gebhart/patrepeval huggingface dataset:
Accessory cell stimulation of T cell proliferation requires active antigen processing, Ia-restricted antigen presentation, and a separate nonspecific 2nd signal. (1981)

The roles of Ia+ accessory cells in H-2-restricted stimulation of antigen-specific T cell proliferation were explored in an in vitro model. L-glutamic acid60-L-alanine30-L-tyrosine10-(GAT) primed BALB/c nylon wool-passed T cells were depleted of Ia+ antigen-presenting cells (APC) by treatment with monoclonal anti-Ia antibody plus complement. Such cells failed to respond to soluble GAT, or to soluble GAT in the presence of phorbol myristic acetate (PMA), which is known to stimulate production of, or replace, IL-1 in vitro. Addition of gamma-irradiated syngeneic spleen cells reconstituted the response to soluble GAT, but addition of ultraviolet (UV) light-irradiated spleen cells did not, even in the presence of PMA. Preincubation of cells with GAT for 24 hr, followed by washing, then gamma irradiation, generated a cell population able to stimulate GAT-primed T cells to proliferate. The same pulsed cells exposed to UV irradiation failed to stimulate T cell responses unless PMA was added to the cultures. The relevant cells in this UV-irradiated population are Ia+. It is concluded that a finite period of time for interaction of metabolically intact APC with antigen is required before creation of an appropriate (Ia + antigen) signal recognized by the T cell. In addition to such Ia-restricted antigen presentation, however, a 2nd nonspecific signal, again requiring metabolically active APC for elaboration, is necessary for detectable T cell activation. These studies thus define 3 separable activities of APC during the process of H-2 restricted T cell activation.
Preparation and crystal structure of the recombinant α1/α2 catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib (2001)

The intracellular form of mammalian platelet activating factor acetylhydrolase found in brain (PAF-AH Ib) is thought to play a critical role in control in neuronal migration during cortex development. This oligomeric complex consists of a homodimer of the 45 kDa (beta) LIS1 protein, the product of the causative gene for type I lissencephaly, and, depending on the developmental stage and species, one of three possible pairs of two homologous approximately 26 kDa alpha-subunits, which harbor all of the catalytic activity. The exact composition of this complex depends on the expression patterns of the alpha(1) and alpha(2) genes, exhibiting tissue specificity and developmental control. All three possible dimers (alpha(1)/alpha(1), alpha(1)/alpha(2) and alpha(2)/alpha(2)) were identified in tissues. The alpha(1)/alpha(2) heterodimer is thought to play an important role in fetal brain. The structure of the alpha(1)/alpha(1) homodimer was solved earlier in our laboratory at 1.7 A. We report here the preparation of recombinant alpha(1)/alpha(2) heterodimers using a specially constructed bi-cistronic expression vector. The approach may be useful in studies of other systems where pure heterodimers of recombinant proteins are required. The alpha(1)/alpha(2) dimer has been crystallized and its structure was solved at 2.1 A resolution by molecular replacement. These results set the stage for a detailed characterization of the PAF-AH Ib complex.
The Bacillussubtilis Histone-like Protein Hbsu Is Required for DNA Resolution and DNA Inversion Mediated by the β Recombinase of Plasmid pSM19035 (1995)

The beta recombinase, encoded by the Gram-positive bacterial plasmid pSM19035, is unable to mediate DNA recombination in vitro unless a host factor is provided. The factor has now been identified as the Bacillus subtilis Hbsu protein. Hbsu is a nonspecific DNA-binding and DNA-bending protein. The beta recombinase, in the presence of highly purified Hbsu protein, is able to catalyze in vitro intramolecular recombination between two specific recombination sites on a supercoiled DNA molecule. DNA resolution was obtained when the two crossing over sites (six sites) were directly oriented, whereas DNA inversion was the product when the six sites were in inverse orientation. The ability of the Escherichia coli chromatin-associated proteins HU, IHF, Fis, and H-NS to substitute for Hbsu was investigated. HU efficiently stimulated beta-mediated recombination, while the effect of IHF was partial and that of Fis and H-NS was undetectable. In addition, the beta protein was able to mediate DNA recombination in both wild-type and IHF-deficient E. coli cells, but failed to do so in an HU-deficient strain. The data presented provide direct evidence that a chromatin-associated protein is strictly required for beta-mediated recombination.
Editorial Comment (1983)

No AccessJournal of Urology1 Jan 1983Editorial Comment E. Darracott Vaughan E. Darracott VaughanE. Darracott Vaughan View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)51893-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial Comment." The Journal of Urology, 129(1), p. 10 © 1983 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 129Issue 1January 1983Page: 10 Advertisement Copyright & Permissions© 1983 by The American Urological Association Education and Research, Inc.MetricsAuthor Information E. Darracott Vaughan More articles by this author Expand All Advertisement PDF downloadLoading ...
Fault Detection and Diagnosis in Industrial Systems (2001)

