gebhart/patrepeval huggingface dataset:
Detection of Hepatocellular Carcinoma in a High-Risk Population by a Mass Spectrometry-Based Test (2021)

Hepatocellular carcinoma (HCC) is one of the fastest growing causes of cancer-related death. Guidelines recommend obtaining a screening ultrasound with or without alpha-fetoprotein (AFP) every 6 months in at-risk adults. AFP as a screening biomarker is plagued by low sensitivity/specificity, prompting interest in discovering alternatives. Mass spectrometry-based techniques are promising in their ability to identify potential biomarkers. This study aimed to use machine learning utilizing spectral data and AFP to create a model for early detection. Serum samples were collected from three separate cohorts, and data were compiled to make Development, Internal Validation, and Independent Validation sets. AFP levels were measured, and Deep MALDI<sup>®</sup> analysis was used to generate mass spectra. Spectral data were input into the VeriStrat<sup>®</sup> classification algorithm. Machine learning techniques then classified each sample as "Cancer" or "No Cancer". Sensitivity and specificity of the test were >80% to detect HCC. High specificity of the test was independent of cause and severity of underlying disease. When compared to AFP, there was improved cancer detection for all tumor sizes, especially small lesions. Overall, a machine learning algorithm incorporating mass spectral data and AFP values from serum samples offers a novel approach to diagnose HCC. Given the small sample size of the Independent Validation set, a further independent, prospective study is warranted.
Antenna-coupled infrared focal plane array (2005)

Uncooled bolometric detectors used in infrared-imaging systems have slow time constants (∼15 ms), which makes them impractical for fast-frame-rate applications. Antenna-coupled microbolometers are fast uncooled detectors with good sensitivity and directivity, and they can be polarization and wavelength selective. These detectors have collection areas in the order of 10 μm2, which are too small for infrared imaging systems where a typical pixel area ranges from 20 × 20 μm2 to 50 × 50 μm2. To solve this problem, 2D arrays of antenna-coupled detectors, which can be used as pixels in infrared-imaging systems, are fabricated. In this paper, antenna-coupled pixels are fabricated on a commercial readout integrated circuit (ROIC), resulting in the first antenna-coupled infrared focal plane array (IR-FPA). Measurements made on this antenna-coupled infrared focal plane array show that the integration of antenna-coupled detectors to a commercial ROIC is possible. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 48: 165–166, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.21294
Uniform and Multizone Liner Results for the International Forum for Aviation Research (2020)

This paper provides detailed results achieved by NASA in response to two liner research challenges supporting the International Forum for Aviation Research (IFAR) collaboration. The IFAR consists of representatives from a number of national research laboratories and is established to enable information exchange on aviation research activities. Over the past three years, members of IFAR have investigated three liner research topics of mutual interest. The first is intended to compare experimental methods and impedance eduction methodologies for evaluation of uniform liners. The second is to evaluate the ability of 3D duct propagation codes to predict the effects of spanwise variable-impedance liners on the acoustic pressure field. The third is to explore different approaches to simultaneously educe the impedances for each zone of a three-zone axially segmented liner. Since each challenge was conducted as a blind test, the NASA paper presented at the 2019 AIAA/CEAS Aeroacoustics Conference was limited to preliminary data for the first and third challenges (detailed NASA results for the second challenge were presented in an earlier paper). The purpose of this paper is to provide more extensive results for these two challenges to enable more thorough comparison with the results from the IFAR partners.
Baculovirus Expression, Purification and Evaluation of Recombinant Pneumococcal Surface Adhesin A of <i>Streptococcus pneumoniae</i> (1999)

