gebhart/patrepeval huggingface dataset:
Cell Culture Adaptation of Hepatitis C Virus and In Vivo Viability of an Adapted Variant (2007)

Production of infectious hepatitis C virus in cell culture has become possible because of the unique properties of the JFH1 isolate. However, virus titers are rather low, limiting the utility of this system. Here we describe the generation of cell culture-adapted JFH1 variants yielding higher titers of infectious particles and enhanced spread of infection in cultured cells. Sequence analysis of adapted genomes revealed a complex pattern of mutations that differed in two independent experiments. Adaptive mutations were observed both in the structural and in the nonstructural regions, with the latter having the highest impact on enhancement of virus titers. The major adaptive mutation was identified in NS5A, and it enhanced titers of three intergenotypic chimeras consisting of the structural region of a genotype 1a, 1b, or 3a isolate and the remainder of the JFH1 isolate. The mutation resides at the P3 position of the NS5A-B cleavage site and slows down processing, implying that subtle differences in replication complex formation appear to determine the efficiency of virus formation. Highly adapted JFH1 viruses carrying six mutations established a robust infection in uPA-transgenic SCID mice xenografted with human hepatocytes. However, the mutation in NS5A which enhanced virus titers in cell culture the most had reverted to wild type in nearly half of the viral genomes isolated from these animals at 15 weeks postinoculation. These results argue for some level of impaired fitness of this mutant in vivo.
Carbon nanotube-based digital vacuum electronics and miniature instrumentation for space exploration (2010)

JPL has developed high performance cold cathodes using arrays of carbon nanotube bundles that produce &gt; 15 A/cm<sup>2</sup> at applied fields of 5 to 8 V/&mu;m without any beam focusing. They have exhibited robust operation in poor vacuums of 10<sup>-6</sup> to 10<sup>-4</sup> Torr- a typically achievable range inside hermetically sealed microcavities. Using these CNT cathodes JPL has developed miniature X-ray tubes capable of delivering sufficient photon flux at acceleration voltages of &lt;20kV to perform definitive mineralogy on planetary surfaces; mass ionizers that offer two orders of magnitude power savings, and S/N ratio better by a factor of five over conventional ionizers. JPL has also developed a new class of programmable logic gates using CNT vacuum electronics potentially for Venus in situ missions and defense applications. These "digital" vacuum electronic devices are inherently high-temperature tolerant and radiation insensitive. Device design, fabrication and DC switching operation at temperatures up to 700&deg; C are presented in this paper.
Chemistry of Boranes. XXIV. Carbonylation of Derivatives of B10H102- and B12H122- with Oxalyl Chloride (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of Boranes. XXIV. Carbonylation of Derivatives of B10H102- and B12H122- with Oxalyl ChlorideWalter R. Hertler, Walter H. Knoth, and Earl L. MuettertiesCite this: Inorg. Chem. 1965, 4, 3, 288–293Publication Date (Print):March 1, 1965Publication History Published online1 May 2002Published inissue 1 March 1965https://pubs.acs.org/doi/10.1021/ic50025a005https://doi.org/10.1021/ic50025a005research-articleACS PublicationsRequest reuse permissionsArticle Views212Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Review of Horizontal Methods and Drilling Technology (1991)

Abstract This paper covers the geology of the Rocky Mountains, low permeable hydrocarbon producing formations and the problems associated with horizontal drilling tools in these regions. The paper includes representative horizontal well data from the Rocky Mountain region and low permeable hydrocarbon producing formations outside the United States. Oil producing trends with respect to fracture and formation are described as they pertain to horizontal drilling tools. Where applicable emphasis is placed on solutions to problems associated with horizontal tools.
Public International Law and Private Enterprise: Damages for a killing in East Timor (1996)

(1996). Public International Law and Private Enterprise: Damages for a killing in East Timor. Australian Journal of Human Rights: Vol. 3, No. 1, pp. 21-39.
Effect of Troglitazone on Insulin Sensitivity and Pancreatic β-Cell Function in Women at High Risk for NIDDM (1996)

