gebhart/patrepeval huggingface dataset:
Stochastic Reservoir Simulation Using Neural Networks Trained on Outcrop Data (1998)

Abstract Extensive outcrop data or photographs of present day depositions or even simple drawings from expert geologists contain precious structural information about spatial continuity that is beyond the present tools of geostatistics essentially limited to two-point statistics (histograms and covariances). A neural net can be learned to collect multiple point statistics from various training images, these statistics are then used to generate stochastic models conditioned to actual data. In petroleum applications, the methodology developed can be a substitute for objects based-algorithms when facies geometry and reservoir continuity are too complex to be modeled by simple object such as channels. The performance of the neural net approach is illustrated using training images of increasing complexity, and attempts at explaining that performance is provided in each case. The neural net builds local probability distributions for the facies types (categorical case) or for petrophysical properties (continuous case). These local probabilities include multiple point statistics learned from training images and are sampled with a Metropolis-Hastings sampler which also ensures reproduction of statistics coming from the actual subsurface data such as locally varying facies proportions. P. 321
Frequency Trimming for MEMS Resonator Oscillators (2007)

This paper presents various frequency trimming methodologies with the focus on silicon based micromechanical resonators. The techniques include mechanical trimming and pure electronic trimming. The experimental results showed the frequency accuracy have reached 2.6 ppm for mechanical trimming and lppm for electronic trimming. Furthermore, the technique of digital electronic trimming resolved the temperature compensation issues for MEMS resonators at the same time.
Assay of thyroglobulin in serum with thyroglobulin autoantibodies: an unobtainable goal? (1995)

Measurement of thyroglobulin (Tg) in serum with anti-Tg autoantibodies (TgAb) represents a difficult challenge. Immunoradiometric assays (IRMA) employing monoclonal anti-Tg antibodies not cross-reacting with endogenous TgAb have recently been developed and proposed for Tg assays in TgAb-positive sera. The aim of the present investigation was to assess the clinical reliability of this approach. Assays of serum Tg in patients with and without TgAb using one such monoclonal antibody IRMA (Thyroglobulin IRMA-Pasteur; IRMA-1) were compared with those obtained by a conventional IRMA employing polyclonal anti-Tg antibodies (HTGK-Sorin; IRMA-2). Preliminary studies for assessment of the interference of TgAb showed that the recovery of added Tg was significantly higher (P < 0.01) when determined by IRMA-1 (64.6 +/- 23%) than by IRMA-2 (49.5 +/- 20%). Study groups included 79 patients with differentiated thyroid carcinoma (DTC) treated by total thyroidectomy and radioiodine ablation; 24 had no metastases or residual thyroid tissue, 31 had a thyroid residue, and 24 had metastatic disease. Seventy-five patients with autoimmune thyroid disease (47 with Graves' and 28 with Hashimoto's disease) were also included. In TgAb-negative sera from DTC patients, similar Tg concentrations were found by both IRMA, i.e. undetectable in most patients with no residual thyroid or neoplastic tissue, low to moderately elevated in the majority of those with residual thyroid tissue, and markedly elevated in all patients with metastatic disease. Serum Tg was undetectable by both assays in several TgAb-positive sera from DTC patients with residual thyroid tissue or metastatic disease, respectively, in whom a detectable or even high serum Tg concentration was expected. Despite the lower in vitro interference of TgAb in IRMA-1, there was no difference between the two assays. In the group of patients with thyroid autoimmune disease, serum Tg concentrations were found to be high in TgAb-negative sera and much lower in TgAb-positive sera by both IRMAs. In conclusion, the present study demonstrates that the use of a monoclonal antibody IRMA for serum Tg, although less susceptible to in vitro TgAb interference, does not necessarily provide any substantial advantage with respect to a conventional polyclonal IRMA in detecting Tg in TgAb-positive sera. The finding of undetectable or lower than expected serum Tg by either method in TgAb-positive serum may well reflect a truly reduced serum Tg concentration. This might be due to an accelerated Tg metabolic clearance in the presence of TgAb.(ABSTRACT TRUNCATED AT 400 WORDS)
A Quadripotential Mesenchymal Progenitor Cell Isolated from the Marrow of an Adult Mouse (1999)

