gebhart/patrepeval huggingface dataset:
An end-to-end approach to host mobility (2000)

We present the design and implementation of an end-to-end architecture for Internet host mobility using dynamic updates to the Domain Name System (DNS) to track host location. Existing TCP connections are retained using secure and efficient connection migration, enabling established connections to seamlessly negotiate a change in endpoint IP addresses without the need for a third party. Our architecture is secure—name updates are effected via the secure DNS update protocol, while TCP connection migration uses a novel set of Migrate options—and provides a pure end-system alternative to routing-based approaches such as Mobile IP.
Molecular Similarity (2011)

In order to identify new molecules susceptible to become medicines, the pharmaceutical research has more and more resort to new technologies to synthesize big number of molecules simultaneously and to test their actions on given therapeutic target. This data can be exploited to construct the models permitting to predict the properties of molecules not yet tested, even not yet synthesized. Such predictive models are very important because they make it possible to suggest the synthesis of new molecules, and to eliminate very early in the the molecule’s search process the molecules whose properties would prevent their use as medicine. The authors call it virtual sifting. It is within this framework that research by similarity is registered. It is a practical approach to identify molecules candidates (to become medicines) from the data bases or the virtual chemical libraries by comparing the compounds two by two. Many statistical models and learning tools have been developed to correlate the molecule’s structure with their chemical, physical or biological properties. The large majority of these methods start by transforming each molecule in a vector of great dimension (using molecular descriptors), then use a learning algorithm on these vectorial descriptions. The objective of this chapter is to study molecular similarity using a particular type of neural networks: the Kohonen networks (also called “SOM” Self- Organizing Maps), applying the nearest neighbor algorithm to the projection of the molecules (coordinates) in the constructed MAP.
Increasing bacterial disease resistance in plants utilizing antibacterial genes from insects (1987)

Abstract The introduction of genes into plants encoding potent antibacterial proteins, derived from insects, may significantly augment the level of their resistance to bacterial disease. Using modern techniques, genes of choice can be introduced into plant tissue and this tissue can be manipulated to produce viable plants. The potato has been chosen as the model system, not only because of its plasticity of development, which allows for the relatively easy regeneration of whole plants from transformed tissue, but also because the potato ranks among the top four plants in the world in terms of economic importance.
Genome-wide search for loss of heterozygosity using laser capture microdissected tissue of breast carcinoma: an implication for mutator phenotype and breast cancer pathogenesis. (2000)

Breast cancer is considered to display a high degree of intratumor heterogeneity, without any obvious morphological and pathological steps to define sequential evolution, and its progression may vary among individual tumors. In an attempt to elucidate these etiological and phenotypic complexities, the present study, based on the fundamental concept that genomic instability is the engine of both tumor progression and tumor heterogeneity, was conducted to test the hypothesis that breast cancer pathogenesis is driven by double-strand break (DSB)-initiated chromosome instability (CIN). The rationale underlying this hypothesis is derived from the clues provided by family breast cancer syndromes, in which susceptibility genes, including p53, ATM, BRCA1 and BRCA2, are involved within the common functional pathway of DSB-related checkpoint/ repair. Because genomic deletion caused by DSB is reflected in the genetic mechanism of loss of heterozygosity (LOH), this genome-wide LOH study was conducted, using 100 tumors and 400 microsatellite markers. To minimize the effect of heterogeneity within tumors, the experimental technique of laser capture microdissection was used to ensure that genetic and phenotypic examinations were based on the same tumor cells. Support for our hypothesis comes from the observations that: (a) the extent of DSB-initiated CIN in tumors significantly increased as tumors progressed to poorer grades or later stages; (b) in the sequential steps toward CIN, the loci of p53 and ATM, the key checkpoint genes against DSB, were lost at the earliest stage; and (c) many loci identified to be important in breast tumorigenesis were the genomic sites possibly harboring the genes involved in DSB-related checkpoint/repair (including RAD51, RAD52, and BRCA1) or CIN (including FA-A, FA-D, and WRN), and a higher number of these loci showing LOH was significantly associated with increased level of DSB-initiated CIN (P < 0.0001). Breast cancers are thus considered to be sequentially progressive with CIN. However, CIN might also cause genetic heterogeneity, which was revealed by the findings that LOH at some markers was observed only in the component of ductal carcinoma in situ but not in the invasive component of the same tumors. In addition, some markers were found to preferentially lose at specific tumor grades, implying their contribution to genetic heterogeneity during tumor development. Therefore, this study suggests that breast cancer progression is clonal with regard to CIN, but different breast cancers would present distinct molecular profiles resulting from genetic heterogeneity caused by CIN.
Bioluminescence in the sea: photoprotein systems. (1985)

