gebhart/patrepeval huggingface dataset:
The application of value-driven decision-making in air combat simulation (2002)

The use of constructive computer simulations of air-to-air combat has long been a tool used to evaluate the effectiveness of hardware improvements, to investigate new or improved tactics, to provide threats for man-in-the-loop simulators, and to provide environment generators for hardware-in-the-loop systems. Value-driven based decision models, used in air-to-air combat models such as BRAWLER (aircraft) and TRACES (helicopters), are based upon a relatively straightforward paradigm much like the one used implicitly by many chess players. Using this approach, the selection of a course of action consists of: (1) the selection of a set alternative courses of actions which span the decision space, (2) projection of each alternative into the future, (3) evaluation (scoring) of the future for each alternative using a value function, and (4) selection of the highest scoring alternative. Since the value function is constructed to be sensitive to the many goals of a given decision, it intrinsically performs tradeoffs among conflicting objectives. In addition, the effects of orders from higher level entities in the decision hierarchy are easily implemented by passing weights to the decision-maker which affect the importance of various components of his value scoring function.
Capacitive RF discharges modelled by particle-in-cell Monte Carlo simulation. I. Analysis of numerical techniques (1993)

Particle-in-cell Monte Carlo simulation has become a very effective tool in exploring processing plasmas and in particular capacitive RF discharges. We describe the conventional particle-in-cell (PIC) simulation and its limitations in terms of computational efficiency, review the implicit subcycling methods used to improve computational efficiency for many problems, and analyse conventional and implicit subcycling PIC simulation performances on an RF discharge model. Implementation of the implicit subcycling scheme in our bounded one-dimensional electrostatic code, PDP, resulted in an order of magnitude reduction in the simulation run time when the accuracy conditions were satisfied.
Temperature transients in heavily doped and undoped silicon using rapid thermal annealing (1985)

Optical coupling by absorption and reflection of a wafer during rapid thermal anneals (RTA) determines the temperature transients during heating, and the behavior of thermally activated processes. It is shown experimentally that the heating rate and temperatures during the early phases of a RTA cycle depend on the doping of the wafer being heated. High doping is accompanied by high free carrier absorption which results in a relatively rapid increase in temperature. Differences of heating rates of 50 °C/sec and temperatures several hundred degrees centigrade are obtained in the first 5 sec of a RTA cycle for N+ and N− wafers and significant effects on the heating rate of heavily implanted wafers are also seen. Experiments were carried out using thermocouples, optical pyrometer and also by observing the lateral solid-phase growth of silicon on sapphire (SOS). A simple theoretical description is given for the enhanced heating rate for N+ and heavily implanted wafers.
Mouse model of G M2 activator deficiency manifests cerebellar pathology and motor impairment (1997)

The GM2 activator deficiency (also known as the AB variant), Tay-Sachs disease, and Sandhoff disease are the major forms of the GM2 gangliosidoses, disorders caused by defective degradation of GM2 ganglioside. Tay-Sachs and Sandhoff diseases are caused by mutations in the genes (HEXA and HEXB) encoding the subunits of beta-hexosaminidase A. The GM2 activator deficiency is caused by mutations in the GM2A gene encoding the GM2 activator protein. For degradation of GM2 ganglioside by beta-hexosamindase A, the GM2 activator protein must participate by forming a soluble complex with the ganglioside. In each of the disorders, GM2 ganglioside and related lipids accumulate to pathologic levels in neuronal lysosomes, resulting in clinically similar disorders with an onset in the first year of life, progressive neurodegeneration, and death by early childhood. We previously have described mouse models of Tay-Sachs (Hexa -/-) and Sandhoff (Hexb -/-) diseases with vastly different clinical phenotypes. The Hexa -/- mice were asymptomatic whereas the Hexb -/- mice were severely affected. Through gene disruption in embryonic stem cells we now have established a mouse model of the GM2 activator deficiency that manifests an intermediate phenotype. The Gm2a -/- mice demonstrated neuronal storage but only in restricted regions of the brain (piriform, entorhinal cortex, amygdala, and hypothalamic nuclei) reminiscent of the asymptomatic Tay-Sachs model mice. However, unlike the Tay-Sachs mice, the Gm2a -/- mice displayed significant storage in the cerebellum and defects in balance and coordination. The abnormal ganglioside storage in the Gm2a -/- mice consisted of GM2 with a low amount of GA2. The results demonstrate that the activator protein is required for GM2 degradation and also may indicate a role for the GM2 activator in GA2 degradation.
Sequence requirements for cleavage activation of influenza virus hemagglutinin expressed in mammalian cells. (1988)

