprisingly, a zoom-in camera that expanded the image as the movable camera did, however, was ineffective probably because of a lack of motion parallax. Although we explained nothing about the camera, most subjects noticed that their walking caused the view's expansion. If a remote person initiated the camera's movement, social telepresence could not be enhanced.
Changes in absorbance of monolayer of living cells induced by laser radiation at 633, 670, and 820 nm (2001)

Redox absorbance changes in living cells (monolayer of HeLa cells) under laser irradiation at 633, 670, and 820 nm have been studied by the method of multichannel recording in spectral range 530-890 nm. It has been found that the irradiation causes changes in the absorption spectrum of the cells in two regions, near 754-795 nm (maxima at 757, 775, and 795 nm) and near 812-873 nm (maxima at 819, 837, 858, and 873 nm). Changes occur in band parameters (peak positions, width, and integral intensity). Virtually no changes occur in the red spectral region and a few changes are recorded in the green region near 556-565 nm. The results obtained evidence that cytochrome c oxidase becomes more oxidized (which means that the oxidative metabolism is increased) due to irradiation at all wavelengths used. The results of present experiment support the suggestion (Karu, Lasers Life Sci., 2:53, 1988) that the mechanism of low-power laser therapy at the cellular level is based on the electronic excitation of chromophores in cytochrome c oxidase which modulates /spl alpha/ redox status of the molecule and enhances its functional activity.
Oncogene expression cloning by retroviral transduction of adenovirus E1A-immortalized rat kidney RK3E cells: transformation of a host with epithelial features by c-MYC and the zinc finger protein GKLF. (1999)

The function of several known oncogenes is restricted to specific host cells in vitro, suggesting that new genes may be identified by using alternate hosts. RK3E cells exhibit characteristics of epithelia and are susceptible to transformation by the G protein RAS and the zinc finger protein GLI. Expression cloning identified the major transforming activities in squamous cell carcinoma cell lines as c-MYC and the zinc finger protein gut-enriched Kruppel-like factor (GKLF)/epithelial zinc finger. In oral squamous epithelium, GKLF expression was detected in the upper, differentiating cell layers. In dysplastic epithelium, expression was prominently increased and was detected diffusely throughout the entire epithelium, indicating that GKLF is misexpressed in the basal compartment early during tumor progression. The results demonstrate transformation of epithelioid cells to be a sensitive and specific assay for oncogenes activated during tumorigenesis in vivo, and identify GKLF as an oncogene that may function as a regulator of proliferation or differentiation in epithelia.
An Extensive Class of Small RNAs in Caenorhabditis elegans (2001)

The lin-4 and let-7 antisense RNAs are temporal regulators that control the timing of developmental events in Caenorhabditis elegans by inhibiting translation of target mRNAs. let-7 RNA is conserved among bilaterian animals, suggesting that this class of small RNAs [microRNAs (miRNAs)] is evolutionarily ancient. Using bioinformatics and cDNA cloning, we found 15 new miRNA genes in C. elegans. Several of these genes express small transcripts that vary in abundance during C. elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse.
Prospective Multi-Institutional Study Evaluating the Performance of Prostate Cancer Risk Calculators (2011)

The SRC performed better than the PRC, but neither one added clinical benefit for risk thresholds of less than 30%. Further research is needed to improve the AUCs of the risk calculators, particularly for higher-grade cancer.
Transduction of Phosphatase and Tensin Homolog Deleted on Chromosome 10 into Eosinophils Attenuates Survival, Chemotaxis, and Airway Inflammation (2007)

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is part of a complex signaling system that affects a variety of important cell functions. PTEN antagonizes the action of PI3K by dephosphorylating the signaling lipid phosphatidylinositol 3,4,5-triphosphate. In the present study, we used a TAT fusion protein transduction system to elucidate the role of PTEN in eosinophils and airway inflammation. A small region of the HIV TAT protein (YGRKKRRQRRR), a protein transduction domain known to enter mammalian cells efficiently, was fused to the N terminus of PTEN. Flow cytometric analysis of annexin V- and propidium iodide-stained cells was used to assess eosinophil survival. A chemotaxis assay was performed using a Boyden chamber. Cell analysis in bronchoalveolar lavage fluid and histological examinations were performed using OVA-challenged A/J mice. We found that TAT-PTEN was successfully internalized into eosinophils and functioned as a phosphatase in situ. TAT-PTEN, but not a TAT-GFP control protein, blocked the ability of IL-5 to prevent the apoptosis of eosinophils from allergic subjects. The eotaxin-induced eosinophil chemotaxis was inhibited by TAT-PTEN in a dose-dependent manner. Intranasal pretreatment with TAT-PTEN, but not TAT-GFP, significantly inhibited the OVA-induced eosinophil infiltration in bronchoalveolar lavage fluid. Histological examination of the lung, including H&E and Alcian blue/periodic acid-Schiff staining, revealed that TAT-PTEN, but not TAT-GFP, abrogated eosinophilic inflammation and mucus production. Our results suggest that PTEN negatively regulates eosinophil survival, chemotaxis, and allergic inflammation. The pharmacological targeting of PTEN may constitute a new strategy for the treatment of eosinophilic disorders.
Collagen-Poly(HEMA) Hydrogels for the Controlled Release of Anticancer Drugs—Preparation and Characterization (1990)

