gebhart/patrepeval huggingface dataset:
GROVV"TH FACTOR RECEPTOR TYRO'SINE KINASES (1988)

STRUCTURAL CHARACTERISTICS AND CLASSIFICATION OF RECEPTOR TYlROSINE KINASES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444 Prototypic Structure and Membrane Topology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444 Three Types of RTKs. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . 446 RTK Domain Organization. . . . . . . . . . . . . . . . . . . .... . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . 447 Receptor-Derived Oncogenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ,.,,. 452 Other Receptorlike Tyrosine Kinases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455 Evolution of RTKs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ,,., . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455 RECEPTOR FUNCTION AND REGULATION: BIOCHEMICAL AND GENETIC ANALYSES, . ... , . . . . . . ,... . . . . . . . . . . . . . . . . .. . . . 457 . P Ligand Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458 Transmembrane Signaling . . . . . . .. . . . . . . . . . . . ., . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ,, . . . . . . . 459 Tyrosine Kinase Activity ., . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461 Heterologous Regulation of RTK Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464 ONCOGENIC POTENTIAL OF RTKs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466 Structural Basis of RTK Transforming Potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467 Autocrine Mechanisms . . . . . . . . . . .,', . . . . . . . . . . . . . . . . . . . . . . . . . . . ., . . . . . . . . . . . . . . . . . . . . ., . . . . 468 Overexpression of RTKs .. . . . . . . . . . . . . . . . . . .... .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469 RECEPTOR-ACTIVATED SIGNALING PATHWAYS . . . . . . . . . . . . . ...... . .. ......... . . . . . . . . 470 Endogenous Substrates of RTKs . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471 Induction ('if Nuclear Oncogenes . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471
TCR Engagement Regulates Differential Responsiveness of Human Memory T Cells to Fas (CD95)-Mediated Apoptosis (1999)

In this work, we have tried to establish whether human memory T cells may be protected from Fas (CD95)-induced apoptosis when correctly activated by Ag, and not protected when nonspecifically or incorrectly activated. In particular, we wanted to investigate the molecular mechanisms that regulate the fate of memory T cells following an antigenic challenge. To address this issue, we chose an experimental system that closely mimics physiological T cell activation such as human T cell lines and clones specific for viral peptides or alloantigens. We demonstrate that memory T cells acquire an activation-induced cell death (AICD)-resistant phenotype when TCRs are properly engaged by specific Ag bound to MHC molecules. Ag concentration and costimulation are critical parameters in regulating the protective effect. The analysis of the mechanisms involved in the block of CD95 signal transduction pathways revealed that the crucial events are the inhibition of CD95-associated IL-1beta-converting enzyme (ICE)-like protease (FLICE) activation and poly(ADP)-ribose polymerase cleavage, and the mRNA expression of FLICE-like inhibitory protein. Furthermore, we have observed that TCR-mediated neosynthesis of FLICE-like inhibitory protein mRNA is suppressed either by protein tyrosine kinase inhibitors or cyclosporin A. In conclusion, the present analysis of the effects of TCR triggering on the regulation of AICD suggests that AICD could be inhibited in human memory T cells activated in vivo by a foreign Ag, but may become operative when the Ag has been cleared.
Combining quote-driven and order-driven trading systems in next-generation stock markets: an experimental investigation (2002)

We use computer-based simulations of a stock market as a background environment for experimental tests of the integration of an order-driven trading system into a dealer/quote-driven market. Experimental subjects traded using a traditional dealer quote screen (such as Nasdaq or SEAQ), to which a limit order facility was added. Subjects' trading decisions revealed that: (1) when available, the limit order facility attracted investor orders that would have otherwise gone to dealers, and reduced trading costs; (2) the relative use of market orders and limit orders was affected by the bid-ask spread, wider spreads led subjects to substitute limit orders for market orders; (3) limit order use was reduced when the dealers were provided with an informational advantage; (4) while the introduction of a limit order facility did not have an adverse effect on dealer profit margins, dealers' activities as a percentage of total volume declined. Overall, the simulation environment provides insights into the effects of market design changes, and guidance on market structure issues, such as how best to incorporate a limit order facility into a dealer market.
Human T cells express CD25 and Foxp3 upon activation and exhibit effector/memory phenotypes without any regulatory/suppressor function (2009)