Adult marrow contains mesenchymal progenitor cells (MPCs) that have multiple differentiation potentials. A conditionally immortalized MPC clone, BMC9, has been identified that exhibits four mesenchymal cell phenotypes: chondrocyte, adipocyte, stromal (support osteoclast formation), and osteoblast. The BMC9 clone, control brain fibroblasts and another marrow-derived clone, BMC10, were isolated from a transgenic mouse (H-2Kb-tsA58) containing a gene for conditional immortality. To test for chondrogenic potential, cells were cultured in defined medium containing 10 ng/ml transforming growth factor beta and 10-7 M dexamethasone in 15-ml polypropylene tubes ("aggregate cultures"). Adipogenic potential was quantitated by flow cytometry of Nile Red-stained cells cultured for 1 and 2 weeks in medium containing isobutyl methylxanthine, indomethacin, insulin, and dexamethasone. Support of osteoclast formation was measured by quantitating multinucleated tartrate-resistant acid phosphatase-positive cells in spleen cell cocultures of test clones (immortomouse clones and positive control ST2 cells) cultured in the presence of 10-7 M vitamin D3 and 150 mM ascorbate-2-phosphate. In vivo osteogenic potential was assayed by histologic examination of bone formation in subcutaneous implants, into athymic mouse hosts, of a composite of cells combined with porous calcium phosphate ceramics. The bone marrow-derived clone BMC9 has the potential to express each of the four mesenchymal characteristics tested, while brain fibroblasts, tested under identical conditions, did not exhibit any of these four mesenchymal characteristics. BMC10 cells exhibited osteogenic and chondrogenic phenotypes, but showed only minimal expression of adipocytic or osteoclast-supportive phenotypes. Clone BMC9 is, minimally, a quadripotential MPC isolated from the marrow of an adult mouse that can differentiate into cartilage and adipose, support osteoclast formation, and form bone. The BMC9 clone is an example of an adult-derived multipotential progenitor cell that is situated early in the mesenchymal lineage.
Concomitant S‐, N‐, and heme‐nitros(yl)ation in biological tissues and fluids: implications for the fate of NO in vivo (2002)

There is growing evidence for the involvement of nitric oxide (NO) -mediated nitrosation in cell signaling and pathology. Although S-nitrosothiols (RSNOs) have been frequently implicated in these processes, it is unclear whether NO forms nitrosyl adducts with moieties other than thiols. A major obstacle in assessing the significance of formation of nitrosated species is the limited reliability of available analytical techniques for measurements in complex biological matrices. Here we report on the presence of nitrosated compounds in plasma and erythrocytes of rats, mice, guinea pigs, and monkeys under basal conditions, in immunologically challenged murine macrophages in vitro and laboratory animals in vivo. Besides RSNOs, all biological samples also contained mercury-stable nitroso species, indicating the additional involvement of amine and heme nitros(yl)ation reactions. Significant differences in the amounts and ratios of RSNOs over N- and heme-nitros(yl)ated compounds were found between species and organs. These observations were made possible by the development of a novel gas-phase chemiluminescence-based technique that allows detection of nitroso species in tissues and biological fluids without prior extraction or deproteinization. The method can quantify as little as 100 fmol bound NO and has been validated extensively for use in different biological matrices. Discrimination between nitrite, RSNOs, and N-nitroso or nitrosylheme compounds is accomplished by use of group-specific reagents. Our findings suggest that NO generation in vivo leads to concomitant formation of RSNOs, nitrosamines, and nitrosylhemes with considerable variation between rodents and primates, highlighting the difficulty in comparing data between different animal models and extrapolating results from experimental animals to human physiology.
Immunization with Mimotopes Prevents Growth of Carcinoembryonic Antigen–Positive Tumors in BALB/c Mice (2007)

