gebhart/patrepeval huggingface dataset:
Preserving digital data in heterogeneous environments (2009)

Digital preservation aims at maintaining digital objects accessible over a long period of time, regardless of the challenges of organizational or technological changes or failures. In particular, data produced in e-Science domains could be reliably stored in today's data grids, taking advantage of the natural properties of this kind of infrastructure to support redundancy. However, to achieve reliability we must take into account failure interdependency. Taking into account the fact that correlated failures can affect multiple components and potentially cause complete loss of data, we propose a solution to evaluate redundancy strategies in the context of heterogeneous environments such as data grids. This solution is based on a simulation engine that can be used not only to support the process of designing the preservation environment and related policies, but also later on to observe and control the deployed system.
IgE-Dependent Mast Cell Activation Potentiates Airway Responses in Murine Asthma Models (2002)

We have studied murine models of asthma using FcepsilonRIalpha-chain-deficient (FcepsilonRIalpha(-/-)) mice to investigate the role of IgE-dependent mast cell activation in these models. When mice were either 1) immunized once with OVA in alum i.p. and then challenged with OVA intranasally, or 2) repeatedly immunized with OVA in the absence of adjuvant and subsequently challenged with nebulized OVA, FcepsilonRalpha(-/-) mice had significantly fewer eosinophils and lower IL-4 levels in their bronchoalveolar lavage fluid compared with wild-type mice. When mice were given anti-IL-5 antibody before OVA challenge in protocol 1, eosinophilic infiltration into the airways was significantly suppressed in both genotypes, but only FcepsilonRIalpha(-/-) mice showed significantly reduced airway hyperresponsiveness (AHR). In addition, when mice immunized and challenged with OVA also received a late OVA provocation at a higher concentration and were then exposed to methacholine, only wild-type mice developed a substantial increase in AHR. Since FcepsilonRI is expressed mainly on mast cells in mouse airways, we conclude that IgE-dependent activation of this cell type plays an important role in the development of allergic airway inflammation and AHR in mice. The models used may be of value for testing inhibitors of IgE or mast cells for development of therapeutic agents for human asthma.
8B/10B Codec for Efficient PAPR Reduction in OFDM Communication Systems (2005)

High peak-to-average power ratio (PAPR) of the transmitted signal is a major drawback of orthogonal frequency division multiplexing (OFDM) communication systems. The PAPR reduces the power efficiency of the RF high power amplifier (HPA) in the transmitter and causes distortion in the system. In this paper, we propose a new PAPR reduction method, which uses a DC-balanced 8B/10B code in the time domain of OFDM system to reduce PAPR. The simulation result shows that the proposed method can reduce the peak PAPR value of a 16 sub-carrier OFDM system utilizing QPSK modulation to 7.4dB. The theoretical peak PAPR for the same system would be 12dB. Moreover, the proposed method has very low complexity and the complexity does not increase as the number of OFDM subcarriers increases.
Distributed Routing for Very Large Networks Based on Link Vectors (1997)

Routing is the network-layer function that selects the paths that data packets travel from a source to a destination in a computer communication network. This thesis is on distributed adaptive routing algorithms for large packet-switched networks. A new type of routing algorithms for computer networks, the link-vector algorithm (LVA) is introduced. LVAs use selective dissemination of topology information. Each router running an maintains a subset of the topology that corresponds to adjacent links and those links used by its neighbor routers in their preferred paths to known destinations. Based on that subset of topology information, the router derives its own preferred paths and communicates the corresponding link-state information to its neighbors. An update message contains a vector of updates; each such update specifies a link and its parameters. LVAs can be used for different types of routing policies. LVAs are shown to have better performance than the ideal link-state algorithm based on flooding and the distributed Bellman-Ford algorithm.
Pharmacokinetics of an anti—human immunodeficiency virus antisense oligodeoxynucleotide phosphorothioate (GEM 91) in HIV-infected subjects* (1995)