Copolymeric hydrogels of collagen and poly(hydroxyethyl meth acrylate) [poly(HEMA)] were prepared and were characterized using FT-IR spectroscopy, thermogravimetric analysis (TGA) and scanning electron micros copy (SEM). It was found that hydrogels containing about 5-10% (w/w) collagen were stable and resilient. As the collagen content was increased, there was a corresponding decrease in the resiliency and stability of the hydrogel in retain ing its physical form. The cumulative in vitro release profile of 5-fluorouracil from collagen-poly(HEMA) hydrogel matrix showed a zero-order pattern with a release rate of about 270 μg/day for a period of 10 days.
A 20-Nucleotide (A + U)-rich Element of β2-Adrenergic Receptor (β2AR) mRNA Mediates Binding to β2AR-binding Protein and Is Obligate for Agonist-induced Destabilization of Receptor mRNA (1997)

The Mr 35,000 beta-adrenergic receptor mRNA-binding protein, termed betaARB protein, is induced by beta-adrenergic agonists and binds to beta2-receptor mRNAs that display agonist-induced destabilization. A cognate sequence in the mRNA was identified previously that provides for betaARB protein binding in vitro. In the present work, the sequence established in vitro for binding of betaARB protein to hamster beta2-adrenergic receptor mRNA was probed in vivo by site-directed mutagenesis of the 3'-untranslated region and expression in Chinese hamster ovary cells. A 20-nucleotide, (A + U)-rich region in the 3'-untranslated region consisting of an AUUUUA hexamer flanked by defined U-rich regions constitutes the binding domain for betaARB protein. U to G substitution in the hexamer region attenuates the binding of betaARB protein, whereas U to G substitution of hexamer and flanking U-rich domains abolishes binding of betaARB protein and stabilizes beta2-adrenergic receptor mRNA levels in transfectant clones challenged with either isoproterenol or cyclic AMP. These results demonstrate that binding of betaARB protein to the 20-nucleotide, (A + U)-rich domain mediates the agonist and cyclic AMP-induced mRNA decay of G protein-linked receptors, such as the beta2-adrenergic receptor.
Thermoplastic film camera for holographic recording of extended objects in industrial applications (1982)

Optimization of a thermoplastic film recording camera and its performance for holography of extended objects are reported. Special corona geometry and accurate control of development heat by constant current heating and high-resolution measurement of the development temperature enable easy recording of reproducible, large aperture holograms. Experimental results for transfer characteristics, diffraction efficiency characteristics, and spatial frequency response are given.
Production and characterization of a bispecific IgG capable of inducing T-cell-mediated lysis of malignant B cells (1993)

Bispecific monoclonal antibodies (bsabs) recognizing both CD3 and a tumor antigen can redirect T-cell-mediated cytotoxicity toward cells bearing that antigen. Such bsabs have been shown to be more effective than monospecific monoclonal antibodies (MoAbs) at preventing tumor growth in animal models of B-cell malignancy. The current studies describe the production and preliminary evaluation of a bsab designed to induce the lysis of malignant human B cells by human T cells. The bsab was obtained from a hybrid-hybridoma cell line produced by fusing OKT3-secreting hybridoma cells with hybridoma cells that secrete 1D10. 1D10 is an MoAb that recognizes an antigen found on a majority of malignant human B cells that has not been detected to a significant degree on normal resting or activated lymphocytes. High performance liquid chromatography (HPLC) was used to separate bsab from monospecific antibodies that were also present in the hybrid-hybridoma antibody product. The bsab was then evaluated in vitro for its ability to induce lysis of malignant B cells by activated T cells. The bsab consistently induced extensive lysis in vitro of 1D10 (+) cells, including both cell lines and cells obtained from patients with a variety of B-cell malignancies. No such effect was seen with activated T cells alone or activated T cells with monospecific antibody. No increased lysis was seen with 1D10 (-) cell lines. The bsab also mediated lysis of malignant B cells by autologous T cells. We conclude bsab containing an OKT3 arm and a 1D10 arm can induce T-cell-mediated lysis in a manner that is both potent and specific. This supports further evaluation of this bsab as a potential immunotherapy of B-cell malignancy.
Primase couples leading- and lagging-strand DNA synthesis from oriC. (1994)

