gebhart/patrepeval huggingface dataset:
Generation of human antibody fragments recognizing distinct epitopes of the nucleocapsid (N) SARS-CoV protein using a phage display approach (2005)

Abstract Background Severe acute respiratory syndrome (SARS)-CoV is a newly emerging virus that causes SARS with high mortality rate in infected people. Successful control of the global SARS epidemic will require rapid and sensitive diagnostic tests to monitor its spread, as well as, the development of vaccines and new antiviral compounds including neutralizing antibodies that effectively prevent or treat this disease. Methods The human synthetic single-chain fragment variable (scFv) ETH-2 phage antibody library was used for the isolation of scFvs against the nucleocapsid (N) protein of SARS-CoV using a bio panning-based strategy. The selected scFvs were characterized under genetics-molecular aspects and for SARS-CoV N protein detection in ELISA, western blotting and immunocytochemistry. Results Human scFv antibodies to N protein of SARS-CoV can be easily isolated by selecting the ETH-2 phage library on immunotubes coated with antigen. These in vitro selected human scFvs specifically recognize in ELISA and western blotting studies distinct epitopes in N protein domains and detect in immunohistochemistry investigations SARS-CoV particles in infected Vero cells. Conclusion The human scFv antibodies isolated and described in this study represent useful reagents for rapid detection of N SARS-CoV protein and SARS virus particles in infected target cells.
Network analysis of named entity co-occurrences in written texts (2016)

The use of methods borrowed from statistics and physics to analyze written texts has allowed the discovery of unprecedent patterns of human behavior and cognition by establishing links between models features and language structure. While current models have been useful to unveil patterns via analysis of syntactical and semantical networks, only a few works have probed the relevance of investigating the structure arising from the relationship between relevant entities such as characters, locations and organizations. In this study, we represent entities appearing in the same context as a co-occurrence network, where links are established according to a null model based on random, shuffled texts. Computational simulations performed in novels revealed that the proposed model displays interesting topological features, such as the small world feature, characterized by high values of clustering coefficient. The effectiveness of our model was verified in a practical pattern recognition task in real networks. When compared with traditional word adjacency networks, our model displayed optimized results in identifying unknown references in texts. Because the proposed representation plays a complementary role in characterizing unstructured documents via topological analysis of named entities, we believe that it could be useful to improve the characterization of written texts (and related systems), specially if combined with traditional approaches based on statistical and deeper paradigms.
Investigation and Reduction of Acoustical Noise from Switched Reluctance Drives in Current and Voltage Control (1994)

Vol. 3, pp. 589-594
Growth of the Ectomycorrhizal Fungus Pisolithus Microcarpus in different nutritional conditions (2011)

The most important plant species employed in reforestation programs depend on ectomycorrhizal fungi for their establishment and growth. The exploitation of this symbiosis to improve forest productivity requires fungal inoculants in a large scale level. To develop such a technology it is necessary to define the optimal composition of the culture medium for each fungus. With these objectives in mind, the effect of the composition of the culture medium on biomass production of the ectomycorrhizal fungus Pisolithus microcarpus (isolate UFSC-Pt116) was studied. The original composition of two culture media, already employed for cultivation of ectomycorrhizal fungi, was submitted to several variations with the C/N ratio as the main variable. A variation of the Pridham-Gottlieb medium was the most efficient for the production of biomass. Therefore, it was submitted to a factorial assay where glucose, peptone and yeast extract components were the factors analyzed. Results showed that the glucose concentration may be increased up to 40 % in order to promote higher biomass production. Peptone had a positive effect on this variable, whereas yeast extract promoted a deleterious effect. These results indicate that it is advisable to eliminate yeast extract from the medium and replace it with peptone prior to use.
Salicylic acid has a role in regulating gene expression during leaf senescence (2000)

Leaf senescence is a complex process that is controlled by multiple developmental and environmental signals and is manifested by induced expression of a large number of different genes. In this paper we describe experiments that show, for the first time, that the salicylic acid (SA)-signalling pathway has a role in the control of gene expression during developmental senescence. Arabidopsis plants defective in the SA-signalling pathway (npr1 and pad4 mutants and NahG transgenic plants) were used to investigate senescence-enhanced gene expression, and a number of genes showed altered expression patterns. Senescence-induced expression of the cysteine protease gene SAG12, for example, was conditional on the presence of SA, together with another unidentified senescence-specific factor. Changes in gene expression patterns were accompanied by a delayed yellowing and reduced necrosis in the mutant plants defective in SA-signalling, suggesting a role for SA in the cell death that occurs at the final stage of senescence. We propose the presence of a minimum of three senescence-enhanced signalling factors in senescing leaves, one of which is SA. We also suggest that a combination of signalling factors is required for the optimum expression of many genes during senescence.
The production of transgenic potato plants expressing human alpha-interferon using lipofectin-mediated transformation. (2002)