Human pharmacokinetics of an antisense oligodeoxynucleotide phosphorothioate (GEM 91) developed as an anti-human immunodeficiency virus (HIV) agent was carried out in this study. 35S-Labeled GEM 91 was administered to six HIV-infected individuals by means of 2-hour intravenous infusions at a dose of 0.1 mg/kg. Plasma disappearance curves for GEM 91-derived radioactivity could be described by the sum of two exponentials, with half-life values of 0.18 +/- 0.04 and 26.71 +/- 1.67 hours. The radioactivity in plasma was further evaluated by polyacrylamide gel electrophoresis, showing the presence of both intact GEM 91 and lower molecular weight metabolites. Urinary excretion represented the major pathway of elimination, with 49.15% +/- 6.80% of the administered dose excreted within 24 hours and 70.37% +/- 6.72% over 96 hours after dosing. The radioactivity in urine was associated with lower molecular weight metabolites. No drug-related toxicity was observed.
Nonmuscle and Muscle Tropomyosin Isoforms Are Expressed from a Single Gene by Alternative RNA Splicing and Polyadenylation (1986)

The molecular basis for the expression of rat embryonic fibroblast tropomyosin 1 and skeletal muscle beta-tropomyosin was determined. cDNA clones encoding these tropomyosin isoforms exhibit complete identity except for two carboxy-proximal regions (amino acids 189 to 213 and 258 to 284) and different 3'-untranslated sequences. The isoform-specific regions delineate the troponin T-binding domains of skeletal muscle tropomyosin. Analysis of genomic clones indicates that there are two separate loci in the rat genome that contain sequences complementary to these mRNAs. One locus is a pseudogene. The other locus contains a single gene made up of 11 exons and spans approximately 10 kilobases. Sequences common to all mRNAs were found in exons 1 through 5 (amino acids 1 to 188) and exons 8 and 9 (amino acids 214 to 257). Exons 6 and 11 are specific for fibroblast mRNA (amino acids 189 to 213 and 258 to 284, respectively), while exons 7 and 10 are specific for skeletal muscle mRNA (amino acids 189 to 213 and 258 to 284, respectively). In addition, exons 10 and 11 each contain the entire 3'-untranslated sequences of the respective mRNAs including the polyadenylation site. Although the gene is also expressed in smooth muscle (stomach, uterus, and vas deferens), only the fibroblast-type splice products can be detected in these tissues. S1 and primer extension analyses indicate that all mRNAs expressed from this gene are transcribed from a single promoter. The promoter was found to contain G-C-rich sequences, a TATA-like sequence TTTTA, no identifiable CCAAT box, and two putative Sp1-binding sites.
Absence of Mycoplasma species DNA in chronic fatigue syndrome (2003)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Plasma and Thermal ALD of Al[sub 2]O[sub 3] in a Commercial 200 mm ALD Reactor (2007)

The deposition of Al 2 O 3 by remote plasma atomic layer deposition ALD in the Oxford Instruments FlexAL reactor was studied and compared with results from thermal ALD in the same reactor. Trimethylaluminum AlCH 3 3 was used as the metal precursor and O 2 plasma and H 2 O were used as oxidizing agents for the plasma and thermal processes, respectively. For remote plasma ALD with a total cycle time of 4 s, the growth per cycle decreased monotonically with substrate temperature, from 1.7 /cycle at 25C to 1.0 /cycle at 300C. This growth per cycle was consistently higher than that obtained for thermal ALD. For the latter a maximum growth per cycle of 1.0 /cycle was found at 200C. The film properties investigated were nearly independent of oxidant source for temperatures between 100 and 300C, with a slightly higher mass density for the remote plasma ALD Al 2 O 3 films. Films deposited at 200 and 300C were stoichiometric with a mass density of 3.0 g/cm 3 and low C 1 atom % and H 3 atom % contents. At lower substrate temperatures, oxygen-rich films were obtained with a lower mass density and higher H-content. Remote plasma ALD produced uniform Al 2 O 3 films with nonuniformities of less than 2% over 200 mm diam substrates. Excellent conformality was obtained for films deposited in macropores with an aspect ratio of 8 2.0-2.5 m diam. Preliminary results on electrical properties of remote plasma deposited films showed high dielectric constants of 7.8 and 8.9 for as-deposited and forming gas annealed Al 2 O 3 , respectively.
Cloning, characterization, and functional studies of human and mouse glycoprotein VI: a platelet-specific collagen receptor from the immunoglobulin superfamily (2000)

