gebhart/patrepeval huggingface dataset:
Production Improvement in Gas-Condensate Reservoirs by Elimination of Condensate Blockages Through Wettability Alteration (2023)

Summary Pressure below the dew point during production from gas-condensate reservoirs causes condensate to accumulate in the vicinity of the wellbore. The liquid build-up reduces the gas relative permeability, resulting in inefficient gas production. In near-wellbore regions, chemical treatments are used to alter rock wettability to stimulate gas-condensate wells and maintain high productivity. In this study, we investigate the effect of the anti-scratch coating (SCC), as a new ethanol-based nanofluid, on production assessment by altering the wettability of sandstone/carbonate rocks from a liquid-wetting to intermediate gas-wetting state. Static contact angle and spontaneous imbibition measurements were carried out to examine the aforementioned phenomenon. Besides, the coreflooding experiments were conducted to analyze the two-phase fluid flow through porous media. All experiments were conducted in presence of the methane gas. According to the results, SCC can significantly reduce the surface free energy of sandstone by reducing the contact angle. For sandstone rocks, spontaneous imbibition experiments showed that imbibed n-decane and brine were reduced by factors of 0.2 and 0.01, respectively. However, these factors were reported as 0.26 (for n-decane) and 0.068 (for brine) for carbonate rocks. Additionally, a reduction in pressure drop by a factor of 0.3814 in high-permeability sandstone core was observed.
Resolvent Analysis of Compressible Laminar and Turbulent Cavity Flows (2019)

The present work demonstrates the use of a resolvent analysis to obtain physical insights for open-cavity flows. A resolvent analysis identifies the flow response to harmonic forcing, given a steady base state, in terms of the response and forcing modes and the amplification gain. The response and forcing modes reveal the spatial structures associated with this amplification process. In this study, a resolvent analysis is performed on both laminar and turbulent flows over a rectangular cavity with a length-to-depth ratio of at a freestream Mach number of in a spanwise periodic setting. Based on the dominant instability of the base state, a discount parameter is introduced to a resolvent analysis to examine the harmonic characteristics over a finite-time window. First, the underlying flow physics is uncovered and the findings are interpreted from laminar flow at . These findings from laminar flow are extended to a more practical cavity flow example at a much higher Reynolds number of . The features of response and forcing modes from the turbulent cavity flow are similar to the spatial structures from the laminar analysis. It is further found that the large amplification of energy in the flow response is associated with the high frequency for turbulent flow, whereas the flow is more responsive to the low-frequency excitation in the laminar case. These findings from the resolvent analysis provide valuable insights for flow control studies with regard to parameter selection and the placement of actuators and sensors.
Growth of E mu-myc transgenic B-lymphoid cells in vitro and their evolution toward autonomy. (1988)

Constitutive expression of the c-myc oncogene in the B lymphoid cells of E mu-myc transgenic mice promotes cellular proliferation and predisposes to lymphomagenesis. To delineate further how the pre-B cells of prelymphomatous mice have been altered, we have investigated their growth in vitro. They were not autonomous, since they died rapidly when cultured without feeder cells. When cultured on bone marrow stromal cells, E mu-myc cells initially grew to only slightly higher densities than B lineage cells from normal mice, but were larger and showed more cell cycle activity. After 14 weeks, all cultures appeared oligo- or monoclonal, as judged by analysis of Ig gene rearrangements. While the growth of the normal cells was constant, the E mu-myc cells started to grow to 10-fold higher densities after 14-20 weeks, implying a reduced requirement for growth factors. They remained dependent on feeder cells and were non-tumorigenic. By 25 weeks, however, the one remaining culture had become feeder-independent and tumorigenic. We suggest that deregulated c-myc expression in B cell precursors increases the rate of cell turnover, thereby increasing the frequency of genetic changes conductive to autonomous growth.
Tryptic transpeptidation products observed in proteome analysis by liquid chromatography‐tandem mass spectrometry (2005)

