gebhart/patrepeval huggingface dataset:
TNF- <i>alpha</i> stimulation of fibroblast proliferation. Dependence on platelet-derived growth factor (PDGF) secretion and alteration of PDGF receptor expression. (1995)

TNF-alpha stimulates DNA synthesis and proliferation of cultured human fibroblasts. Maximal DNA synthesis in response to TNF-alpha occurs approximately 28 h after addition of TNF-alpha to quiescent fibroblasts, a delay of about 12 to 14 h as compared with DNA synthesis elicited by platelet-derived growth factor (PDGF). TNF-alpha induces PDGF A chain gene expression with a maximum at 4 h. DNA synthesis is abrogated in response to TNF-alpha by a goat anti-PDGF IgG but not by nonimmune goat IgG, suggesting induction of an autocrine PDGF-AA loop by TNF-alpha. The response to PDGF-AA requires the presence of PDGF receptor alpha-receptors. TNF-alpha does not significantly affect PDGF alpha-receptor mRNA or protein expression, nor does it alter the proliferative response to externally added PDGF-AA. In contrast, TNF-alpha reduces the levels of PDGF beta-receptor mRNA, protein expression, and cell proliferation in response to PDGF-BB. Thus, DNA synthesis in response to TNF-alpha depends upon autocrinely induced PDGF-AA. At the same time, TNF-alpha may alter the response to PDGF-BB from exogenous sources.
Turning the postal system into a generic digital communication mechanism (2004)

The phenomenon that rural residents and people with low incomes lag behind in Internet access is known as the "digital divide." This problem is particularly acute in developing countries, where most of the world's population lives. Bridging this digital divide, especially by attempting to increase the accessibility of broadband connectivity, can be challenging. The improvement of wide-area connectivity is constrained by factors such as how quickly we can dig ditches to bury fibers in the ground; and the cost of furnishing "last-mile" wiring can be prohibitively high.In this paper, we explore the use of digital storage media transported by the postal system as a general digital communication mechanism. While some companies have used the postal system to deliver software and movies, none of them has turned the postal system into a truly generic digital communication medium supporting a wide variety of applications. We call such a generic system a Postmanet . Compared to traditional wide-area connectivity options, the Postmanet has several important advantages, including wide global reach, great bandwidth potential and low cost.Manually preparing mobile storage devices for shipment may appear deceptively simple, but with many applications, communicating parties and messages, manual management becomes infeasible, and systems support at several levels becomes necessary. We explore the simultaneous exploitation of the Internet and the Postmanet, so we can combine their latency and bandwidth advantages to enable sophisticated bandwidth-intensive applications.
Generation of a strong magnetic field by an intense<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>laser pulse (1986)

A strong magnetic field of 600 kG (60 T) is generated at the center of a 2-mm-diam one-turn coil in which the current is driven by a ${\mathrm{CO}}_{2}$ laser. The magnetic field, current, and voltage are measured as functions of the separation distance of the gap where the high voltage is induced by the laser irradiation in the coil loop at a fixed intensity of 1.3\ifmmode\times\else\texttimes\fi{}${10}^{14}$ W/${\mathrm{cm}}^{2}$. These results are analyzed on the basis of hot-electron E\ifmmode\times\else\texttimes\fi{}B drift and plasma expansion inside the gap. The analysis indicates how to design the target and the laser pulse for generation of a magnetic field of a few megagauss.
Radiographic Applications of Receiver Operating Characteristic (ROC) Curves (1974)

The basic concepts underlying the theory and experimental determination of receiver operating characteristic (ROC) curves are discussed. Such curves were used to describe the detectability of the image of 2 mm Lucite beads (similar to certain small gallstones) in a noisy background of radiographic mottle. Results are shown for four typical radiographic screen-film combinations with differing optical, sensitometric, and noise properties. In some cases there was qualitative correlation between the detectability described by the ROC curves and the mathematical model describing radiographic mottle.
<i>In Vivo</i>Stimulation of Bone Formation by Transforming Growth Factor-β (1989)