Expression of Foxp3 does not necessarily convey regulatory function in human CD4+CD25+ T cells. Increased FoxP3 on CD44+ effector and CD44+CD62L+ memory T cells upon stimulation suggest the activation-induced regulation of FoxP3 expression.
Collagen-Binding Peptidoglycans Inhibit MMP Mediated Collagen Degradation and Reduce Dermal Scarring (2011)

Scarring of the skin is a large unmet clinical problem that is of high patient concern and impact. Wound healing is complex and involves numerous pathways that are highly orchestrated, leaving the skin sealed, but with abnormal organization and composition of tissue components, namely collagen and proteoglycans, that are then remodeled over time. To improve healing and reduce or eliminate scarring, more rapid restoration of healthy tissue composition and organization offers a unique approach for development of new therapeutics. A synthetic collagen-binding peptidoglycan has been developed that inhibits matrix metalloproteinase-1 and 13 (MMP-1 and MMP-13) mediated collagen degradation. We investigated the synthetic peptidoglycan in a rat incisional model in which a single dose was delivered in a hyaluronic acid (HA) vehicle at the time of surgery prior to wound closure. The peptidoglycan treatment resulted in a significant reduction in scar tissue at 21 days as measured by histology and visual analysis. Improved collagen architecture of the treated wounds was demonstrated by increased tensile strength and transmission electron microscopy (TEM) analysis of collagen fibril diameters compared to untreated and HA controls. The peptidoglycan's mechanism of action includes masking existing collagen and inhibiting MMP-mediated collagen degradation while modulating collagen organization. The peptidoglycan can be synthesized at low cost with unique design control, and together with demonstrated preclinical efficacy in reducing scarring, warrants further investigation for dermal wound healing.
Analysis of rapid thermocycling for the polymerase chain reaction (2004)

PCR (polymerase chain reaction) has become an important diagnostic tool for the identification of pathogens. There has been a dramatic increase in usage of PCR since the late eighties and it is expected that future use will increase even more. PCR devices continue to evolve and performance should increase significantly at reduced cost. This study focuses on the principles of rapid PCR with the PCRJet. The PCRJet is a new thermocycler patented by Megabase Research Products (Lincoln, NE). Performance of the PCRJet is thoroughly analyzed-including (1) an engineering approach to study the PCRJet's performance and (2) a biochemical approach to amplification of a number of different DNA fragments. This PCRJet study is necessary to develop a rapid and portable Ranque-Hilsch based PCRJet machine in a joint project between Megabase Research Products and the University of Nebraska. More than 600 PCR experiments have been performed in several versions of the PCRJet machine. The fastest PCR accomplished to date has been for an 85 base pair DNA fragment; thirty cycles for this amplicon required only 78 sec. The longest fragment the PCRJet has amplified has been 2331 base pairs; thirty cycles in the PCRJet took 10.3 min . The PCRJet speed compares favorably to commercially available devices which require thirty minutes to three hours to complete thirty PCR cycles. The PCRJet speed originates in its heat transfer by convection using high velocity gasses. In PCR, a small volume of an aqueous solution containing the template DNA, primers, polymerase, and other chemicals is cycled through a defined, sequential temperature protocol. Of the three modes of heat transfer, thermal conduction has been the choice for most devices to attain the temperature protocol. Consequently, most of the time in a thermal block PCR cycle is spent non-productively in transition between DNA denaturation, primer annealing, and enzymatic elongation temperatures. Aspects of the convective heat transfer utilized by the PCRJet are analyzed within this dissertation. Some computational fluid dynamics results of the PCRJet heat transfer are shown.
PHOG: probabilistic model for code (2016)

