gebhart/patrepeval huggingface dataset:
Exploiting the Redundancy in the Immune System (2003)

The fields of vaccinology and immunology have had a long-standing and complicated relationship. The view that vaccinology is a branch of immunology is more perception than reality. Vaccinology is older, practical, and often idiosyncratic, with its prime focus on the development of functional vaccines that protect a host against a particular microbe. Immunology is younger, conceptual, and strives to explain how a remarkably complex system recognizes and protects against internal and external threats without committing suicide. Vaccinology has been largely microbe-centered, clinically successful, and mostly empirical, whereas immunology has been largely host-centered, having struggled to translate its theoretical success and potential into clinical applicability. In this commentary, we examine the divide between vaccinology and immunology and put forth the view that vaccines often protect against infectious diseases by eliciting ‘unnatural’ immunity: immune responses that differ from and may even counteract those that arise during the development of natural immunity to
FOXP3 is a novel transcriptional repressor for the breast cancer oncogene SKP2 (2007)

S-phase kinase-associated protein 2 (SKP2) is a component of the E3 ubiquitin ligase SKP1-Cul1-Fbox complex. Overexpression of SKP2 results in cell cycle dysregulation and carcinogenesis; however, the genetic lesions that cause this upregulation are poorly understood. We recently demonstrated that forkhead box P3 (FOXP3) is an X-linked breast cancer suppressor and an important repressor of the oncogene ERBB2/HER2. Since FOXP3 suppresses tumor growth regardless of whether the tumors overexpress ERBB2/HER2, additional FOXP3 targets may be involved in its tumor suppressor activity. Here, we show that mammary carcinomas from mice heterozygous for a Foxp3 mutation exhibited increased Skp2 expression. Ectopic expression of FOXP3 in mouse mammary cancer cells repressed SKP2 expression with a corresponding increase in p27 and polyploidy. Conversely, siRNA silencing of the FOXP3 gene in human mammary epithelial cells increased SKP2 expression. We also show that Foxp3 directly interacted with and repressed the Skp2 promoter. Moreover, the analysis of over 200 primary breast cancer samples revealed an inverse correlation between FOXP3 and SKP2 levels. Finally, we demonstrated that downregulation of SKP2 was critical for FOXP3-mediated growth inhibition in breast cancer cells that do not overexpress ERBB2/HER2. Our data provide genetic, biochemical, and functional evidence that FOXP3 is a novel transcriptional repressor for the oncogene SKP2.
Phosphinoyl Radicals:  Structure and Reactivity. A Laser Flash Photolysis and Time-Resolved ESR Investigation (1998)

The photochemistry of a series of bis(acyl)phosphine oxides and the rate constants of the reactions of their phosphorus radicals with n-butylacrylate, thiophenol, bromotrichloromethane, oxygen, and methyl viologen have been investigated by laser flash photolysis. The results were compared to a mono(acyl)phosphine oxide ((2,4,6-trimethylbenzoyl)diphenylphosphine oxide). The variation in reactivity of the different phosphorus radicals was correlated with the degree of radical localization and s-character on the phosphorus atom, as reflected by the 31P hyperfine coupling constant, which was measured by time-resolved ESR. High 31P hyperfine splitting is observed for high degree of spin localization in a σ-orbital. It was shown that typical radical reactions (addition to monomers and oxygen, and atom abstractions) correlate well with the 31P hyperfine coupling. An inverse correlation was observed for electron-transfer reactions (reduction of methyl viologen), were a higher p-character of a localized orbital enhances the reaction.
Phage‐display as a tool for quantifying protein stability determinants (2004)

