gebhart/patrepeval huggingface dataset:
Naming Plan for Internet Directory-Enabled Applications (1998)

Application of the conventional X.500 approach to naming has heretofore, in the experience of the authors, proven to be an obstacle to the wide deployment of directory-enabled applications on the Internet. We propose a new directory naming plan that leverages the strengths of the most popular and successful Internet naming schemes for naming objects in a hierarchical directory. This plan can, we believe, by extending the X.500 approach to naming, facilitate the creation of an Internet White Pages Service (IWPS) and other directory-enabled applications by overcoming the problems encountered by those using the conventional X.500 approach.
Simulating Mobile Agent Based Network Management Using Network Simulator (2000)

Large, heterogeneous computer and telecommunication networks with ever changing topology and size are typical environments todays network management (NM) systems struggle to control. Unexpected events occur frequently in these complex networks, and many of the events result in failure situations where the NM system is required to intervene and restabilize the network. By distributing the NM system throughout the network efficiency and dependability can be improved. This is indeed what todays NM system providers and operators are focusing on. Efforts are currently being made to increase the level of distribution of the most popular management architectures in use today (SNMP, OSI, TMN).
Internal deletion mutants ofXenopustranscription factor IIIA (1989)

Xenopus transcription factor IIIA (TFIIIA) or TFIIIA mutants with internal deletions were expressed in E. coli utilizing a bacteriophage T7 RNA polymerase system. TFIIIA or deletion mutant TFIIIAs, isolated from E.coli cell extracts, were identified by SDS PAGE and immunoblotting with rabbit antiserum against native TFIIIA purified from Xenopus immature oocytes. Specific DNA binding of intact or internally deleted TFIIIA was compared by analyzing their abilities to protect the internal control gene (ICR) of the Xenopus 5S RNA gene from DNase I digestion. Intact protein, synthesized from a full-length TFIIIA cDNA, bound specifically to the entire ICR (+96 to +43) and promoted 5S RNA gene transcription in vitro. One TFIIIA deletion mutant, expressed from cDNA lacking the coding sequence for the putative fourth zinc finger (designated from the N-terminus, amino acids 103-132) protected the ICR from DNase I digestion from nucleotide positions +96 to +78. A second TFIIIA mutant resulting from fusion of putative zinc fingers 7 and 8 (deletion of amino acids 200-224) protected the 5S gene ICR from positions +96 to +63. The DNase I protection patterns of these mutant proteins are consistent with the formation of strong ICR contacts by those regions of the protein on the N-terminal side of the mutation but not by those regions on the C-terminal side of the mutation. The regions of the protein comprising the N-terminal 3 fingers and N-terminal six fingers appear to be in contact with approximately 18 and 33 bp of DNA respectively on the 3' side of the 5S gene ICR. These internal deletion mutants promoted 5S RNA synthesis in vitro and DNA renaturation.
The absorption and conjugation of methyldopa in patients with coeliac and Crohn's diseases during treatment. (1983)

The absorption and elimination of a single 500 mg dose of methyldopa has been studied after oral administration to 10 normal volunteers, 10 patients with coeliac disease, who were on a gluten-free diet, and to five patients with Crohn's disease. In patients with Crohn's disease the percentage of the dose recovered in urine (24%) was about one-half of normal (50%). This decreased absorption was associated with reduced plasma concentrations of both free and conjugated methyldopa and a decreased pharmacological response. In patients with coeliac disease the percentage of dose recovered in urine (43%) was similar to normals, indicating a normal absorption of the drug. However, the plasma concentrations of both free and conjugated methyldopa were significantly higher than normal, although there was no increase in drug-related effects. These findings confirm the importance of using indices other than drug plasma concentrations in the assessment of bioavailability in disease states.
PyIgClassify: a database of antibody CDR structural classifications (2014)