We conducted a randomized placebo-controlled study to determine the effects of the thiazolidinedione compound troglitazone on whole-body insulin sensitivity (SI), pancreatic beta-cell function, and glucose tolerance in 42 Latino women with impaired glucose tolerance (IGT) and a history of gestational diabetes mellitus (GDM), characteristics that carry an 80% risk of developing NIDDM within 5 years. After baseline oral (OGTT) and intravenous (IVGTT) glucose tolerance testing, subjects were assigned to take placebo or 200 or 400 mg troglitazone daily for 12 weeks (14 subjects per treatment group). An OGTT and IVGTT were repeated during the 12th week of treatment. Five subjects failed to complete the trial for personal reasons, and medication compliance averaged 90% in the remaining subjects, none of whom experienced a serious adverse event. SI, calculated by minimal model analysis of IVGTT results, changed by only 4 +/- 14% during 12 weeks of placebo administration, but increased 40 +/- 22 and 88 +/- 22% above basal during treatment with 200 and 400 mg troglitazone, respectively (P = 0.01 among groups). Troglitazone administration was also associated with a dose-dependent reduction in the total insulin area during IVGTTs, which was highly significant (P < 0.001), and with a reduction during OGTTs, which approached statistical significance (P = 0.09). Glucose tolerance improved slightly in all groups, but the magnitude of change did not differ significantly among groups, whether it was assessed as the number of subjects who continued to manifest IGT at 12 weeks (P = 0.64 among groups), the change in total glucose area during OGTTs (P = 0.58), or the change in fractional glucose disappearance rates during IVGTTs (P = 0.28). Among the women who received troglitazone, the greatest improvement in SI occurred in the women who had the highest diastolic blood pressures and the best IVGTT insulin responses during baseline testing. Our findings indicate that troglitazone improved whole-body insulin sensitivity and lowered circulating insulin concentrations in women with prior GDM who are at very high risk for NIDDM. The lack of improvement in glucose tolerance despite improved insulin sensitivity may be a manifestation of the beta-cell defect that predisposes the women to NIDDM. The overall pattern of response to troglitazone in our high-risk patients indicates that the drug is an ideal agent with which to test whether the amelioration of insulin resistance can delay or prevent diabetes in women with limited beta-cell reserve.
LJ Interviews Linus Torvalds (1998)

With 2.2 on the horizon, LJ once again talks to the man who started it all --Linus Torvalds
Reconstruction of a 3D Virtual Colon Structure and Camera Motion for Screening Colonoscopy (2017)

Background/PurposeOptical colonoscopy is the gold standard for detection and prevention of Colorectal cancer. However, any lesion outside the field of view of the camera during colonoscopy is missed, and can develop from a polyp into a cancer or from a small cancer into a large, metastatic cancer. Hence, viewing the colon mucosa as much as possible is desirable. The ultimate goal is to use the reconstruction results to mark the area likely unobserved during colonoscopy where polyps may be hidden.Materials and Methods:This paper presents a novel method for reconstructing (i) a 3D virtual colon structure from a sequence of 2D colonoscopic images and (ii) the endoscope camera navigation path. Unlike existing work that focus on reconstruction of accurate colon surface for a computer-aided surgery, this work focuses on estimating the alignment of the colon haustral folds, thickness and protrusion of the folds, and the camera path for computer-aided screening colonoscopy to inspect as much as possible of the colon mucosa.Results:On endoscopy video of a synthetic colon model, we achieved at least 73% and 90% accuracy in estimating the directions of camera translation and rotation motions, respectively. The average percentage of the depth error is about 10% (8.5/85.8) of the average depth of all the folds seen in all the image sequences. The average percentage of the circumference error is about 10% (17/178.2) of the average circumference of all the folds seen in all the image sequences. The results are promising and give further insight to address this challenging problem.Conclusions:We present the work on reconstruction of a colon structure and endoscope motion from a colonoscopic image sequence for screening colonoscopy. We overcame several challenges such as the scale difference of consecutive reconstructed models, estimating closed fold contours from tracked fold edges, and registering the models. As future work, we will investigate a multi-frame registration approach to further reduce the depth and circumference estimation errors by registering nearby frames that are more similar in fold shape together.
Electrically gated ionic channels in lipid bilayers (1977)