Photoproteins are the primary reactants of the light-emitting reactions of various bioluminescent organisms. A photoprotein emits light in proportion to its amount, like a luciferin, but its light-emitting reaction does not require a luciferase. There are about two dozen types of bioluminescent organisms for which substantial biochemical knowledge is presently available, and about one third of them involve photoproteins. Most photoproteins are found in marine organisms. There are various types of photoproteins: the photoproteins of coelenterates, ctenophores and radiolarians require Ca2+ to trigger their luminescence; the photoproteins of the bivalve Pholas and of the scale worm appear to involve superoxide radicals and O2 in their light-emitting reactions; the photoprotein of euphausiid shrimps emits light only in the presence of a special fluorescent compound; the photoprotein of the millipede Luminodesmus, the only known example of terrestrial origin, requires ATP and Mg2+ to emit light. The Ca2+-sensitive photoproteins of coelenterates have been most frequently studied and most widely used. Therefore, they are overwhelmingly popular compared with other types. All coelenterate photoproteins, including aequorin, halistaurin, obelin and phialidin, have relative molecular masses close to 20 000, contain an identical functional group, and emit blue light in aqueous solution when a trace of Ca2+ is added, in the presence or absence of molecular oxygen. Aequorin contains an oxygenated form of coelenterazine in its functional group. When Ca2+ is added, aequorin decomposes into three parts, i.e., apo-aequorin, coelenteramide and CO2, accompanied by the emission of light. Apo-aequorin can be reconstituted into active aequorin indistinguishable from the original sample, by incubation with an excess of coelenterazine in a buffer containing 5 mM-EDTA and a trace of 2-mercaptoethanol, even at 0 degree C. Thus, aequorin and other coelenterate photoproteins can be luminesced and recharged repeatedly. The regeneration of coelenterate photoproteins in this manner probably takes place in vivo, utilizing stored coelenterazine. The photoproteins of coelenterates, and their chemically modified forms, are useful in measuring and monitoring calcium ions in biological systems, especially in single cells.
A randomized controlled clinical trial of actarit in the treatment of r heumatoid arthritis (2002)

OBJECTIVE To evaluate the efficacy and safety of a ctarit and methotrexate in the treatment of patients with rheumatoid arthritis(R A).METHODS Randomized, double or single blind, controlled an d multi center clinical trial of actarit versus methotrexate was performed. The 313 patients were given po with actarit 100 mg tid and another 167 patients wer e given po with methotrexate 10 mg once weekly for 12 weeks.Naproxen or oxaprozi n was gived together in the first 4～6 weeks.RESULTS ①The t otal efficacy rates of actarit and methotrexate were 68.06% and 76.65% after 12 weeks treatment, respectively( P 0.05).②Actarit and methotrexate improved t he symptoms and signs of rheumatoid arthritis,decreased ESR,C reactive protein and rheumatoid factor(RF) level respectively.Methotrexate improved morning stiff ness, grasp strength of two hand, tenderness joint count(TJC), ESR and RF level better than those of actarit( P 0.05).③The incidences of adverse effects of actarit and methotrexate were 7.03% and 22.35%( P 0.05).The adverse effects of actarit were gastrointestinal effects,SGPT increased slightly and etc.CONCLUSION Actarit is a safe and effective antirhematic drug in t he treatment of RA.The efficacy of actarit was lower than that of methotrexate, while the tolerance of actarit is better than that of methotrexate.
The Kinetic Mechanism of Phosphomevalonate Kinase (2003)