Classification of the structures of the complementarity determining regions (CDRs) of antibodies is critically important for antibody structure prediction and computational design. We have previously performed a clustering of antibody CDR conformations and defined a systematic nomenclature consisting of the CDR, length and an integer starting from the largest to the smallest cluster in the data set (e.g. L1-11-1). We present PyIgClassify (for Python-based immunoglobulin classification; available at http://dunbrack2.fccc.edu/pyigclassify/), a database and web server that provides access to assignments of all CDR structures in the PDB to our classification system. The database includes assignments to the IMGT germline V regions for heavy and light chains for several species. For humanized antibodies, the assignment of the frameworks is to human germlines and the CDRs to the germlines of mice or other species sources. The database can be searched by PDB entry, cluster identifier and IMGT germline group (e.g. human IGHV1). The entire database is downloadable so that users may filter the data as needed for antibody structure analysis, prediction and design.
Method for Comparing Percutaneous Absorption of Steroids (1962)

A simple method for assessing the percutaneous absorption of steroid preparations is suggested. Using vasoconstriction as an index of absorption, occlusion of the skin surface with Saran Wrap results in a 100-fold difference in absorption over simple topical application.
Thrombolysis for acute ischaemic stroke (2003)

Overall, thrombolytic therapy appears to result in a significant net reduction in the proportion of patients dead or dependent in activities of daily living. However, this appears to be net of an increase in deaths within the first seven to ten days, symptomatic intracranial haemorrhage, and deaths at follow-up at three to six months. The data from trials using intravenous recombinant tissue plasminogen activator, from which there are the most evidence on thrombolytic therapy so far, suggest that it may be associated with less hazard and more benefit. There was heterogeneity between the trials for some outcomes and the optimum criteria to identify the patients most likely to benefit and least likely to be harmed, the latest time window, the agent, dose, and route of administration, are not clear. The data are promising and may justify the use of thrombolytic therapy with intravenous recombinant tissue plasminogen activator in experienced centres in highly selected patients where a licence exists. However, the data do not support the widespread use of thrombolytic therapy in routine clinical practice at this time, but suggest that further trials are needed to identify which patients are most likely to benefit from treatment and the environment in which it may best be given. To avoid the problem of data missing from some trials for some key outcomes encountered in this review to date, and to assist future metaanalyses, future trialists should try to collect data in such a way as to be compatible with the basic outcome assessments reviewed here (eg early death, fatal intracranial haemorrhage, poor functional outcome).
Controlled Deposition of Size-Selected Silver Nanoclusters (1996)

Variable-temperature scanning tunneling microscopy was used to study the effect of kinetic cluster energy and rare-gas buffer layers on the deposition process of size-selected silver nanoclusters on a platinum(111) surface. Clusters with impact energies of </=1 electron volt per atom could be landed nondestructively on the bare substrate, whereas at higher kinetic energies fragmentation and substrate damage were observed. Clusters with elevated impact energy could be soft-landed via an argon buffer layer on the platinum substrate, which efficiently dissipated the kinetic energy. Nondestructive cluster deposition represents a promising method to produce monodispersed nanostructures at surfaces.
Purification of E1 and E1-Like Enzymes (2005)

Ubiquitin-activating enzyme is the archetype for a family of enzymes catalyzing the ATP-coupled activation of ubiquitin and other class 1 ubiquitin-like proteins required for their subsequent conjugation to cellular targets. The general physical and mechanistic features of the E1 family appear well conserved. Formation of an obligatory E1-ubiquitin thiol ester intermediate forms the basis of a one-step covalent purification of the enzyme on ubiquitin-linked affinity columns that has been adapted for the isolation of E1 paralogs. We describe the facile purification of active E1 from outdated human red blood cells in yields (2-4 nmol/U of blood) that make this an attractive alternative to expression of the proteolytically labile recombinant protein. In addition, two stoichiometric activity assays are described that rely on formation of the E1 125I-ubiquitin thiol ester and ubiquitin [2,8-3H]adenylate intermediates.
Elevated frequencies of natural killer T lymphocytes in myasthenia gravis (1999)

T lymphocytes are considered to exert a regulatory function in the development of antiacetylcholine receptor antibodies, but no clear T-cell alterations in patients with myasthenia gravis (MG) have yet been found. The authors report a significant increase of recently identified natural killer T lymphocytes expressing T-cell receptor Valpha24. A possible role in disease initiation or maintenance is suggested by the observed strong synthesis of interferon-gamma as well as of interleukin 4.
Production of a high-density and high-temperature plasma with an intense high-contrast subpicosecond laser (1993)