To address questions of protein stability, researchers have increasingly turned to combinatorial approaches that permit the rapid analysis of libraries of protein variants. Phage-display has proved to be a powerful tool for analyzing protein stability due to the large library size and the robustness of the phage particle to a variety of denaturing conditions. With the B1 domain of protein G (GB1) and a camelid heavy chain antibody as model systems, we are using phage-display libraries to experimentally address questions that have generally been addressed in silico, either through computational studies or statistical analysis of known protein structures. One effort has focused on identifying novel solutions to repacking the hydrophobic core of GB1, while maintaining stability comparable to the wild type protein. In a second study, a small set of substitutions in complimentarity-determining region 3 was found to stabilize the framework of the camelid antibody. Another major focus has been to obtain quantitative data on beta-sheet stability determinants. We have successfully adapted a phage-display method for quantitating affinities of protein variants (shotgun alanine scanning) to analysis of GB1 stability. Using this method, we have analyzed the energetic contributions of cross-strand side chain-side chain interactions. Finally, we discuss parameters to consider in using phage-display to discriminate subtle stability differences among fully folded variants. Overall, this method provides a fast approach for quantitatively addressing biophysical questions.
Coarse-grained distributed optimal power flow (1997)

We present an approach to parallelizing optimal power flow (OPF) that is suitable for coarse-grained distributed implementation and is applicable to very large interconnected power systems. We demonstrate the approach on several medium size systems, including IEEE Test Systems and parts of the ERCOT system. Our simulations demonstrate the feasibility of distributed implementation of OPF. Rough estimates are made of parallel efficiencies and speed-ups.
Zeroing in on ROS1 Rearrangements in Non–Small Cell Lung Cancer (2012)

Rimkunas and colleagues report on the development and validation of an immunohistochemical assay evaluating non-small cell lung cancers (NSCLC) for the presence of ROS1 fusions. The diagnostic was validated in a screen of 556 NSCLCs, identifying 9 (1.6%) tumors with oncogenic ROS1 rearrangements. These patients are candidates for ROS1-targeted therapies.
FACTS, mejora del rendimiento de las redes eléctricas (2002)

El sector del suministro de energía esta evolucionando rápidamente por causa de la desregula-ción y privatización. Durante años, las inversiones en la red de transmisión de muchos mercados no han sido suficientes y esto ha centrado finalmente la atención en el aumento de utilización de las líneas de transmisión existentes, en la cooperación multidisciplinar y en el problema de la calidad de la energía. La consecuencia es el gran interés actual por soluciones, tanto nuevas como clásicas. Precisamente se trata de las soluciones FACTS (Flexible AC Transmission Systems), entre ellas SVC, SVC Light(®), TCSC y otras. Estas soluciones, que se benefician de los importantes avances técnicos de la última década, hoy son las soluciones más actuales para muchas y varia-das necesidades. Una aplicación típica consistiría en aumentar la capacidad de cualquier línea de transmisión, pero en este artículo nos limitaremos a describir varios casos especiales y el modo en que se han afrontado los requerimientos específicos de los mismos
A Fully Convolutional Neural Network for Cardiac Segmentation in Short-Axis MRI (2016)

Automated cardiac segmentation from magnetic resonance imaging datasets is an essential step in the timely diagnosis and management of cardiac pathologies. We propose to tackle the problem of automated left and right ventricle segmentation through the application of a deep fully convolutional neural network architecture. Our model is efficiently trained end-to-end in a single learning stage from whole-image inputs and ground truths to make inference at every pixel. To our knowledge, this is the first application of a fully convolutional neural network architecture for pixel-wise labeling in cardiac magnetic resonance imaging. Numerical experiments demonstrate that our model is robust to outperform previous fully automated methods across multiple evaluation measures on a range of cardiac datasets. Moreover, our model is fast and can leverage commodity compute resources such as the graphics processing unit to enable state-of-the-art cardiac segmentation at massive scales. The models and code are available at https://github.com/vuptran/cardiac-segmentation
<title>Imaging spectroscopy using tunable filters: a review</title> (2000)

Major spin-offs from NASA's multi- and hyper spectral imaging remote sensing technology developed for Earth resources monitoring, are creative techniques that combine and integrate spectral with spatial methods. Such techniques are finding use in medicine, agriculture, manufacturing, forensics, and an e er expanding list of other applications. Many such applications are easier to implement using a sensor design different from the pushbroom or whiskbroom air- or space-borne counterparts. This need is met by using a variety of electronically tunable filters that are mounted in front of a monochrome camera to produce a stack of images at a sequence of wavelengths, forming the familiar 'image cube'. The combined spectral/spatial analysis offered by such image cubes takes advantage of tools borrowed form spatial image processing, chemometrics and specifically spectroscopy, and new custom exploitation tools developed specifically for these applications. Imaging spectroscopy is particularly useful for non homogeneous samples or scenes. examples include spatial classification based on spectral signatures, use of spectral libraries for material identification, mixture composition analysis, plume detection, etc. This paper reviews available tunable filters ,system design considerations, general analysis techniques for retrieving the intrinsic scene properties from the measurements, and applications and examples.
Genome-wide identification and characterization of novel genes involved in terpenoid biosynthesis in Salvia miltiorrhiza (2012)

