gebhart/patrepeval huggingface dataset:
Discovery of a novel regulatory pathway in cholesterol metabolism (2007)

We recently identified and synthesized a novel sulfated oxysterol, 5‐cholesten‐3β, 25‐diol 3‐sulphate (25HC3S), whose concentration increased dramatically in the mitochondria and the nuclei of primary rat hepatocytes in response to over‐expression of cholesterol mitochondria delivery protein, StarD1. This oxysterol was also found in human liver nuclei. The addition of synthesized 25HC3S to HepG2 cell culture increased cholesterol uptake and inhibited expression of HMG‐CoA reductase, suggesting this nuclear oxysterol is a regulatory molecule. The present study demonstrates a pathway for biosynthesis of 25HC3S in hepatocytes. Assays using mitochondria isolated from rat liver and CYP27A1 − knock out mouse liver indicated that 25‐hydroxycholesterol is synthesized by CYP27A1 in mitochondria. Incubation of mitochondrial and cytosol fractions resulted in synthesis of the sulfated oxysterol. RT‐PCR analysis showed the presence of the highly regulated hydroxycholesterol sulfotransferase 2B1b (SULT2B1b) in hepatocytes. Its expression could be down‐regulated by addition of 25HC3S but not by 25‐hydroxycholesterol. The results indicate that the mitochondria synthesize 25‐OH‐cholesterol which is subsequently 3β‐sulfonated to form 25HC3S. The current findings imply the presence of a regulatory pathway in hepatocytes which play an important role in cholesterol homeostasis.
Nucleophilic Difluoromethylation of Primary Alkyl Halides Using Difluoromethyl Phenyl Sulfone as a Difluoromethyl Anion Equivalent (2004)

A facile and efficient nucleophilic difluoromethylation of primary alkyl halides has been disclosed through a novel nucleophilic substitution-reductive desulfonylation strategy, using difluoromethyl phenyl sulfone as a difluoromethyl anion ("CF(2)H(-)") equivalent.
Optical motion tracking to improve image quality in MRI of the brain (2012)

Magnetic resonance imaging (MRI) of the brain is highly sensitivity to head motion. Prospective motion correction is a promising new method to prevent artifacts resulting from this effect. The image volume is continuously updated based on head tracking information, ensuring that the magnetic fields used for imaging maintain a constant geometric relationship relative to the object. This paper reviews current developments and methods of performing prospective correction. Optical tracking using cameras has major advantages over other methods used to obtain head pose information, as it does not affect the MR imaging process or interfere with the sequence timing. Results show that motion artifacts can be almost completely prevented for most imaging sequences. Despite this success, there are still engineering challenges to be solved before the technique becomes widely accepted in the clinic. These include improvements in miniaturization, marker fixation and MR compatibility.
Flavivirus DNA vaccines: current status and potential. (2001)

The use of DNA-based vaccines is a novel and promising immunization approach for the development of flavivirus vaccines. This approach has been attempted in vaccine development for various virus species, including St. Louis encephalitis, Russian spring-summer encephalitis, Central European encephalitis, dengue serotypes 1 and 2, Murray Valley encephalitis, Japanese encephalitis, and West Nile viruses. However, very little is known about the factors affecting its efficacy. Recently, we demonstrated that a single intramuscular immunization of DNA vaccine of Japanese encephalitis and West Nile viruses protected mice and horses from virus challenge. Administration of these recombinant plasmid vectors resulted in endogenous expression and secretion of extracellular virus-like particles that correlated well with the induction of protective immunity. These results provided evidence that the virus-like particles composed of premembrane/membrane and envelope proteins are essential for eliciting immune responses similar to those induced by live, attenuated virus vaccines. The biosynthesis and protein processing of premembrane/membrane and envelope proteins that preserve the native conformation and glycosylation profiles identical to virion proteins could be determined by the effectiveness of the transmembrane signal sequence located at the amino-terminus of premembrane protein. The use of DNA vaccines in multivalent and/or combination vaccines designed to immunize against multiple flaviviruses is also a promising area of development.
A Device and Method for Sprayer Calibration (1993)

A device and method have been developed and patented for spray calibration. The device can be used to determine the steady-state flow rate of the actual spray liquid. The modular design of the device permits its use with any kind of sprayer utilizing any number of hydraulic nozzles. The device can be used indoors or outdoors without any site contamination.
Quantitative Measurement of Nano‐/Microparticle Endocytosis by Cell Mass Spectrometry (2010)