The effect of transforming growth factor-beta (TGF beta) on bone in vivo was examined. Twelve daily injections of 1 microgram TGF beta directly onto the periostea of parietal bones of neonatal rats stimulated the formation of periosteal woven bone. The thickness of the treated parietal bones increased at least 2-fold in a dose-dependent manner. This TGF beta effect was localized at the sites of injection, and no change was observed in contralateral parietal bones and tibiae. The body weight in these growing rats was not affected by TGF beta 1. TGF beta 2 had effects similar to those of TGF beta 1 on the parietal bones in vivo. These results reveal for the first time that TGF beta stimulates bone formation in vivo and indicate its anabolic role in local bone metabolism.
Lack of Induced Systemic Resistance in Peanut to Late Leaf Spot Disease by Plant Growth-Promoting Rhizobacteria and Chemical Elicitors (2001)

A disease assay was optimized for late leaf spot disease of peanut using Cercosporidium per-sonatum in the greenhouse, and this assay was used in attempts to elicit induced systemic resistance using strains of plant growth-promoting rhizobacteria (PGPR) and chemical elicitors. Nineteen strains of spore-forming bacilli PGPR, including strains of Paenibacillus macerans, Brevibacillus brevis, Bacillus laterosporus, B. subtilis, B. pumilus, B. amyloliquefaciens, B. sphaericus, B. cereus, and B. pasteurii, which previously elicited systemic disease control activity on other crops, were evaluated in greenhouse assays. Seven PGPR strains elicited significant disease reduction in a single experiment; however, none repeated significant protection achieved in the greenhouse assay, while significant protection consistently occurred with the fungicide chlorothalonil (Bravo). In other greenhouse trials, neither stem injections of C. personatum nor foliar sprays of chemicals, including salicylic acid, sodium salicylate, isonicotinic acid, or benzo[1,2,3]thiadiazole-7-carbothioc acid S-methyl ester (Actigard), which elicit systemic acquired resistance on other crops, elicited significant disease protection. In contrast, foliar sprays with DL-β-amino-n-butyric acid (BABA), which is an elicitor of localized acquired resistance, resulted in significantly less late leaf spot disease in one of two tests. Combination treatments of four PGPR strains with BABA in the greenhouse did not significantly protect peanut from late leaf spot. Field trials conducted over two growing seasons indicated that none of the 19 PGPR strains, applied as seed treatments at two concentrations, significantly reduced late leaf spot disease. The same chemical elicitors tested in the greenhouse, including BABA, did not elicit significant disease protection. Some combinations of four PGPR and BABA significantly reduced the disease at one but not at two sample times. Collectively, these results suggest that late leaf spot resistance in peanut is not systemically inducible in the same manner as is resistance to diseases in other crops by PGPR and chemical inducers.
A Lightweight Approach to Authenticated Web Caching (2005)

Distributed caching is increasingly used to shorten the response time of Web servers and balance the load on the network by avoiding repeated transmission of the same content. An important research issue is the provision of access control mechanisms in the cache servers in order to service only authenticated client requests. In this paper, we provide a solution based on the distribution of secure cookies, avoiding the distribution and replication of sensitive information to the cache servers. With respect to previous proposals, our solution is lightweight, since it does not rely on computational heavy security mechanisms. We analyze two scenarios for authenticated caching involving different participants and, in both cases, describe a viable caching scheme.
Chitosan-Decorated Doxorubicin-Encapsulated Nanoparticle Targets and Eliminates Tumor Reinitiating Cancer Stem-like Cells (2015)

Tumor reinitiating cancer stem-like cells are responsible for cancer recurrence associated with conventional chemotherapy. We developed a doxorubicin-encapsulated polymeric nanoparticle surface-decorated with chitosan that can specifically target the CD44 receptors of these cells. This nanoparticle system was engineered to release the doxorubicin in acidic environments, which occurs when the nanoparticles are localized in the acidic tumor microenvironment and when they are internalized and localized in the cellular endosomes/lysosomes. This nanoparticle design strategy increases the cytotoxicity of the doxorubicin by six times in comparison to the use of free doxorubicin for eliminating CD44(+) cancer stem-like cells residing in 3D mammary tumor spheroids (i.e., mammospheres). We further show these nanoparticles reduced the size of tumors in an orthotopic xenograft tumor model with no evident systemic toxicity. The development of nanoparticle system to target cancer stem-like cells with low systemic toxicity provides a new treatment arsenal for improving the survival of cancer patients.
Male Chronic Pelvic Pain Syndrome (2013)