The generation of action potentials in nerve and muscle requires cell membranes with steeply voltage-dependent ionic permeabilities. The voltage-dependent, ion-selective pathways responsible for excitation have been characterized for numerous excitable tissues such as nerve axon, muscle, electric organ, algae and epithelia (Aidley, 1971; Hodgkin, 1964; Cole, 1968). The process of activating ionic pathways by some stimulus, such as a change in membrane potential, is called gating.
A shift in the Th1/Th2 ratio accompanies the clinical remission of systemic lupus erythematosus in patients with end-stage renal disease (2002)

SLE patients with preserved renal function show a bias in the differentiation of Th cells towards Th(2). Once ESRD occurs, the Th(1)/Th(2) ratio normalizes. This may contribute to the remission of Th(2)-mediated autoimmune diseases such as SLE.
Interferon-β1afor the treatment of multiple sclerosis (2007)

At present, two types of recombinant human interferon (IFN)-beta are in clinical use. IFN-beta1a is produced in genetically engineered Chinese hamster ovary cells, and its amino acid sequence and glycosylation pattern are identical to those of endogenous human IFN-beta. The beneficial effect of IFN-beta in multiple sclerosis (MS) probably results from different mechanisms of action, such as a direct effect on plasma cells modulating IgG synthesis, an increase of interleukin (IL)-10 levels, the inhibition of IL-1beta and tumour necrosis factor alpha, the stimulation of IL-1 receptor antagonist production, the inhibition of proliferation of leukocytes, a decreased antigen presentation in microglia, a reduction of T cell migration into the brain by inhibition of the activity of T cell matrix metalloproteinases, and a downregulation of adhesion molecules. IFN-beta1a has been shown by several multicenter controlled trials to be effective in relapsing-remitting MS. It reduces relapse rate by 30-50%, magnetic resonance imaging signs of disease activity in 30-80% and disability progression by 30%. It is also effective in preventing conversion to clinically definite MS when given at the time of a first demyelinating event (i.e., at the very beginning of the clinical disease). No clear evidence of the persistence of the efficacy over the long-term has stood out from a systematic analysis of published trials. A Cochrane review concluded that, in fact, the clinical effect beyond the first year of treatment is not clear. Finally, no efficacy has been shown in secondary progressive or primary progressive MS. However, IFN-beta1a is very well tolerated and the most frequent side effects are mild (local skin reaction and flu-like symptoms) and decline in frequency or disappear after the first 3-6 months of treatment. Although the optimal frequency between once weekly or multiple weekly administrations is still controversial, all protocols require multiple monthly injections. Some patients might find it hard to cope with such a treatment regimen over the long term. Ongoing trials with new powerful immunomodulatory drugs, such as monoclonal antibodies, that require only monthly or bimonthly parenteral administrations will probably offer a better tolerated treatment option in the near future.
Interactive modeling of plants (1999)

We present a rule-based approach combined with traditional geometric modelling techniques that allows easy generation of many branching objects including flowers, bushes, trees, and even nonbotanical objects. A set of components describing structural and geometrical elements of plants maps to a graph that forms the description of a specific plant and generates the geometry. Users get immediate feedback on what they've created-geometrical parameters, tropisms, and free-form deformations can control the overall shape of a plant. We demonstrate that our method handles the complexity of most real plants.
A Polycomb Repression Signature in Metastatic Prostate Cancer Predicts Cancer Outcome (2007)