Cleavage of the hemagglutinin (HA) in tissue culture systems has been correlated with virulence of avian influenza viruses. To examine the structural requirements for cleavage of the HA, the HA gene from a virulent H5 influenza virus was expressed in mammalian cells (CV-1), and the cleavage site of the HA was explored by using site-specific mutagenesis. The expressed HA protein exhibited normal cleavage, transport to the cell membrane, and ability to adsorb and to fuse erythrocytes at pH 5. Site-specific mutagenesis of the HA directly established that (i) most of the basic amino acids at this site are critical for cleavage activation; (ii) besides the connecting peptide sequence, at least one other structural feature of the HA is required for enzyme recognition; and (iii) the length of the connecting peptide can abrogate the structural feature(s).
The PR4G VHF ECCM system: extensive tactical communications for the battlefield (2003)

PR4G, a complete system for ECCM (electronic counter countermeasures) VHF tactical radio communications, is described. It has been developed to meet the requirements of the French army. Its characteristics, including enhancements and integration into the French C3I (command, control, communications, and intelligence) systems, are presented. The program and program management methodology are described. Program management uses such techniques as functional and value analysis, total quality, integrated logistics support, and design to cost. A preplanned enhancement program is under way, including new services like time-division multiple access, packet access service, and low data rate vocoders.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enediyne Antitumor Antibiotic Maduropeptin Biosynthesis Featuring a C-Methyltransferase That Acts on a CoA-Tethered Aromatic Substrate (2010)

The enediyne antitumor antibiotic maduropeptin (MDP) is produced by Actinomadura madurae ATCC 39144. The biosynthetic pathway for the 3,6-dimethylsalicylic acid moiety of the MDP chromophore is proposed to be comprised of four enzymes: MdpB, MdpB1, MdpB2, and MdpB3. Based on the previously characterized biosynthesis of the naphthoic acid moiety of neocarzinostatin (NCS), we expected a biosynthetic pathway featuring carboxylic acid activation by the MdpB2 CoA ligase immediately before its coupling to an enediyne core intermediate. Surprisingly, the MDP aromatic acid biosynthetic pathway employs an unusual logic in which MdpB2-catalyzed CoA activation occurs before MdpB1-catalyzed C-methylation, demonstrating that MdpB1 is apparently unique in its ability to C-methylate a CoA-tethered aromatic acid. MdpB2 is a promiscuous CoA ligase capable of activating a variety of salicylic acid analogues, a property that could be potentially exploited to engineer MDP analogues.
α-Amino-β-hydroxy Acids in the Total Synthesis of Amino Sugars (1993)

The use of suitably protected serine- and threonine-derived aldehydes as chirons offers many new possibilities in stereocontrolled synthesis of amino sugars. The application of these chirons to various reactions such as metalloorganic addition, [4+2] cycloaddition, and cyclocondensation enabled the development of a unique methodology for highly controlled formation of new chiral centers. For illustration of this methodology, a survey of total synthesis of selected, naturally occurring amino sugars is presented. 1. Introduction 2. Developed Methodology: Scope and Limitations 3. Practical Tests of the Developed Methodology: Total Syntheses of Selected Amino Sugars 4. Conclusion
The pathogenesis of choroidal neovascularization in patients with age-related macular degeneration. (1999)