Injuries to the vessel wall and subsequent exposure of collagen from the subendothelial matrix result in thrombus formation. In physiological conditions, the platelet plug limits blood loss. However, in pathologic conditions, such as rupture of atherosclerotic plaques, platelet-collagen interactions are associated with cardiovascular and cerebral vascular diseases. Platelet glycoprotein VI (GPVI) plays a crucial role in collagen-induced activation and aggregation of platelets, and people who are deficient in GPVI suffer from bleeding disorders. Based on the fact that GPVI is coupled to the Fc receptor (FcR)-gamma chain and thus should share homology with the FcR chains, the genes encoding human and mouse GPVI were identified. They belong to the immunoglobulin (Ig) superfamily and share 64% homology at the protein level. Functional evidence demonstrating the identity of the recombinant protein with GPVI was shown by binding to its natural ligand collagen; binding to convulxin (Cvx), a GPVI-specific ligand from snake venom; binding of anti-GPVI IgG isolated from a patient; and association to the FcR-gamma chain. The study also demonstrated that the soluble protein blocks Cvx and collagen-induced platelet aggregation and that GPVI expression is restricted to megakaryocytes and platelets. Finally, human GPVI was mapped to chromosome 19, long arm, region 1, band 3 (19q13), in the same region as multiple members of the Ig superfamily. This work offers the opportunity to explore the involvement of GPVI in thrombotic disease, to develop alternative antithrombotic compounds, and to characterize the mechanism involved in GPVI genetic deficiencies. (Blood. 2000;96:1798-1807)
Millimeter-wave spatial and quasi-optical power combining techniques (2005)

Spatial and quasi-optical power combining techniques applicable at millimeter-wave frequencies have been developed. The combiners are formed by combining the output power from the active elements in free space or in open resonators.
Nucleic Acid–Gold Nanoparticle Conjugates as Mimics of microRNA (2011)

Novel conjugates of gold nanoparticles functionalized with synthetic microRNAs can enter cells without the aid of cationic co-carriers and mimic the function of endogenous microRNAs. These conjugates can regulate multiple proteins through interactions with the 3′ untranslated region of the target messenger RNA and control cell behavior. The conjugates are promising new tools for studying microRNA function and are candidates for microRNA replacement therapies. 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.
Biological subtypes of breast cancer: Prognostic and therapeutic implications (2014)

Breast cancer is a heterogeneous complex of diseases, a spectrum of many subtypes with distinct biological features that lead to differences in response patterns to various treatment modalities and clinical outcomes. Traditional classification systems regarding biological characteristics may have limitations for patient-tailored treatment strategies. Tumors with similar clinical and pathological presentations may have different behaviors. Analyses of breast cancer with new molecular techniques now hold promise for the development of more accurate tests for the prediction of recurrence. Gene signatures have been developed as predictors of response to therapy and protein gene products that have direct roles in driving the biology and clinical behavior of cancer cells are potential targets for the development of novel therapeutics. The present review summarizes current knowledge in breast cancer molecular biology, focusing on novel prognostic and predictive factors.
Tumor hypoxia and reoxygenation: the yin and yang for radiotherapy (2016)