Terpenoids are the largest class of plant secondary metabolites and have attracted widespread interest. Salvia miltiorrhiza, belonging to the largest and most widely distributed genus in the mint family, is a model medicinal plant with great economic and medicinal value. Diterpenoid tanshinones are the major lipophilic bioactive components in S. miltiorrhiza. Systematic analysis of genes involved in terpenoid biosynthesis has not been reported to date. Searching the recently available working draft of the S. miltiorrhiza genome, 40 terpenoid biosynthesis-related genes were identified, of which 27 are novel. These genes are members of 19 families, which encode all of the enzymes involved in the biosynthesis of the universal isoprene precursor isopentenyl diphosphate and its isomer dimethylallyl diphosphate, and two enzymes associated with the biosynthesis of labdane-related diterpenoids. Through a systematic analysis, it was found that 20 of the 40 genes could be involved in tanshinone biosynthesis. Using a comprehensive approach, the intron/exon structures and expression patterns of all identified genes and their responses to methyl jasmonate treatment were analysed. The conserved domains and phylogenetic relationships among the deduced S. miltiorrhiza proteins and their homologues isolated from other plant species were revealed. It was discovered that some of the key enzymes, such as 1-deoxy-D-xylulose 5-phosphate synthase, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, hydroxymethylglutaryl-CoA reductase, and geranylgeranyl diphosphate synthase, are encoded by multiple gene members with different expression patterns and subcellular localizations, and both homomeric and heteromeric geranyl diphosphate synthases exist in S. miltiorrhiza. The results suggest the complexity of terpenoid biosynthesis and the existence of metabolic channels for diverse terpenoids in S. miltiorrhiza and provide useful information for improving tanshinone production through genetic engineering.
A low on resistance 700V charge balanced LDMOS with intersected WELL structure (2004)

A new 700V rate charge balanced LDMOS structure is proposed. The key feature of this structure is the intersected N-Well and P-Well that divides drift region into multi parallel conduction path. Ron,sp can be reduced by considerably high doped N-Well region and surface electric field can be dispersed by each Well junction. Ron,sp of the proposed LDMOS is reduced by 55% compared with conventional LDMOS. This value nearly gets to the limit of LDMOS made by bulk silicon. The surface electric field that can cause fatal failure of LDMOS in reliability characteristics is decreased by 30% compared with conventional LDMOS. The position occurring breakdown was moved from surface to bulk below drain contact in the proposed LDMOS.
Study on the protection of CDP-choline against nicotine intoxication. (1983)

Cytidine diphosphate choline (CDP-choline, citicoline, Somazina) was orally administered to a group of mice at a dose of 1 g/kg for 4 days. Simultaneously, another group of mice were treated under similar conditions with 0.25% agar suspension. Then, animals were distributed into subgroups of 10 mice each and intravenous increasing doses of nicotine bitartrate were administered. By comparing the toxicity induced by nicotine in the animals receiving CDP-choline with that in animals receiving agar solution, a remarkable difference of the LD50 was observed between both groups.
Preferential adhesion of prostate cancer cells to bone is mediated by binding to bone marrow endothelial cells as compared to extracellular matrix components in vitro. (2000)