Commonly, prior to mass spectrometry based analysis of proteins or protein mixtures, the proteins are subjected to specific enzymatic proteolysis. For this purpose trypsin is most frequently used. However, the process of proteolysis is not unflawed. For example, some side activities of trypsin are known and have already been described in the literature (e.g., chymotryptic activity). Here, we describe the occurrence of transpeptidated peptides during standard proteome analysis using two-dimensional polyacrylamide gel electrophoresis followed by mass spectrometric protein identification. Different types of transpeptidated peptides have been detected. The most frequently observed transpeptidation reaction is N-terminal addition of arginine or lysine to peptides. Furthermore, addition of two amino acids to the N-terminus of a peptide has also been detected. Another transpeptidation that we observed, is combination of two peptides, which were originally located in different regions of the analyzed protein. Currently, the full amount of peptides generated by transpeptidation is not clear. However, it should be recognized that protein information is presently lost as these effects are not detectable with available database search software.
Power conservative multi-attribute queries on data broadcast (2002)

Studies power conservation techniques for multi-attribute queries on wireless data broadcast channels. Indexing data on broadcast channels can improve the client filtering capability, while clustering and scheduling can reduce both the access time and the tune-in time. Thus, indexing techniques should be coupled with clustering and scheduling methods to reduce the battery power consumption of mobile computers. In this study, three indexing schemes for multi-attribute queries, namely the index tree, signature and hybrid index, are discussed. We develop cost models for these three indexing schemes and evaluate their performance based on multi-attribute queries on wireless data broadcast channels.
Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity (2023)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern challenge the efficacy of approved vaccines, emphasizing the need for updated spike antigens. Here, we use an evolutionary-based design aimed at boosting protein expression levels of S-2P and improving immunogenic outcomes in mice. Thirty-six prototype antigens were generated in silico and 15 were produced for biochemical analysis. S2D14, which contains 20 computationally designed mutations within the S2 domain and a rationally engineered D614G mutation in the SD2 domain, has an ~11-fold increase in protein yield and retains RBD antigenicity. Cryo-electron microscopy structures reveal a mixture of populations in various RBD conformational states. Vaccination of mice with adjuvanted S2D14 elicited higher cross-neutralizing antibody titers than adjuvanted S-2P against the SARS-CoV-2 Wuhan strain and four variants of concern. S2D14 may be a useful scaffold or tool for the design of future coronavirus vaccines, and the approaches used for the design of S2D14 may be broadly applicable to streamline vaccine discovery.
1717 Identification of Structural Matrices Based on A Concept of Self-Identification Using Variable Geometric Parameters (2005)

This paper proposes a method for the identification of structural matrices using a concept of self-identification with variable geometric parameters. The method is theoretically formulated by using the change of eigenvalues and eigenvectors according to change of the variable geometric vector. A modal expansion technique is introduced to obtain the eigenvectors under the lack of sensors. Numerical examples show that the stiffness matrix of a two-dimensional variable geometry truss is exactly identified with enough number of the linearly independent eigenvectors changed by one variable length member of the truss.
Strength-duration properties of sensory and motor axons in amyotrophic lateral sclerosis (1998)

In normal subjects, the strength-duration time constant is longer for cutaneous afferents than for motor axons, probably because the former express a greater non-inactivating (persistent) Na+ conductance that is active at threshold. Using a threshold-tracking system the strength-duration properties of cutaneous afferents and motor axons were recorded from 23 patients with amyotrophic lateral sclerosis, and compared with those of 32 healthy subjects. In control subjects and patients, the strength-duration time constant of sensory fibres declined with age, and there was no difference between the two groups when age was taken into account. The motor time constant did not change with age when expressed as a percentage of the time constant for sensory fibres in the same nerve, but was significantly longer for the patients than control subjects. In addition, motor rheobase was significantly lower for the patients, when expressed as a percentage of sensory rheobase. There was an inverse relationship between the time constant and rheobase for sensory and motor axons, and this was the same for the patients and the control subjects, suggesting that the variations in time constant within and between the groups were related to the expression of a common factor. Measurements of refractoriness and supernormality provided no evidence for a difference in resting membrane potential between the patients and control subjects. These findings are consistent with the interpretation that motor axons of the patients with amyotrophic lateral sclerosis have a greater persistent Na+ conductance than normal motor axons. This could contribute to the ectopic activity responsible for fasciculation.
Experiments with a thin-walled stainless-steel vacuum chamber (2000)