All present and accounted for? Cell mass spectrometry was used to determine the quantity of both gold and polystyrene nano-/microparticles taken up into cells (see picture). The uptake amounts measured for gold nanoparticles were similar to those determined by inductively coupled plasma mass spectrometry, a technique which can not be used to measure the cellular uptake of nonmetal particles.
Comparison of an in-house PCR assay, direct fluorescence assay and the Roche AMPLICOR Chlamydia trachomatis kit for detection of C. trachomatis (2009)

To improve the control of Chlamydia trachomatis infection in India, a rapid, specific and cost-effective method is much needed. We developed an in-house PCR assay by targeting a unique genomic sequence encoding a protein from the C. trachomatis phospholipase D endonuclease superfamily that produces an amplified fragment of 368 bp. The specificity of the primers was confirmed using genomic DNA from other sexually transmitted disease-causing and related micro-organisms and from humans. The assay was highly sensitive and could detect as low as 10 fg C. trachomatis DNA. Clinical evaluation of the in-house-developed PCR was carried out using 450 endocervical specimens that were divided in two groups. In group I (n=274), in-house PCR was evaluated against the direct fluorescence assay. The resolved sensitivity of the in-house PCR method was 97.22 % compared with 88 % for the direct fluorescent antibody assay. In group II (n=176), the in-house PCR was compared with the commercial Roche AMPLICOR MWP CT detection kit. The resolved sensitivity of the in-house PCR assay reported here was 93.1 % and the specificity was 97.46 %, making it a cost-effective alternative for routine diagnosis of genital infection by C. trachomatis. The method should facilitate early detection leading to better prevention and treatment of genital infection in India.
An enzyme immunoassay for galactosyltransferase isoenzyme II, and its clinical application to cancer diagnosis (1990)

In this "sandwich"-type enzyme immunoassay of galactosyltransferase isoenzyme II (GT-II), we used the monoclonal antibody MAb 3872 previously established and characterized to be specific for GT-II. Plastic beads coated with MAb 3872 were incubated with serum and buffer, washed, then incubated with MAb 3872 conjugated with horseradish peroxidase and again washed. Peroxidase activity remaining on the beads was measured by color development with o-phenylenediamine. The assay standard curve was linear from 0 to 150 kU/L. Inter- and intra-assay CVs were less than 9% and less than 7%, respectively. Mean GT-II values for 370 normal controls were 6.8 (SD 3.4) kU/L with no significant sex-, smoking-, or blood-type-related differences. We also assayed serum from patients with 11 different cancers or with matched benign diseases. The diagnostic sensitivity of GT-II for liver and esophageal cancer was 0.91 and 0.72, respectively, apparently higher than for carcinoembryonic antigen (CEA) or alpha-fetoprotein. GT-II and CEA concentrations in sera were not correlated. Evidently this assay may be useful as a cancer diagnostic test to supplement existing serological methods.
Heterologous prime–boost vaccinations for poverty-related diseases: advantages and future prospects (2009)

Classical vaccination approaches, based on a single vaccine administered in a homologous prime–boost schedule and optimized to induce primarily neutralizing antibodies, are unlikely to be sufficiently efficacious to prevent TB, malaria or HIV infections. Novel vaccines, capable of inducing a more powerful immune response, in particular T-cell immunity, are desperately needed. Combining different vaccine modalities that are able to complement each other and induce broad and sustainable immunity is a promising approach. This review provides an overview of heterologous prime–boost vaccination modalities currently in development for the ‘big three’ poverty-related diseases and emphasizes the need for innovative vaccination approaches.
Efficient up-conversion pumping at 800 nm of an erbium-doped fluoride fibre laser operating at 850 nm (1990)

An erbium-doped fluorozirconate fibre laser has been constructed which uses up-conversion pumping at 801 nm to excite a higher-level laser transition at 850 nm. A slope efficiency of 38% was measured.
Quantifying accuracy and heterogeneity in single-molecule super-resolution microscopy (2020)

The resolution and accuracy of single-molecule localization microscopes (SMLMs) are routinely benchmarked using simulated data, calibration rulers, or comparisons to secondary imaging modalities. However, these methods cannot quantify the nanoscale accuracy of an arbitrary SMLM dataset. Here, we show that by computing localization stability under a well-chosen perturbation with accurate knowledge of the imaging system, we can robustly measure the confidence of individual localizations without ground-truth knowledge of the sample. We demonstrate that our method, termed Wasserstein-induced flux (WIF), measures the accuracy of various reconstruction algorithms directly on experimental 2D and 3D data of microtubules and amyloid fibrils. We further show that WIF confidences can be used to evaluate the mismatch between computational models and imaging data, enhance the accuracy and resolution of reconstructed structures, and discover hidden molecular heterogeneities. As a computational methodology, WIF is broadly applicable to any SMLM dataset, imaging system, and localization algorithm.
A novel high speed low power logic family: Race logic (2000)