We introduce a new generative model for code called probabilistic higher order grammar (PHOG). PHOG generalizes probabilistic context free grammars (PCFGs) by allowing conditioning of a production rule beyond the parent non-terminal, thus capturing rich contexts relevant to programs. Even though PHOG is more powerful than a PCFG, it can be learned from data just as efficiently. We trained a PHOG model on a large JavaScript code corpus and show that it is more precise than existing models, while similarly fast. As a result, PHOG can immediately benefit existing programming tools based on probabilistic models of code.
Microfluidics in Inorganic Chemistry (2010)

Abstract The application of microfluidics in chemistry has gained significant importance in the recent years. Miniaturized chemistry platforms provide controlled fluid transport, rapid chemical reactions, and cost‐saving advantages over conventional reactors. The advantages of microfluidics have been clearly established in the field of analytical and bioanalytical sciences and in the field of organic synthesis. It is less true in the field of inorganic chemistry and materials science; however in inorganic chemistry it has mostly been used for the separation and selective extraction of metal ions. Microfluidics has been used in materials science mainly for the improvement of nanoparticle synthesis, namely metal, metal oxide, and semiconductor nanoparticles. Microfluidic devices can also be used for the formulation of more advanced and sophisticated inorganic materials or hybrids.
Oropharyngeal Candidiasis as a Marker for Esophageal Candidiasis in Patients with Cancer (1998)

The present study was designed to determine the frequency of candidal esophagitis in cancer patients with oral thrush. Patients with clinically and microbiologically diagnosed oral candidiasis were evaluated by endoscopy for concurrent esophageal candidiasis. Esophageal involvement was documented by mucosal lesions, microbiological findings of candidal infection in smears of brushing material, positive cultures of brushing material, and histological evidence of mucosal invasion by the yeast. For 21 of the 22 patients studied, there were endoscopic and microbiological findings of candidal esophagitis. Cultures of the brushing material from all 22 patients were positive, while histological evidence was found for 14 patients. Only 10 of the patients had mild esophageal symptoms. It is concluded that oral thrush represents a reliable marker for esophageal candidiasis in patients with cancer. Routine endoscopy is not necessary to confirm the diagnosis; this procedure should be reserved for patients with persistent thrush and symptoms despite antifungal therapy.
Isolation and characterization of a novel antifreeze protein from carrot (Daucus carota) (1999)

A modified assay for inhibition of ice recrystallization which allows unequivocal identification of activity in plant extracts is described. Using this assay a novel, cold-induced, 36 kDa antifreeze protein has been isolated from the tap root of cold-acclimated carrot (Daucus carota) plants. This protein inhibits the recrystallization of ice and exhibits thermal-hysteresis activity. The polypeptide behaves as monomer in solution and is N-glycosylated. The corresponding gene is unique in the carrot genome and induced by cold. The antifreeze protein appears to be localized within the apoplast.
Polymer Electrolyte-Gated Carbon Nanotube Field-Effect Transistor (2004)

Single-walled carbon nanotube field-effect transistors were fabricated using solid electrolyte (PEO plus LiClO4) as gating materials. The SWNT FETs demonstrated strong gate-channel coupling with improved device characteristics compared with back-gated devices. More importantly, the nanotubes can be easily doped using different concentrations of electron acceptor mixed in the polymer materials. The transport type of the devices can be easily controlled through doping.
Single-Agent Rituximab as First-Line and Maintenance Treatment for Patients With Chronic Lymphocytic Leukemia or Small Lymphocytic Lymphoma: A Phase II Trial of the Minnie Pearl Cancer Research Network (2003)

Single-agent rituximab, used at a standard dose and schedule, is active in the first-line treatment of patients with CLL/SLL, producing substantially higher response rates than previously reported in relapsed or refractory patients (51% v 13%, respectively). Re-treatment with rituximab at 6-month intervals is well tolerated. The PFS time of 18.6 months in patients with CLL/SLL seems shorter than the 36- to 40-month median PFSs previously reported with first-line plus maintenance rituximab in patients with follicular lymphoma. Additional follow-up is required to fully assess the impact of this treatment strategy.
The pKO2 Linear Plasmid Prophage ofKlebsiella oxytoca (2004)

Temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only phages N15 and PY54 are known to have a linear plasmid prophage with closed hairpin telomeres. We report here the complete nucleotide sequence of the 51,601-bp Klebsiella oxytoca linear plasmid pKO2, and we demonstrate experimentally that it is also a prophage. We call this bacteriophage phiKO2. An analysis of the 64 predicted phiKO2 genes indicate that it is a fairly close relative of phage N15; they share a mosaic relationship that is typical of different members of double-stranded DNA tailed-phage groups. Although the head, tail shaft, and lysis genes are not recognizably homologous between these phages, other genes such as the plasmid partitioning, replicase, prophage repressor, and protelomerase genes (and their putative targets) are so similar that we predict that they must have nearly identical DNA binding specificities. The phiKO2 virion is unusual in that its phage lambda-like tails have an exceptionally long (3,433 amino acids) central tip tail fiber protein. The phiKO2 genome also carries putative homologues of bacterial dinI and umuD genes, both of which are involved in the host SOS response. We show that these divergently transcribed genes are regulated by LexA protein binding to a single target site that overlaps both promoters.
Synthesis of 3-Amino-4-fluoropyrazoles (2011)

Fluorinated pyrazoles bearing additional functional groups that allow further functionalization are of considerable interest as building blocks in medicinal chemistry. The developed synthetic strategy for new 3-amino-4-fluoropyrazoles consists of a monofluorination of β-methylthio-β-enaminoketones using 1-(chloromethyl)-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate) (Selectfluor) toward the corresponding monofluorinated enaminoketones, followed by condensation with different hydrazines.
Two Approaches to Scheduling Outfitting Processes in Shipbuilding (2009)

In shipbuilding, outfitting is the process of installing non-structural components, like equipment, pipes, cables, ducts, etc., which can run through several structural compartments. Pre-outfitting is defined as outfitting activities that take place before hull erection, thus during panel, section and block assembly. The outfitting process is characterized by interferences between yard and many subcontractors, disturbances by unexpected delays, and technological constraints concerning the installation of main propulsion machinery. Scheduling of this process is therefore quite complex and a difficult topic to research. According to extensive literature study, there have been some relevant paper published more than twenty years ago[1],[2],[3],although since then the topic has not received much attention.. Traditionally, the initial outfitting process planning is generated largely manually by experts with the help of computer software, like Microsoft Project and Primavera. These tools allow some limited plan checking and evaluation. As soon as special simulation tools, for example based on eM-Plant or, Arena, are fully developed, plans can be tested, analyzed and optimized in a more accurate way. Even though the digitalization of downstream work is being developed, the initial plan depends greatly on experts. They have to be trained and then gain their expertise from practice. It generally takes over five years for someone to acquire sufficient expertise in a particular area[4]. Furthermore, the knowledge the experts gained by their years of experience may be lost, due to retirement and personnel quitting the company. Hence, it is indispensable to make such tacit knowledge explicit through models. It means that in order to optimize the facilities, maximize the production efficiency and minimize the building time, it is necessary to develop a system to automatically generate plans for outfitting processes, which can also support the simulation models afterwards for verification purposes. The research discussed in this paper looks into the possibilities to automatically generate an outfitting sequence and planning, based on two approaches. The first approach is an analytical approach, where the focus lies on the most convenient installation sequence on a system or compartment level. This sequence considers all relations between activities within one system and with activities of other systems, and relations within one compartment and its adjacent compartments. Then a mathematical approach is discussed. Physical constraints between the pipes, ducts, cable trays, etc. are introduced and represented. A model is made to generate an installation sequence of these components in one compartment.
Congenital Deficiency of a Factor in Normal Plasma That Reverses Microangiopathic Hemolysis and Thrombocytopenia (1978)