The application of a reasonably thin stainless-steel wall has been recently suggested as an alternative approach in ultra-high-vacuum (UHV) chamber construction, since the hydrogen outgassing rate qout can be decreased much easily to the level required to reach UHV and EXV. Two identical stainless-steel chambers (AISI type 304, volume 12 l) with uniform wall thickness (0.6 mm) were constructed. Each was equipped with a miniature ion-getter pump and spinning rotor gauge (SRG) thimble. They were pumped down and initially degassed by a moderate bakeout (2.5 h, 150 °C) using a turbomolecular pump system. The gas accumulation method was applied for the determination of qout and the total amount of released gases. A capacitance manometer was used during bakeout but a SRG was applied after the chamber was sealed off. The qout at room temperature after initial bakeout was in the order of ≅3×10−12 mbar l/(cm2 s). SRG measurements of qout at 50 °C over several days showed a tendency of slight decrease. The bakeout of the chambers was being repeated in a duration of 72 h at 200 °C. The amount of released hydrogen was much smaller than expected, whereas the decrease of qout was noticeable. In fact, it was one tenth of the value before the bakeout. The results show the benefit of using a moderately thin wall and agree with the model of recombination-limited hydrogen outgassing from stainless steel.
[Experimental gene therapy in models of inflammatory arthritis]. (1996)

Gene therapy is rheumatoid arthritis is presently in an experimental phase. Genes encoding for antiinflammatory proteins can be transfected in joint cells. Therefore gene encoding for interleukin-1 receptor antagonist has been transfected into synovial cells or into chondrocytes. Gene expression can be maintained as long as 8 weeks after cell transfer. We have reported that clinical and histopathological parameters of collagen-induced arthritis (an animal model of rheumatoid arthritis) can be reduced by engraftment of CHO cells transfected with genes encoding for antiinflammatory cytokines such as interleukine-4 or interleukine-13. Some of the questions which need to be assessed before planning clinical trial are the choice of vectors and the most efficient target cells; and the genes to be transfected have to be chosen among many candidates.
Performance of the upgraded H.E.S.S. cameras (2018)

The 14 years old cameras of the H.E.S.S. 12-m telescopes have been upgraded in 2015/2016, with the goals of reducing the system failure rate, reducing the dead time and improving the overall performance of the array. This conference contribution describes the various tests that were carried out on the cameras and their sub-components both in the lab and on site. It also gives an overview of the commissioning and calibration procedures adopted during and after the installation, including e.g. flat-fielding and trigger threshold scans. Finally, it reports in detail about the overall performance of the four new H.E.S.S-I cameras, using very recent data.
SUV39H1 Represses the Expression of Cytotoxic T-Lymphocyte Effector Genes to Promote Colon Tumor Immune Evasion (2019)

Despite the presence of CTLs in the tumor microenvironment, the majority of immunogenic human colon cancer does not respond to immune checkpoint inhibitor immunotherapy, and microsatellite instable (MSI) tumors are not naturally eliminated. The molecular mechanism underlying the inactivity of tumor-infiltrating CTLs is unknown. We report here that CTLs were present in both MSI and microsatellite stable colon tumors. The expression of the H3K9me3-specific histone methyltransferase SUV39H1 was significantly elevated in human colon carcinoma compared with normal colon tissues. Using a mouse colon carcinoma model, we further determined that tumor-infiltrating CTLs in the colon tumor microenvironment have high expression of SUV39H1. To target SUV39H1 in the tumor microenvironment, a virtual chemical library was screened on the basis of the SET (suppressor of variegation 3-9, enhancer of zeste and trithorax) domain structure of the human SUV39H1 protein. Functional enzymatic activity assays identified a small molecule that inhibits SUV39H1 enzymatic activity. On the basis of the structure of this small molecule, we modified it and chemically synthesized a small molecule, termed F5446, which has an EC<sub>50</sub> of 0.496 μmol/L for SUV39H1 enzymatic activity. H3K9me3 was enriched in the promoters of <i>GZMB, PRF1, FASLG</i>, and <i>IFNG</i> in quiescent T cells. F5446 inhibited H3K9me3, thereby upregulating expression of these effectors in tumor-infiltrating CTLs and suppressing colon carcinoma growth in a CD8<sup>+</sup> CTL-dependent manner <i>in vivo</i> Our data indicate that SUV39H1 represses CTL effector gene expression and, in doing so, confers colon cancer immune escape.
Magnetic field of an asymmetric ring head with an underlayer (1993)