Coupling of leading- and lagging-strand DNA synthesis at replication forks formed at Escherichia coli oriC has been studied in vitro using a replication system reconstituted with purified proteins. At low concentrations of primase (8 nM), the major replication products were multigenome-length molecules, generated by a rolling circle-type mechanism, and unit-length molecules. Rolling circle DNA replication was inhibited at high concentrations of primase (80 nM) and the major replication products were half-unit-length leading strands and a distinct population of short Okazaki fragments. At low primase concentrations, an asymmetric mode of DNA synthesis occurred. Each strand was made independently and initiation could occur outside of oriC. At high primase concentrations, initiation occurred exclusively at oriC and two coupled replication forks proceeded bidirectionally around the plasmid. Presumably, at low concentrations of primase, DnaB (the replication fork helicase) unwound the plasmid DNA before replication forks could form, leading to initiation at sites other than oriC. On the other hand, high concentrations of primase resulted in successful capture of the helicase leading to the formation at oriC of coupled replication forks capable of coordinated leading- and lagging-strand synthesis.
Demonstration of Nondeterministic Quantum Logic Operations Using Linear Optical Elements (2002)

Knill, Laflamme, and Milburn [Nature (London) 409, 46 (2001)] recently showed that nondeterministic quantum logic operations could be performed using linear optical elements, additional photons (ancilla), and postselection based on the output of single-photon detectors. Here we report the experimental demonstration of two logic devices of this kind, a destructive controlled-NOT (CNOT) gate and a quantum parity check. These two devices can be combined with a pair of entangled photons to implement a conventional (nondestructive) CNOT that succeeds with a probability of 1/4.
Antidepressants for major depressive disorder in patients with a co-morbid axis-III disorder (2010)

The objective of this study is to assess whether the antidepressants are effective in treating major depressive disorder (MDD) in patients with a co-morbid axis-III disorder, and to compare the relative efficacy (vs. placebo) of antidepressants between these patients and those enrolled in general MDD trials. Medline/Pubmed publication databases were searched. We selected for randomized, double-blind, placebo-controlled trials of antidepressants for MDD, whether conducted in a general population, or in populations with an axis-III disorder. Antidepressants were more effective than placebo in patients with axis-III disorders overall [risk ratio for response (RR)=1.42, P<0.0001], as well as specifically for post-stroke (RR=1.43, P=0.04), human-immunodeficiency virus positive or acquired immunodeficiency syndrome (RR=1.66, P=0.005), but not cancer patients (RR=1.26, P=0.19). There was a trend for higher placebo response rates in studies, which did (41.2%) versus those which did not (37.7%) select for axis-III disorders (P=0.06), and significantly higher antidepressant response rates in studies which did (57.4%) versus those which did not (53.5%) select for axis-III disorders (P=0.01). Antidepressants are effective for MDD in patients who present with co-morbid axis-III disorders and as effective (vs. placebo) in this population as they are in the general MDD population. Higher general response rates observed in the co-morbid MDD population are intriguing, and require replication.
Cardiac Na+Channel Dysfunction in Brugada Syndrome Is Aggravated by β1-Subunit (2000)

It is suggested that coexpression of hbeta(1) exposes a more severe functional defect that results in a greater overlap in the relationship between channel inactivation and activation (window current) in T1620M, which is proposed to be a potential pathophysiological mechanism of IVF in vivo. One possible explanation for our finding is an altered alpha-/beta(1)-subunit association in the mutant.
Effects of a 3-Month Endurance Event on Physical Performance and Body Composition: The G2 Trans-Greenland Expedition☆ (2003)

Although the number of subjects was limited, this observational study demonstrated that well-trained and experienced long-distance ski trekkers who eat an adequate high-calorie diet can perform endurance treks in severe cold, with little or no loss of lean mass and physical capability.
Catalytic Antisense DNA Molecules Targeting Egr-1 Inhibit Neointima Formation following Permanent Ligation of Rat Common Carotid Arteries (2002)

Animal models of neointima (NI) formation have proven useful in gaining insights into the mechanisms of restenosis after coronary angioplasty and stenting, but the events at a molecular level remain incompletely understood. Here, we describe a technically straightforward, rat model of NI formation, involving complete ligation of the common carotid artery and demonstrate the importance of the immediate-early gene and zinc finger transcription factor Egr-1 in this process. Acute cessation of common carotid blood flow by vessel ligation, was followed by the expression of Egr-1 in the arterial media within 3 h and NI formation proximal to the point of ligation at 18 days. Local delivery of catalytic oligodeoxynucleotides (ODN) targeting rat Egr-1 mRNA at the time of ligation reduced both Egr-1 expression and NI formation in this model. In contrast, a scrambled version of this ODN had no inhibitory effect. These studies demonstrate for the first time that arterial intimal thickening following artery ligation is critically-dependent on the activation of Egr-1.