gebhart/patrepeval huggingface dataset:
A large-scale multi-center independent validation study of a panel of seven biomarkers for the detection of ovarian cancer (2006)

5057 Background: Previously we discovered seven serum biomarkers: ITIH4, transthyretin, ApoA1, CTAPIII, hepcidin, transferrin, and SAA, for the detection of ovarian cancer. They are fragments, cleavages, or PTMs of circulating proteins that are difficult to measure by conventional immunoassays. Using optimzed mass spectrometry assays, we evaluated these biomarkers in a large-scale multi-center study. Methods: A total of 607 serum samples from five sites were analyzed using SELDI TOF-MS protocols optimized for the seven biomarkers. They included 234 women with benign gynecologic diseases, and 373 patients with invasive epithelial ovarian cancer (101 early stage, 231 late stage, and 40 stage unknown). Among them, 165 benigns and 228 cancers had a CA125 available at time of analysis. The median and quartiles of CA125 for benign, early stage, and late or unknown stage were 26/11/57 IU, 80/22/434 IU, and 234/40/1114 IU, respectively. The biomarkers were assessed individually using the Mann-Whitney U Test. A linear composite index was derived in an unsupervised fashion using data from one site and then calculated for the remaining data using the fixed formula. ROC curve analyses were performed on data from individual sites and all sites combined. Results: All seven biomarkers individually demonstrated statistically significant differentiating power, and the majority had p-value<0.00001. AUCs of the composite index in ROC analyses for the six sites were 0.602, 0.566, 0.821, 0.813, and 0.592 in detecting cancer at all stages from benign. On the combined data, the differences in AUC between the index and CA125 were not statistically significant for the detection of cancer at all stages (AUC=0.706 vs. 0.725) or early stages only (AUC=0.534 vs. 0.653). However, the index did better at the high-sensitivity range. At a fixed sensitivity of 86%, the specificity of the index was 34% (77/226) compared to CA125 at 26% (42/163). For early stage cases, at a fixed sensitivity of 84%, the specificity of the index was 24% (55/226) compared to CA125 at 14%% (22/163). Conclusions: We validated seven previously discovered biomarkers, individually and in combination. Prospective studies and assay development are under way to further characterize their clinical utility. [Table: see text]
Single-shot high-quality facial geometry and skin appearance capture (2020)

We propose a new light-weight face capture system capable of reconstructing both high-quality geometry and detailed appearance maps from a single exposure. Unlike currently employed appearance acquisition systems, the proposed technology does not require active illumination and hence can readily be integrated with passive photogrammetry solutions. These solutions are in widespread use for 3D scanning humans as they can be assembled from off-the-shelf hardware components, but lack the capability of estimating appearance. This paper proposes a solution to overcome this limitation, by adding appearance capture to photogrammetry systems. The only additional hardware requirement to these solutions is that a subset of the cameras are cross-polarized with respect to the illumination, and the remaining cameras are parallel-polarized. The proposed algorithm leverages the images with the two different polarization states to reconstruct the geometry and to recover appearance properties. We do so by means of an inverse rendering framework, which solves per texel diffuse albedo, specular intensity, and high-resolution normals, as well as global specular roughness considering the subsurface scattering nature of skin. We show results for a variety of human subjects of different ages and skin typology, illustrating how the captured fine-detail skin surface and subsurface scattering effects lead to realistic renderings of their digital doubles, also in different illumination conditions.
Fiber-optic dc and low-frequency electric-field sensor (1991)

We demonstrate an interferometric fiber-optic dc and low-frequency electric-field sensor based on the electrostrictive effect. The quadratic relationship between the applied electric field E and the induced strain e in electrostrictive ceramics (e.g., Ba:PZT) allows for the detection of low-frequency signals as sidebands of a high-frequency carrier. A preliminary investigation of the sensor has yielded a minimum detectable E field of 0.35 (V/m)/ Hz at 5 Hz for a sensor with 3 cm of fiber.
A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium (2012)