Phosphomevalonate kinase catalyzes an essential step in the so-called mevalonate pathway, which appears to be the sole pathway for the biosynthesis of sterols and other isoprenoids in mammals and archea. Despite the well documented importance of this pathway in the cause and prevention of human disease and that it is the biosynthetic root of an enormous diverse class of metabolites, the mechanism of phosphomevalonate kinase from any organism is not yet well characterized. The first structure of a phosphomevalonate kinase from Streptococcus pneumoniae was solved recently. The enzyme exhibits an atypical P-loop that is a conserved defining feature of the GHMP kinase superfamily. In this study, the kinetic mechanism of the S. pneumoniae enzyme is characterized in the forward and reverse directions using a combination of classical initial-rate methods including alternate substrate inhibition using ADPbetaS. The inhibition patterns strongly support that in either direction the substrates bind randomly to the enzyme prior to chemistry, a random sequential bi-bi mechanism. The kinetic constants are as follows: k(cat(forward)) = 3.4 s(-1), K(i(ATP)) = 137 microm, K(m(ATP)) = 74 microm, K(i(pmev)) = 7.7 microm, K(m(pmev)) = 4.2 microm; k(cat(reverse)) = 3.9 s(-1), K(i(ADP)) = 410 microm, K(m(ADP)) = 350 microm, K(i(ppmev)) = 14 microm, K(m(ppmev)) = 12 microm, where pmev and ppmev represent phosphomevalonate and diphosphomevalonate, respectively.
Implementation of Adaptive Modulation and Coding Technique using (2011)

Index Terms—. Adaptive Modulation and Coding (AMC), Cognitive Radio (CR), LTE, Software Defined Radio (SDR), WiMAX. —————————— a —————————— 1 I The growth in the use of the information networks lead to the need for new communication networks with higher data rates. The telecommunication industry is also changing, with a demand for a greater range of services, such as video conferences, or applications with multimedia contents. The increased reliance on computer networking and the Internet has resulted in a wider demand for connectivity to be provided where, any time, leading to a rise in the requirements for higher capacity and high reliability broadband wireless access Broadband wireless Access (BWA) telecommunication systems. BWA intensively focused in the last few years. Thus, various new technologies with high transmission abilities have been designed. The BWA has become the best way to meet escalating business demand for rapid Internet connection and integrated triple play services. That is the very base of the HSPA, WiMAX, and LTE concept: a wireless transmission infrastructure that allows a fast deployment as well as low maintenance costs. The emergent demand of all types of services, not only voice and data but also multimedia services, aims for the design of increasingly more intelligent and agile communication systems, capable of providing spectrally efficient and flexible data rate access. These systems are able to adapt and adjust the transmission parameters based on the link quality, improving the spectrum efficiency of the system, and reaching, in this way, the capacity limits of the underlying wireless channel. Link adaptation techniques, often referred to as adaptive modulation and coding (AMC), are a good way for reaching the cited requirements. They are designed to track the channel variations, thus changing the modulation and coding scheme to yield a higher throughput by transmitting with high information rates under favorable channel conditions and reducing the information rate in response to channel degradation.
The CRIT Study: Anemia and blood transfusion in the critically ill—Current clinical practice in the United States* (2004)

Anemia is common in the critically ill and results in a large number of RBC transfusions. Transfusion practice has changed little during the past decade. The number of RBC units transfused is an independent predictor of worse clinical outcome.
Effect of Allogenic Freeze‐Dried Demineralized Bone Matrix on Guided Tissue Regeneration in Dogs (1998)