Laser photocoagulation and several experimental treatments for choroidal neovascularization (CNV) in patients with age-related macular degeneration attempt to ablate the neovascularization, but do not address underlying angiogenic stimuli. As a result, recurrences are a major problem. Drug treatment to counter the growth of CNV would be a major advance, but its development is impeded by lack of knowledge concerning the stimuli and other molecular signals involved in the pathogenesis of CNV. Herein we explore clues that can be gleaned from clinical, epidemiological, pathological, and experimental data. These suggest that abnormalities of the extracellular matrix of retinal pigmented epithelial (RPE) cells may promote a pro-angiogenic RPE phenotype that contributes to the development of CNV. This provides a general hypothesis that can be tested, but it is also necessary to test hypotheses regarding the specific alterations in gene expression that contribute to CNV. Identification of alterations in gene expression will provide targets for rational design of drug treatment.
Is field intubation useful? (2003)

The establishment and maintenance of an adequate airway is often the single most important initial therapy provided to a victim of severe injury. This may be accomplished by simple techniques such as placement of an oral or nasopharyngeal airway as well as bag-mask ventilation techniques. More advanced techniques such as endotracheal intubation require a higher level of training and expertise for both prehospital and hospital providers. Although paramedics routinely practice endotracheal intubation in the field, there are increasing reports on the many potential risks associated with these procedures as well as increased morbidity and mortality in both pediatric and adult patients. These data have important implications for field airway management in the critically ill trauma patient.
Primer3—new capabilities and interfaces (2012)

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3's functionality. In this article, we describe Primer3's current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement-a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
Specific Newborn Individualized Developmental Care and Assessment Program Movements Are Associated With Acute Pain in Preterm Infants in the Neonatal Intensive Care Unit (2004)

Of the 85 NIDCAP behaviors, a subset of 8 NIDCAP movements were associated with pain. Particularly for infants who are born at early GAs, addition of these movements to commonly used measures may improve the accuracy of pain assessment.
Molecular cloning of the murine BP-1/6C3 antigen: a member of the zinc-dependent metallopeptidase family. (1990)

The BP-1/6C3 antigen is a phosphorylated cell surface glycoprotein that can be identified by monoclonal antibodies on mouse pre-B cells, immature B cells, and certain stromal cell lines from bone marrow. Expression of this antigen is increased in stromal-dependent pre-B cell lines and retrovirally transformed pre-B cells. Expression of the BP-1/6C3 antigen thus correlates with proliferation and transformation of immature B-lineage cells. In this study, we report the isolation and characterization of cDNAs encoding the BP-1/6C3 antigen. Northern blot analysis revealed a major 4.1-kilobase mRNA in all BP-1/6C3+ mouse pre-B lines and in a human pre-B cell line. BP-1/6C3 mRNA was either absent or truncated in BP-1/6C3- cell lines. The cDNA sequence predicts a type II integral membrane protein of 945 amino acids with an intracytoplasmic amino terminus of only 17 amino acids and a typical zinc-binding motif in its extracellular domain. BP-1/6C3 has significant homology to aminopeptidase N and is the second member of the zinc-dependent metallopeptidase gene family to be found on the surface of early B-lineage cells.
A comprehensive search for DNA amplification in lung cancer identifies inhibitors of apoptosis cIAP1 and cIAP2 as candidate oncogenes (2003)