We propose an efficient method for compressing Vietnamese text using <i>n</i>-gram dictionaries. It has a significant compression ratio in comparison with those of state-of-the-art methods on the same dataset. Given a text, first, the proposed method splits it into <i>n</i>-grams and then encodes them based on <i>n</i>-gram dictionaries. In the encoding phase, we use a sliding window with a size that ranges from bigram to five grams to obtain the best encoding stream. Each <i>n</i>-gram is encoded by two to four bytes accordingly based on its corresponding <i>n</i>-gram dictionary. We collected 2.5 GB text corpus from some Vietnamese news agencies to build <i>n</i>-gram dictionaries from unigram to five grams and achieve dictionaries with a size of 12 GB in total. In order to evaluate our method, we collected a testing set of 10 different text files with different sizes. The experimental results indicate that our method achieves compression ratio around 90% and outperforms state-of-the-art methods.
A cobalt-catalyzed steroid synthesis (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA cobalt-catalyzed steroid synthesisRaymond L. Funk and K. Peter C. VollhardtCite this: J. Am. Chem. Soc. 1977, 99, 16, 5483–5484Publication Date (Print):August 1, 1977Publication History Published online1 May 2002Published inissue 1 August 1977https://pubs.acs.org/doi/10.1021/ja00458a044https://doi.org/10.1021/ja00458a044research-articleACS PublicationsRequest reuse permissionsArticle Views918Altmetric-Citations96LEARN 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
<title>keV-electron-based table-top soft x-ray source</title> (2001)

A novel soft X-ray source has been developed that generates soft X-rays of 2.36 nm wavelength. The source is based on focusing a 10 keV electron beam on a continuous jet of water, exciting oxygen K<SUB>(alpha</SUB> ) characteristic radiation. A high-resolution spectrum was recorded which shows a background-free peak at 2.36 nm with a FWHM of 0.017 nm. The brightness of this source is limited by the amount of electron energy that can be dissipated inside the water jet, without endangering the stability of the source. We succeeded in focusing 60 (mu) A onto one side of the jet, at which value the brightness is ~5*10<SUP>8</SUP> photons/(sec sr micrometers <SUP>2</SUP>). The source is of potential interest for use in tabletop soft X-ray microscopy, because the line radiation falls just within the water window, the wavelength region that is employed in this type of microscopy.
ChemInform Abstract: Microchips as Controlled Drug‐Delivery Devices (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals (2004)

Abstract Plants belonging to the legume family develop nitrogen-fixing root nodules in symbiosis with bacteria commonly known as rhizobia. The legume host encodes all of the functions necessary to build the specialized symbiotic organ, the nodule, but the process is elicited by the bacteria1, 2, 3. Molecular communication initiates the interaction, and signals, usually flavones, secreted by the legume root induce the bacteria to produce a lipochitin-oligosaccharide signal molecule (Nod-factor), which in turn triggers the plant organogenic process4, 5, 6, 7. An important determinant of bacterial host specificity is the structure of the Nod-factor, suggesting that a plant receptor is involved in signal perception and signal transduction initiating the plant developmental response8, 9. Here we describe the cloning of a putative Nod-factor receptor kinase gene (NFR5) from Lotus japonicus. NFR5 is essential for Nod-factor perception and encodes an unusual transmembrane serine/threonine receptor-like kinase required for the earliest detectable plant responses to bacteria and Nod-factor. The extracellular domain of the putative receptor has three modules with similarity to LysM domains known from peptidoglycan-binding proteins and chitinases. Together with an atypical kinase domain structure this characterizes an unusual receptor-like kinase.
Translating with Scarce Resources (2000)

Current corpus-based machine translation techniques do not work very well when given scarce linguistic resources. To examine the gap between human and machine translators, we created an experiment in which human beings were asked to translate an unknown language into English on the sole basis of a very small bilingual text. Participants performed quite well, and debriefings revealed a number of valuable strategies. We discuss these strategies and apply some of them to a statistical translation system. Introduction Corpus-based approaches to machine translation (MT) have been on the rise recently, partly because of their promise to automate a great deal of dictionary construction and rule writing, partly because they simply represent a new way of attacking a stubborn problem, and partly because they have performed relatively well in MT evaluations (such as those performed by DARPA and the German Verbmobil program). These approaches generally rely on a large bilingual text cor...
Superconducting optoelectronic loop neurons (2019)