THE patient described below has been under observation for 11 years. Evidence to be presented suggests that she has the congenital deficiency of a factor in normal plasma that appears under some circumstances to be important in platelet and red-cell survival.Case ReportThe patient, now 29 years old, was noted at birth to have a rudimentary right radius and ulna, and a lobster-claw deformity of the right hand.From the age of six months to 12 years she had six to 10 episodes yearly characterized by the acute onset of high fever, generalized petechial rash, usually a clinically determinable . . .
Melt-quenched KCl:Eu2+ films for photostimulated luminescence applications (1998)

Using a conventional melt-quenching method, Eu2+-doped KCl films have been prepared. These films yield intense photostimulated luminescence (PSL) with the stimulated excitation maximum shifting to longer wavelengths as compared to the reports on the single-crystal analog. This will be advantageous for image reading by a He–Ne laser or red-emitting diode lasers when used in the PSL applications. Several types of centers have been found. Further, in the electron paramagnetic resonance spectrum, the hyperfine structure due to the Eu2+ centers has been observed to disappear at low temperatures (∼5 K). This can be attributed to the formation of complexes by the trapping of defect centers at the Eu2+ site(s). Crystallization effects and paramagnetic centers as well as optical properties of these films are discussed.
Paraneoplastic pemphigus triggered by radiotherapy (1995)

Paraneoplastic pemphigus is a recently described autoimmune disease characterized by painful mucosal ulceration and polymorphous skin lesions in association with an underlying neoplasm. Distinct autoantibodies bind desmoplakin I, desmoplakin II, bullous pemphigoid antigen and an uncharacterized 190 kDa antigen. A case is presented of paraneoplastic pemphigus that developed after radiotherapy for non-Hodgkin's lymphoma in a 53 year old man. Multiple skin biopsies showed a lichenoid reaction without acantholysis. Immunofluorescence and mucosal biopsies were required to establish the correct diagnosis. Corneal opacities resembling lichenoid graft-versus-host disease and retinal haemorrhages, which developed in the patient, have not been previously documented. Despite high doses of immunosuppressive agents and plasmaphoresis, the patient eventually died from respiratory failure.
Crystal structure of 2,5-diketo- d -gluconic acid reductase A complexed with NADPH at 2.1-Å resolution (1998)

The three-dimensional structure of Corynebacterium 2, 5-diketo-D-gluconic acid reductase A (2,5-DKGR A; EC 1.1.1.-), in complex with cofactor NADPH, has been solved by using x-ray crystallographic data to 2.1-A resolution. This enzyme catalyzes stereospecific reduction of 2,5-diketo-D-gluconate (2,5-DKG) to 2-keto-L-gulonate. Thus the three-dimensional structure has now been solved for a prokaryotic example of the aldo-keto reductase superfamily. The details of the binding of the NADPH cofactor help to explain why 2,5-DKGR exhibits lower binding affinity for cofactor than the related human aldose reductase does. Furthermore, changes in the local loop structure near the cofactor suggest that 2,5-DKGR will not exhibit the biphasic cofactor binding characteristics observed in aldose reductase. Although the crystal structure does not include substrate, the two ordered water molecules present within the substrate-binding pocket are postulated to provide positional landmarks for the substrate 5-keto and 4-hydroxyl groups. The structural basis for several previously described active-site mutants of 2,5-DKGR A is also proposed. Recent research efforts have described a novel approach to the synthesis of L-ascorbate (vitamin C) by using a genetically engineered microorganism that is capable of synthesizing 2,5-DKG from glucose and subsequently is transformed with the gene for 2,5-DKGR. These modifications create a microorganism capable of direct production of 2-keto-L-gulonate from D-glucose, and the gulonate can subsequently be converted into vitamin C. In economic terms, vitamin C is the single most important specialty chemical manufactured in the world. Understanding the structural determinants of specificity, catalysis, and stability for 2,5-DKGR A is of substantial commercial interest.