The appearance of this book is quite timely as it provides a much needed state-of-the-art exposition on fault detection and diagnosis, a topic of much interest to industrialists. The material included is well organized with logical and clearly identified parts; the list of references is quite comprehensive and will be of interest to readers who wish to explore a particular subject in depth.
Biomechanics of the Anterior Human Corneal Tissue Investigated with Atomic Force Microscopy (2012)

At microscale level, the mechanical response of the most anterior stroma is complex and nonlinear. The microstructure (fibers' packing, number of cross-links, water content) and the combination of elastic (collagen fibers) and viscous (matrix) components of the tissue influence the type of viscoelastic response. Efforts in modeling the biomechanics of human corneal tissue at micrometric level are needed.
Microbiological safety of the first clinical pig islet xenotransplantation trial in New Zealand (2014)

Abstract Background Xenotransplantation using pig cells, tissues, or organs may be associated with the transmission of porcine microorganisms and the development of zoonoses. Among all porcine microorganisms porcine endogenous retroviruses ( PERV s) represent a special risk because they are integrated in the genome of all pigs and able to infect human cells. In previous preclinical and retrospective clinical trials of xenotransplantation, no transmission of PERV was observed. The first clinical trial of (alginate‐encapsulated) porcine islet cell transplantation in New Zealand, which was approved by the New Zealand Government as an open‐label phase I/ II a safety/efficacy trial, offers the possibility to analyze microbiological safety in a prospective clinical study. Methods Before the trial started, a multilevel testing strategy was used to screen for 26 microorganisms in donor pigs of the Auckland Island strain and the islet cell preparations used for treatment. Donor testing was performed using molecular methods including multiplex real‐time PCR . Blood samples from 14 pig islet cell recipients were also investigated by molecular biological methods at weeks 1, 4, 8, 12, 24, and 52 post‐transplant for the transmission of porcine microorganisms. Sera were also monitored at these time points for antibodies against PERV s. Results Beginning in 2009, fourteen patients with severe unaware hypoglycemia were treated with one of four different dosages of alginate‐encapsulated porcine islets ranging from 5000–20 000 islet equivalents delivered in a single dose. No transmission of either PERV s or other porcine microorganisms was detected by PCR and immunological methods. Conclusion These findings support previous results and strongly indicate the safety of xenotransplantation as performed here.
Gene expression of liver-specific proteins in hepatocyte spheroids in primary culture. (1995)

Adult rat hepatocytes assemble to form multicellular spheroids under non-adherent environments such as immobilized chondroitin sulfate-proteoglycan in primary culture. Previously, we demonstrated that hepatocyte spheroids exhibited various differentiated structures as observed in the liver tissue. It was also shown that hepatocyte growth was highly suppressed and several differentiated functions, including albumin production and gluconeogenesis, were well preserved in spheroids. To investigate the differentiated functions of cultured hepatocytes in relation to cell morphology, we compared the expression of the albumin and transferrin genes in spheroids with those in monolayers by Northern blot analysis. Production of these proteins in the culture medium was simultaneously examined by ELISA. Gene expression and protein production of both albumin and transferrin were better preserved in spheroids. We also examined changes in the expression of liver-specific genes in response to IL-6. Reduced mRNA levels of both albumin and transferrin was only found in spheroids and no change was observed in monolayers. These results suggest that the regulation of tissue-specific gene expression is better preserved in spheroids, in which hepatocytes are in close contact with each other.
MABp1 Targeting IL-1α for Moderate to Severe Hidradenitis Suppurativa Not Eligible for Adalimumab: A Randomized Study (2017)

Patients with moderate to severe hidradenitis suppurativa failing adalimumab therapy, or those ineligible to receive it, remain a population with an unmet need. Twenty patients not eligible for adalimumab were randomized to receive 12 weeks of blind treatment with placebo or MABp1, a true human antibody targeting IL-1α. Hidradenitis suppurativa clinical response score at week 12 was the primary endpoint. The primary endpoint was met in 10% and 60% of placebo- and MABp1-treated patients, respectively (odds ratio = 13.50, 95% confidence interval = 1.19-152.51). Clinical efficacy was maintained at 24 weeks in 0% and 40%. Improvement in the visual analog scale was reported by 20% and 85.7%, respectively, of patients failing previous anti-TNF treatment. Ultrasonography showed decreased neovascularization and lesion skin depth in the MABp1 group. MABp1 treatment was associated with decrease of circulating IL-8 and of stimulated production of IL-8 by whole blood. Whole blood production for hBD-2 was negatively associated with changes on ultrasonography in the placebo group but not in the MABp1 group. MABp1 is a promising treatment for patients with hidradenitis suppurativa not eligible for adalimumab. Inhibition of neovascularization and modulation of the production of IL-8 and hBD-2 are suggested mechanisms of action.
Surfactant Solutions Developed for NAPL Recovery in Contaminated Aquifers (1996)