Superconducting optoelectronic hardware has been proposed for large-scale neural computing. In this work, we expand upon the circuit and network designs previously introduced. We investigate circuits using superconducting single-photon detectors and Josephson junctions to perform signal reception, synaptic weighting, and integration. Designs are presented for synapses and neurons that perform integration of rate-coded signals as well as detect coincidence events for temporal coding. A neuron with a single integration loop can receive input from thousands of synaptic connections, and many such loops can be employed for dendritic processing. We show that a synaptic weight can be modified via a superconducting flux-storage loop inductively coupled to the current bias of the synapse. Synapses with hundreds of stable states are designed. Spike-timing-dependent plasticity can be implemented using two photons to strengthen and two photons to weaken the synaptic weight via Hebbian-type learning rules. In addition to the synaptic receiver and plasticity circuits, we describe an amplifier chain that converts the current pulse generated when a neuron reaches threshold to a voltage pulse sufficient to produce light from a semiconductor diode. This light is the signal used to communicate between neurons in the network. We analyze the performance of the elements in the amplifier chain to calculate the energy consumption per photon created. The speed of the amplification sequence allows neuronal firing up to at least 20 MHz, independent of connectivity. We consider these neurons in network configurations to investigate near-term technological potential and long-term physical limitations. By modeling the physical size of superconducting optoelectronic neurons, we calculate the area of these networks. A system with 8100 neurons and 330 430 total synapses will fit on a 1×1cm2 die. Systems of millions of neurons with hundreds of millions of synapses will fit on a 300 mm wafer. For multiwafer assemblies, communication at light speed enables a neuronal pool the size of a large data center (105m2) comprised of trillions of neurons with coherent oscillations at 1 MHz.
Promising Therapy Candidates for Liver Fibrosis (2016)

Liver fibrosis is a wound-healing process in response to repeated and chronic injury to hepatocytes and/or cholangiocytes. Ongoing hepatocyte apoptosis or necrosis lead to increase in ROS production and decrease in antioxidant activity, which recruits inflammatory cells from the blood and activate hepatic stellate cells (HSCs) changing to myofibroblasts. Injury to cholangiocytes also recruits inflammatory cells to the liver and activates portal fibroblasts in the portal area, which release molecules to activate and amplify cholangiocytes. No matter what origin of myofibroblasts, either HSCs or portal fibroblasts, they share similar characteristics, including being positive for α-smooth muscle actin and producing extracellular matrix. Based on the extensive pathogenesis knowledge of liver fibrosis, therapeutic strategies have been designed to target each step of this process, including hepatocyte apoptosis, cholangiocyte proliferation, inflammation, and activation of myofibroblasts to deposit extracellular matrix, yet the current therapies are still in early-phase clinical development. There is an urgent need to translate the molecular mechanism of liver fibrosis to effective and potent reagents or therapies in human.
TLR9 and STING agonists synergistically induce innate and adaptive type‐II IFN (2014)

Agonists for TLR9 and Stimulator of IFN Gene (STING) act as vaccine adjuvants that induce type-1 immune responses. However, currently available CpG oligodeoxynucleotide (ODN) (K-type) induces IFNs only weakly and STING ligands rather induce type-2 immune responses, limiting their potential therapeutic applications. Here, we show a potent synergism between TLR9 and STING agonists. Together, they make an effective type-1 adjuvant and an anticancer agent. The synergistic effect between CpG ODN (K3) and STING-ligand cyclic GMP-AMP (cGAMP), culminating in NK cell IFN-γ (type-II IFN) production, is due to the concurrent effects of IL-12 and type-I IFNs, which are differentially regulated by IRF3/7, STING, and MyD88. The combination of CpG ODN with cGAMP is a potent type-1 adjuvant, capable of inducing strong Th 1-type responses, as demonstrated by enhanced antigen-specific IgG2c and IFN-γ production, as well as cytotoxic CD8(+) T-cell responses. In our murine tumor models, intratumoral injection of CpG ODN and cGAMP together reduced tumor size significantly compared with the singular treatments, acting as an antigen-free anticancer agent. Thus, the combination of CpG ODN and a STING ligand may offer therapeutic application as a potent type-II IFN inducer.
Statistical Pattern Analysis of Partial Discharge Measurements for Quality Assessment of Insulation Systems in High-Voltage Electrical Machinery (2004)

In this paper, we present a new statistical analysis method of phase-resolved partial discharge (PD) measurements for the quality assessment of electrical insulation in high-voltage machinery. The method is based on a supervised classification approach which utilizes histogram similarity analysis. The motivation for choosing histogram similarity analysis is twofold. First, the phase-resolved PD measurement itself is, in fact, a two-dimensional histogram. Therefore, a histogram-matching-based approach suits the very nature of the data. Second, histogram similarity analysis combines the typical statistical parameters, used in PD analysis, in a statistically powerful and rigorous way. In our study, we utilize various histogram types and similarity analysis, including correlation, chi-square, and Kolmogorov-Smirnov tests. Further, we propose a postprocessing method to quantify the accuracy of classification results which enables the user to make soft decisions. Our experimental study on laboratory samples demonstrates that the method shows strong potential in detection and classification of insulation defects. The results from our study suggest that the proposed method provides a powerful, general, and mathematically simple approach to the analysis of phase-resolved PD measurements.
Compendious Concurrent Dual-Band Receiver Based on Multiport Interferometric Architecture (2021)