Male chronic pelvic pain syndrome (MCPPS) is defined as chronic pain, pressure, or discomfort localized to the pelvis, perineum, or genitalia of males lasting more than 3 months that is not due to readily explainable causes. Other names for the disorder include prostatodynia and chronic nonbacterial (abacterial) prostatitis, although it is unclear how the symptoms relate to the prostate. And it appears to be extensive variability in clinical presentation and may result in chronic neuropathic pain and neuromuscular pain. Therefore patients with MCPPS should be cared by multimodal treatment including antihyperalgesics, antidepressants and pain intervention procedures such as caudal block. We report successful care in two men with MCPPS.
Alkali-Stabilized Pt-OH <i> <sub>x</sub> </i> Species Catalyze Low-Temperature Water-Gas Shift Reactions (2010)

We report that alkali ions (sodium or potassium) added in small amounts activate platinum adsorbed on alumina or silica for the low-temperature water-gas shift (WGS) reaction (H(2)O + CO → H(2) + CO(2)) used for producing H(2). The alkali ion-associated surface OH groups are activated by CO at low temperatures (~100°C) in the presence of atomically dispersed platinum. Both experimental evidence and density functional theory calculations suggest that a partially oxidized Pt-alkali-O(x)(OH)(y) species is the active site for the low-temperature Pt-catalyzed WGS reaction. These findings are useful for the design of highly active and stable WGS catalysts that contain only trace amounts of a precious metal without the need for a reducible oxide support such as ceria.
Investigation of effective-medium models of microscopic surface roughness by spectroscopic ellipsometry (1979)

Using measured dielectric function data from 2.1 to 5.5 eV for chemical-vapor-deposition---grown smooth amorphous ($a$-Si) and microscopically rough fine-grained polycrystalline ($p$-Si) films, we show that the dielectric properties of microscopically rough layers of thicknesses 100-500 \AA{}A are accurately modeled in the effective-medium approximation. These microscopically rough layers show essentially no macroscopic light scattering, and thus are inaccessible to measurement by usual scattering techniques. The unambiguous identification of microscopic roughness, as opposed to, e.g., an overlying oxide, is shown to require a spectroscopic capability. Statistical-analysis techniques are introduced to determine model parameters systematically and objectively, and also to establish correlations and confidence limits that show which parameters are defined by the data and which are statistically indeterminate. A best-fit five-parameter model for the sample with the thickest surface region shows that the density profile is characteristic of hemispherical, not pyramidal, irregularities. This indicates that surface roughness arises from a three-dimensional nucleation and growth process in these samples. In a comparison of the three one-parameter effective-medium models, Bruggeman and Maxwell Garnett(2) theories are found to adequately represent the data, while the Lorentz-Lorenz model, previously used exclusively to model roughness in single-wavelength applications, predicts only qualitatively the spectral dependence and gives poor results.
Evolving fuzzy systems (2008)