Abstract Phase diagrams can be used to select surfactant solutions for diesel dissolution and extraction in contaminated aquifers. They indicate the active matter concentrations which can be injected into an aquifer. Due to surfactant precipitation or fine particles dispersion in sediments, surfactant solutions concentration greater than 5% and less than their solubility limit can be used for injections. Surfactant solution effects on interfacial tension (IFT) are consistent with predictions from phase diagrams. For similar active matter concentrations, IFT are lower for surfactant solutions that dissolve more diesel. IFT values between equilibrated diesel and surfactant solutions and observation of the oil‐in‐water microemulsions in column effluents confirm that solubilization of oil can occur in a Winsor type I system without oil mobilization. More than 50 sand column experiments were done for this study and a good agreement is observed between diesel dissolved in sand column experiments (with downward injection) and diesel dissolution predicted from phase diagrams. However, sand columns experiments showed significant decrease in efficiency with a drop in temperature from 25° C to 8° C (phase diagrams predict no change) and they are essential to check efficiencies of washing solution selected by phase diagrams. Optimal injection concentration of solutions decreases as the alcohols ratio (n‐AmOH:n‐BuOH) increases and as the temperature decreases. In columns, optimal concentration of surfactant solutions has a maximum efficiency of 0.4 (dissolved diesel/active matter). This limited performance is explained by: (1) the use of water to push a slug of washing solution creates dilution and thus demixing of the oil‐in‐water microemulsion in the column; (2) the limited interfacial area between diesel and washing solution in the porous media; (3) surface effects on the solid phase. Diesel extraction in sand columns is strongly influenced by the flow direction (up/down), the volume of the solution, and to a lesser extent by water salinity. Small modifications of flow velocity (three times faster) do not have a significant effect on diesel dissolution. Efficiency of diesel dissolution by surfactant solutions decreases as washing progresses because interfacial area (diesel/surfactant solution) decreases. The selection of a surfactant for diesel recovery is not based on efficiency alone but must also consider the costs of the ingredients.
Screening for L -sorbose and L -sorbosone dehydrogenase producing microbes for 2-keto- L -gulonic acid production (1999)

Acetic acid bacteria incompletely oxidize L-sorbose to 2-keto-L-gulonic acid (2KLG) by L-sorbose- and L-sorbosone dehydrogenases. In order to isolate novel microorganisms with these enzyme activities, a new screening method has been studied with a presumption that microorganisms reuse their metabolic products when principal carbon sources are exhausted. When various keto-aldonic acid-producing microorganisms were tested for the ability to grow in minimal media containing such products as 2,5-diketo-gluconic acid, 2-keto-D-gluconic acid, 5-keto-D-gluconic acid or 2-keto-L-gulonic acid, they grew with these keto-aldonic acids as the sole carbon source. By enriching the isolates collected from screening samples for their growth in minimal medium containing 2KLG as the sole carbon source, as much as 50% of selected strains showed L-sorbose- and L-sorbosone dehydrogenase activities. In spite of the presence of these enzymes, no significant amount of 2KLG was detected in the culture broth, possibly due to 2KLG reductase activity, indicating that the direct screening for 2KLG producer microorganisms would be less successful. These results suggest that the screening strategy using 2KLG as a carbon source is a useful method for the selective screening of microorganisms with L-sorbose- and L-sorbosone dehydrogenases, and that a similar strategy may be applied to other cases.
Bisimulation through probabilistic testing (preliminary report) (1989)

We propose a language for testing concurrent processes and examine its strength in terms of the processes that are distinguished by a test. By using probabilistic transition systems as the underlying semantic model, we show how a testing algorithm with a probability arbitrary close to 1 can distinguish processes that are not bisimulation equivalent. We also show a similar result (in a slightly stronger form) for a new process relation called 2/3-bisimulation — lying strictly between that of simulation and bisimulation. Finally, the ultimately strength of the testing language is shown to identify an even stronger process relation, called probabilistic bisimulation.
In Vitro Processing of Aleurain, a Barley Vacuolar Thiol Protease. (1990)

