gebhart/patrepeval huggingface dataset:
Versatile Oligo( N ‐Substituted) Glycines: The Many Roles of Peptoids in Drug Discovery (2004)

Introduction Peptoid Synthesis Solid-Phase Synthesis Sub-monomer Solid-Phase Method Side Reactions Post-Synthetic Analysis Drug Discovery via Small-Molecule Peptoid Libraries Peptoid Drugs from Combinatorial Libraries Peptoid Inhibitors of RNA-Protein Interactions Peptoid-Based Drug Delivery and Molecular Transporters: Cellular Uptake Peptoid Mimics of HIV-Tat Protein Cellular Delivery of Nucleic Acids Peptoid Mimics of Peptide Ligands Peptoids with Folded Structure Restricting Conformational Space Peptoid Helices CD and NMR Studies of a Helical Peptoid Pentamer with α-Chiral Aromatic Side Chains CD Studies of Longer Peptoid Helices Containing α-Chiral Aromatic Side Chains Structural Studies of Peptoids with Aliphatic Side Chains by CD, NMR, and X-ray Crystallography Summary Protein-mimetic Structures Biomimetic Peptoid Structures for Therapeutic Applications Peptoid Mimics of Antibacterial Peptides Peptoid-Based Mimics of Lung Surfactant Proteins Collagen-based Structures Containing Peptoid Residues Obstacles to the Development of Biomedically-useful Peptoids Enhance the Diversity of Secondary Structure in Peptoid Foldamers Improve Understanding of Peptoid Sequence/Structure Relationships Translate Bioactive Peptide Sequences into Bioactive Peptoid Sequences Develop Peptoids with Stable Tertiary Structure Develop Peptoid Shuttles for Intracellular Import of Xenobiotic Agents Optimize Pharmacological Profile of Oligopeptoids Conclusion References
Basic fibroblast growth factor, a protein devoid of secretory signal sequence, is released by cells via a pathway independent of the endoplasmic reticulum‐Golgi complex (1992)

Basic fibroblast growth factor (bFGF) modulates functions of a variety of cell types. Whereas bFGF is known to act extracellularly, the protein lacks a transient signal peptide. No defined mechanism for bFGF secretion has been characterized besides release from dead or injured cells. To study this problem we devised an experimental system to examine bFGF-mediated migration of isolated single cells. Under these conditions individual cells are not affected by bFGF derived from other cells. By this method we have previously shown that bFGF released by NIH 3T3 cells transfected with bFGF cDNA modulates migration in an autocrine manner. We have now examined the effects on cell motility of drugs or treatments known to affect various pathways of protein secretion. Drugs that block secretion via the endoplasmic reticulum (ER)-Golgi complex or via multidrug resistance proteins did not inhibit cell motility. Migration was enhanced by the calcium ionophore A23187, which stimulates exocytosis, and was inhibited by methylamine, serum-free, and low temperature (18 degrees C) conditions, which block endo- and exocytosis. The reversal of these effects by the concomitant addition of affinity-purified anti-bFGF IgG or recombinant bFGF showed that the alterations in cell migration were mediated by changes in bFGF externalization. Thus bFGF can be released via a mechanism of exocytosis independent of the ER-Golgi pathway.
On the Decomposition of Synthetic Gibbsite Studied by Neutron Thermodiffractometry (2006)

The thermal decomposition mechanism of synthetic Al(OH) 3 (gibbsite) was studied in situ by neutron thermodiffractometry in an ambient atmosphere from room temperature to 600°C with 50°C steps. Gibbsite decomposed to yield AlO·(OH) (boehmite) and then poorly crystallized χ‐Al 2 O 3 . Rietveld analysis was used to refine the cell parameters' variation of gibbsite and its thermal expansion coefficients were obtained: for the a ‐axis: 15±1 × 10 −6 K −1 , for b : 10±2 × 10 −6 K −1 , and for c : 17±2 × 10 −6 K −1 .
Performance analysis of MAC protocols for wireless control area network (2002)