We report on the observation of high-electron-density (ne ≈ 15nc where nc is the critical density, 4 × 1021 cm−3 for λ = 0.53 μm) and high-temperature (Te ≈ 400 eV) plasma obtained when an intense high-contrast 400-fs laser pulse interacts with a solid Al target. After the laser intensity is increased from 1016 to 5 × 1017 W/cm2, the kiloelectron-volt x-ray emission is brighter by approximately an order of magnitude and is still produced from very dense plasma (6 × 1022 cm−3).
IGOR: Image guided operating robot. Methodology, applications (1992)

Existing imaging devices can be used to plan complex medical and surgical interventions. Recent advances in Robotics provide the opportunity of assisting the physician or the surgeon in performing the intervention. Assisting both planning and performing of interventions raise problems of information modelling, data registration, surgical planning and specific problems for using partially autonomous systems. A general methodology for computer assisted medical interventions is proposed, which turns out to be a particular case of the classical loop of Perception Decision Action. Clinical applications are presented.
Molecular mechanisms of DNA damage initiated by alpha, beta-unsaturated carbonyl compounds as criteria for genotoxicity and mutagenicity. (1990)

alpha, beta-Unsaturated carbonyl compounds are important not only from a theoretical but also a practical standpoint. These ubiquitous compounds can interact with DNA through various mechanisms. The predominant interaction is the formation of cyclic 1,N2-deoxyguanosine adducts; 7,8-cyclic guanine adducts are also found. We have synthesized and characterized the stereoisomers of adducts formed by about 20 alpha, beta-unsaturated carbonyl compounds. The different types of adducts and the mutagenic and genotoxic response can be explained by the molecular structures of the agents. Compounds forming saturated cyclic adducts are mutagenic in S. typhimurium strain TA100 and to a lesser extent in TA1535. Substances with a leaving group at the C-3 position form unsaturated conjugated cyclic adducts and are mutagenic only in the His D3052 frameshift strains with an intact excision repair system (no urvA mutation). Metabolic epoxidation of the double bond and other metabolic activation, e.g., activation of the nitrogroups via nitroreductases, were also found to contribute to genotoxic and mutagenic activities. Our results have further elucidated the genotoxic mechanisms of these compounds; however, additional investigations are required for a complete understanding of the genotoxic activity of this class of compounds.
Cyclin‐Dependent Kinase‐2 (Cdk2) Forms an Inactive Complex with Cyclin D1 Since Cdk2 Associated with Cyclin D1 is Not Phosphorylated by Cdk7–Cyclin‐H (1996)

Cyclin-dependent kinases (Cdks) form complexes with cyclins, and as a consequence they generally express kinase activities. One of these Cdks, Cdk2, is known to bind with cyclins A and E, and plays an important role in the progression of the cell cycle via phosphorylation of target proteins such as the product of the retinoblastoma tumor-suppressor gene (pRB). It has been suggested that Cdk2 bound with cyclin D1 and Cdk2-cyclin-D1 complex show neither H1 histone nor pRB kinase activity. However, it is not clear whether Cdk2-cyclin-D1 has unknown targets and why Cdk2 is not activated by binding with cyclin D1. We investigated these questions using Cdk, cyclin and Cdk-cyclin complexes produced in a baculovirus expression system. Cdk2 formed a complex with cyclin D1 in this system. After extensive purification, Cdk2 was still bound to cyclin D1. The Cdk2-cyclin-D1 complex did not phosphorylate any tested substrates, such as H1 histone, pRB, SV40 large T antigen, p53, E2F-1 or a preparation of nuclear proteins from HeLa cells; in contrast, Cdk2-cyclin-E and Cdk2-cyclin-A phosphorylated these proteins. Moreover, the Cdk2-cyclin-D1 complex was not activated by incubation with Cdk4 or cyclin E. Thus, Cdk2 and cyclin D1 formed a stable complex that was not activated. In order to determine why Cdk2-cyclin-D1 lacks kinase activity, we investigated the phosphorylation of Cdk2. Under-shifted Cdk2, the active form of Cdk2, was not detected in the Cdk2-cyclin-D1 complex in the baculovirus system. In human WI-38 cells, cyclin D1 began to form a complex with Cdk2 as well as with Cdk4 from the mid-G1 phase of the cell cycle. The Cdk2 bound to cyclin D1 in human cells was also the inactive form that was slowly migrated. Moreover, we found that Cdk2 bound to cyclin D1 was not phosphorylated by Cdk7-cyclin-H, while Cdk2 bound to cyclin E, as well as free Cdk2, was was phosphorylated by Cdk7-cyclin-H. Additionally, Cdk2 phosphorylated by Cdk7-cyclin-H did not bind to cyclin D1. These results strongly suggest that Cdk2 forms a stable complex with cyclin D1 but is not activated because the Cdk2 molecule in the complex is not phosphorylated by Cdk7-cyclin-H and the phosphorylated Cdk2, an active form, does not bind to cyclin D1.
Copper(I)‐Catalyzed Cycloaddition of Organic Azides and 1‐Iodoalkynes (2009)