A new logic family, Race Logic, is proposed for high speed and low power applications. Race Logic does not use transistors but utilise timing difference between two racing signals to implement boolean logic operations. Because the number of transistors is very small compared to conventional logic styles, delay time from clock to output is very small and the power consumption is also minimized. Various kinds of combinational circuits are simulated, and a 64bit carry look-ahead adder is fabricated using Race Logic.
Metal–Organic Frameworks Stabilize Mono(phosphine)–Metal Complexes for Broad-Scope Catalytic Reactions (2016)

Mono(phosphine)-M (M-PR3; M = Rh and Ir) complexes selectively prepared by postsynthetic metalation of a porous triarylphosphine-based metal-organic framework (MOF) exhibited excellent activity in the hydrosilylation of ketones and alkenes, the hydrogenation of alkenes, and the C-H borylation of arenes. The recyclable and reusable MOF catalysts significantly outperformed their homogeneous counterparts, presumably via stabilizing M-PR3 intermediates by preventing deleterious disproportionation reactions/ligand exchanges in the catalytic cycles.
Aminoalkylation of 10‐Hydroxycamptothecin Using Methylene Chloride Under Solid–Liquid Phase Transfer Catalysis: A New Approach for the Preparation of Topotecan (2004)

Abstract The use of dichloromethane as a reagent, for the preparation of Topotecan {(4S)‐10‐(dimethylamino)methyl‐4‐ethyl‐4,9‐dihydroxy‐1‐H‐pyrano[3′,4′:6,7]indolizino‐[1,2‐b]quinoline‐3,14(4H,12H)dione} from 10‐hydroxy‐camptothecin under solid–liquid phase transfer catalysis, which behaves both as a solvent and a reagent serving as for C‐1 unit source for amino‐alkylation of 10‐hydroxy‐(4S)‐camptothecin.
Low-Energy Distillation-Membrane Separation Process (2010)

A low-energy separation process combining distillation and membrane vapor permeation is introduced as an alternative to conventional distillation. The process can be applied to any liquid mixture for which appropriate selective membranes are available. However, in this paper, the discussion is limited to water/organic solvent mixtures using membranes that preferentially permeate water. Such membranes are available. The process is illustrated with two mixtures: ethanol (light component)/water (heavy component) and acetic acid (heavy component)/water (light component) mixtures. In both cases, the combination process reduces the energy consumption of the separation to half that of simple distillation.
Optofluidic surface-enhanced Raman spectroscopy with nanoparticle-functionalized flow-through multihole capillary (2012)

Surface-enhanced Raman scattering (SERS) has emerged as a powerful analytical technique for direct detection of chemical and biological analytes because of high sensitivity, selectivity, and rapid response. Here we propose and develop a novel optofluidic SERS structure, i.e., nanoparticle-functionalized flow-through multihole capillary. This unique platform provides many advantages. First, its 3-dimensional (3-D) structure, similar to nanoporous aluminum membranes, nanoporous polymer monoliths, and photonic crystal fibers (PCFs), provides large surface area for the deposition of noble nanoparticles or nanoclusters to achieve high SERS intensity. Second, it has well-defined flow-through channels. It provides robust and controllable nanoparticle immobilization like PCFs, but much higher nanoparticle density thus large SERS-active sites due to large surface within the detection volume, and also enables fast and convenient analyte delivery for real-time, online detection. Third, the well-defined multihole capillary can also confine and transmit light along the longitudinal direction, accumulating large SERS signal like PCFs. Fourth, it is easy to integrate with other sensing platforms, such as label-free biosensors, to provide comprehensive information on molecular interaction. Moreover, the multihole capillary can be mass-produced easily and cost effectively using the fiber drawing method. In this report, using a capillary consisting of thousands of micrometer-sized holes adsorbed with gold nanoparticles, we investigated the proposed optofluidic SERS system using the transverse and longitudinal detection methods, where the SERS excitation and collection were perpendicular to and along the capillary, respectively. A detection limit better than 100 fM for rhodamine 6G was achieved with an enhancement factor exceeding 10<sup>8</sup>.
Laser Created X-Ray Sources For Microlithography (1986)

Laser created X-ray sources have been investigated both theoretically and experimentally using λ = 1.06 μm and λ = 0.26 μm and short pulses (0.5 nsec). Some preliminary results are given with UV radiation obtained with a long pulse (25 nsec) excimer laser. The con-version efficiency of the X-ray emission in the sub-keV (0.1-0.75 keV) and keV (0.75-2 keV) ranges is given for various atomic numbers and a large range of laser intensities. Using these results and resist sensitivities, we discuss the characteristics of the laser required for X-ray lithography.
Built-In Self-Test for Automatic Analog Frequency Response Measurement (2005)