Pneumococcal surface adhesin A (PsaA), with a molecular mass of approximately 37 kD by SDS-PAGE, is a common surface protein expressed by all 90 serotypes of Streptococcus pneumoniae. S. pneumoniae serotype 6B genomic DNA was amplified to generate a DNA fragment carrying the full-length psaA sequence and was cloned into a baculovirus expression system. We expressed either cell-associated or cell-free nonfusion PsaA polypeptides using two insect cell lines, Spodoptera frugiperda (Sf9) and Trichoplusia ni 5B1-4 (High-Five). Recombinant PsaA (rPsaA) polypeptides were partially purified by partitioning in PBS/Triton X-114 buffers and by weakly basic ion exchange filter chromatography. Membrane-bound 'hydrophobic rPsaA' (hrPsaA) expressed by either Sf9 or High-Five cells had a molecular mass of approximately 38 kD by SDS-PAGE and partitioned in a Triton X-114 phase, it reacted with both rabbit polyclonal and five monoclonal anti-PsaA antibodies by dot blot or Western blot analysis. High-Five-cell-expressed 'soluble rPsaA' (srPsaA) with a molecular mass of approximately 37 kD by SDS-PAGE, was isolated from the serum-free culture medium and did not partition in the Triton X-114 phase; it reacted with anti-PsaA rabbit polyclonal and mouse monoclonal antibodies by ELISA and Western blot analysis. Both rPsaA polypeptide forms were immunogenic in Swiss-Webster adult female mice. In an infant mouse model of bacteremia, survival rates for mice given mouse anti-rPsaA immune serum (from mice immunized with High-Five-expressed srPsaA; 20 microl, 1:50,000 titer) 24 h before bacteremic challenge were greater than for the control group (48 h postchallenge, 20 vs. 90% survival rates) when challenged with S. pneumoniae serotype 6B. These results indicate that rPsaA is immunogenic and elicits protective antibody in mice similar to native protein.
Mogrol represents a novel leukemia therapeutic, via ERK and STAT3 inhibition. (2015)

Unlike solid tumors, the primary strategy for leukemia treatment is chemotherapy. However, leukemia chemotherapy is associated with adverse drug effects and drug resistance. Therefore, it is imperative to identify novel agents that effectively treat leukemia while minimizing adverse effects. The Raf/MEK/extracellular regulated kinase (ERK) and signal transducer and activator of transcription 3 (STAT3) pathways have been implicated in leukemia carcinogenesis, and provide novel molecular targets for therapeutic intervention in cancer. Mogrol, a biometabolite of mogrosides found in Siraitia grosvenorii, has exhibited anti-cancer activities; however, the underlying mechanism of this effect remains unclear. To clarify its anti-cancer activity and mechanism of action, we treated K562 leukemia cells with mogrol. Mogrol suppressed leukemia cell growth via inhibition of the ERK1/2 and STAT3 pathways, in particular, through the suppression of p-ERK1/2 and p-STAT3. Inhibition of these pathways suppressed Bcl-2 expression, thereby inducing K562 cell apoptosis. Furthermore, mogrol enhanced p21 expression, resulting in G0/G1 cell cycle arrest. The findings provide new perspectives regarding the role of mogrol in leukemia treatment.
Date and their processing byproducts as substrates for bioactive compounds production (2014)

Date is the most popular fruit in middle-east countries. However, the date production process is accompanied by a substantial increase of loss during picking, storage, commercialization and conditioning process. Date and their byproducts have many essential elements for the growth of microorganisms. Thus, they can be converted into value-added compounds through biotechnology. In this paper, date and their processing byproducts used as substrates for producing value-added products such as organic acids, exopolysaccharide, antibiotics, date flavored probiotic fermented dairy, bakery yeast, etc, were reviewed.
Nanoscale Control of Homoepitaxial Growth on a Two‐Dimensional Zeolite (2016)

Nanoscale crystal growth control is crucial for tailoring two-dimensional (2D) zeolites (crystallites with thickness less than two unit cells) and thicker zeolite nanosheets for applications in separation membranes and as hierarchical catalysts. However, methods to control zeolite crystal growth with nanometer precision are still in their infancy. Herein, we report solution-based growth conditions leading to anisotropic epitaxial growth of 2D zeolites with rates as low as few nanometers per day. Contributions from misoriented surface nucleation and rotational intergrowths are eliminated. Growth monitoring at the single-unit-cell level reveals novel nanoscale crystal-growth phenomena associated with the lateral size and surface curvature of 2D zeolites.
Bioplastics from waste glycerol derived from biodiesel industry (2013)