High fidelity: 1-Iodoalkynes react rapidly and selectively with organic azides in the presence of copper(I) catalysts (see scheme; TTTA=tris((1-tert-butyl-1H-1,2,3-triazolyl)methyl)amine). The reaction is compatible with many functional groups and solvents, and 5-iodotriazole products were usually obtained in excellent yield. These products can be further functionalized to give fully substituted 1,2,3-triazoles. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Novel ALK inhibitors in clinical use and development (2015)

Anaplastic lymphoma kinase 1 (ALK-1) is a member of the insulin receptor tyrosine kinase family. ALK-1 was initially found in anaplastic large cell lymphoma (ALCL). ALK mutations have also been implicated in the pathogenesis of non-small cell lung cancer (NSCLC) and other solid tumors. Multiple small molecule inhibitors with activity against ALK and related oncoproteins are under clinical development. Two of them, crizotinib and ceritinib, have been approved by FDA for treatment of locally advanced and metastatic NSCLC. More agents (alectinib, ASP3026, X396) with improved safety, selectivity, and potency are in the pipeline. Dual inhibitors targeting ALK and EGFRm (AP26113), TRK (TSR011), FAK (CEP-37440), or ROS1 (RXDX-101, PF-06463922) are under active clinical development.
Image coding using vector quantization: a review (1988)

A review of vector quantization techniques used for encoding digital images is presented. First, the concept of vector quantization is introduced, then its application to digital images is explained. Spatial, predictive, transform, hybrid, binary, and subband vector quantizers are reviewed. The emphasis is on the usefulness of the vector quantization when it is combined with conventional image coding techniques, or when it is used in different domains.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Monovalent fragments (Fab) of monoclonal antibodies to a sporozoite surface antigen (Pb44) protect mice against malarial infection. (1980)

Monoclonal antibodies (IG1, k) directed against a surface component of Plasmodium berghei sporozoites (Pb-44) confer complete protection to mice against a lethal inoculum of parasites. The degree of protection is a function of the number of parasites used in the challenge and of the antibody concentration in serum. Passive transfer of 10 micrograms of antibody per mouse abolished or profoundly diminished the infectivity of 10(3) sporozoites, but much higher amounts of antibody were required for complete protection against challenge with 10(4) parasites. Fab fragments of the monoclonal antibodies were as effective as the intact antibodies in mediating protection as determined by the neutralizing assay. This observation suggests that the antibodies interfere with a parasite function necessary for its infectivity, such as, for example, the ability to penetrate into the target cell or to multiply in the hepatocytes. When sporozoites are incubated with the intact monoclonal antibodies at 37 degrees C, a long filament appears at its posterior end (circumsporzoite precipitation [CSP] reaction). Fab fragments are ineffective at high concentrations. However, if after treatment with Fab, the sporozoites are incubated with rabbit antibodies to mouse k-chains, a strong CSP reaction is observed. We conclude that the CSP reaction can result from the cross-linking of Pb44 and that it has the characteristics of a capping reaction followed by the shedding of the immune complexes.
Digital Correlation Demodulator Design for RFID Reader Receiver (2007)

