gebhart/patrepeval huggingface dataset:
The serum concentration of human kallikrein 10 represents a novel biomarker for ovarian cancer diagnosis and prognosis. (2003)

Human kallikrein 10 (hK10) is a secreted serine protease that is highly expressed in ovarian tissue. We hypothesized that hK10 might represent a novel serological marker for ovarian cancer. We quantified by immunoassay, hK10 in sera from 97 normal women (controls), 141 patients with benign gynecologic diseases, and 146 patients with ovarian cancer. We then examined the diagnostic and prognostic value of this measurement in ovarian cancer. We found that normal serum hK10 ranged from 50 to 1040 ng/liter (mean = 439 ng/liter). hK10 concentration is significantly elevated in serum of presurgical ovarian cancer patients (range: 106-11,746 ng/liter; mean = 1067 ng/liter) but not in serum of patients with benign gynecologic diseases (range: 120-1200 ng/liter; mean = 447 ng/liter). When a cutoff of 700 ng/liter was selected (diagnostic specificity = 90%), the diagnostic sensitivity for ovarian cancer is 54%. About 35% of CA125-negative ovarian cancer patients (CA125 < 23 kU/liter) were hK10 positive at 90% specificity. In patients with stage I/II ovarian cancer, use of these two markers in combination results in a 21% increase in sensitivity, at 90% specificity, compared with CA125 alone. High serum hK10 was strongly associated with serous epithelial type, late-stage, advanced grade, large residual tumor (>1 cm), suboptimal debulking, and no response to chemotherapy (all Ps < 0.001). In univariate Cox survival analysis, high serum hK10 is associated with increased risk for relapse and death (hazard ratio = 2.59 and 3.15, respectively, P </= 0.003). This prognostic value remains significant for overall survival in the multivariate analysis. Kaplan-Meier survival curves demonstrated similar findings. Serum hK10 represents a novel biomarker for ovarian cancer. We conclude that preoperative serum hK10 concentration is a strong and independent unfavorable prognostic marker for ovarian cancer.
Synthetic Aperture Fourier Holographic Optical Microscopy (2006)

We report a new synthetic aperture optical microscopy in which high-resolution, wide-field amplitude and phase images are synthesized from a set of Fourier holograms. Each hologram records a region of the complex two-dimensional spatial frequency spectrum of an object, determined by the illumination field's spatial and spectral properties and the collection angle and solid angle. We demonstrate synthetic microscopic imaging in which spatial frequencies that are well outside the modulation transfer function of the collection optical system are recorded while maintaining the long working distance and wide field of view.
Multifunctional Mesoporous Silica Nanoparticles as a Universal Platform for Drug Delivery (2013)

Nanosized mesoporous silica particles with high colloidal stability attract growing attention as drug delivery systems for targeted cancer treatment and as bioimaging devices. This Perspective describes recent breakthroughs in mesoporous silica nanoparticle design to demonstrate their high potential as multifunctional drug delivery nanocarriers. These types of nanoparticles can feature a well-defined and tunable porosity at the nanometer scale, high loading capacity, and multiple functionality for targeting and entering different types of cells. We focus on the requirements for an efficient stimuli-responsive and thus controllable release of cargo into cancer cells and discuss design principles for smart and autonomous nanocarrier systems. Mesoporous silica nanoparticles are viewed as a promising and flexible platform for numerous biomedical applications.
Design of Water-lubricated Components for Hydraulic Systems (1980)

The use of water-based fire-resistant fluids in hydraulic systems offers benefits in safety, conservation of petroleum products, and ecology. However, the properties of such fluids introduce significant design problems, particularly in the area of lubrication. This paper reviews some of the work that has been done in the development of design criteria for systems using waterbased fluids. The application of lubrication mechanics to the selection of materials and to the determination of geometric design details is discussed.
Estrogen suppresses mu-opioid- and GABAB-mediated hyperpolarization of hypothalamic arcuate neurons (1992)

