gebhart/patrepeval huggingface dataset:
Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates (1991)

Telomeric DNA consists of G- and C-rich strands that are always polarized such that the G-rich strand extends past the 3' end of the duplex to form a 12-16-base overhang. These overhanging strands can self-associate in vitro to form intramolecular structures that have several unusual physical properties and at least one common feature, the presence of non-Watson-Crick G.G base pairs. The term "G-DNA" was coined for this class of structures (Cech, 1988). On the basis of gel electrophoresis, imino proton NMR, and circular dichroism (CD) results, we find that changing the counterions from sodium to potassium (in 20 mM phosphate buffers) specifically induces conformational transitions in the G-rich telomeric DNA from Tetrahymena, d(T2G4)4 (TET4), which results in a change from the intramolecular species to an apparent multistranded structure, accompanied by an increase in the melting temperature of the base pairs of greater than 25 degrees, as monitored by loss of the imino proton NMR signals. NMR semiselective spin-lattice relaxation rate measurements and HPLC size-exclusion chromatography studies show that in 20 mM potassium phosphate (pH 7) buffer (KP) TET4 is approximately twice the length of the form obtained in 20 mM sodium phosphate (pH 7) buffer (NaP) and that mixtures of Na+ and K+ produce mixtures of the two forms whose populations depend on the ratio of the cations. Since K+ and NH4+ are known to stabilize a parallel-stranded quadruplex structure of poly[r(I)4], we infer that the multistranded structure is a quadruplex. Our results indicate that specific differences in ionic interactions can result in a switch in telomeric DNAs between intramolecular hairpin-like or quadruplex-containing species and intermolecular quadruplex structures, all of which involve G.G base pairing interactions. We propose a model in which duplex or hairpin forms of G-DNA are folding intermediates in the formation of either 1-, 2-, or 4-stranded quadruplex structures. In this model monovalent cations stabilize the duplex and quadruplex forms via two distinct mechanisms, counterion condensation and octahedral coordination to the carbonyl groups in stacked planar guanine "quartet" base assemblies. Substituting one of the guanosine residues in each of the repeats of the Tetrahymena sequence to give the human telomeric DNA, d(T2AG3)4, results in less effective K(+)-dependent stabilization. Thus, the ion-dependent stabilization is attenuated by altering the sequence. Upon addition of the Watson-Crick (WC) complementary strand, only the Na(+)-stabilized structure dissociates quickly to form a WC double helix.(ABSTRACT TRUNCATED AT 400 WORDS)
Quantitative structure-activity studies of insect growth regulators: XVI. Substituent effects of dibenzoylhydrazines on the insecticidal activity to Colorado potato beetleLeptinotarsa decemlineata (1999)

Insecticidal activity against the Colorado potato beetle, Leptinotarsa decemlineata, was measured for a series of substituted N-tert-butyl-dibenzoylhydrazines, in which one of the benzoyl moieties closer to the tert-butyl group was fixed as being 2-chloro-substitued and the other variously substituted singly or doubly. The effects of substituents on the activity were quantitatively analysed using the classical quantitative structure–activity relationship (QSAR) procedure. The activity against the Colorado potato beetle increases with the molecular hydrophobicity. In addition, various types of steric effect are at work, depending upon the positions. Hydrogen-bonding acceptor substituents at the para position enhance the activity. There seem to be threshold (or optimum) values, albeit position-dependent, in the molecular hydrophobicity, above which the activity starts to decrease. This biphasic contribution of the molecular hydrophobicity to activity against coleopterous larvae is the most conspicuous difference in substituent effects from those found for similar compounds against lepidopterous pest insects, and may be the basis of the variations in the activity spectrum for certain compounds in this series. The introduction of bulkier substituents into the meta- and para-positions of the benzene ring, apart from the tert-butyl group, is unfavorable to activity. LD50 values against Colorado potato beetle larvae of methoxyfenozide (RH-2485) and tebufenozide (RH-5992) were in the order of 10−7 mol per insect, whereas those of RH-5849, and halofenozide (RH-0345) were very low, 10−9–10−10 mol per insect being selective to the coleopterous larvae. © 1999 Society of Chemical Industry
Coagulation Factor VII Gln100 → Arg (1998)