From our results, we can conclude that the Col-1 epitope of the glycoprotein CEA can be translated into an immunogenic peptide mimic. The mimotope-induced antibodies recognize CEA and do effectively inhibit growth of CEA-positive tumors. Based on these finding, we suggest that the generated mimotopes are candidates for active immunotherapy of CEA-expressing tumors.
The immune regulatory protein B7-H3 promotes osteoblast differentiation and bone mineralization (2004)

B7-H3, a member of the B7 family of the Ig superfamily proteins, is expressed on the surface of the antigen-presenting cells and down-regulates T cell functions by engaging an unknown counterreceptor on T cells. Although B7-H3 is ubiquitously expressed, its potential nonimmune functions have not been addressed. We found that B7-H3 is highly expressed in developing bones during embryogenesis and that its expression increases as osteoblast precursor cells differentiate into mature osteoblasts. In vitro bone formation by osteoblastic cells was inhibited when B7-H3 function was interrupted by the soluble recombinant protein B7-H3-Fc. Analysis of calvarial cells derived from neonatal B7-H3 knockout (KO) mice revealed normal numbers of osteoblast precursor cells possessing a normal proliferative capacity. However, the B7-H3-deficient calvarial cells exhibited impaired osteogenic differentiation, resulting in decreased mineralized bone formation in vitro. These results suggest that B7-H3 is required for the later phase of osteoblast differentiation. Although B7-H3 KO mice had no gross skeletal abnormalities, they displayed a lower bone mineral density in cortical (but not trabecular) bones compared with WT controls. Consistent with the reduced bone mineral density, the femurs of B7-H3 KO mice were more susceptible to bone fracture compared with those of WT mice. Taken together, these results indicate that B7-H3 and its unknown counterreceptor play a positive regulatory role in bone formation. In addition, our findings identified B7-H3 as another molecule that has a dual role in the bone-immune interface.
Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens (1990)

The rotavirus gene segment coding for the major outer capsid glycoprotein vp7 was amplified directly from stool specimens by the polymerase chain reaction (PCR). Double-stranded RNA extracted from stool samples was used as the template for reverse transcription, which was followed immediately and in the same reaction mix with amplification, using the Taq polymerase. Various conditions were examined to optimize the yield of the amplified gene. The concentrations of MgCl2, dimethyl sulfoxide, and template RNA were critical. The choice of primer pairs allowed amplification of the entire segment or specific portions. By using type-specific primers derived from distinct regions on the gene, we devised a PCR typing method in which each human serotype virus produced a characteristic segment size, readily identifiable in agarose gels. The PCR typing method was applied to 10 rotavirus reference strains, including all 6 known human serotypes (serotypes 1, 2, 3, 4, 8, and 9), and to 34 stool specimens previously serotyped by an enzyme immunoassay with monoclonal antibodies. An absolute correlation was found between the molecular and serologic methods. In addition, 14 stool specimens nonserotypable by an enzyme immunoassay with monoclonal antibodies could be typed by the PCR method. Besides the application for rotavirus detection and typing directly from stools, the PCR method provides a rapid and efficient means of obtaining large quantities of cDNA suitable for sequencing, cloning, and other genetic studies, precluding the need for cell culture and virus purification.
Enhanced Flux and Electrochemical Cleaning of Silicate Scaling on Carbon Nanotube-Coated Membrane Distillation Membranes Treating Geothermal Brines (2017)

The desalination of inland brackish groundwater offers the opportunity to provide potable drinking water to residents and industrial cooling water to industries located in arid regions. Geothermal brines are used to generate electricity, but often contain high concentrations of dissolved salt. Here, we demonstrate how the residual heat left in spent geothermal brines can be used to drive a membrane distillation (MD) process and recover desalinated water. Porous polypropylene membranes were coated with a carbon nanotube (CNT)/poly(vinyl alcohol) layer, resulting in composite membranes having a binary structure that combines the hydrophobic properties critical for MD with the hydrophilic and conductive properties of the CNTs. We demonstrate that the addition of the CNT layer increases membrane flux due to enhanced heat transport from the bulk feed to the membrane surface, a result of CNT's high thermal transport properties. Furthermore, we show how hydroxide ion generation, driven by water electrolysis on the electrically conducting membrane surface, can be used to efficiently dissolve silicate scaling that developed during the process of desalinating the geothermal brine, negating the need for chemical cleaning.
Asking about well‐being gets you half an answer: Intra‐individual processes of implicit and explicit job attitudes (2011)