Abstract Polyhydroxyalkanoates (PHAs) are polyesters that can be biologically synthesized by many microorganisms and engineered plants that have been investigated by microbiologists, biochemists, polymer scientists, material engineers, and medical researchers for several decades. Research on microbial production of PHAs has been extensively focused on using pure carbon sources, such as sugars and fatty acids. Practical considerations of production costs of PHAs have resulted in research efforts to use alternative renewable and inexpensive feedstocks. One potential feedstock for the production of PHA polymers is the glycerol waste byproduct of biodiesel production. The major focus of this review is the production of PHA polymers from glycerol. A review of biosynthetic pathways for PHAs production from glycerol, current production of waste glycerol in biodiesel industry, physical and mechanical properties of PHAs, and applications of PHAs in the areas of packaging industry, implant materials, drug carrier, biofuels, are covered. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
The light-scattering whole blood aggregometer: a novel device for assessment of platelet aggregation in undiluted blood. (1998)

The novel light-scattering whole blood aggregometer has been shown to be a valid device to measure platelet aggregation and may be well suited for the assessment of platelet function in research and clinical blood samples.
Epitaxial Growth of Indium Arsenide Nanowires on Silicon Using Nucleation Templates Formed by Self‐Assembled Organic Coatings (2007)

Indium arsenide nanowires are grown directly on silicon substrates (see figure and cover) using a method employing self-assembled organic coatings to create oxide-based growth templates. High-performance materials, such as InAs, could have great impact on future nanoelectronics if integrated with Si, but integration has so far been hard to realize with other methods.
<title>Local resolved spectroscopy at the human ocular fundus in vivo: technique and clinical examples</title> (1996)

Ocular fundus reflectometry is known as a method for the determination of the optical density of pigments at the eye ground. This has been described for diagnostic investigations at single locations. The new technique of imaging spectroscopy enables the recording of one dimensional local distribution of spectra from the fundus which is illuminated confocal to the entrance slit of a spectrograph. A fundus reflectometer consisting of a Zeiss fundus camera, an imaging spectrograph, and an intensified CCD-camera are presented. The local resolved spectra gained by this apparatus are approximated by a mathematical model on the basis of the anatomy of the fundus as a structure of layers with different optical properties. Each spectrum is assumed to be described by a function of the absorption spectra of the pigments found in the retinal and choroidal tissue. Assuming the existence of parameters which are independent from the fundus location we have to approximate the measured local distribution of spectra by a system of coupled non-linear equations. By a least square fit the local distribution of the extinction of melanin, xantophyll and hemoglobin may be obtained as well as the extension of pathologic alterations at the fundus. The benefits of the method for clinical diagnostics are discussed at first measurements from physiological and pathological examples.
Regulation of angiogenesis and choroidal neovascularization by members of microRNA-23∼27∼24 clusters (2011)

MicroRNAs (miRNAs) modulate complex physiological and pathological processes by repressing expression of multiple components of cellular regulatory networks. Here we demonstrate that miRNAs encoded by the miR-23∼27∼24 gene clusters are enriched in endothelial cells and highly vascularized tissues. Inhibition of miR-23 and miR-27 function by locked nucleic acid-modified anti-miRNAs represses angiogenesis in vitro and postnatal retinal vascular development in vivo. Moreover, miR-23 and miR-27 are required for pathological angiogenesis in a laser-induced choroidal neovascularization mouse model. MiR-23 and miR-27 enhance angiogenesis by promoting angiogenic signaling through targeting Sprouty2 and Sema6A proteins, which exert antiangiogenic activity. Manipulating miR-23/27 levels may have important therapeutic implications in neovascular age-related macular degeneration and other vascular disorders.
Passive Inter-Photon Imaging (2021)