We have used recombinant mammalian expression and purification of the factor VII (FVII) variant Gln100 --> Arg (Q100RFVII) to study FVII deficiency in subjects with this mutation. Q100RFVII was secreted poorly in comparison with wild-type FVII (WTFVII) in a stable mammalian expression system, and purified variant protein was found to have undetectable clotting activity. Following activation by immobilized factor Xa, Q100RFVIIa had amidolytic activity similar to WTFVIIa in the absence of soluble tissue factor (sTF); however, unlike WTFVIIa no typical increase in activity was seen after addition of sTF. In a factor X activation assay using relipidated transmembrane truncated tissue factor (residues 1-243), Q100RFVIIa showed less than 5% of the ability of WTFVIIa to activate factor X. We performed direct binding analysis of WT and Q100RFVII/FVIIa to immobilized sTF using surface plasmon resonance, and severely reduced binding of both non-activated and activated Q100RFVII to sTF was seen, indicating a pronounced defect in tissue factor (TF) interaction with this variant. In the sTF-FVIIa crystal structure the candidate residue Gln100 is not in contact with TF but is at the epidermal growth factor 2-protease domain interface. We suggest that the mutation results in a global fold change severely reducing tissue factor interaction; mutation of FVII residues not directly involved in the interaction with TF may still result in variant FVII unable to take part in the initiation of coagulation.
Cationic Liposomes and DNA Delivery (1993)

AbstractLiposome technology offers several potential advantages for delivering functioning DNA to cells in intact animals. A particular advantage of cationic liposomes is simplicity. The use of chargecharge interaction as a device for forming DNA-liposome complexes circumvents the necessity to incorporate DNA into the liposome during process of manufacturing the liposomes. In addition, cationic liposomes complexed to DNA may behave differently in. vivo than other liposomes. In the lungs, transgenes can be expressed following either intravenous or airway delivery of cationic liposome-DNA complexes. Aerosol delivery of such complexes may prove a particularly useful clinical approach. The ability to target liposomes to particular cell populations by incorporating into the liposome proteins with affinities for different cells may be a particularly useful strategy for selective delivery of DNA to sub-populations of cells in the lungs and other organs. The fact that cationic liposomes can effectively deliver transgenes to the lungs as well as other organs makes it likely that this technology will be one of the clinical approaches which proves useful.
Correlation between nicotine-induced inhibition of hematopoiesis and decreased CD44 expression on bone marrow stromal cells (2001)

This study demonstrates that in vivo exposure to cigarette smoke (CS) and in vitro treatment of long-term bone marrow cultures (LTBMCs) with nicotine, a major constituent of CS, result in inhibition of hematopoiesis. Nicotine treatment significantly delayed the onset of hematopoietic foci and reduced their size. Furthermore, the number of long-term culture-initiating cells (LTC-ICs) within an adherent layer of LTBMCs was significantly reduced in cultures treated with nicotine. Although the production of nonadherent mature cells and their progenitors in nicotine-treated LTBMCs was inhibited, this treatment failed to influence the proliferation of committed hematopoietic progenitors when added into methylcellulose cultures. Bone marrow stromal cells are an integral component of the hematopoietic microenvironment and play a critical role in the regulation of hematopoietic stem cell proliferation and self-renewal. Exposure to nicotine decreased CD44 surface expression on primary bone marrow-derived fibroblastlike stromal cells and MS-5 stromal cell line, but not on hematopoietic cells. In addition, mainstream CS altered the trafficking of hematopoietic stem/progenitor cells (HSPC) in vivo. Exposure of mice to CS resulted in the inhibition of HSPC homing into bone marrow. Nicotine and cotinine treatment resulted in reduction of CD44 surface expression on lung microvascular endothelial cell line (LEISVO) and bone marrow-derived (STR-12) endothelial cell line. Nicotine treatment increased E-selectin expression on LEISVO cells, but not on STR-12 cells. These findings demonstrate that nicotine can modulate hematopoiesis by affecting the functions of the hematopoiesis-supportive stromal microenvironment, resulting in the inhibition of bone marrow seeding by LTC-ICs and interfering with stem cell homing by targeting microvascular endothelial cells.
Serum leptin concentration and advanced gastrointestinal cancers: a case controlled study (2004)