This paper presents the performance analysis of the wireless medium access control (WMAC) protocol and the remote frame medium access control (RFMAC) protocol for a wireless control area network (WCAN). These two MAC protocols are suggested for distributed and centralised wireless communications respectively, as part of the complete WCAN project. The performances of the protocols are evaluated by simulating the models of the protocols using set of signals called the "SAE benchmark". The benchmark table provides an example to illustrate the application of control area network (CAN) system. This paper discusses the applicability of the wireless MAC protocols and validates its usefulness for real-time communications based on the parameters in the benchmark table.
Detection of Diverse New Francisella -Like Bacteria in Environmental Samples (2005)

Following detection of putative Francisella species in aerosol samples from Houston, Texas, we surveyed soil and water samples from the area for the agent of tularemia, Francisella tularensis, and related species. The initial survey used 16S rRNA gene primers to detect Francisella species and related organisms by PCR amplification of DNA extracts from environmental samples. This analysis indicated that sequences related to Francisella were present in one water and seven soil samples. This is the first report of the detection of Francisella-related species in soil samples by DNA-based methods. Cloning and sequencing of PCR products indicated the presence of a wide variety of Francisella-related species. Sequences from two soil samples were 99.9% similar to previously reported sequences from F. tularensis isolates and may represent new subspecies. Additional analyses with primer sets developed for detection and differentiation of F. tularensis subspecies support the finding of very close relatives to known F. tularensis strains in some samples. While the pathogenicity of these organisms is unknown, they have the potential to be detected in F. tularensis-specific assays. Similarly, a potential new subspecies of Francisella philomiragia was identified. The majority of sequences obtained, while more similar to those of Francisella than to any other genus, were phylogenetically distinct from known species and formed several new clades potentially representing new species or genera. The results of this study revise our understanding of the diversity and distribution of Francisella and have implications for tularemia epidemiology and our ability to detect bioterrorist activities.
Tissue-type plasminogen activator (t-PA) : physiological and clinical aspects (1988)

This book is made possible by the enthusiastic contributions of the authors of the chapters. They have been invited from young and active scientists in the field of t-PA research. I am grateful for their contribution and for the fact that all accepted the specifications of their chapter in order to obtain a structured book. Inevitably, some overlap does exist; on the one hand to enable controversial or unsettled areas to be discussed by the different experts with a different approach and background.It is a particular pleasure and honor that Dr. T. Astrup, as an eye-witness and essential contributor to the history of t-PA discovery and research, gives a unique account of the history of t-PA research in the first chapter of the book.
Cutting Edge: Immunosuppressant as Adjuvant for Tolerogenic Immunization (2008)

Vaccination for autoimmune and alloimmune diseases has long been an attractive idea. Yet, there is no suitable adjuvant to forcefully steer the immune response toward tolerance. In this study we show that dexamethasone, a potent glucocorticoid immunosuppressant, can function as a tolerogenic adjuvant when applied together with peptide immunogen. BALB/c mice with pre-established delayed-type hypersensitivity to hen OVA were immunized with an OVA-derived, MHC II-restricted peptide (OVA(323-339)) in the presence of dexamethasone. The treatment caused long-term desensitization in treated animals to hen OVA via a dexamethasone-dependent tolerogenic mechanism that blocks maturation of dendritic cells and expands OVA(323-339)-specific CD4(+)CD25(+)Foxp3(+) regulatory T cells in vivo. Similar treatment of NOD mice using dexamethasone and an insulin-derived, MHC II-restricted peptide (B:9-23) prevented predisposed spontaneous diabetes. Remarkably, in both models, dexamethasone-augmented immunization induced long-term persistent, Ag-specific regulatory T cells responsive to recall Ags. These results reveal for the first time the potential usefulness of immunosuppressants as tolerogenic adjuvants.
Two-step shape recovery in heating-responsive shape memory polytetrafluoroethylene and its thermally assisted self-healing (2013)

In this paper, the heating-responsive shape memory effect (SME) in commercial polytetrafluoroethylene (PTFE) programmed by means of tension and compression is investigated systematically. The focus is on the influence of the glass transition (Tg) and the melting transition (Tm) on the shape recovery performance. Two-step shape recovery upon heating to over the glass transition range and then the melting transition range is observed. The key parameters in programming, namely the programming temperature, programming strain and deformation method, are examined. In addition, we study the feasibility of utilizing the high melting temperature nature of PTFE as a high temperature shape memory polymer (SMP) and for thermally assisted self-healing.
Piroxicam and other cyclooxygenase inhibitors: Potential for cancer chemoprevention (1992)