Digital camera pixels measure image intensities by converting incident light energy into an analog electrical current, and then digitizing it into a fixed-width binary representation. This direct measurement method, while conceptually simple, suffers from limited dynamic range and poor performance under extreme illumination — electronic noise dominates under low illumination, and pixel full-well capacity results in saturation under bright illumination. We propose a novel intensity cue based on measuring inter-photon timing, defined as the time delay between detection of successive photons. Based on the statistics of inter-photon times measured by a time-resolved single-photon sensor, we develop theory and algorithms for a scene brightness estimator which works over extreme dynamic range; we experimentally demonstrate imaging scenes with a dynamic range of over ten million to one. The proposed techniques, aided by the emergence of single-photon sensors such as single-photon avalanche diodes (SPADs) with picosecond timing resolution, will have implications for a wide range of imaging applications: robotics, consumer photography, astronomy, microscopy and biomedical imaging.
Real-time code-division multi-tag localization with centimeter accuracy (2017)

In conventional indoor passive radio frequency identification (RFID) systems, time-division multiple access (TDMA) protocols are designed to counter multi-path interference and inter-tag collision for digital ID retrieval. However, high-accuracy (centimeter-level and below) localization to track multiple tags simultaneously still awaits a feasible solution. Overlap on the same carrier frequency of the downlink (from reader to tags) and uplink (from tags to reader) leads to severe self-jamming and reader collision, which makes tag localization especially difficult. The present narrow bandwidth also limits the localization accuracy and reliability. Starting from the polling process and synchronization by TDMA, we propose the code division multiple access (CDMA) within the broadband harmonic backscatter RFID system to enable the simultaneous real-time (15 Hz) tag localization with centimeter accuracy and millimeter deviation. We investigate the impacts of the number of tags with respect to the sampling rate, tag power consumption and locating errors originated from the inter-tag collision, and then present an experimental prototype for verification.
New Natural-Product Diversity From Marine Actinomycetes (2007)

There is currently renewed interest in the study of microorganisms as a source of structurally unique and pharmacologically active natural products. Actinomycetes, being the single most productive source of naturally occurring antibiotics, are a logical component of these studies, and success with this group will be enhanced by the inclusion of previously unknown taxa. Recent studies of marine-derived actinomycetes have revealed the widespread distribution of unique marine taxa residing in ocean sediments. Chemical studies of these strains, focusing on members of the new genus Salinospora, have led to a high rate of novel secondary metabolite discovery, including molecules with potent biological activity. Given the encouraging results from preliminary studies of these newly described marine bacteria, it seems clear that marine actinomycetes represent an important future resource for small-molecule drug discovery.
Enhanced Adaptive Interpolation Filters for Video Coding (2010)

H.264/AVC uses motion compensated prediction with fractional-pixel precision to reduce temporal redundancy of the input video signal. It has been shown that the Adaptive Interpolation Filter (AIF) framework [3] can significantly improve accuracy of the motion compensated prediction. In this paper, we present the Enhanced Adaptive Interpolation Filters (E-AIF) scheme, which enhances the AIF framework with a number of useful features, aimed at both improving performance and reducing complexity. These features include the full-pixel position filter and the filter offset, the radial-shaped 12-position filter support, and a RD-based filter selection. Simulations show that E-AIF can achieve up to 20% bit rate reduction compared to H.264/AVC. Compared to all other AIF schemes, E-AIF further reduces the bit rate by up to 6%, and demonstrates the highest performance consistently.
Double Interpolation for Digital-to-Analog Conversion (1986)

Interpolative digital-to-analog converters generate an output that has only a few analog levels. They provide fine resolution by oscillating rapidly between these levels in such a manner that the average output represents the value of the applied code. Here we describe an improved method of interpolating that results in reduced noise in the signal band. A theory of the interpolation, confirmed by experiments, demonstrates that switching between only two levels at 1.3 mHz could provide 16 bit resolution for telephone signals.
Recent Insights into the Molecular Pathogenesis of Huntington Disease (1999)