We have demonstrated previously that the preferential adhesion of prostate cancer cells to human bone marrow endothelial (HBME) cells may contribute to their preferential metastasis to bone. Although a subject of debate, it has been postulated that the endothelial cells of the bone marrow are fenestrated. It is unknown therefore whether prostate cancer cells adhere preferentially to the extracellular matrix (ECM) or the endothelial cells. It has also been demonstrated in other organ systems that the types of cell adhesion molecules on the surface of endothelial cells lining the organ microvasculature are determined, in part, by the ECM of the organ. We investigated how prostate cancer cell adhesion to HBME cells is affected by growing HBME cells on selected organ-derived ECM proteins in vitro. Growth of HBME cells and immortalized human aortic endothelial cells on bone, kidney, and placenta ECM proteins significantly increased their ability to bind PC-3 cells. This increased adhesion was not dose dependent and was not demonstrated with human dermal microvascular endothelial cells. Scanning electron microscopic analysis demonstrated that prostate cancer cells adhered directly to the endothelial cells and not to the underlying substrata. These results suggest that unidentified cell adhesion molecules are expressed or up-regulated on the apical surfaces of human aortic endothelial cells and HBME cells grown on bone, kidney, and placenta ECMs. These results also strongly demonstrate that the adhesion of prostate cancer cells to bone may be initiated by direct binding to endothelial cells rather than direct binding to exposed ECM components.
5-azacytidine and 5-azadeoxycytidine inhibit human immunodeficiency virus type 1 replication in vitro (1990)

Chemotherapeutic agents which affect the integration, stability, or inducibility of the human immunodeficiency virus (HIV) provirus would have considerable value in treating acquired immunodeficiency syndrome. Two nucleoside analogs of cytosine, 5-azacytidine and 5-azadeoxycytidine, which seem to have such value because of their capabilities to affect both the stability and the methylation patterns of the nucleic acids into which they are incorporated, were tested for their ability to inhibit the replication of HIV type 1 (HIV-1) in human CEM T cells in vitro. 5-Azadeoxycytidine (1 microM) completely inhibited HIV replication in CEM cells, by the criteria of reduced viral antigen expression and decreased supernatant reverse transcriptase activity, with little toxicity for the treated cells. 5-azacytidine (1 microM) also inhibited HIV replication, but less effectively. When added 2 or more h after CEM cells were infected with HIV-1, both 5-azacytosine derivatives were less effective than they were when added at the time of infection. Even 2 h of exposure to 5-azadeoxycytidine was sufficient for inhibition of HIV replication. Although long exposure to either analog at concentrations of 1 microM would result in pronounced cellular cytotoxicity, the the fact that short exposures to the same dose of drug inhibit HIV replication but are not toxic for the cells implies that cellular toxicity itself is not an important mechanism of the antiviral action of the analogs.
Unusual C3 and C4 metabolism in the chemoautotroph Alcaligenes eutrophus (1984)

Phosphoenolpyruvate (PEP) carboxykinase was identified to be the only C3-carboxylating enzyme in Alcaligenes eutrophus. The enzyme requires GDP or inosine diphosphate (GTP or inosine triphosphate) for activity. Pyruvate- and other PEP-dependent CO2-fixing enzyme activities were not detected, regardless of whether the cells were grown autotrophically or heterotrophically. It is suggested that two pathways are present in the organism for the formation of PEP from C4 dicarboxylic acids. Besides decarboxylation of oxaloacetate by PEP carboxykinase, the consecutive action of NADP+-malic enzyme and PEP synthetase can also accomplish this synthesis. An oxaloacetate decarboxylase activity observed in the cell extracts may also contribute to the latter route. The properties of a mutant deficient in PEP synthetase supported the biochemical data. This mutant was unable to grow on pyruvate or lactate and grew slower than the wild type on direct or indirect metabolites of the tricarboxylic acid cycle such as succinate, glutamate, or acetate. Growth on fructose and autotrophic growth were not affected by the enzyme defect. The findings suggest that, depending on the growth substrate utilized, PEP carboxykinase can serve a dual physiological function in A. eutrophus, an anaplerotic function in oxaloacetate synthesis from PEP, or a gluconeogenic function in PEP synthesis from oxaloacetate.
Fear in the Presence of Others (2001)

Article Abstract Because this piece has no abstract, we have provided for your benefit the first 3 sentences of the full text. We have all met people who are somewhat shy, selfconscious,and introverted and minimize their social contact. This personality style falls within that portionof the bell-shaped curve that we consider to representthe "normal personality."It seems clear, however, that some people are substantiallyrestricted by what appears to be a similar constellationof traits.
Inactivation and activation of Ras by the neurotrophin receptor p75 (2004)