This randomized, split-mouth study was designed to evaluate the adjunctive effect of allogenic, freeze-dried, demineralized bone matrix (DBM) to guided tissue regeneration (GTR). Contralateral fenestration defects (6 x 4 mm) were created 6 mm apical to the buccal alveolar crest on maxillary canine teeth in 6 beagle dogs. DBM was implanted into one randomly selected fenestration defect. Expanded polytetrafluoroethylene (ePTFE) membranes were used to provide bilateral GTR. Tissue blocks including defects with overlying membranes and soft tissues were harvested following a four-week healing interval and prepared for histometric analysis. Differences between GTR+DBM and GTR defects were evaluated using a paired t-test (N = 6). DBM was discernible in all GTR+DBM defects with limited, if any, evidence of bone metabolic activity. Rather, the DBM particles appeared solidified within a dense connective tissue matrix, often in close contact to the instrumented root. There were no statistically significant differences between the GTR+DBM versus the GTR condition for any histometric parameter examined. Fenestration defect height averaged 3.7+/-0.3 and 3.9+/-0.3 mm, total bone regeneration 0.8+/-0.6 and 1.5+/-0.8 mm, and total cementum regeneration 2.0+/-1.3 and 1.6+/-1.7 mm for GTR+DBM and GTR defects, respectively. The histologic and histometric observations, in concert, suggest that allogenic freeze-dried DBM has no adjunctive effect to GTR in periodontal fenestration defects over a four-week healing interval. The critical findings were 1) the DBM particles remained, embedded in dense connective tissue without evidence of bone metabolic activity; and 2) limited and similar amounts of bone and cementum regeneration were observed for both the GTR+DBM and GTR defects.
Lentivirus Vectors Using Human and Simian Immunodeficiency Virus Elements (1999)

Lentivirus vectors based on human immunodeficiency virus (HIV) type 1 (HIV-1) constitute a recent development in the field of gene therapy. A key property of HIV-1-derived vectors is their ability to infect nondividing cells. Although high-titer HIV-1-derived vectors have been produced, concerns regarding safety still exist. Safety concerns arise mainly from the possibility of recombination between transfer and packaging vectors, which may give rise to replication-competent viruses with pathogenic potential. We describe a novel lentivirus vector which is based on HIV, simian immunodeficiency virus (SIV), and vesicular stomatitis virus (VSV) and which we refer to as HIV/SIVpack/G. In this system, an HIV-1-derived genome is encapsidated by SIVmac core particles. These core particles are pseudotyped with VSV glycoprotein G. Because the nucleotide homology between HIV-1 and SIVmac is low, the likelihood of recombination between vector elements should be reduced. In addition, the packaging construct (SIVpack) for this lentivirus system was derived from SIVmac1A11, a nonvirulent SIV strain. Thus, the potential for pathogenicity with this vector system is minimal. The transduction ability of HIV/SIVpack/G was demonstrated with immortalized human lymphocytes, human primary macrophages, human bone marrow-derived CD34(+) cells, and primary mouse neurons. To our knowledge, these experiments constitute the first demonstration that the HIV-1-derived genome can be packaged by an SIVmac capsid. We demonstrate that the lentivirus vector described here recapitulates the biological properties of HIV-1-derived vectors, although with increased potential for safety in humans.
Organic electroluminescent devices fabricated using a diamine doped MgF2 thin film as a hole-transporting layer (1995)

Organic electroluminescent (EL) devices have been fabricated which have a MgF2 layer doped with N, N′-diphenyl-N, N′-bis(3-methylphenyl)-[1,1′-biphenyl]-4, 4′-diamine (TPD) as the hole- transporting layer, and the emitting layer of tris-(8-hydroxyquinoline) aluminum (Alq). For the organic EL devices, bright green emission with 2600 cd/m2 is observed at a voltage of 15 V. The luminous efficiency is about 0.3 lm/W at a current density of 100 mA/cm2. This high efficiency indicates that the diamine doped MgF2 layer plays the role of hole transport and confinement of electrons in the emitting layer. It is also found that the thermal stability of the organic EL device is higher than that of the conventional organic EL device.
Neutrophil-induced Transmigration of Tumour Cells Treated with Tumour-conditioned Medium is Facilitated by Granulocyte-macrophage Colony-stimulating Factor (2000)

These results indicate that the GM-CSF that is present in tumour-conditioned medium may be involved, at least in part, in alterations in PMN function mediated by the medium and subsequently PMN-induced transmigration of tumour cells.
Mapping of RNA- temperature-sensitive mutants of Sindbis virus: assignment of complementation groups A, B, and G to nonstructural proteins (1989)