The lipofectin system was used to transform potato protoplasts with plasmid DNA (pIG3031), which contains human alpha-interferon cDNA and codes for the selectable neomycin phosphotransferase II gene (NPT II). Both genes are under the control of the bi-directional plant active transcriptional promoter from Agrobacterium tumefaciens T-DNA. The criteria of phenotype stability after selective pressure removal, in vitro activity assay of NPT II, the biological analysis of alpha-interferon activity, Southern blot analysis and RNA slot blot were used to confirm the mitotic stability of the foreign gene and its expression and stable integration into the host genome. These studies demonstrate that human alpha-interferon cDNA can be correctly expressed in potato cells.
Power independent ignition energy measurements (2023)

A portion of the electrical energy supplied to hot-wire ignitable materials is dissipated, largely through thermal conduction, to the unignited portion of the charge and to the containment and igniter system. The remainder of the energy deposited by the igniter wire raises the mass of material required for sustained reaction to the critical reaction temperature. The amount of energy dissipated is a direct function of the time from first application of power, to ignition. Time to ignition can be controlled by altering firing pulse power. Integration of the power pulse from start until ignition yields the ignition energy. Repetition of this procedure at different power levels permits one to plot energy versus firing time. Since conduction losses are time dependent, extrapolation of the resulting curve to zero time yields an ignition energy value that is independent of losses due to thermal conduction. A key to the success of the procedure is accurate observation of ignition time. It was found that the reaction energy released at ignition causes a discernible deflection in the firing current record. By comparison of light emission and current traces, it was found that the onset of deflagration occurs at the inflection point of the current trace deflection. This procedure has been successfully applied to hot pressed thermite samples, yielding ignition energies that are in qualitative agreement with the expected sensitivities of the samples.
Optimization of data prefetch helper threads with path-expression based statistical modeling (2007)

This paper investigates helper threads that improve performance by prefetching data on behalf of an application's main thread. The focus is data prefetch helper threads that lack branch instructions and which generate prefetches for one dynamic instance of a delinquent load instruction per spawned helper thread. This form of helper thread, some-times called a simple p-thread, has been studied previously by Roth et al. [29, 26] who proposed a framework for optimizing their impact. A key step in that framework is predicting the performance impact of a helper thread. In this paper we propose and evaluate a novel performance prediction technique that achieves comparable results yet requires less detailed information about dynamic program behavior. This technique extends a path expression based statistical modeling framework [2] by incorporating information about branch correlation (which we show is important) and by considering data flow information in a statistical manner. Significantly, the profile information we use is similar to that provided within current optimizing compilers. This paper also provides the first comprehensive assessment of the sources of modeling error relevant to predicting the performance impact of simple p-threads.
CpG Island Methylator Phenotype Association with Elevated Serum α-Fetoprotein Level in Hepatocellular Carcinoma (2007)

Positive correlation of CIMP and AFP levels in HCC suggests that CIMP can serve as a molecular marker of late-stage HCC development.
An Efficient File Hierarchy Attribute-Based Encryption Scheme in Cloud Computing (2016)

Ciphertext-policy attribute-based encryption (CP-ABE) has been a preferred encryption technology to solve the challenging problem of secure data sharing in cloud computing. The shared data files generally have the characteristic of multilevel hierarchy, particularly in the area of healthcare and the military. However, the hierarchy structure of shared files has not been explored in CP-ABE. In this paper, an efficient file hierarchy attribute-based encryption scheme is proposed in cloud computing. The layered access structures are integrated into a single access structure, and then, the hierarchical files are encrypted with the integrated access structure. The ciphertext components related to attributes could be shared by the files. Therefore, both ciphertext storage and time cost of encryption are saved. Moreover, the proposed scheme is proved to be secure under the standard assumption. Experimental simulation shows that the proposed scheme is highly efficient in terms of encryption and decryption. With the number of the files increasing, the advantages of our scheme become more and more conspicuous.
Comparison of Interleukin-4 Gene Expression and NF-AT Activity in Neonates and Adults Peripheral Blood Mononuclear Cells (2001)

The mechanisms of lowered IL 4 gene expression in neonates was studied by comparing the differences of IL 4 gene expression and nuclear factor of activated T cell (NF AT) activities between neonatal cord blood mononuclear cells (CBMC) and adult PBMC The levels of IL 4 and its mRNA were detected by using ELISA and RT PCR respectively,and the activity of NF AT was detected by using electrophoresis mobility shift assay (EMSA) Results showed that,after stimulation with anti CD3 and PMA,the concentrations of IL 4 in supernatants of CBMC were significant lower than those in PBMC In our test system,the activities of NF AT in CBMC were almost undetectable,but stronger in PBMC The results of this study suggest that lack of the regulation by NF AT at transcription level may be associated with insufficient transcription of IL 4 gene in neonates,and thus result in insufficient IL 4 gene expression in neonates
AI for dynamic team-mate adaptation in games (2010)