Aleurain, originally described from its cDNA as a thiol protease [Rogers, J.C., Dean, D., and Heck, G.R. (1985). Proc. Natl. Acad. Sci. USA 82, 6512-6516], is characterized here as a glycoprotein that is targeted to a distinct vacuolar compartment in aleurone cells. Monospecific antibodies to a bacterial trpE-aleurain fusion protein were used to show that aleurain is made as a 42-kilodalton (kD) proenzyme (proaleurain) that is proteolytically processed in a post-Golgi compartment in two steps to form a 32-kD protein. The first processing step is the discrete loss of 9 kD from proaleurain to yield a 33-kD intermediate that is further processed by the gradual loss of 1 kD resulting in mature 32-kD aleurain. Using proaleurain secreted from Xenopus oocytes as a substrate, we established an in vitro system using aleurone cell extracts that correctly processes proaleurain to a stable protein that is indistinguishable from native barley aleurain as judged by partial digestion with staphylococcal V8 protease. Proaleurain is not capable of self-cleavage in the absence of aleurone cell extracts and mature aleurain appears not to participate in processing in vitro.
Shp-2 Tyrosine Phosphatase Functions as a Negative Regulator of the Interferon-Stimulated Jak/STAT Pathway (1999)

Shp-2 is an SH2 domain-containing protein tyrosine phosphatase. Although the mechanism remains to be defined, substantial experimental data suggest that Shp-2 is primarily a positive regulator in cell growth and development. We present evidence here that Shp-2, while acting to promote mitogenic signals, also functions as a negative effector in interferon (IFN)-induced growth-inhibitory and apoptotic pathways. Treatment of mouse fibroblast cells lacking a functional Shp-2 with IFN-alpha or IFN-gamma resulted in an augmented suppression of cell viability compared to that of wild-type cells. To dissect the molecular mechanism, we examined IFN-induced activation of signal transducers and activators of transcription (STATs) by electrophoretic mobility shift assay, using a specific DNA probe (hSIE). The amounts of STAT proteins bound to hSIE upon IFN-alpha or IFN-gamma stimulation were significantly increased in Shp-2(-/-) cells. Consistently, tyrosine phosphorylation levels of Stat1 upon IFN-gamma treatment and, to a lesser extent, upon IFN-alpha stimulation were markedly elevated in mutant cells. Furthermore, IFN-gamma induced a higher level of caspase 1 expression in Shp-2(-/-) cells than in wild-type cells. Reintroduction of wild-type Shp-2 protein reversed the hypersensitivity of Shp-2(-/-) fibroblasts to the cytotoxic effect of IFN-alpha and IFN-gamma. Excessive activation of STATs by IFNs was also diminished in mutant cells in which Shp-2 had been reintroduced. Together, these results establish that Shp-2 functions as a negative regulator of the Jak/STAT pathway. We propose that Shp-2 acts to promote cell growth and survival through two mechanisms, i.e., the stimulation of growth factor-initiated mitogenic pathways and the suppression of cytotoxic effect elicited by cytokines, such as IFNs.
Highly predictive blacklisting (2008)

The notion of blacklisting communication sources has been a well-established defensive measure since the origins of the Internet community. In particular, the practice of compiling and sharing lists of the worst offenders of unwanted traffic is a blacklisting strategy that has remained virtually unquestioned over many years. But do the individuals who incorporate such blacklists into their perimeter defenses benefit from the blacklisting contents as much as they could from other list-generation strategies? In this paper, we will argue that there exist better alternative blacklist generation strategies that can produce higher-quality results for an individual network. In particular, we introduce a blacklisting system based on a relevance ranking scheme borrowed from the linkanalysis community. The system produces customized blacklists for individuals who choose to contribute data to a centralized log-sharing infrastructure. The ranking scheme measures how closely related an attack source is to a contributor, using that attacker’s history and the contributor’s recent log production patterns. The blacklisting system also integrates substantive log prefiltering and a severity metric that captures the degree to which an attacker’s alert patterns match those of common malwarepropagation behavior. Our intent is to yield individualized blacklists that not only produce significantly higher hit rates, but that also incorporate source addresses that pose the greatest potential threat. We tested our scheme on a corpus of over 700 million log entries produced from the DShield data center and the result shows that our blacklists not only enhance hit counts but also can proactively incorporate attacker addresses in a timely fashion. An early form of our system have been fielded to DShield contributors over the last year. 1
Genetic optimization of a self organizing fuzzy-neural network for load forecasting (2002)

In this paper a self-organizing fuzzy-neural network with a new learning mechanism and rule optimization using genetic algorithm (GA) is proposed for load forecasting. The number of rules in the inferencing layer is optimized using a genetic algorithm and an appropriate fitness function. We devise a learning algorithm for updating the connecting weights as well as the structure of the membership functions of the network. The proposed algorithm exploits the notion of error back propagation. The network weights are initialized with random weights instead of any preselected ones. The performance of the network is validated by extensive simulation results using practical data ranging over a period of two years. The optimized fuzzy neural network provides an accurate prediction of electrical load in a time frame varying from 24 to 168 hours ahead. The algorithm is adaptive and performs much better than the existing ANN techniques used for load forecasting.