Abstract Job attitudes, as indicators of well‐being, vary within individuals across cognitive processes and not just time. Research on employee well‐being has relied primarily on self‐reported measures of explicit job and life attitudes. Our work takes a different perspective on this issue by examining the role of implicit attitudes regarding one's organization, coworkers, and supervisor as indicators of well‐being. Implicit attitudes are automatic, introspectively inaccessible, and predict behavior in socially sensitive contexts in which self‐report measures may be impaired by impression management. The results of a field study demonstrate that implicit and explicit job attitudes reflect relatively independent intra‐individual processes. Additionally, this study demonstrates that job performance and citizenship behaviors are best predicted by a combination of implicit and explicit job attitudes, and that a dissociation between implicit and explicit attitudes impacts organizational identification. We conclude with a discussion of how capturing implicit cognition in the workplace can better describe and subsequently help improve employee well‐being. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Characterization of neutralizing monoclonal antibodies to murine cytomegalovirus (1990)

Monoclonal antibodies (MAbs) and polyclonal antibodies raised in mice to murine cytomegalovirus (MCMV) were characterized in vitro by their virus-neutralizing activity and their reactivity with MCMV polypeptides and MCMV-infected mouse embryo fibroblasts (MEF). MCMV was neutralized by the MAbs prior to virus adsorption to MEF by a complement-dependent mechanism. Although the neutralization of MCMV prior to virus adsorption to MEF by polyclonal antibodies was enhanced in the presence of complement, MCMV was also neutralized by a complement-independent mechanism after virus adsorption. No correlation was observed between the level of neutralization of MCMV and the ability of MAbs or polyclonal antibodies to interfere with the binding of the virus to MEF. As the neutralization of MCMV with polyclonal antibodies by both complement-dependent and -independent mechanisms may reflect the interaction of antibodies with different specificities, the ability of each MAb to interact with a second MAb was investigated. One MAb, 1E8, inhibited the neutralizing activity of several other MAbs. Several MAbs reacted with multiple polypeptides by immunoprecipitation and Western blotting analysis; MAb AC1 cross-reacted with a neutralizing 92K/98K MCMV domain and a 70K ribonucleoprotein, the latter with which sera from patients with connective tissue diseases also reacted. This suggests that an homology exists between these proteins, which may lead to the development of autoimmune manifestations in vivo.
RAM2, an essential gene of yeast, and RAM1 encode the two polypeptide components of the farnesyltransferase that prenylates a-factor and Ras proteins. (1991)

In the yeast Saccharomyces cerevisiae, mutations in either of two unlinked genes, RAM1 or RAM2, abolish the farnesyltransferase activity responsible for prenylation of Ras proteins and the a-factor mating pheromone. Here we report that the function of RAM1 and RAM2 genes is required for the membrane localization of Ras proteins and a-factor. The RAM2 gene was sequenced and can encode a 38-kDa protein. We examined the functional interaction of RAM2 and RAM1 by expressing the genes in Escherichia coli. Extracts derived from an E. coli strain that coexpressed RAM1 and RAM2 efficiently farnesylated a-factor peptide and Ras protein substrates. In contrast, extracts derived from E. coli strains that expressed either RAM gene alone were devoid of activity; however, when the latter extracts were mixed, protein farnesyltransferase activity was reconstituted. These results indicate that the yeast farnesyl-protein transferase is comprised of Ram1 and Ram2 polypeptides. Although Ram1 is a component of the enzyme, disruption of the RAM1 gene in yeast was not lethal, indicating that the Ram1-Ram2 farnesyltransferase is not essential for viability. In contrast, disruption of RAM2 was lethal, suggesting that Ram2 has an essential function in addition to its role with Ram1 in protein farnesylation.
Analysis of MTF degradation in the imaging of cells in a flow system (1994)