A high performance digital demodulator for RFID reader receiver is proposed. After carefully analyzing the characteristics of the received data, correlation operation is introduced into the demodulator to estimate the frequency of the received data and decode them. Simulation result indicates that this demodulator can work well under the 6dB input signal-to-noise ratio (SNR) with +/- 22% frequency deviation tolerance. FPGA implementation result shows that the communication distance between reader and tag can be extended to 5m above by the use of this demodulator.
Intravenous ferric derisomaltose for the treatment of iron deficiency anemia (2021)

Intravenous (IV) iron is the therapy of choice when oral iron is ineffective or poorly tolerated, yet use has been limited by fears of hypersensitivity reactions (HSRs). Newer formulations that bind iron more tightly and release it more slowly have made the risk of serious or severe HSRs very low. One such formulation, ferric derisomaltose, has been approved in the United States for delivery of 1000 mg iron in a single IV infusion. Ferric derisomaltose rapidly repletes iron parameters with low rates of serious or severe HSRs. Single-infusion iron repletion offers convenience, eliminates adherence concerns, and reduces healthcare resource utilization.
Gene therapy and molecular approaches to the treatment of hereditary muscular disorders (2000)

Gene therapy for inherited muscle disease is an active area of research and development. Initial emphasis has been on gene replacement but alternative approaches are increasingly being considered in order to overcome difficulties, such as the immune rejection of transduced cells, the need for appropriate and tissue-specific control of expression, and the requirement for systemic spread in some conditions. However, the most significant obstacles to the clinical success of gene therapy are still the lack of efficiency and accuracy of gene medicine delivery.
Antibacterial activity of lactic acid bacteria isolated from vacuum‐packaged meats (1990)

Lactic acid bacteria isolated from vacuum-packaged fresh meat stored at 4 degrees C were shown to produce antagonistic substances active against closely related bacteria. Growth medium, pH and growth temperature all affected the production of the inhibitory substances. Ten strains including aciduric Lactobacillus-type organisms, Carnobacterium spp. and Leuconostoc spp. were selected that produced protein-aceous substances that caused inhibition of indicator strains. These were considered to be bacteriocins or bacteriocin-like compounds based on their inactivation with protease, generally narrow spectra of antibacterial activity and bactericidal or bacteriostatic modes of action. Activity was not lost from supernatant fluids as a result of heat treatment at 62 degrees C for 30 min, except for the Leuconostoc strains. Inhibitory spectra of some strains included Enterococcus spp. and Listeria monocytogenes. Some strains were of interest because their inhibitory substances were detected in the supernatant fluid early in the growth cycle. The inhibitory substances differed in characteristics between strains and there is evidence that more than one bacteriocin-like substance may be produced by some strains.
Tumor cell senescence in cancer treatment. (2003)

Cell senescence is broadly defined as the physiological program of terminal growth arrest, which can be triggered by alterations of telomeres or by different forms of stress. Neoplastic transformation involves events that inhibit the program of senescence, and tumor cells were believed until recently to have lost the ability to senesce. It has now become apparent, however, that tumor cells can be readily induced to undergo senescence by genetic manipulations or by treatment with chemotherapeutic drugs, radiation, or differentiating agents. Treatment-induced senescence, which has both similarities with, and differences from, replicative senescence of normal cells, was shown to be one of the key determinants of tumor response to therapy in vitro and in vivo. Although senescent cells do not proliferate, they remain metabolically active and produce secreted proteins with both tumor-suppressing and tumor-promoting activities. Expression of tumor-promoting factors by senescent cells is mediated, at least in part, by senescence-associated cyclin-dependent kinase inhibitors such as p21(Waf1/Cip1/Sdi1). Clinical and preclinical studies indicate that expression of different biological classes of senescence-associated growth-regulatory genes in tumor cells has significant prognostic implications. Elucidation of the genes and regulatory mechanisms that determine different aspects of tumor senescence makes it possible to design new therapeutic approaches to improving the efficacy and to decreasing the side effects of cancer therapy.