Amplification of oncogenes is an important mechanism that can cause gene overexpression and contributes to tumor development. The identification of amplified regions might have both prognostic and therapeutic significance. We used primary lung carcinomas and lung cancer cell lines for restriction landmark genomic scanning (RLGS) to identify novel amplified sequences. Enhanced RLGS fragments that indicate gene amplification were observed in primary tumors and lung cancer cell lines of both non-small cell lung cancer and small cell lung cancer. We identified one novel amplicon on chromosome 11q22, in addition to previously reported amplicons that include oncogenes MYCC, MYCL1 and previously identified amplification of chromosomal regions 6q21 and 3q26-27. Amplification of 11q22 has been reported in other types of cancer and was refined to an approximately 1.19 Mbp region for which the complete sequence is available. Based on a patient sample with a small region of low-level amplification we were able to further narrow this region to 0.92 Mbp. Genes localized in this region include two inhibitors of apoptosis (cIAP1 and cIAP2). Immunohistochemistry and western blot analysis identified cIAP1 and cIAP2 as potential oncogenes in this region as both are overexpressed in multiple lung cancers with or without higher copy numbers.
Selection and affinity maturation of IgNAR variable domains targeting Plasmodium falciparum AMA1 (2004)

The new antigen receptor (IgNAR) is an antibody unique to sharks and consists of a disulphide-bonded dimer of two protein chains, each containing a single variable and five constant domains. The individual variable (V(NAR)) domains bind antigen independently, and are candidates for the smallest antibody-based immune recognition units. We have previously produced a library of V(NAR) domains with extensive variability in the CDR1 and CDR3 loops displayed on the surface of bacteriophage. Now, to test the efficacy of this library, and further explore the dynamics of V(NAR) antigen binding we have performed selection experiments against an infectious disease target, the malarial Apical Membrane Antigen-1 (AMA1) from Plasmodium falciparum. Two related V(NAR) clones were selected, characterized by long (16- and 18-residue) CDR3 loops. These recombinant V(NAR)s could be harvested at yields approaching 5mg/L of monomeric protein from the E. coli periplasm, and bound AMA1 with nanomolar affinities (K(D)= approximately 2 x 10(-7) M). One clone, designated 12Y-2, was affinity-matured by error prone PCR, resulting in several variants with mutations mapping to the CDR1 and CDR3 loops. The best of these variants showed approximately 10-fold enhanced affinity over 12Y-2 and was Plasmodium falciparum strain-specific. Importantly, we demonstrated that this monovalent V(NAR) co-localized with rabbit anti-AMA1 antisera on the surface of malarial parasites and thus may have utility in diagnostic applications.
An open environment for standard cell and gate array library development (2003)

Standard cell and gate array libraries are assembled in this powerful environment, which automates SPICE characterization and datasheet generation while providing simulation models whose accuracy may be verified, for many simulators. Any of several third-party EDA tools may be utilized at each stage in the development cycle.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solid malignancies among patients in the Wegener's granulomatosis etanercept trial (2006)

Data from the WGET, the first substantial reported experience of the combined use of etanercept and cyclophosphamide in the treatment of WG, indicate that the combination of TNF inhibition and cyclophosphamide may heighten the risk of cancer beyond that observed with cyclophosphamide alone.
The Fourth Armadillo Repeat of Plakoglobin ( -Catenin) Is Required for Its High Affinity Binding to the Cytoplasmic Domains of E-Cadherin and Desmosomal Cadherin Dsg2, and the Tumor Suppressor APC Protein (1995)

Plakoglobin is a member of a protein family with a repeated amino acid motif, the armadillo repeat, and is a cytoplasmic protein found in both adherens junctions and desmosomes. Plakoglobin has been shown to form distinct complexes with cadherins or desmosomal cadherins. Also, plakoglobin has been shown to complex with APC, the tumor suppressor gene product. Recently we isolated a cDNA clone encoding plakoglobin lacking the fourth armadillo repeat of the original 13-repeat protein [Ozawa et al. (1995) J. Biochem. 118, 836-840]. In this study, we established an in vitro assay system to study the molecular interaction of plakoglobin with cadherins, the APC gene product, and alpha-catenin. Establishment of the system and cloning of an alternate form of plakoglobin cDNA allowed us to examine the biological activity of plakoglobin lacking the fourth armadillo repeat. Experiments with the bacterially expressed 12-repeat plakoglobin revealed that the protein binds to E-cadherin, desmoglein (Dsg2), and APC with lower affinity than the 13-repeat form does. Consistent with the observation that the affinity of alpha-catenin for these two alternate forms was similar, we found amino acid residues 104 to 145 of plakoglobin, the residues present in both isoforms, are sufficient for its binding to alpha-catenin.
Laboratory Measures of Exercise Capacity and Ventricular Characteristics and Function Are Weakly Associated With Functional Health Status After Fontan Procedure (2009)