The effects of estrogen on the response of hypothalamic arcuate neurons to mu-opioid and GABAB agonists were investigated. Intracellular recordings were made from arcuate neurons in slices prepared from ovariectomized guinea pigs that were pretreated with estrogen or vehicle. Estrogen shifted the dose-response curve to the mu-opioid agonist DAMGO (Tyr-D-Ala-Gly-MePhe-Gly-ol) by 3.4-fold; the EC50 for DAMGO was 240 +/- 25 nM in estrogen-treated females versus 70 +/- 12 nM in the controls. The maximal hyperpolarization induced by DAMGO was equivalent in neurons from both groups. The Ke for the naloxone antagonism of the DAMGO response was similar in both groups, which would indicate that the affinity of the mu-receptor was unchanged. To explore where in the receptor/G-protein/K+ channel cascade estrogen may be acting to attenuate the mu-opioid-mediated hyperpolarization, the response to the GABAB agonist baclofen was also tested. Estrogen treatment also shifted the dose-response curve for the baclofen-induced hyperpolarization by 3.3-fold without altering the maximum hyperpolarization; the EC50 shifted from 11.0 +/- 4.0 microM to 36.0 +/- 5.0 microM. All of the neurons were identified after linking the intracellular biocytin with streptavidin-FITC, and a subpopulation of cells in both groups were immunoreactive for beta-endorphin. We conclude that estrogen decreases the functional coupling of the mu-opioid and GABAB receptors to the inwardly rectifying K+ channel possibly through an action on the G-protein.
Computer translation of IUPAC systematic organic chemical nomenclature. 5. Steroid nomenclature (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer translation of IUPAC systematic organic chemical nomenclature. 5. Steroid nomenclatureD. I. Cooke-Fox, G. H. Kirby, M. R. Lord, and J. D. RaynerCite this: J. Chem. Inf. Comput. Sci. 1990, 30, 2, 128–132Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/ci00066a005https://doi.org/10.1021/ci00066a005research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-Citations8LEARN 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 options Get e-Alerts
An approach for the analysis of relapse and marrow reconstitution after autologous marrow transplantation using retrovirus-mediated gene transfer (1992)

Autologous bone marrow transplantation (ABMT) is widely used as treatment for malignant disease. Although the major cause of treatment failure is relapse, it is unknown if this arises entirely because of residual disease in the patient or whether contaminating cells in the rescuing marrow contribute. Attempts to purge marrow of its putative residual malignant cells may delay hematopoietic reconstitution and are of uncertain efficacy. We now describe how retrovirus-mediated gene transfer may be used to elucidate the source of relapse after ABMT for acute myeloid leukemia and to evaluate the efficacy of purging. Clonogenic myeloid leukemic blast cells in patient marrow can be transduced with the NeoR gene-containing helper-free retrovirus, LNL6, with an efficacy of 0% to 23.5% (mean, 10.5%). Transduced colonies grow in selective media and the presence of the marker gene can be confirmed in individual malignant colonies by polymerase chain reaction. If such malignant cells remain in harvested “remission” marrow, they will therefore be marked after exposure to LNL6. Detection of the marker gene in the malignant cells present at any later relapse would be firm evidence that residual disease contributed to disease recurrence, and would permit rapid subsequent evaluation of purging techniques. The technique also marks normal marrow progenitors from patients with acute myeloblastic leukemia. These colony-forming cells can be detected in long-term marrow cultures at a frequency of 1% to 18% for up to 10 weeks after exposure to the vector. Animal models and analysis of probability tables both suggest that these levels of marking in vitro are sufficient to provide information about the mechanisms of relapse and the biology of marrow regeneration in vivo. These preclinical data form part of the basis for current clinical studies of gene transfer into marrow before ABMT.
Evaluation of Combination Chemotherapy (2004)

Isobologram and combination index (CI) analyses are the two most popular methods for evaluating drug interactions in combination cancer chemotherapy. As the commonly used CI-based software program uses linear regression, our first objective was to evaluate the effects of logarithmic data transformation on data analysis and conclusions. Monte-Carlo simulations were conducted with experimentally relevant parameter values to generate error-containing effect or concentration-effect data of single agents and combinations. The simulated data were then analyzed with linear and nonlinear regression. The results showed that data transformation reduced the accuracy and precision of the regression-derived IC(50), curve shape parameter and CI values. Furthermore, as neither isobologram nor CI analyses provide output of concentration-effect curves for investigator evaluation, our second objective was to develop a method and the associated computer program/algorithm to (a) normalize drug concentrations in IC(50) equivalents and thereby enable simultaneous presentation of the curves for single agents and combinations in a single plot for visual inspection of potential curve shifts, (b) analyze concentration-effect data with nonlinear regression, and (c) use the curve shift analysis simultaneously with isobologram and CI analyses. The applicability of this method was shown with experimentally obtained data for single agent doxorubicin and suramin and their combinations in cultured tumor cells. In summary, this method, by incorporating nonlinear regression and curve shift analysis, although retaining the attractive features of isobologram and CI analyses, reduced the potential errors introduced by logarithmic data transformation, enabled visual inspection of data variability and goodness of fit of regression analysis, and simultaneously provided information on the extent of drug interaction at different combination ratios/concentrations and at different effect levels.
A prefusion SARS-CoV-2 spike RNA vaccine is highly immunogenic and prevents lung infection in non-human primates (2020)