There is a long tradition of developing games in which the difficulty level is dynamically adapted to the performance of human players. However, there has been less work on the creation of game systems that perform dynamic team-mate adaption - and even less on developing team-mate NPCs (Non Player Characters) that adaptively support players in the face of opponents that adaptively increase the difficulty for the player. This paper is based on preliminary research to identify the key elements involved in developing “buddy” NPC team-mates that dynamically adapt to the needs and behaviors of human players while cooperating to compete against adaptive AI opponents. We discuss the computational and design challenges involved in developing such agents in the context of a simple test game called Capture the Gunner (CTG). The main contributions of the paper include: a proposed vocabulary and framework for understanding/modeling team-mate systems with adaptive difficulty, a particular technique for adaptive team-mate cooperation in the face of an adaptive opponent, and the identification of several significant new issues that arise in the process of developing computer games that involve adaptive NPC team-mates that cooperate with the player in the face of adaptive opponents.
Soil Fertility and Fertilizers: An Introduction to Nutrient Management (1998)

1. Introduction. 2. Basic Soil-Plant Relationships. 3. Soil Acidity and Alkalinity. 4. Nitrogen. 5. Phosphorus. 6. Potassium. 7. Sulfur, Calcium, and Magnesium. 8. Micronutrients. 9. Soil Fertility Evaluation. 10. Basics of Nutrient Management. 11. Nutrients, Water Use, and Other Interactions. 12. Economics of Plant-Nutrient Use. 13. Agricultural Productivity and Environmental Quality. Index.
WEClustering: word embeddings based text clustering technique for large datasets (2021)

A massive amount of textual data now exists in digital repositories in the form of research articles, news articles, reviews, Wikipedia articles, and books, etc. Text clustering is a fundamental data mining technique to perform categorization, topic extraction, and information retrieval. Textual datasets, especially which contain a large number of documents are sparse and have high dimensionality. Hence, traditional clustering techniques such as K-means, Agglomerative clustering, and DBSCAN cannot perform well. In this paper, a clustering technique especially suitable to large text datasets is proposed that overcome these limitations. The proposed technique is based on word embeddings derived from a recent deep learning model named "Bidirectional Encoders Representations using Transformers". The proposed technique is named as WEClustering. The proposed technique deals with the problem of high dimensionality in an effective manner, hence, more accurate clusters are formed. The technique is validated on several datasets of varying sizes and its performance is compared with other widely used and state of the art clustering techniques. The experimental comparison shows that the proposed clustering technique gives a significant improvement over other techniques as measured by metrics such Purity and Adjusted Rand Index.
A Review of Low-Dose Ritonavir in Protease Inhibitor Combination Therapy (2003)

The pharmacokinetics of protease inhibitors center around the microsomal enzyme cytochrome P-450 3A4. As a potent inhibitor of this enzyme, ritonavir can increase the bioavailability and half-life of coadministered protease inhibitors. Evidence suggests that increased exposure to protease inhibitors is clinically relevant. Antiretroviral treatment with low-dose ritonavir-boosted lopinavir, indinavir, and saquinavir has durable virological activity and shows impressive immune reconstitution. Although tolerable in most cases, gastrointestinal side effects, hepatotoxicity, and blood lipid abnormalities remain relevant issues. Additional study will elucidate the advantages and disadvantages of twice-daily, low-dose ritonavir-boosted regimens and determine whether once-daily regimens based on this principle will have a lasting role in clinical practice.
[The Infucommand. A PCA (patient-controlled analgesia) device using pulsoximetric bolus control]. (1990)

A physician who treats his patients with patient-controlled analgesia (PCA) must be aware of the possibility of unnoticed respiratory depression. A new device has been developed (Infucommand), which uses a pulsoximeter to monitor respiration and stops the infusion pump if the level of O2 saturation falls below a preset value. Thus, the danger of opioid overdosage can be reduced.
Cristobalite Phase Formation in Glass/Ceramic Composites (1995)