In relatively healthy Fontan patients, laboratory measures account for a small proportion of the variation in functional health status and therefore may not be optimal surrogate end points for trials of therapeutic interventions.
Quantifying similarity between motifs (2007)

A common question within the context of de novo motif discovery is whether a newly discovered, putative motif resembles any previously discovered motif in an existing database. To answer this question, we define a statistical measure of motif-motif similarity, and we describe an algorithm, called Tomtom, for searching a database of motifs with a given query motif. Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs.
Thromboembolic and bleeding complications in patients with mechanical heart valve prostheses. (1994)

These data provide a reference for future studies and give adequate risk estimates for clinical decision making.
The Net Charge of the First 18 Residues of the Mature Sequence Affects Protein Translocation across the Cytoplasmic Membrane of Gram-Negative Bacteria (2000)

This statistical study shows that in proteins of gram-negative bacteria exported by the Sec-dependent pathway, the first 14 to 18 residues of the mature sequences have the highest deviation between the observed and expected net charge distributions. Moreover, almost all sequences have either neutral or negative net charge in this region. This rule is restricted to gram-negative bacteria, since neither eukaryotic nor gram-positive bacterial exported proteins have this charge bias. Subsequent experiments performed with a series of Escherichia coli alkaline phosphatase mutants confirmed that this charge bias is associated with protein translocation across the cytoplasmic membrane. Two consecutive basic residues inhibit translocation effectively when placed within the first 14 residues of the mature protein but not when placed in positions 19 and 20. The sensitivity to arginine partially reappeared again 30 residues away from the signal sequence. These data provide new insight into the mechanism of protein export in gram-negative bacteria and lead to practical recommendations for successful secretion of hybrid proteins.
The liver stage of Plasmodium berghei inhibits host cell apoptosis (2005)

Plasmodium berghei is the causative agent of rodent malaria and is widely used as a model system to study the liver stage of Plasmodium parasites. The entry of P. berghei sporozoites into hepatocytes has extensively been studied, but little is known about parasite-host interaction during later developmental stages of the intracellular parasite. Growth of the parasite far beyond the normal size of the host cell is an important stress factor for the infected cell. Cell stress is known to trigger programmed cell death (apoptosis) and we examined several apoptotic markers in P. berghei-infected cells and compared their level of expression and their distribution to that of non-infected cells. As none of the apoptotic markers investigated were found altered in infected cells, we hypothesized that parasite infection might confer resistance to apoptosis of the host cell. Treatment with peroxide or serum deprivation induced apoptosis in non-infected HepG2 cells, whereas P. berghei-infected cells appeared protected, indicating that the parasite interferes indeed with the apoptotic machinery of the host cell. To prove the physiological relevance of these results, mice were infected with high numbers of P. berghei sporozoites and treated with tumour necrosis factor (TNF)-alpha/D-galactosamine to induce massive liver apoptosis. Liver sections of these mice, stained for degraded DNA, confirmed that infected cells containing viable parasites were protected from programmed cell death. However, in non-treated control mice as well as in TNF-alpha-treated mice a small proportion of dead intracellular parasites with degraded DNA were detected. Most hepatocytes containing dead parasites provoked an infiltration of immunocompetent cells, indicating that these cells are no longer protected from cell death.