Abstract To contain the coronavirus disease 2019 (COVID-19) pandemic, a safe and effective vaccine against the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is urgently needed in quantities sufficient to immunise large populations. In this study, we report the design, preclinical development, immunogenicity and anti-viral protective effect in rhesus macaques of the BNT162b2 vaccine candidate. BNT162b2 contains an LNP-formulated nucleoside-modified mRNA that encodes the spike glycoprotein captured in its prefusion conformation. After expression of the BNT162b2 coding sequence in cells, approximately 20% of the spike molecules are in the one-RBD ‘up’, two-RBD ‘down’ state. Immunisation of mice with a single dose of BNT162b2 induced dose level-dependent increases in pseudovirus neutralisation titers. Prime-boost vaccination of rhesus macaques elicited authentic SARS-CoV-2 neutralising geometric mean titers 10.2 to 18.0 times that of a SARS-CoV-2 convalescent human serum panel. BNT162b2 generated strong T H 1 type CD4 + and IFNγ + CD8 + T-cell responses in mice and rhesus macaques. The BNT162b2 vaccine candidate fully protected the lungs of immunised rhesus macaques from infectious SARS-CoV-2 challenge. BNT162b2 is currently being evaluated in a global, pivotal Phase 2/3 trial ( NCT04368728 ).
Clinical Immunogenicity of rHuPH20, a Hyaluronidase Enabling Subcutaneous Drug Administration (2015)

Recombinant human PH20 hyaluronidase (rHuPH20) is used to facilitate dispersion of subcutaneously delivered fluids and drugs. This report summarizes rHuPH20 immunogenicity findings from clinical trials where rHuPH20 was co-administered with SC human immunoglobulin, trastuzumab, rituximab, or insulin. Plasma samples were obtained from evaluable subjects participating in ten different clinical trials as well as from healthy plasma donors. A bridging immunoassay and a modified hyaluronidase activity assay were used to determine rHuPH20-reactive antibody titers and neutralizing antibodies, respectively. rHuPH20-binding antibody populations from selected subjects with positive titers were affinity-purified and subjected to further characterization such as cross-reactivity with endogenous PH20. Among individual trials, the prevalence of pre-existing rHuPH20-reactive antibodies varied between 3 and 12%, excepting the primary immunodeficiency (PID) studies. Incidence of treatment-induced rHuPH20 antibodies was 2 to 18%, with the highest titers (81,920) observed in PID. No neutralizing antibodies were observed. Within most trials, the kinetics of antibody responses were comparable between pre-existing and treatment-induced antibody responses, although responses classified as persistent were more common in subjects with pre-existing titers. There was no association between antibody positivity and either local or systemic adverse events. Pre-existing and treatment-induced antibody populations were of similar immunoglobulin isotypes and cross-reacted to endogenous PH20 to similar extents. No cross-reactivity to PH20 paralogs was detected. rHuPH20 induces only modest immunogenicity which has no association with adverse events. In addition, antibodies purified from baseline-positive individuals are qualitatively similar to those purified from individuals developing rHuPH20-reactive antibodies following exposure to the enzyme.
Hydrogen Storage in Carbon Single-wall Nanotubes (2002)

Carbon single-wall nanotubes (SWNTs) and other nanostructured carbon materials have attracted considerable interest recently due to several reports of high hydrogen storage capacities at room temperatures. Other reports indicate room temperature storage capacities are ~ 0 wt%. All in all, the reported capacities on these materials range from 0 to 60 wt%. Careful work at NREL indicates a maximum capacity for adsorption of hydrogen on SWNTs is ~8 wt%. Samples displaying this maximum value were prepared by sonicating purified SWNTs in a dilute nitric acid solution with a high-energy probe. The process cuts the SWNT into shorter segments and introduces a Ti-6Al-4V alloy due to the disintegration of the ultrasonic probe. The Ti-6Al-4V alloy is a well-known metal hydride and its contribution to the measured hydrogen uptake must be accounted for in order to assess the amount of hydrogen stored on the SWNT fraction. One way to evaluate the relative importance of the cutting and the presence of the alloy in producing active SWNT materials is to produce cut samples that do not contain metal impurities. Metal hydrides may then be subsequently introduced in a controlled manner. This paper describes the experiments used to evaluate the hydrogen storage capacity of the sonicated SWNTs, and introduces new methods for cutting SWNTs that avoid the introduction of the impurity alloy. A Raman spectroscopy technique was also developed which enables the degree of cutting to be tracked. This year we also developed a method for growing SWNTs by chemical vapor deposition from methane that promises, when scaled-up, to produce SWNTs for approximately $1/kg. This latter work will not be discussed here, but will soon be submitted to the peer-reviewed literature.
Heparanase expression in human colorectal cancer and its relationship to tumor angiogenesis, hematogenous metastasis, and prognosis (2004)