The Polycomb Group (PcG) protein EZH2 is a critical component of a multiprotein complex that methylates Lys(27) of histone 3 (H3K27), which consequently leads to the repression of target gene expression. We have previously reported that EZH2 is overexpressed in metastatic prostate cancer and is a marker of aggressive diseases in clinically localized solid tumors. However, the global set of genes directly regulated by PcG in tumors is largely unknown, and thus how PcG mediates tumor progression remains unclear. Herein we mapped genome-wide H3K27 methylation in aggressive, disseminated human prostate cancer tissues. Integrative analysis revealed that a significant subset of these genes are also targets of PcG in embryonic stem cells, and their repression in tumors is associated with poor prognosis. By stepwise cross-validation, we developed a "Polycomb repression signature" composed of 14 direct targets of PcG in metastatic tumors. Notably, solid tumor subtypes in which this gene signature is repressed show poor clinical outcome in multiple microarray data sets of tumors including breast and prostate cancer. Taken together, our results show a fingerprint of PcG-mediated transcriptional repression in metastatic prostate cancer that is reminiscent of stem cells and associated with cancer progression. Therefore, PcG proteins play a central role in the epigenetic silencing of target genes and functionally link stem cells, metastasis, and cancer survival.
GPS Multipath Mitigation for Urban Area Using Omnidirectional Infrared Camera (2009)

This paper describes a precision positioning technique that can be applied to vehicles in urban areas. The proposed technique mitigates Global Positioning System (GPS) multipath by means of an omnidirectional infrared (IR) camera that can eliminate the need for invisible satellites [a satellite detected by the receiver but without line of sight (LOS)] by using IR images. Some simple GPS multipath mitigation techniques, such as the installation of antennas away from buildings and using choke ring antennas, are well known. Further, various correlator techniques can also be employed. However, when a direct signal cannot be received by the antenna, these techniques do not provide satisfactory results because they presume that the antenna chiefly receives direct signals. On the other hand, the proposed technique can mitigate GPS multipath, even if a direct signal cannot be received because it can recognize the surrounding environment by means of an omnidirectional IR camera. With the IR camera, the sky appears distinctively dark; this facilitates the detection of the borderline between the sky and the surrounding buildings, which are captured in white, due to the difference in the atmospheric transmittance rate between visible light and IR rays. Positioning is performed only with visible satellites having fewer multipath errors and without using invisible satellites. With the proposed system, static and kinematic evaluations in which invisible satellites are discriminated through observation using an omnidirectional IR camera are conducted. Hence, signals are received even if satellites are hidden behind buildings; furthermore, the exclusion of satellites having large errors from the positioning computation becomes possible. The evaluation results confirm the effectiveness of the proposed technique and the feasibility of highly accurate positioning.
THE ONBROWSER ONTOLOGY MANAGER: MANAGING ONTOLOGIES ON THE GRID (2004)

Although many tools and methodologies exist for ontology editing and management, complete, integrated ontology management systems working on the Grid are needed. Moreover, such ontology management systems should allow the use of knowledge coded into ontologies to different applications in a standard way. In this paper we consider the role of ontology management systems that using metadata spread on the Grid can help Grid programming. The paper presents the design and a first implementation of OnBrowser , an ontology manager that provides access to “knowledge objects” coding ontology portions and referring to Grid metadata, through both user interfaces and application programming interfaces.
Phosphorothioate Oligonucleotides Inhibit Human Immunodeficiency Virus Type 1 Fusion by Blocking gp41 Core Formation (2006)