The neurotrophin receptor p75 induces neurotrophic and/or apoptotic signalling pathways and can also cooperate with the neurotrophic Trk receptor tyrosine kinases. Its intracellular part encloses a so-called 'death domain' with a segment similar to the wasp venom mastoparan which binds small GTPases such as Rho. To study possible interactions of p75 and Ras (and Rho) we used wild-type and mutant genes of p75 stably expressed by MDCK cells which normally have neither Trk nor p75. We found that p75 can directly bind the GTPases Ras and Rho and that the unstimulated p75 inactivates total cellular Ras through a differential influence on the dissociation of GDP and GTP from Ras and an exchange of bound Ras.GDP for free Ras.GTP. These properties of p75 could also be demonstrated in vitro and should therefore be cell type-independent. Stimulation of p75 with nerve growth factor causes Ras activation via adapter proteins known from Trk signalling and induces rapid outgrowth of cellular processes. Both inactivation and activation of Ras by p75 are controlled by the phosphorylation state of the receptor's two intracellular tyrosines. p75 also influences Rho activation and inactivation, and the combined interactions of the receptor with the two GTPases Ras and Rho can regulate neurite formation in an efficient, synergistic way.
Purification and Some Characteristics of Extracellular Lipase fromFusarium oxysporumf. sp.lini (1992)

An extracellular lipase was isolated from a culture filtrate of Fusarium oxysporum f. sp. lini SUF 402 by hydrophobic chromatography. Purity of the preparation was 38-fold and recovery yield was 32%. The molecular mass of the isolated enzyme was 30 kDa. The lipase had a sugar chain, and the N-terminal amino acid was modified. The optimun pH at 37°C was 7.0. The enzyme had higher activity toward p-nitrophenyl esters with long and middle chain fatty acids (C8-C18) than with a short chain fatty acid (C4). The enzyme was not inhibited by phenylmethylsulfonyl fluoride or 2-mercaptoethanol. In the case of the lipase, both the hydrolysis rate of tristearin and final concentration of fatty acid content were higher than those of triolein. The lipase was examined with respect to its ability of concentrating the n-3 polyunsaturated fatty acid (n-3 PUFA) content of partially hydrolyzed glycerides (TG and DG) obtained from two kinds of fish oil (cod liver oil and refined sardine oil). The lipase gave increases in n-3 PUFA contents as the hydrolysis progressed. The lipase concentrated only docosahexaenoic acid with little increase in icosapentaenoic acid. Maximal total n-3 PUFA contents were about 30% in both fish oils.
Battery‐Powered Implantable Nerve Stimulator for Chronic Activation of Two Skeletal Muscles Using Multichannel Techniques (1999)

Chronic activation of skeletal muscle is used clinically in representative numbers for diaphragm pacing to restore breathing and for dynamic graciloplasty to achieve fecal continence. The 3 different stimulation techniques currently used for electrophrenic respiration (EPR) all apply high frequency powered implants. It was our goal to make these stimulation methods applicable for EPR by a battery-powered nerve stimulator that would maximize the patient's freedom of movement. Additionally, the system should allow the implementation of multichannel techniques and alternating stimulation of 2 skeletal muscles as a further improvement in graciloplasty. Generally, the developed implantable nerve stimulator can be used for simultaneous and alternating activation of 2 skeletal muscles. Stimulation of the motor nerve is achieved by either single channel or multichannel methods. Carousel stimulation and sequential stimulation can be used for graciloplasty as well as for EPR. For EPR we calculated an operating time of the implant battery of 4.1 years based on the clinically used stimulation parameters with carousel stimulation. The multichannel pulse generator is hermetically sealed in a titanium case sized 65 x 17 mm (diameter x height) and weighs 88 g.
Traffic dispersion graph based anomaly detection (2011)

Detecting and diagnosing anomalous traffic are important aspects of managing IP networks. In this paper, we propose a novel approach to detect anomalous network traffic based on graph theory concepts such as degree distribution, maximum degree and dK-2 distance. In this approach, we have used the traffic dispersion graphs (TDG) to model network traffic over time. We analyze differences of TDG graphs in time series to detect anomalies and introduce a method to identify attack patterns in anomalous traffic. The approach has been validated by using network traces from POSTECH and CAIDA. © 2011 ACM.