Abstract The time‐delay and integration method can be used with a charge‐coupled device array to acquire images of cell in a flow cytometer. The loss of high spatial frequency components in images acquired with this technique is studied by deriving the modulation transfer function (MTF) for each of the main causes of image degradation: finite sampling aperture, nonsynchronism between image movement and charge transfer rate, discrete charge motion, transfer inefficiency, and axis misalignment. The system MTF and resolution in the horizontal and vertical directions are then examined.©1994 John Wiley &amp; Sons Inc
Effects of nandrolone decanoate and antiresorptive therapy on vertebral density in osteoporotic postmenopausal women (1989)

Conventional antiresorptive therapy for osteoporosis can delay bone loss, but secondary inhibition of bone formation appears to prevent an increase in bone density. Recently, anabolic steroid therapy has been shown to increase total body calcium and forearm density in osteoporotic patients, perhaps by causing an increase in bone formation. It is not known if these agents affect vertebral density. We have measured vertebral mineral density in 71 postmenopausal osteoporotic women before and after treatment with either the anabolic steroid nandrolone decanoate or antiresorptive therapy. After a mean treatment period of 14 months, there was a mean increase of 20% in vertebral mineral density in the former group, and no significant change in the latter group. The difference in the time-weighted mean rates of change between the two groups was significant. The results suggest that nandrolone decanoate therapy increases bone formation.
Comprehensive Study on Structure−Activity Relationships of Rifamycins:  Discussion of Molecular and Crystal Structure and Spectroscopic and Thermochemical Properties of Rifamycin O (1998)

The mechanism of action of rifamycins against bacterial DNA-dependent RNA polymerase has been explained on the basis of the spatial arrangement of four oxygens which can form hydrogen bonds with the enzyme. Structural descriptors are derived from X-ray diffraction crystal structures of 25 active and nonactive rifamycins. Principal component analysis is used to find the combination of structural parameters which better discriminate between active and nonactive rifamycins. Two possible mechanisms of molecular rearrangement are described which can convert nonactive into active conformations. The energy involved for conformational rearrangements is studied by molecular modeling techniques. Methyl C34 is found to play a key role for determining the geometry of the pharmacophore. Rifamycin O, reported to be active, is obtained by oxidation of rifamycin B and is studied by X-ray single-crystal diffractometry, by solution IR and NMR spectroscopy, and by thermal analysis. Surprisingly the oxidation process is totally stereospecific, and an explanation is given based on solution spectroscopic evidence. The conformation found in the solid state is typical of nonactive compounds, and molecular mechanics calculations show that a molecular rearrangement to the active conformation would require about 15 kcal/mol. Thermal analysis confirms that rifamycin O has a sterically constrained conformation. Therefore, it is likely that the antibiotic activity of rifamycin O is due either to chemical modification prior to reaching the enzyme or to conformational activation.
Electrodes for transcutaneous (surface) electrical stimulation (2008)

In therapeutic and functional applications transcutaneous electrical stimulation (TES) is still the most frequently applied technique for muscle and nerve activation despite the huge efforts made to improve implantable technologies. Stimulation electrodes play the important role in interfacing the tissue with the stimulation unit. Between the electrode and the excitable tissue there are a number of obstacles in form of tissue resistivities and permittivities that can only be circumvented by magnetic fields but not by electric fields and currents. However, the generation of magnetic fields needed for the activation of excitable tissues in the human body requires large and bulky equipment. TES devices on the other hand can be built cheap, small and light weight. The weak part in TES is the electrode that cannot be brought close enough to the excitable tissue and has to fulfill a number of requirements to be able to act as efficient as possible. The present review article summarizes the most important factors that influence efficient TES, presents and discusses currently used electrode materials, designs and configurations, and points out findings that have been obtained through modeling, simulation and testing.