Piroxicam is a nonsteroidal anti-inflammatory drug (NSAID) widely used for treatment of inflammatory arthritis. Recent experimental and clinical studies suggest that piroxicam, as well as other NSAIDs, may be useful for chemoprevention of colon cancer. While there is less information regarding NSAIDs for chemoprevention of urinary bladder malignancy, there are compelling data which suggest that this should be evaluated. A major effect of NSAIDs is inhibition of cyclooxygenase, the rate-limiting enzyme for conversion of arachidonic acid to important signal molecules, including prostaglandins, which profoundly affect cellular functions in many tissues. The initial enzyme reaction leading to formation of prostaglandin H can be accompanied by cooxidation of xenobiotics resulting in extrahepatic and local tissue production of reactive products which are carcinogenic. The end product prostaglandins, especially prostaglandin E2 (PGE2), are biological modifiers which can significantly affect cell proliferation and tumor growth. High levels of PGE2 stimulate growth of certain tumor cell lines while inhibition of prostaglandin synthesis with indomethacin or piroxicam can cause suppression. The mechanisms for this effect are unclear. Studies in cultured cells exposed to indomethacin show inhibition of G1-to-S phase progression of the cell cycle and a reduction in overall DNA synthesis. It is unclear whether this effect on cell growth results from some direct action of the NSAID or a reduction in prostaglandins or indirectly from modulation of important control signals, such as calcium flux. In addition to cyclooxygenase, NSAIDs can inhibit activity of other enzymes, including phosphodiesterases and cyclic GMP-AMP protein kinases, which may be central to cancer initiation and promotion. NSAIDs can also interfere with transmembrane ion fluxes and with cell-to-cell binding. Prostaglandins can modulate a variety of immunological responses and thereby play an important role in host antitumor immunity. For example, high levels of tissue PGE2 are frequently associated with suppression of immune surveillance and killing of malignant cells. Conversely, immune responses are generally enhanced by drugs that inhibit prostaglandin synthesis. PGE2 can act as a feedback inhibitor for cellular immune processes, such as T-cell proliferation, lymphokine production, and cytotoxicity. This effect is also seen for macrophage activity and natural killer cell toxicity. In general, either increased production of PGE2 or increased sensitivity to normal amounts of PGE2 results in depressed cellular immunity. Cyclooxygenase inhibitors (NSAIDs) such as piroxicam which decrease PGE2 production can stimulate cellular immune function both in vitro and in vivo. A variety of tumor cell lines and human malignancies produce large quantities of prostaglandins.(ABSTRACT TRUNCATED AT 400 WORDS)
Inflow Performance Relationship (IPR) For Solution Gas-Drive Reservoirs—Analytical Considerations (2007)

Abstract This work provides the analytical development of "Vogel"-type Inflow Performance Relation (or IPR) correlations for solution gas-drive reservoir systems using characteristic flow behavior. Specifically, we provide the following results: An analytical form of the quadratic (Vogel) IPR correlation: q o q o , max = 1 − v [ p w f p ¯ ] − ( 1 − v ) [ p w f p ¯ ] 2 Where the v-parameter is defined for the solution gas-drive reservoir case using the oil mobility function (i.e., [(ko/(μoBo)]) — this definition is given by: v = 2 [ k o / ( μ o B o ) ] p ¯ = 0 [ k o / ( μ o B o ) ] p ¯ + [ k o / ( μ o B o ) ] p ¯ = 0 The analytical form for a cubic IPR correlation: q o q o , max = 1 − α [ p w f p ¯ ] − β [ p w f p ¯ ] 2 − γ [ p w f p ¯ ] 3 The analytical form for a quartic IPR correlation: q 0 q 0 , max = 1 − ε [ p w f p ¯ ] − σ [ p w f p ¯ ] 2 − η [ p w f p ¯ ] 3 − θ [ p w f p ¯ ] 4 The practical value of this work is that we have proven that an IPR can be written for a given solution gas-drive reservoir system directly from rock-fluid properties and fluid properties. The "theoretical" value of this work is that we provide a "characteristic" formulation of the oil mobility profile [ko/(μoBo)], which is given as: [ 1 − [ k o / ( μ o B o ) ] p [ k o / ( μ o B o ) ] p i ] = 1 − ζ [ p ¯ p i ] + ( 1 − ζ ) [ p ¯ p i ] 2 − 2 ( 1 − ζ ) [ p ¯ p i ] 3 ( ζ ≤ 1 ) This proposed "characteristic" mobility model is validated against numerical simulation results from the literature and from work performed as part of this study. Note that the characteristic mobility is only a function of the characteristic parameter (ζ), the initial and average reservoir pressures (pi and p¯), and the oil-phase mobility evaluated at the initial reservoir pressure [ko/(μoBo)]pi.
Water Soluble Polymers for Pharmaceutical Applications (2011)