Independently from the site of gastrointestinal tract, serum leptin concentration in advanced gastrointestinal cancer is lower than controls and it is not a determinant factor in weight loss. In contrast to healthy subjects, gender does not effect the serum leptin concentration in patients with advanced gastrointestinal cancer.
The art of computer virus research and defense (2005)

Of all the computer-related books I've read recently, this one influenced my thoughts about security the most. There is very little trustworthy information about computer viruses. Peter Szor is one of the best virus analysts in the world and has the perfect credentials to write this book.-Halvar Flake, Reverse Engineer, SABRE Security GmbHSymantec's chief antivirus researcher has written the definitive guide to contemporary virus threats, defense techniques, and analysis tools. Unlike most books on computer viruses, The Art of Computer Virus Research and Defense is a reference written strictly for white hats: IT and security professionals responsible for protecting their organizations against malware. Peter Szor systematically covers everything you need to know, including virus behavior and classification, protection strategies, antivirus and worm-blocking techniques, and much more.Szor presents the state-of-the-art in both malware and protection, providing the full technical detail that professionals need to handle increasingly complex attacks. Along the way, he provides extensive information on code metamorphism and other emerging techniques, so you can anticipate and prepare for future threats.Szor also offers the most thorough and practical primer on virus analysis ever published-addressing everything from creating your own personal laboratory to automating the analysis process. This book's coverage includes Discovering how malicious code attacks on a variety of platforms Classifying malware strategies for infection, in-memory operation, self-protection, payload delivery, exploitation, and more Identifying and responding to code obfuscation threats: encrypted, polymorphic, and metamorphic Mastering empirical methods for analyzing malicious code-and what to do with what you learn Reverse-engineering malicious code with disassemblers, debuggers, emulators, and virtual machines Implementing technical defenses: scanning, code emulation, disinfection, inoculation, integrity checking, sandboxing, honeypots, behavior blocking, and much more Using worm blocking, host-based intrusion prevention, and network-level defense strategies © Copyright Pearson Education. All rights reserved.
Resource partitioning in general purpose operating systems (1999)

The principal role of the operating system is that of resource management. Its task is to present a set of appropriate services to the applications and users it supports. Traditionally, general-purpose operating systems, including Windows NT, federate resource sharing in a fair manner, with the predominant goal of efficient resource utilisation. As a result the chosen scheduling algorithms are not suited to applications that have stringent Quality-of-Service (QoS) and resource management requirements, such as continuous media streaming applications. Several approaches to resource management that are able to meet these requirements, including the use of deterministic schedulers, are well established. Operating systems already exist that provide services for fine-grained resource partitioning and QoS based allocations. Nevertheless, the question arises: can we introduce suitable management mechanisms into general-purpose operating systems that will provide adequate support for the majority of resource sensitive applications, particularly multimedia? Or are there inherent problems in general-purpose operating system architectures that demand significant re-engineering?We attempt to answer this question by proposing the Protected Virtual Machine (PVM) architecture. This introduces mechanisms into Windows NT that enable partitioning of resources and protection from resource interference. The functionality of the PVM architecture is two-fold. First it introduces the necessary scheduling mechanisms and atomic resource abstractions into the operating system, and second it provides a higher level reservation and admission service directly to applications. The resulting system is able to provide both a best-effort service for applications with less stringent needs and a guaranteed service for multimedia and other resource critical processing in a shared environment, By enhancing the existing operating system, legacy applications can still be supported, thus avoiding a prominent obstacle in existing real-time and multimedia operating systems.
Distribution of serotonin 5‐HT1C receptor mRNA in adult rat brain (1989)