Four complementation groups of temperature-sensitive (ts) mutants of Sindbis virus that fail to make RNA at the nonpermissive temperature are known, and we have previously shown that group F mutants have defects in nsP4. Here we map representatives of groups A, B, and G. Restriction fragments from a full-length clone of Sindbis virus, Toto1101, were replaced with the corresponding fragments from the various mutants. These hybrid plasmids were transcribed in vitro by SP6 RNA polymerase to produce infectious RNA transcripts, and the virus recovered was tested for temperature sensitivity. After each lesion was mapped to a specific region, cDNA clones of both mutants and revertants were sequenced in order to determine the precise nucleotide change responsible for each mutation. Synthesis of viral RNA and complementation by rescued mutants were also examined in order to study the phenotype of each mutation in a uniform genetic background. The single mutant of group B, ts11, had a defect in nsP1 (Ala-348 to Thr). All of the group A and group G mutants examined had lesions in nsP2 (Ala-517 to Thr in ts17, Cys-304 to Tyr in ts21, and Gly-736 to Ser in ts24 for three group A mutants, and Phe-509 to Leu in ts18 and Asp-522 to Asn in ts7 for two group G mutants). In addition, ts7 had a change in nsP3 (Phe-312 to Ser) which also rendered the virus temperature sensitive and RNA-. Thus, changes in any of the four nonstructural proteins can lead to failure to synthesize RNA at a nonpermissive temperature, indicating that all four are involved in RNA synthesis. From the results presented here and from previous results, several of the activities of the nonstructural proteins can be deduced. It appears that nsP1 may be involved in the initiation of minus-strand RNA synthesis. nsP2 appears to be involved in the initiation of 26S RNA synthesis, and in addition it appears to be a protease that cleaves the nonstructural polyprotein precursors. It may also be involved in shutoff of minus-strand RNA synthesis. nsP4 appears to function as the viral polymerase or elongation factor. The functions of nsP3 are as yet unresolved.
Inability of anti-epidermal growth factor receptor monoclonal antibody to block “autocrine” growth stimulation in transforming growth factor-secreting melanoma cells. (1984)

Mouse monoclonal antibodies to the human epidermal growth factor (EGF) receptor were raised by immunizing with plasma membrane vesicles prepared from A431 cells. This paper describes the characterization of one of the IgG anti-receptor monoclonal antibodies generated and its use to probe the role of transforming growth factor (TGF) in the autonomous growth of a melanoma cell line in culture. This antibody blocks: 1) the binding of 125I-EGF to the A431 EGF receptor; 2) the EGF stimulation of the EGF-dependent protein kinase in vitro; and 3) human fibroblast DNA synthesis and proliferation in culture. It can precipitate the EGF receptor from metabolically labeled A431 cells and human fibroblasts and these receptors have indistinguishable peptide maps. No EGF receptor could be detected by immunoprecipitation after fibroblasts were treated with EGF or conditioned medium from the melanoma cells which secrete EGF-like TGF (alpha TGF). The antibody itself did not down-regulate the receptor but could block down-regulation caused by EGF and alpha TGF. Despite its ability to block EGF-stimulated growth and down-regulation in fibroblasts, the antibody was unable to block the growth and soft agar colony formation of alpha TGF-secreting melanoma cells, nor could the antibody detect EGF receptor in these cells under the conditions developed to prevent down-regulation and lysosomal degradation of the EGF receptor. These studies suggest that these melanoma cells do not have the intact EGF receptor and that the secretion of alpha TGF by these cells plays no role in their growth in culture. The absence of receptor cannot be explained by down-regulation by secreted alpha TGF.
Umbilical cord blood cells and brain stroke injury: bringing in fresh blood to address an old problem (2004)

Degeneration of brain tissue following stroke leads to functional impairment with limited brain self-repair. New evidence suggests that delivery of circulating CD34(+) human umbilical cord blood cells can produce functional recovery in an animal stroke model with concurrent angiogenesis and neurogenesis leading to some restoration of cortical tissue. While some alternative interpretations of this data are offered herein, the study provides encouraging evidence of functional recovery from stroke in an animal model using stem cell therapy.