Advances in polymer science have led to the development of novel drug delivery systems. Some polymers are obtained from natural resources and then chemically modified for various applications, while others are chemically synthesized and used. A large number of natural and synthetic polymers are available. In the present paper, only water soluble polymers are described. They have been explained in two categories (1) synthetic and (2) natural. Drug polymer conjugates, block copolymers, hydrogels and other water soluble drug polymer complexes have also been explained. The general properties and applications of different water soluble polymers in the formulation of different dosage forms, novel delivery systems and biomedical applications will be discussed.
Availability Modeling and Analysis of a Virtualized System (2009)

This paper develops an availability model of a virtualized system. We construct non-virtualized and virtualized two hosts system models using a two-level hierarchical approach in which fault trees are used in the upper level and homogeneous continuous time Markov chains (CTMC) are used to represent sub-models in lower level. In the models, we incorporate not only hardware failures (e.g., CPU, memory, power, etc) but also software failures including Virtual Machine Monitor (VMM), Virtual Machine (VM), and application failures. We also incorporate high availability (HA) service and VM live migration in the virtualized system. Metrics we use are system steady state availability, downtime in minutes per year and capacity oriented availability.
Ontology-Driven Automatic Entity Disambiguation in Unstructured Text (2006)

Abstract. Precisely identifying entities in web documents is essential for document indexing, web search and data integration. Entity disambiguation is the challenge of determining the correct entity out of various candidate entities. Our novel method utilizes background knowledge in the form of a populated ontology. Additionally, it does not rely on the existence of any structure in a document or the appearance of data items that can provide strong evidence, such as email addresses, for disambiguating person names. Originality of our method is demonstrated in the way it uses different relationships in a document as well as from the ontology to provide clues in determining the correct entity. We demonstrate the applicability of our method by disambiguating names of researchers appearing in a collection of DBWorld posts using a large scale, realworld ontology extracted from the DBLP bibliography website. The precision and recall measurements provide encouraging results. Keywords: Entity disambiguation, ontology, semantic web, DBLP, DBWorld. 1
Macromolecular Design via the Interchange of Xanthates (MADIX): Polymerization of Styrene with O‐Ethyl Xanthates as Controlling Agents (2002)

Abstract Control of the free‐radical polymerization of styrene was achieved using a series of eight xanthates of the general structure RS(CS)OEt as reversible addition fragmentation chain‐transfer agents. The influence of the nature of the R leaving group was explored. It was found that the transfer ability of the xanthate is markedly improved with increasing stability of R and its steric hindrance. Group R strongly influences the M n evolution profile during polymerization, but only influences the polydispersities to a small extent. The cyanoisopropyl group was shown to be the best leaving group, leading to an increase in the molecular weight during polymerization that was close to linearity. The living character of the polymerization and the high purity of the chain structures were supported by matrix‐assisted laser desorption ionization time‐of‐flight (MALDI‐TOF) mass spectrometry and 13 C NMR spectroscopy. A zero‐order dependence of the kinetics of polymerization on the xanthate concentration was observed. Conversion versus time plots for thermal bulk polymerizations of styrene at 110 °C in the presence of various xanthates. magnified image Conversion versus time plots for thermal bulk polymerizations of styrene at 110 °C in the presence of various xanthates.
Protease-induced leukocyte chemotaxis and activation: roles in host defense and inflammation. (2001)