Based on in situ hybridization histochemistry (ISHH), we describe the anatomical distribution of the serotonin 5-HT1C receptor mRNA. In addition to the very high levels in epithelial cells of the choroid plexus, 5-HT1C receptor mRNA is found throughout the limbic system, in catecholaminergic cells and in serotonergic neurons. Receptor transcripts are also present in the hypothalamus, numerous motor nuclei and the subthalamus. Our results correlate well with serotonin (5-HT) innervation and receptor binding. Receptor mRNA is present in many brain structures in addition to regions previously shown to have 5-HT1C receptor binding. The distribution of this receptor mRNA suggests that the 5-HT1C receptor may mediate a number of the central effects of 5-HT.
SYNTHESIS AND BIOLOGICAL ACTIVITY OF BRANCHED CHAIN-SUGAR NUCLEOSIDES1 (1989)

Abstract 2′-Alkyl derivatives of cytidine and thymidine have been synthesized. 2′-Deoxy-6,2′-methanocytidine has also been prepared. Among them, 2′-deoxy-2′-methylidene-cytidine exhibited potent antitumor activities.
EntityRank: searching entities directly and holistically (2007)

As the Web has evolved into a data-rich repository, with the standard “page view, ” current search engines are becoming increasingly inadequate for a wide range of query tasks. While we often search for various data “entities ” (e.g., phone number, paper PDF, date), today’s engines only take us indirectly to pages. While entities appear in many pages, current engines only find each page individually. Toward searching directly and holistically for finding information of finer granularity, we study the problem of entity search, a significant departure from traditional document retrieval. We focus on the core challenge of ranking entities, by distilling its underlying conceptual model Impression Model and developing a probabilistic ranking framework, EntityRank, that is able to seamlessly integrate both local and global information in ranking. We evaluate our online prototype over a 2TB Web corpus, and show that EntityRank performs effectively. 1.
A review of localization algorithms for distributed wireless sensor networks in manufacturing (2008)

Abstract\n Wireless Sensor Networks (WSN) typically consist of a large number of densely populated sensor nodes. Due to important advances in integrated circuits and radio technologies, the use of distributed sensor networks is more and more widespread for a variety of applications, such as indoor navigation, environmental monitoring, people and objects tracking, logistics, industrial diagnostics, quality control, and other activities in manufacturing. In many cases, such as in objects tracking, knowing the physical location of network nodes is essential. Locating elements of WSNs is not a trivial task. Manual methods are wearisome and may be inaccurate, especially for large-scale networks. Therefore, many self-locating methods ? where nodes cooperate with each other without human involvement ? have recently been studied and implemented. &#13;\nThe purpose of this work is to analyse the most significant methods for automatic locating of distributed WSNs. The first part of the paper provides a description of the most common criteria to categorize existing network localization algorithms. Then, we suggest a taxonomy which may be an useful tool to help evaluating, comparing, and selecting them. Five of the most representative algorithms are deeply explained and discussed, in order to identify their strong points, and their limitations.
Aseptic meningitis and encephalitis: the role of PCR in the diagnostic laboratory (1997)

In this study we have devised a simple and robust PCR strategy to detect a wide range of viruses, bacteria, and parasites, all of which are capable of causing aseptic meningitis and encephalitis. The techniques developed have been used in a routine diagnostic virology laboratory to test prospectively 2,233 cerebrospinal fluid specimens. A virus was detected in 147 specimens of cerebrospinal fluid from 143 patients. Four sets of primers were sufficient to detect the virus in 135 (94%) of the PCR-positive patients. We conclude that with appropriate primers, PCR can be systematically and economically applied to test for a range of organisms in a routine diagnostic laboratory. In our opinion, PCR will soon become the "gold standard" test for viral infections of the central nervous system.
Transfer of Cytoplasmic Male Sterility Tetraploid Radish, Raphanus sativus L., to Raphanobrassica by Means of Successive Backcrosses (1986)

departmental bulletin paper
Relative contribution of renal nerve and adrenal gland to renal vascular tone during prolonged canine hemorrhagic hypotension. (1993)