The effect of several different aluminum‐containing ceramic additions to borosilicate glass on suppressing cris‐tobalite precipitation has been examined. The results showed that mullite or aluminum nitride suppresses cristo‐balite formation more effectively than alumina or spinel. Although both follow a simple rule of mixtures, glass/mullite composites can be fabricated with lower dielectric constants than glass/alumina composites, while maintaining a thermal expansion coefficient close to Si. Electron micro‐analysis using X‐ray energy dispersive spectroscope showed that the measured interdiffusion coefficient between alumina and glass is in good agreement with the data which have already been published.
ChemInform Abstract: Enzyme‐Mediated H2O2 Oxidation of (E)‐Stilbene‐3,4‐diol. (1988)

Abstract The title reaction of (I) is investigated in order to gain insight into oxidation processes of natural stilbenes.
Unified formulation of dynamics for serial rigid multibody systems (1991)

There has been a growing interest in the development of new and efficient algorithms for multibody dynamics in recent years. Serial rigid multibody systems form the basic subcomponents of general multibody systems, and a variety of algorithms to solve the serial chain forward dynamics problem have been proposed. In this paper, the economy of representation and analysis tools provided by the spatial operator algebra are used to clarify the inherent structure of these algorithms, to identify those that are similar, and to study the relationships among the ones that are distinct. For the purposes of this study, the algorithms are categorized into three classes: algorithms that require the explicit computation of the mass matrix, algorithms that are completely recursive in nature, and algorithms of intermediate complexity. In addition, alternative factorizations for the mass matrix and closed form expressions for its inverse are derived. These results provide a unifying perspective, within which these diverse dynamics algorithms arise naturally as a consequence of a progressive exploitation of the structure of the mass matrix.
Temporal Consistency of Integrity-Ensuring Computations and Applications to Embedded Systems Security (2018)

Assuring integrity of information (e.g., data and/or software) is usually accomplished by cryptographic means, such as hash functions or message authentication codes (MACs). Computing such integrity-ensuring functions can be time-consuming if the amount of input data is large and/or the computing platform is weak. At the same time, in real-time or safety-critical settings, it is often impractical or even undesirable to guarantee atomicity of computing a time-consuming integrity-ensuring function. Meanwhile, standard correctness and security definitions of such functions assume that input data (regardless of its size) remains consistent throughout computation. However, temporal consistency may be lost if another process interrupts execution of an integrity-ensuring function and modifies portions of input that either or both: (1) were already processed, or (2) were not processed yet. Lack of temporal consistency might yield an integrity result that is non-sensical or simply incorrect. Such subtleties and discrepancies between (implicit) assumptions in definitions and implementations can be a source of inconsistenceies, which might lead to vulnerabilities.
Myogenic Control of Airways Smooth Muscle and Cell-to-Cell Coupling (1994)

In smooth muscle in general, contraction is the physiologically relevant endpoint and is a Ca2+-dependent event. In addition, many of the ion conductances in smooth muscle are regulated by Ca2+ and/or are permeable to Ca2+. As a prerequisite to this discussion of myogenic contractile and electrical activity in airways smooth muscle (ASM), then, it is necessary to review briefly the regulation of contractile activity and of Ca2+-homeostasis in smooth muscle. Many of these issues will be dealt with in more detail in subsequent chapters and volumes of this series.
Homoepitaxial Chemical Vapor Deposition of 6H-SiC at Low Temperatures on {0114} Substrates (1992)

Homoepitaxial chemical vapor deposition of 6H-SiC at low temperatures on {011̄4} substrates has been investigated. The crystal growth was carried out using a SiH 4 -C 3 H 8 -H 2 system in the temperature range of 1000∼1500°C. Crystallinity of grown layers was characterized by means of reflection high-energy electron diffraction and etch-pit observation. The influences of surface polarity and growth conditions on crystallinity of grown layers were investigated. Significant effects of C/Si ratio on the growth were observed. Homoepitaxial growth of 6H-SiC was realized on (01̄14̄)C-face substrates at temperatures as low as 1100°C, which is 700°C lower than that on {0001} basal planes.
Changing the Face of Kynurenines and Neurotoxicity: Therapeutic Considerations (2015)

Kynurenines are the products of tryptophan metabolism. Among them, kynurenine and kynurenic acid are generally thought to have neuroprotective properties, while 3-hydroxykynurenine, 3-hydroxyanthranilic acid and quinolinic acid are considered neurotoxic. They participate in immunoregulation and inflammation and possess pro- or anti-excitotoxic properties, and their involvement in oxidative stress has also been suggested. Consequently, it is not surprising that kynurenines have been closely related to neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis and multiple sclerosis. More information about the less-known metabolites, picolinic and cinnabarinic acid, evaluation of new receptorial targets, such as aryl-hydrocarbon receptors, and intensive research on the field of the immunomodulatory function of kynurenines delineated the high importance of this pathway in general homeostasis. Emerging knowledge about the kynurenine pathway provides new target points for the development of therapeutical solutions against neurodegenerative diseases.