The migration of leukocytes such as neutrophils, monocytes and lymphocytes into inflamed lesions is one of the critical events of inflammation. Although the traditional function of neutrophil-derived antimicrobial proteases is to ingest and kill bacteria, some neutrophil serine proteases have been shown to induce leukocyte migration and activation. Mast cell-derived chymase also has the chemotactic activity for leukocytes. During the acute phase of inflammatory and allergic diseases, the predominantly migrated cells are neutrophils and mast cells, respectively, and in the subsequent chronic phase, monocytes and lymphocytes are mainly migrated. The chemotactic activity for monocytes and lymphocytes of neutrophil-derived serine proteases and mast cell-derived chymase may have a role in switching acute inflammation to chronic inflammation and delayed-type hypersensitivity. Recently, aminopeptidase N and endothelin were shown to induce chemotactic migration of leukocytes. Thus, protease-induced leukocyte chemotaxis and activation may play an important role in immunologic events of inflammatory and allergic diseases.
GORDIAN: VLSI placement by quadratic programming and slicing optimization (1991)

The authors present a placement method for cell-based layout styles. It is composed of alternating and interacting global optimization and partitioning steps that are followed by an optimization of the area utilization. Methods using the divide-and-conquer paradigm usually lose the global view by generating smaller and smaller subproblems. In contrast, GORDIAN maintains the simultaneous treatment of all cells over all global optimization steps, thereby considering constraints that reflect the current dissection of the circuit. The global optimizations are performed by solving quadratic programming problems that possess unique global minima. Improved partitioning schemes for the stepwise refinement of the placement are introduced. The area utilization is optimized by an exhaustive slicing procedure. The placement method is applied to real-world problems, and excellent results in terms of placement quality and computation time are obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Human Pseudoautosomal Region (PAR): Origin, Function and Future (2007)

The pseudoautosomal regions (PAR1 and PAR2) of the human X and Y chromosomes pair and recombine during meiosis. Thus genes in this region are not inherited in a strictly sex-linked fashion. PAR1 is located at the terminal region of the short arms and PAR2 at the tips of the long arms of these chromosomes. To date, 24 genes have been assigned to the PAR1 region. Half of these have a known function. In contrast, so far only 4 genes have been discovered in the PAR2 region. Deletion of the PAR1 region results in failure of pairing and male sterility. The gene SHOX (short stature homeobox-containing) resides in PAR1. SHOX haploinsufficiency contributes to certain features in Turner syndrome as well as the characteristics of Leri-Weill dyschondrosteosis. Only two of the human PAR1 genes have mouse homologues. These do not, however, reside in the mouse PAR1 region but are autosomal. The PAR regions seem to be relics of differential additions, losses, rearrangements and degradation of the X and Y chromosome in different mammalian lineages. Marsupials have three homologues of human PAR1 genes in their autosomes, although, in contrast to mouse, do not have a PAR region at all. The disappearance of PAR from other species seems likely and this region will only be rescued by the addition of genes to both X and Y, as has occurred already in lemmings. The present review summarizes the current understanding of the evolution of PAR and provides up-to-date information about individual genes residing in this region.
Demonstration of in Vitro Infection of Chimpanzee Hepatocytes with Hepatitis C Virus Using Strand-Specific RT/PCR (1994)

Analysis of hepatitis C virus (HCV) replication has been hampered due to the difficulty encountered in in vitro cultivation of the virus in conventional tissue culture systems. In this study, primary chimpanzee hepatocyte cultures maintained in a serum-free medium formulation were susceptible to in vitro infection with HCV. In order to document infection, two new methods of reverse transcription/polymerase chain reaction were developed that permit accurate distinction between positive and negative strand HCV RNA. One method relied upon the use of a tagged cDNA primer, while the second method employed a thermostable reverse transcriptase. Following inoculation of chimpanzee hepatocytes with HCV, intracellular positive and negative strand HCV RNA were detectable 4 days postinfection and throughout the remainder of the experimental period, 25 days. Analysis of HCV-inoculated baboon hepatocytes revealed a total absence of negative strand HCV RNA, while residual positive strand RNA from the inoculum could be detected for up to 11 days. The in vitro replication of HCV RNA in chimpanzee hepatocytes could be suppressed by alpha-interferon. This system should be amenable to the study of HCV replication, antiviral compounds, and the development of neutralization assays.