Tumor hypoxia, a common feature occurring in nearly all human solid tumors is a major contributing factor for failures of anticancer therapies. Because ionizing radiation depends heavily on the presence of molecular oxygen to produce cytotoxic effect, the negative impact of tumor hypoxia had long been recognized. In this review, we will highlight some of the past attempts to overcome tumor hypoxia including hypoxic radiosensitizers and hypoxia-selective cytotoxin. Although they were (still are) a very clever idea, they lacked clinical efficacy largely because of 'reoxygenation' phenomenon occurring in the conventional low dose hyperfractionation radiotherapy prevented proper activation of these compounds. Recent meta-analysis and imaging studies do however indicate that there may be a significant clinical benefit in lowering the locoregional failures by using these compounds. Latest technological advancement in radiotherapy has allowed to deliver high doses of radiation conformally to the tumor volume. Although this technology has brought superb clinical responses for many types of cancer, recent modeling studies have predicted that tumor hypoxia is even more serious because 'reoxygenation' is low thereby leaving a large portion of hypoxic tumor cells behind. Wouldn't it be then reasonable to combine hypoxic radiosensitizers and/or hypoxia-selective cytotoxin with the latest radiotherapy? We will provide some preclinical and clinical evidence to support this idea hoping to revamp an enthusiasm for hypoxic radiosensitizers or hypoxia-selective cytotoxins as an adjunct therapy for radiotherapy.
Antifreeze protein genes are tandemly linked and clustered in the genome of the winter flounder. (1985)

We have used genomic Southern blots and restriction maps of genomic clones to examine the organization of the antifreeze protein multigene family in the winter flounder. The majority of the approximately equal to 40 antifreeze protein (AFP) genes in this fish are present in 7- to 8-kilobase-pair (kbp) elements of DNA, which are iterated as tandem direct repeats. Each repeat contains a single antifreeze protein gene that is 1 kbp long, and all of these genes have the same transcriptional orientation. Although the repeated elements are highly homologous, they do show some restriction site and restriction length polymorphisms. When flounder genomic DNA is digested with restriction endonucleases that do not cut within the repeats, most of the antifreeze protein genes reside in fragments that are at least 40 kbp long, representing clusters of five or more repeats in tandem. After genomic DNA is digested with Xba I or Xho I, these genes are present in fragments of exceptionally high molecular weight, suggesting that the clusters themselves are grouped together in the genome. The AFP gene locus may have evolved by gene amplification as recently as 10(6) years ago in response to the onset of the Cenozoic ice age.
A Double-blind, Placebo-Controlled Study of Oral Nalmefene for Alcohol Dependence (1999)

Treatment with nalmefene was effective in preventing relapse to heavy drinking relative to placebo in alcohol-dependent outpatients and was accompanied by acceptable side effects.
A Urokinase Receptor–Bim Signaling Axis Emerges during EGFR Inhibitor Resistance in Mutant EGFR Glioblastoma (2014)

EGFR is the most common genetically altered oncogene in glioblastoma (GBM), but small-molecule EGFR tyrosine kinase inhibitors (TKI) have failed to yield durable clinical benefit. Here, we show that in two novel model systems of acquired resistance to EGFR TKIs, elevated expression of urokinase plasminogen activator (uPA) drives signaling through the MAPK pathway, which results in suppression of the proapoptotic BCL2-family member protein BIM (BCL2L11). In patient-derived GBM cells and genetic GBM models, uPA is shown to suppress BIM levels through ERK1/2 phosphorylation, which can be reversed by siRNA-mediated knockdown of uPA. TKI-resistant GBMs are resensitized to EGFR TKIs by pharmacologic inhibition of MEK or a BH3 mimetic drug to replace BIM function. A link between the uPA-uPAR-ERK1/2 pathway and BIM has not been previously demonstrated in GBM, and involvement of this signaling axis in resistance provides rationale for a new strategy to target EGFR TKI-resistant GBM.
High-Dose Vancomycin Therapy for Methicillin-Resistant Staphylococcus aureus Infections (2006)

High prevalence of clinical MRSA strains with elevated vancomycin MIC (2 microg/mL) requires aggressive empirical vancomycin dosing to achieve a trough greater than 15 microg/mL. Combination or alternative therapy should be considered for invasive infections caused by these strains.
Polycaprolactone-poly(ethylene-glycol) block copolymer. IV: Biodegradation behaviorin vitro andin vivo (1997)