Fuzzy Sets and Fuzzy Logic were introduced by Lotfi Zadeh in 1965 in his seminal paper [71]. During the last decade of the previous century there was an increase of the various applications of fuzzy logic-based systems mainly due to the introduction of fuzzy logic controllers (FLC) by Ebrahim Mamdani in 1975 [54], the introduction of the fuzzily blended linear systems construct called Takagi–Sugeno (TS) fuzzy systems in 1985 [65], and the the oretical proof that FRB systems are universal approxima tors (that is any arbitrary non-linear function in the [0; 1] range can be asymptotically approximated by a FRB system [68]). Historically, the FRB systems where first being designed based entirely or predominantly on human expert knowledge [54,71]. This offers advantages and was a novel technique at that time for incorporating uncertain, subjective information, preferences, experience, intuition, which are difficult or impossible to be described other- wise. However, it poses enormous difficulties for the pro cess of designing and routine use of these systems, especially in real industrial environments and in on-line and real-time modes. TS fuzzy systems made possible the de- velopment of efficient algorithms for their design not only in off-line, but also in on-line mode [14]. This is facili- tated by their dual nature – they combine a fuzzy linguistic premise (antecedent) part with a functional (usually linear) consequent part [65]. With the invention of the concept of EFS [2,5] the problem of the design was completely automated and data-driven. Thismeans, EFS systems self-develop their model, respectively system structure as well as adapt their parameters “from scratch” on the fly using experimental data and efficient recursive learning mechanisms. Human expert knowledge is not compulsory, not limiting, not essential (especially if it is difficult to obtain in real-time). This does not necessarily mean that such knowledge is prohibited or not possible to be used. On the contrary, the concept of EFS makes possible the use of such knowledge in initialization stages, even during the learning process itself, but this is not essential, it is optional. Examples of EFS are intelligent sensors for oil refineries [52,53], autonomous self-localization algorithms used by mobile robots [75,76], smart agents for machine health monitoring and prognosis in the car industry [30], smart systems for automatic classification of images in CD production process [51] etc. This is a new promising area of research and new applications in different branches of industry are emerging. (c) Springer Verlag
Verifying systems with integer constraints and Boolean predicates (1998)

Symbolic mode, checking has proved highly successful for large finite-state systems, in which states can be compactly encoded using binary decision diagrams (BDDs) or their variants. The inherent limitation of this approach is that it cannot be applied to systems with an infinite number of states --- even those with a single unbounded integer.Alternatively, we recently proposed a model checker for integer-based systems that uses Presburger constraints as the underlying state representation. While this approach easily verified some subtle, infinite-state concurrency problems, it proved inefficient in its treatment of Boolean and (unordered) enumerated types --- which possess no natural mapping to the Euclidean coordinate space.In this paper we describe a model checker which combines the strengths of both approaches. We use a composite model, in which a formula's valuations are encoded in a mixed BDD-Presburger form, depending on the variables used. We demonstrate our technique's effectiveness on a nontrivial requirements specification, which includes a mixture of Booleans, integers and enumerated types.
Transesterification of rapeseed oil in the presence of basic zeolites and related solid catalysts (2001)

Abstract The transesterification of rapeseed oil with methanol was performed by reflux of methanol over cesium‐exchanged NaX faujasites, mixed magnesium‐aluminum oxides, magnesium oxide, and barium hydroxide for different methanol‐to‐oil ratios. Over cesium‐exchanged NaX faujasites and mixed magnesium‐aluminum oxides, a long reaction time and a high methanol‐to‐oil ratio are required to achieve both high oil conversion and high yields in methyl esters. However, over a 300 m 2 /g magnesium oxide, methanol‐to‐oil ratios and reaction times are significantly reduced to obtain both high oil conversion and high yield in the methyl esters, particularly when the hydroxide precursor is calcined at 823 K. Finally, preliminary results with other basic solids such as barium hydroxide have shown a very high activity and a very high yield in esters. This catalyst is particularly effective since, for a methanol‐to‐oil ratio of 6, at reflux of methanol and after a reaction time of only 1 h, the oil conversion is about 80% with a nearly quantitative ester molar fraction.
Finite element and boundary element analysis of electromagnetic NDE phenomena (1992)