This study was designed to determine roles of renal sympathetic nerve activity (RNA) and adrenal catecholamines in the changes of renal vascular resistance during prolonged hemorrhagic shock in anesthetized dogs. In animals with intact baroreceptors, hemorrhagic hypotension (40 mm Hg) caused RNA to increase significantly within 1 min after bleeding, followed by a return to baseline within 10 min. Thereafter, a secondary increase in RNA occurred that was followed by a gradual decline towards the baseline level. The renal perfusion pressure (RPP) showed a progressive and significant increase until the end of the experiment. The initial increase in RNA was abolished by complete denervation of the systemic baroreceptors. The initial increase in RPP, which was observed within 10 min after bleeding in animals with intact baroreceptors, was attenuated by the denervation. In animals with bilateral adrenalectomy, RPP still showed an initial increase, but the progressive increase throughout the entire experimental period did not occur. In animals with baroreceptor denervation and bilateral adrenalectomy, RPP did not show any significant changes during the experiment. These results indicate that the initial renal vasoconstrictive response to hemorrhage is regulated by a reflex sympathetic mechanism. In contrast, a late renal vasoconstriction during hemorrhagic hypotension is predominantly evoked by humoral substances such as adrenal catecholamines.
Sphingomyelin changes in rat cerebral cortex during focal ischemia (1996)

To better define the sphingolipid metabolism during focal brain ischemia, levels of ceramide, sphingomyelin, cerebroside and gangliosides were determined in rat cerebral cortex during focal ischemia produced by occlusion of the middle cerebral artery. Sphingomyelin began to decrease at 2 hours of ischemia and continued to decrease for 96 hours. In contrast, ceramide increased at 6 hours and increased to 4.2-fold at 96 hours after ischemia, and the fatty acid composition of ceramide was solely nonhydroxylated fatty acid similar to sphingomyelin. Hydroxylated fatty acid-linked cerebroside decreased at 6 hours of ischemia, whereas any significant decrease of nonhydroxylated fatty acid-linked cerebroside didn't occur for 96 hours of ischemia. There were no measurable changes in the levels of gangliosides. These results suggested that ceramide was produced in the cerebral cortex by the breakdown of sphingomyelin during early ischemia.
Multiple-Object, Discriminatory Auctions with Bidding Constraints: A Game-Theoretic Analysis (1980)

This paper examines the existence and characterization of pure strategy Nash equilibria in multiple-object auction games in which buyers face a binding constraint on exposure. There are five major results. First, symmetric Nash equilibria exist if and only if there are two or less buyers and two or less items. Second, a Nash equilibrium may not exist if the seller sets a positive reservation bid. Third, asymmetric solutions to symmetrically parameterized games typically involve “high-low” strategies: each buyer submits positive bids only on some restricted subset of the items. Fourth, Nash equilibria typically generate zero “surplus” to the buyers. Fifth, when asymmetric solutions exist and the buyers are identical, these solutions are never unique.
Atroviridins A-C and Neoatroviridins A-D, Novel Peptaibol Antibiotics Produced by Trichoderma atroviride F80317. I. Taxonomy, Fermentation, Isolation and Biological Activities. (2002)

Seven new peptaibols, atroviridins A-C composed of 20 residue amino acids and neoatroviridins A-D with 18 residues, were isolated from the culture broth of fungal strain F80317. The strain F80317 was identified as Trichoderma atroviride from its morphological and cultural characteristics. These compounds showed antimicrobial activity against Gram-positive bacteria and phytopathogenic fungi, and exhibited significant cytotoxicity to human cancer cell lines in vitro. Atroviridins showed significant membrane-perturbing activity responsible to their antibiotic action.
Toward a Biotechnological Heparin through Combined Chemical and Enzymatic Modification of the Escherichia coli K5 Polysaccharide (2001)

A process to generate glycosaminoglycans with heparin- and heparan sulfate-like sequences from the Escherichia coli K5 capsular polysaccharide is described. This polymer has the same structure as N-acetylheparosan, the precursor in heparin/ heparan sulfate biosynthesis. The process involves chemical N-deacetylation and N-sulfation, enzymatic conversion of up to 60% of the D-glucuronic acid to L-iduronic acid residues, and chemical O-sulfation. Because direct sulfation afforded unwanted 3-O-sulfated (instead of 2-O-sulfated) iduronic acid residues, a strategy involving graded solvolytic desulfation of chemically oversulfated C5-epimerized sulfaminoheparosans was assessed using persulfated heparin and heparan sulfate as model compounds. The O-desulfation process was shown to increase the anti-factor Xa activity of oversulfated heparin.