The biodegration behavior of polycaprolactone–poly(ethylene glycol) block copolymer (PCL–b–PEG) was identified by degradation tests in vitro and in vivo. The tests in vitro and in vivo were carried out by immersing samples in pH 5.0, 7.2 and 9.0 buffer solutions with or without lipase at 25.0, 37.0 and 50.0±°C, and implanting samples in the back or small intestine of rats. It was found that the degradation rate of the PCL–b–PEG was increased with increasing PEG content, temperature, acidity or alkalinity, and it was accelerated by the presence of enzyme. The fastest degradation rate was observed in the physiological condition of the sample being implanted in the body of animals. It has been shown that the PCL–b–PEG copolymer is a possible biodegradable polymer. © 1997 John Wiley & Sons, Ltd.
Photon antibunching in the fluorescence of individual color centers in diamond (2000)

We observed photon antibunching in the fluorescent light emitted from a single nitrogen-vacancy center in diamond at room temperature. The possibility of generating triggerable single photons with such a solid-state system is discussed.
Lyophilized plasma attenuates vascular permeability, inflammation and lung injury in hemorrhagic shock (2018)

In severe trauma and hemorrhage the early and empiric use of fresh frozen plasma (FFP) is associated with decreased morbidity and mortality. However, utilization of FFP comes with the significant burden of shipping and storage of frozen blood products. Dried or lyophilized plasma (LP) can be stored at room temperature, transported easily, reconstituted rapidly with ready availability in remote and austere environments. We have previously demonstrated that FFP mitigates the endothelial injury that ensues after hemorrhagic shock (HS). In the current study, we sought to determine whether LP has similar properties to FFP in its ability to modulate endothelial dysfunction in vitro and in vivo. Single donor LP was compared to single donor FFP using the following measures of endothelial cell (EC) function in vitro: permeability and transendothelial monolayer resistance; adherens junction preservation; and leukocyte-EC adhesion. In vivo, using a model of murine HS, LP and FFP were compared in measures of HS- induced pulmonary vascular inflammation and edema. Both in vitro and in vivo in all measures of EC function, LP demonstrated similar effects to FFP. Both FFP and LP similarly reduced EC permeability, increased transendothelial resistance, decreased leukocyte-EC binding and persevered adherens junctions. In vivo, LP and FFP both comparably reduced pulmonary injury, inflammation and vascular leak. Both FFP and LP have similar potent protective effects on the vascular endothelium in vitro and in lung function in vivo following hemorrhagic shock. These data support the further development of LP as an effective plasma product for human use after trauma and hemorrhagic shock.
Nuclear proteins that bind the pre-mRNA 3' splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n. (1993)

HeLa cell nuclear proteins that bind to single-stranded d(TTAGGG)n, the human telomeric DNA repeat, were identified and purified by a gel retardation assay. Immunological data and peptide sequencing experiments indicated that the purified proteins were identical or closely related to the heterogeneous nuclear ribonucleoproteins (hnRNPs) A1, A2-B1, D, and E and to nucleolin. These proteins bound to RNA oligonucleotides having r(UUAGGG) repeats more tightly than to DNA of the same sequence. The binding was sequence specific, as point mutation of any of the first 4 bases [r(UUAG)] abolished it. The fraction containing D and E hnRNPs was shown to bind specifically to a synthetic oligoribonucleotide having the 3' splice site sequence of the human beta-globin intervening sequence 1, which includes the sequence UUAGG. Proteins in this fraction were further identified by two-dimensional gel electrophoresis as D01, D02, D1*, and E0; intriguingly, these members of the hnRNP D and E groups are nuclear proteins that are not stably associated with hnRNP complexes. These studies establish the binding specificities of these D and E hnRNPs. Furthermore, they suggest the possibility that these hnRNPs could perhaps bind to chromosome telomeres, in addition to having a role in pre-mRNA metabolism.