A distinct usage of the conventional multiport architecture is introduced in this work to explore the compendious scheme of a concurrent dual-band interferometric receiver. Dual RF signals at individual frequency channels are received simultaneously, and only a single low-power local oscillator (LO) source is deployed for frequency translation or conversion to the same intermediate frequency (IF) band. Although these signals are spectrally overlapped, they can be extracted with a simple and efficient algorithm with good channel-to-channel isolations. Compared to the conventional multiport configuration, the power detectors are replaced by analog-to-digital converters (ADCs) to process the signals in this proposed scheme. The underlying physics of the concurrent receiving operation is explained and derived analytically. Some experiments are also presented to investigate various performance indexes, including signal linearity, noise behavior, interchannel interference, and so forth. Lastly, multiple M-quadratic-amplitude modulation (QAM) signals are applied to evaluate the communication behavior of the proposed receiver architecture. Distortions due to frequency drift, channel imbalance, and in-phase and quadrature (IQ) imbalance are studied, and bit-error-rates (BER) are measured and compared with their theoretical counterparts. All obtained results confirm that the proposed interferometric receiver provides good communication performances.
Random Extraction from Compressed Data - A Practical Study (2013)

Modern primary storage systems support or intend to add support for real time compression usually based on some flavor of the LZ77 and/or Huffman algorithm. There is a fundamental tradeoff in adding real time (adaptive) compression to such a system: to get good compression the amount of compressed data (the independently compressed block) should be large, to be able to read quickly from random places the blocks should be small. One idea is to let the independently compressed blocks be large but to be able to start decompressing the needed part of the block from a random location inside the compressed block. We explore this idea and compare it with a few alternatives, experimenting with the \zlib\ code base.
Identification of novel tuberculosis diagnostic biomarkers in plasma and saliva (2016)

There is an urgent need for new tools for the rapid diagnosis of tuberculosis (TB) disease, and monitoring of the response to TB treatment, especially in resource-poor settings. Immunodiagnostic approaches might be beneficial, especially if based on the detection of host biomarkers in easily available samples such as serum, plasma or saliva, as they may be easily adaptable into point-of-care tests. The aim of the current study was to identify such candidate biomarkers. We recruited 22 TB patients and 33 individuals with suspected TB, but in whom TB disease was ruled out, at a health centre in Cape Town, South Africa. Using a multiplex platform, we evaluated the levels of 74 host markers in plasma and saliva samples from these individuals, as candidates for the diagnosis of TB disease or monitoring of TB treatment response. The concentrations of 23 host markers detected in plasma and 5 detected in saliva diagnosed TB disease AUC ≥ 0.80. However, the optimal diagnostic biosignature was a combination of neural cell adhesion molecule (NCAM),IL-17A, thrombopoietin(TPO),complement C4 and transthyretin, which diagnosed TB disease with a sensitivity of 100% and specificity of 86% after leave-one-out cross validation. When compared to baseline levels, multiple host markers detected in plasma and saliva were significantly different between diagnosis and end of TB treatment, thereby indicating that they may be potentially useful in monitoring of TB treatment response. In conclusion, we have identified candidate host biomarkers in plasma and saliva samples, which may be useful in the diagnosis of TB disease and monitoring of the response to TB treatment. Our findings require further validation in larger studies.
Endothelialization of Magnetic Graft Materials using SPION-labeled Endothelial Cells (2010)

Seeding vascular grafts with autologous endothelial cells (EC) has been shown to improve in vivo patency, but high cost and development time have prevented widespread clinical use. A technique for loading EC with superparamagnetic iron‐oxide nanospheres (SPIONs) was recently described. SPION‐loaded EC experience magnetic attractive forces in the presence of sufficient magnetic field gradients. Using a multi‐factorial design of experiments approach, the quantity and spatial distribution of magnetizable metal particles within a poly (ether urethane) matrix were systematically varied to produce unique material specimens. Specimens were seeded with SPION‐loaded ECs, and cell coverage was quantified at various post‐seeding time intervals using micrographic image analysis. The effects of changing design parameters on cell capture and sustained cell viability on magnetic substrates were statistically examined. Magnetized ferrites and samarium cobalt demonstrated cell capture, though cytotoxicity prevented sustained cell growth. Cobalt chromium substrates showed effective cell capture and growth to near complete confluence for up to one month.