The fringe field of an asymmetric ring head with an underlayer is obtained using conformal mapping techniques. The Schwartz-Christoffel transformation is used to determine the magnetic field distribution around the head poles, and an analytical field equation is obtained. It is found that an asymmetric ring head with an underlayer is highly suitable for perpendicular recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reputation-based trust model in Vehicular Ad Hoc Networks (2010)

Vehicular Ad Hoc Networks (VANETs) are received more and more researchers' attention with their promising functions in road safety by exchanging real-time warning messages through vehicle-to-infrastructure (V2I) and vehicle-to-vehicle (V2V) communication. However, an inaccurate traffic warning message will impact drivers' decisions, misguide drivers' behavior, and even invoke serious car accidents. In this paper, we proposed an event-based reputation model to filter bogus warning messages. Our solution is classifying all vehicles encounter the same traffic event different roles. A dynamic role-dependent reputation evaluation mechanism is presented to determine whether an incoming traffic message is significant and trustworthy to the driver. The simulation results show that our proposed system can effectively prevent false messages spread on VANET environments.
Growth Factor and Matrix Molecules Preserve Cell Function on Thermally Responsive Culture Surfaces (1999)

Thermally-responsive culture surfaces were designed using copolymers of N-isopropylacrylamide, 4-(aminomethyl)styrene, and acrylic acid. These surfaces contained functional amine and carboxyl groups, which allowed biomolecules to be grafted by amide formation. Epidermal growth factor (EGF), and extracellular matrix (ECM) molecules (collagen type IV, and chondroitin sulfate) were investigated, as surface-grafted biomolecules, for their ability to stimulate cell attachment, proliferation, and function by signaling only from the basal side of cultured cells. Surface analysis of biomolecule-grafted porous inserts showed covalent binding of biomolecules to either amine or carboxyl groups. Multiple attachment to amine and/or carboxyl groups served as cross-linking points that made the polymer hydrogel permanently adherent to the culture surface. Immunofluorescence microscopy techniques gave positive identification of grafted biomolecules. Grafting of EGF improved cell proliferation versus that on nongrafted controls, or controls grafted only with ECM molecules. ECM grafting induced cell attachment on attachment-resistant surfaces. Analysis of trans-epithelial resistance, fluid transport, and polarized g-glutamyl transpeptidase activity indicated that simultaneous grafting of both EGF and ECM produced better polarized cell function than nongrafted controls, or controls grafted with only one type of biomolecule. Covalent grafting of biomolecules did not interfere with cells ability to detach from thermally responsive surfaces upon temperature decrease.
The calmodulin binding domain of chicken smooth muscle myosin light chain kinase contains a pseudosubstrate sequence. (1987)