Huntington disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the HD gene resulting in expression of an uninterrupted polyglutamine stretch within the N-terminus of its protein product huntingtin (htt). In this article we review the clinical, genetic, and neuropathological features of HD and discuss recent insights into the pathogenesis of HD. Examining the role of CAG repeat size on age of onset and penetrance in HD using a refined database of human HD patients has provided further support for the importance of the CAG repeat in the pathogenesis of HD and information leading to a predictive model for the likelihood of being affected by a specific age for a particular CAG expansion. In a YAC transgenic mouse model that replicates key elements of the HD phenotype, the development of selective striatal neurodegeneration is coincident with cleavage of htt and translocation of the N-terminal htt fragment into the nucleus. We also review in vitro evidence that htt is a substrate for cleavage by a group of cysteine proteases involved in apoptotic death-the caspases, and that caspase cleavage of htt results in the generation of a toxic N-terminal fragment. Inhibiting caspase cleavage of huntingtin eliminates the toxicity of the mutant htt protein. These results suggest that cleavage of huntingtin resulting in production of a truncated N-terminal fragment may be a crucial step in the pathogenesis of Huntington disease and that inhibition of this process may be a potential therapeutic strategy for this currently untreatable disorder.
Selective Activation of Sphingosine 1-Phosphate Receptors 1 and 3 Promotes Local Microvascular Network Growth (2010)

Proper spatial and temporal regulation of microvascular remodeling is critical to the formation of functional vascular networks, spanning the various arterial, venous, capillary, and collateral vessel systems. Recently, our group has demonstrated that sustained release of sphingosine 1-phosphate (S1P) from biodegradable polymers promotes microvascular network growth and arteriolar expansion. In this study, we employed S1P receptor-specific compounds to activate and antagonize different combinations of S1P receptors to elucidate those receptors most critical for promotion of pharmacologically induced microvascular network growth. We show that S1P(1) and S1P(3) receptors act synergistically to enhance functional network formation via increased functional length density, arteriolar diameter expansion, and increased vascular branching in the dorsal skinfold window chamber model. FTY720, a potent activator of S1P(1) and S1P(3), promoted a 107% and 153% increase in length density 3 and 7 days after implantation, respectively. It also increased arteriolar diameters by 60% and 85% 3 and 7 days after implantation. FTY720-stimulated branching in venules significantly more than unloaded poly(D, L-lactic-co-glycolic acid). When implanted on the mouse spinotrapezius muscle, FTY720 stimulated an arteriogenic response characterized by increased tortuosity and collateralization of branching microvascular networks. Our results demonstrate the effectiveness of S1P(1) and S1P(3) receptor-selective agonists (such as FTY720) in promoting microvascular growth for tissue engineering applications.
Manipulating Electrical and Fluidic Access in Integrated Nanopore‐Microfluidic Arrays Using Microvalves (2016)

On-chip microvalves regulate electrical and fluidic access to an array of nanopores integrated within microfluidic networks. This configuration allows for on-chip sequestration of biomolecular samples in various flow channels and analysis by independent nanopores.
Inhibitory activity of gold and silica nanospheres to vascular endothelial growth factor (VEGF)-mediated angiogenesis is determined by their sizes (2014)

Nanoparticles can be involved in biological activities such as apoptosis, angiogenesis, and oxidative stress by themselves. In particular, inorganic nanoparticles such as gold and silica nanoparticles are known to inhibit vascular endothelial growth factor (VEGF)-mediated pathological angiogenesis. In this study, we show that anti-angiogenic effect of inorganic nanospheres is determined by their sizes. We demonstrate that 20 nm size gold and silica nanospheres suppress VEGF-induced activation of VEGF receptor-2, in vitro angiogenesis, and in vivo pathological angiogenesis more efficiently than their 100 nm size counterparts. Our results suggest that modulation of the size of gold and silica nanospheres determines their inhibitory activity to VEGF-mediated angiogenesis.