These results indicated that Heparanase expression may be an important role in invasion and hematogenous metastasis, and may be a biologic marker of prognostic significance in colorectal cancer patients.
TACE release of TNF-α mediates mechanotransduction-induced activation of p38 MAPK and myogenesis (2007)

Skeletal muscle responds to mechanical stimulation by activating p38 MAPK, a key signal for myogenesis. However, the mechanotransduction mechanism that activates p38 is unknown. Here we show that mechanical stimulation of myoblasts activates p38 and myogenesis through stimulating TNF-alpha release by TNF-alpha converting enzyme (TACE). In C2C12 or mouse primary myoblasts cultured in growth medium, static stretch activated p38 along with ERK1/2, JNK and AKT. Disrupting TNF-alpha signaling by TNF-alpha-neutralizing antibody or knocking out TNF-alpha receptors blocked stretch activation of p38, but not ERK1/2, JNK or AKT. Stretch also activated differentiation markers MEF2C, myogenin, p21 and myosin heavy chain in a TNF-alpha- and p38-dependent manner. Stretch stimulated the cleavage activity of TACE. Conversely, TACE inhibitor TAPI or TACE siRNA abolished stretch activation of p38. In addition, conditioned medium from stretched myoblast cultures activated p38 in unstretched myoblasts, which required TACE activity in the donor myoblasts, and TNF-alpha receptors in the recipient myoblasts. These results indicate that posttranscriptional activation of TACE mediates the mechanotransduction that activates p38-dependent myogenesis via the release of TNF-alpha.
Sentence segmentation and punctuation recovery for spoken language translation (2008)

Sentence segmentation and punctuation recovery are critical components for effective spoken language translation (SLT). In this paper we describe our recent work on sentence segmentation and punctuation recovery for three different language pairs, namely for English-to-Spanish, Arabic-to-English and Chinese-to-English. We show that the proposed approach works equally well in these very different language pairs. Furthermore, we introduce two features computed from the translation beam-search lattice that indicate if phrasal and target language model context is jeopardized when segmenting at a given word boundary. These features enable us to introduce short intra-sentence segments without degrading translation performance.
An efficient reverse link data rate control scheme for 1xEV-DV system (2002)

Increasing demands in various data services need high speed data transmission. The conventional system cannot support these needs and the 1xEV-DO and 1xEV-DV systems, which are optimized for high-speed packet data services, was proposed. To support high speed transmission in the reverse link in these systems, an efficient data rate control scheme is needed. We propose an enhanced reverse link data rate control scheme for increasing reverse link utilization. The proposed scheme enables both dedicated control and group control with consideration of the location of the access terminal. The proposed scheme is validated through simulation. The result shows that the proposed scheme can increase the average data rate and total amount of transmitted data. Also, the delay can be diminished.
Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters (2011)

The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.
Real-time edge-aware image processing with the bilateral grid (2007)

We present a new data structure---the bilateral grid, that enables fast edge-aware image processing. By working in the bilateral grid, algorithms such as bilateral filtering, edge-aware painting, and local histogram equalization become simple manipulations that are both local and independent. We parallelize our algorithms on modern GPUs to achieve real-time frame rates on high-definition video. We demonstrate our method on a variety of applications such as image editing, transfer of photographic look, and contrast enhancement of medical images.
Machine Learning for High-Speed Corner Detection (2006)

Abstract Where feature points are used in real-time frame-rate applications, a high-speed feature detector is necessary. Feature detectors such as SIFT (DoG), Harris and SUSAN are good methods which yield high quality features, however they are too computationally intensive for use in real-time applications of any complexity. Here we show that machine learning can be used to derive a feature detector which can fully process live PAL video using less than 7 % of the available processing time. By comparison neither the Harris detector (120%) nor the detection stage of SIFT (300%) can operate at full frame rate. Clearly a high-speed detector is of limited use if the features produced are unsuitable for downstream processing. In particular, the same scene viewed from two different positions should yield features which correspond to the same real-world 3D locations[1]. Hence the second contribution of this paper is a comparison corner detectors based on this criterion applied to 3D scenes. This comparison supports a number of claims made elsewhere concerning existing corner detectors. Further, contrary to our initial expectations, we show that despite being principally constructed for speed, our detector significantly outperforms existing feature detectors according to this criterion. 1