Smooth muscle myosin light chain kinase contains a 64 residue sequence that binds calmodulin in a Ca2+-dependent manner (Guerriero, V., Jr., Russo, M. A., and Means, A. R. (1987) Biochemistry, in press). Within this region is a sequence with homology to the corresponding sequence reported for the calmodulin binding region of skeletal muscle myosin light chain kinase (Blumenthal, D. K., Takio, K., Edelman, A. M., Charbonneau, H., Titani, L., Walsh, K. A., and Krebs, E. G. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 3187-3191). Inspection of these sequences reveals that they both share a similar number and spatial arrangement of basic residues with those present in the myosin light chain substrate. We have synthesized a 22-residue peptide corresponding to residues 480-501 (determined from the cDNA) of the smooth muscle myosin light chain kinase. This peptide, Ala-Lys-Lys-Leu-Ser-Lys-Asp-Arg-Met-Lys-Lys-Tyr-Met-Ala-Arg-Arg-Lys-Trp- Gln-Lys-Thr-Gly, inhibited calmodulin-dependent activation of the smooth muscle myosin light chain kinase with an IC50 of 46 nM. At saturating concentrations of calmodulin, the 22-residue peptide inhibited myosin light chain and synthetic peptide substrate phosphorylation competitively with IC50 values of 2.7 and 0.9 microM, respectively. An 11-residue synthetic peptide analog, corresponding to part of the calmodulin-binding sequence in skeletal muscle myosin light chain kinase, Lys-Arg-Arg-Trp-Lys-Lys-Asn-Phe-Ile-Ala-Val, also competitively inhibited synthetic peptide substrate phosphorylation with a Ki of 1 microM. The competitive inhibitory activity of the calmodulin binding regions is similar to the apparent Km of 2.7 microM for phosphorylation of the 23-residue peptide analog of the smooth muscle myosin light chain and raises the possibility that the calmodulin binding region of the myosin light chain kinase may act as a pseudosubstrate inhibitor of the enzyme.
Detection and quantification of live, apoptotic, and necrotic human peripheral lymphocytes by single-laser flow cytometry (1995)

Regulation of peripheral lymphocyte number involves a poorly understood balance between cell renewal and loss. Disrupting this balance leads to a large number of disease states. Methods which allow qualitative and quantitative measurements of cell viability are increasingly valuable to studies directed at revealing the mechanisms underlying apoptotic and necrotic cell death. Here, we have characterized a method using single-laser flow cytometry that differentiates and quantifies the relative number of live, apoptotic, and late-stage apoptotic and necrotic peripheral lymphocytes. Following in vitro gamma irradiation and staining with acridine orange in combination with ethidium bromide, three distinct populations were seen by bivariate analysis of green versus red fluorescence. The identity of each distinct fluorescent population (whether live, apoptotic, or necrotic) was determined by sorting and examination of cellular morphology by electron microscopy. This flow cytometric method is directly compared with the techniques of trypan blue exclusion and DNA fragmentation to quantify cell death following exposure to various doses of in vitro gamma irradiation and postirradiation incubation times. We extend our findings to illustrate the utility of this method beyond analyzing radiation-induced apoptotic peripheral blood mononuclear cells (PBMC); similar fluorescent patterns are shown for radiation- and corticosteroid-treated murine thymocytes, activated human PBMC, and PBMC from human immunodeficiency virus-infected individuals. Our results demonstrate that dual-parameter flow cytometric analysis of acridine orange-ethidium bromide-stained lymphocytes is overall a superior method with increased sensitivity, greater accuracy, and decreased subjectivity in comparison with the other methods tested. By using standard laser and filter settings commonly available to flow cytometric laboratories, this method allows rapid measurement of a large number of cells from a heterogeneous sample.
Rescue of mitomycin C- or psoralen-inactivated Micrococcus radiodurans by additional exposure to radiation or alkylating agents (1982)

The processing of damaged DNA was altered in a mitomycin C-sensitive mutant (mtcA) of Micrococcus radiodurans. Even though the mutant retained resistance to 254-nm UV radiation, it did not, in contrast to the wild-type strain, show any excessive DNA degradation or cell death when incubated with chloramphenicol after sublethal doses of either UV light or mitomycin C. The results suggest the constitutive synthesis of an enzyme system responsible for wild-type proficiency in the repair of mitomycin C-induced damage. An alternative system able to repair damage caused by mitomycin C was demonstrated in the mtcA background. In this strain, additional damage inflicted upon the cellular DNA effected a massive rescue of cells previously inactivated by mitomycin C. Rescue was provoked by ionizing radiation, by UV light, or by simple alkylating agents. Cells treated with psoralen plus near-UV radiation could be rescued only when inactivation was due primarily to psoralen-DNA interstrand cross-links rather than to monoadducts. The rescue of inactivated cells was prevented in the presence of chloramphenicol. These results can be interpreted most readily in terms of an alternative repair system able to overcome DNA interstrand cross-links produced by mitomycin C or psoralen plus near-UV light, but induced only by the more abundant number of damages produced by radiation or simple alkylating agents.