The endeavor to produce quality products coupled with a drive to minimize fail­ ure in major industries such as aerospace, power and transportation is the driving force behind studies of electromagnetic nondestructive evaluation (NDE) methods. Popular domain and integral methods used for the purpose of modeling electromag­ netic NDE phenomena include the finite element and boundary element methods. However no single numerical modeling technique has emerged as the optimal choice for all electromagnetic NDE processes. In a computer aided design environment, where the choice of an optimum modeling technique is critical, an evaluation of the various aspects of different numerical approaches is extremely helpful. In this dissertation, a comparison is made of the relative advantages and disad­ vantages of the finite element (FE) and boundary element (BE) methods as applied to the DC and AC Potential drop (DCPD and ACPD) methods for characterizing fatigue cracks. The comparison covers aspects of robustness, computer resource re­ quirements and ease of numerically implementing the methods. Two dimensional FE and BE models are used to model an infinitely thin fatigue crack using the ACPD method, and a two and three dimensional FE and BE model is used to study the com­ pact tension and single edge notch specimen using the DCPD method. Calibration curves and field plots in the specimen are compared to experimental and analytical data. The FE and BE methods are complementary numerical techniques and are combined to exploit their individual merits in the latter part of this dissertation. A three dimensional hybrid formulation to model eddy current NDE is then developed which discretizes the interior with finite elements and the exterior with boundary, elements. The three dimensional model is applied to an absolute eddy current coil over a finite block. A feasibility study to confirm the validity of the formulation is undertaken by comparing the numerical results for probe lift-off and coil impedance measurements with published data. This comparative study outlined above indicates that when the solution is re­ quired at discrete points, as in the potential drop methods, or the model needs to handle infinite boundaries, as in eddy current NDE, the boundary element model is more suitable. Since it is based on the Green's function, the BE method is lim­ ited to linear problems. Finite element analysis gives full field solutions, making it ideal for studying energy/defect interactions. The hybrid FE/BE formulation han­ dles non-linearity and infinite boundaries naturally, thus utilizing the best of both worlds.
Remote protein homology detection using a modularity-based approach (2011)

Clustering homologous proteins is one of the important tasks in functional genomics. Homologous proteins may share common functions. Annotating proteins of unknown function by transferring annotations from their homologues of known annotations is one of the efficient ways to predict protein function. We use a modularity-based method called CD for grouping together homologous proteins. The method employs a global heuristic search strategy to find the partitioning of the weighted adjacency graph with the largest modularity. The weighted adjacency graph is constructed by the sigmodal transformation of all pairwise sequence similarities between all protein sequences in a given dataset. The method has been extensively tested on several subsets from the superfamily level of the SCOP (Structural Classification of Proteins) database, where some homologous proteins have very low sequence similarity. Compared with a widely used method MCL, we observe that the number of clusters obtained by CD is closer to the number of superfamilies in the dataset, the value of the F-measure given by CD is 10% better than MCL on average, and CD is more tolerant to noise to the sequence similarity. Our results indicate that CD is ideally suitable for clustering homologous proteins when sequence similarity is low.
Most Murine CD8+ Intestinal Intraepithelial Lymphocytes Are Partially But Not Fully Activated T Cells (2002)

Murine small intestine intraepithelial lymphocytes (IELs) bear properties of both activated and nonactivated T cells, although the significance of that dichotomy remains unclear. In this study, we show that although IELs express CD69 in situ and ex vivo, and have cytotoxic activity ex vivo, most CD8(+) IELs from normal mice are phenotypically similar to naive T cells in that they are CD45RB(high), CD44(low/int), and lack or have low levels of expression of CD25, Ly-6C, OX40, Fas ligand (FasL), and intracellular IFN-gamma synthesis. Unlike CD8(+) lymph node cells, IELs express high levels of the FasL gene, but do not express surface FasL until after CD3-mediated stimulation has occurred. Additionally, anti-CD3 stimulation of IELs in the presence of actinomycin-D did not inhibit FasL expression, suggesting that regulation FasL expression on IELs is controlled at least partially at the posttranscriptional level. Following CD3-mediated stimulation, IELs synthesize and secrete IFN-gamma more rapidly and to greater levels than CD8(+) lymph node cells, and they acquire the phenotype of fully activated effector cells as seen by an up-regulation of CD44, Ly-6C, OX40, FasL, and CD25 with the kinetics of memory T cells, with down-regulation of CD45RB expression. These findings indicate that contrary to previous interpretations, most small intestine IELs are not fully activated T cells, but rather that they are semiactivated T cells ready to shift to a fully activated state once a CD3-mediated signal has been received. These data also imply that under appropriate conditions it is possible for T cells to be sustained in a state of partial activation.