Several studies have shown that phosphorothioate oligodeoxynucleotides (PS-ONs) have a sequence-independent antiviral activity against human immunodeficiency virus type 1 (HIV-1). It has also been suggested that PS-ONs inhibit HIV-1 by acting as attachment inhibitors that bind to the V3 loop of gp120 and prevent the gp120-CD4 interaction. Here we show that PS-ONs (and their fully 2'-O-methylated derivatives) are potent inhibitors of HIV-1-mediated membrane fusion and HIV-1 replication in a size-dependent, phosphorothioation-dependent manner. PS-ONs interact with a peptide derived from the N-terminal heptad repeat region of gp41, and the HIV-1 fusion-inhibitory activity of PS-ONs is closely correlated with their ability to block gp41 six-helix bundle formation, a critical step during the process of HIV-1 fusion with the target cell. These results suggest that the increased hydrophobicity of PS-ONs may contribute to their inhibitory activity against HIV-1 fusion and entry, because longer PS-ONs (>or=30 bases) which have a greater hydrophobicity are more potent in blocking the hydrophobic interactions involved in the gp41 six-helix bundle formation and inhibiting the HIV-1-mediated cell-cell fusion than shorter PS-ONs (<30 bases). This novel antiviral mechanism of action of long PS-ONs has implications for therapy against infection by HIV-1 and other enveloped viruses with type I fusion proteins.
Evaluation of direct grafting strategies in Expansion Microscopy (2019)

Abstract High resolution fluorescence microscopy is a key tool in the elucidation of biological fine-structure, providing insights into the distribution and interactions of biomolecular systems down to the nanometer scale. Expansion microscopy is a recently developed approach to achieving nanoscale resolution in optical imaging. In the experiment, biological samples are embedded in a hydrogel, which is isotropicaly swollen. This physically pulls labels apart, allowing more of them to be resolved. However, in the gelation and swelling process, two factors combine to reduce the signal in the final image; signal dilution and the polymerization reaction, which can damage some fluorophores. Here, we show a chemical linking approach that allows covalent grafting of biomolecular target and reporter in expansion microscopy. Through the combination of a targeting ligand, a reporter moiety and a polymerizable group in a single linker, complex constructs can be prepared in a single, labelling step. We show application of this new series of molecules in the targeting of the cell cytoskeleton, a first example of lipid membranes in expansion microscopy; direct immunostaining with primary and secondary antibodies, and direct grafting of ISH probes and signal amplification initiators (HCR and RollFISH). Our probes allow direct, multiplexed targeting of the cellular blueprint and enable a range of novel imaging approaches in combination with expansion microscopy.
Aluminum-wire grid polarizer for a compact magneto-optic pickup device (2002)

A compact magneto-optic pickup device is required to realize magneto-optic disc systems of low cost and fast access. The key is a microminiaturized polarization component. We investigated the optimum fabrication conditions in the resonance domain for S-polarized light using electron-beam direct-writing and the liftoff method, and realized a low-loss wire-grid polarizer of Ts=80 % and Ts/Tp=30, and a high extinction ratio wire-grid polarizer of Ts=54 % and Ts/Tp=1000, for a wavelength of 0.78 /spl mu/m and a period of 0.39 /spl mu/m. These are the best values for wire-grid polarizers in the 0.8 /spl mu/m wavelength band so far reported. We studied the feasibility of using this device for polarization detection in magneto-optic disc systems by measuring the carrier-to-noise ratio (C/N).
Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota (2015)

Variations in the vaginal microbiota, especially shifts away from Lactobacillus-dominant microbiota, are associated with differential risks of acquiring HIV or other sexually transmitted infections. However, emerging evidence suggests that Lactobacillus iners frequently colonizes women with recurring bacterial vaginosis, raising the possibility that L. iners may not be as protective as other Lactobacillus species. Our study was designed to improve understanding of how the cervicovaginal mucus barrier against HIV may vary between women along with the vaginal microbiota and led to the finding that the vaginal microbiota, including specific species of Lactobacillus, can directly alter the diffusional barrier properties of cervicovaginal mucus. This work advances our understanding of the complex barrier properties of mucus and highlights the differential protective ability of different species of Lactobacillus, with Lactobacillus crispatus and possibly other species playing a key role in protection against HIV and other sexually transmitted infections. These findings could lead to the development of novel strategies to protect women against HIV.