We present a built-in self-test (BIST) approach, based on a direct digital synthesizer (DDS), for functional test of analog circuitry in mixed-signal systems. DDS with delta-sigma noise shaping is used to generate test signals with different frequencies and phases. The DDS-based BIST hardware implementation can sweep the frequencies through the interested bands and thus measure the frequency response of the analog circuit. The proposed BIST approach has been implemented in Verilog and synthesized into a field programmable gate array (FPGA). The actual device under test (DUT) was implemented using a field programmable analog array (FPAA) to form a complete BIST testbed for analog functional tests.
A fiber-coupled erbium-doped microsphere laser (2000)

Summary form only given. Optical microsphere cavities, with their very high quality-factor and sub-millimeter dimensions, are attractive new building block for fiber optics and photonics. A microsphere made of laser-active material, with an efficient optical pumping scheme, can be configured as a miniature solid-state laser. Because of the small volume and high Q of whispering-gallery modes, microsphere lasers can combine very low threshold and narrow emission linewidth. Early reports demonstrated the stimulated emission in dye-doped polysterene spheres with relatively low-Q of /spl sim/10/sup 4/ and free-beam pumping/outcoupling. Reports of high-Q microspheres acting as laser cavities were focused on the achievement of extremely low threshold for laser operation with Nd ions. The 1.56 nm lasing in Er-doped ZBLAN spheres have been reported with pumping and outcoupling by means of bulky prism couplers. We present a miniature design that utilizes a novel angle-polished single-mode fiber coupler for both delivering pump power into the sphere and the pickup of laser radiation.
Review of trench and via plasma etch issues for copper dual damascene in undoped and fluorine-doped silicate glass oxide (2003)

Dual damascene dielectric etch technology is emerging as a key enabler for advanced integration schemes. Early implementations of copper dual damascene processes favored the trench-first approach. This approach has now been largely superseded by the via-first scheme for technology nodes below 250 nm. Several etch issues typically arise when implementing either of these approaches. The via-first approach can lead to either via veils or excessive faceting problems when the trench is etched. The traditional trench-first approach requires long via overetches and very high selectivity to the underlayer so that allowance can be made for vias that are misaligned or placed outside the trenches. Trench-first lithography employing organic resists often requires patterning over nonplanar surfaces, which can result in narrow process windows. Both the via-first and trench-first approaches increasingly require etching the trench without a stop layer. This places exacting demands on etch uniformity, etch front control, and sidewall profile angle control. Control of these issues is enhanced when the etch mechanisms responsible for driving them are understood. These and other issues as well as the current understanding of the relevant mechanisms are discussed for implementing copper dual damascene structures in plasma enhanced chemical vapor deposition undoped silicate glass or fluorinated silicate glass oxide films.
Bacterial Nitric-oxide Synthases Operate without a Dedicated Redox Partner (2008)

Bacterial nitric-oxide (NO) synthases (bNOSs) are smaller than their mammalian counterparts. They lack an essential reductase domain that supplies electrons during NO biosynthesis. This and other structural peculiarities have raised doubts about whether bNOSs were capable of producing NO in vivo. Here we demonstrate that bNOS enzymes from Bacillus subtilis and Bacillus anthracis do indeed produce NO in living cells and accomplish this task by hijacking available cellular redox partners that are not normally committed to NO production. These "promiscuous" bacterial reductases also support NO synthesis by the oxygenase domain of mammalian NOS expressed in Escherichia coli. Our results suggest that bNOS is an early precursor of eukaryotic NOS and that it acquired its dedicated reductase domain later in evolution. This work also suggests that alternatively spliced forms of mammalian NOSs lacking their reductase domains could still be functional in vivo. On a practical side, bNOS-containing probiotic bacteria offer a unique advantage over conventional chemical NO donors in generating continuous, readily controllable physiological levels of NO, suggesting a possibility of utilizing such live NO donors for research and clinical needs.
Photonic reservoir computing: a new approach to optical information processing (2010)

Despite ever increasing computational power, recognition and classification problems remain challenging to solve. Recently, advances have been made by the introduction of the new concept of reservoir computing. This is a methodology coming from the field of machine learning and neural networks that has been successfully used in several pattern classification problems, like speech and image recognition. Thus far, most implementations have been in software, limiting their speed and power efficiency. Photonics could be an excellent platform for a hardware implementation of this concept because of its inherent parallelism and unique nonlinear behaviour. Moreover, a photonic implementation offers the promise of massively parallel information processing with low power and high speed. We propose using a network of coupled Semiconductor Optical Amplifiers (SOA) and show in simulation that it could be used as a reservoir by comparing it to conventional software implementations using a benchmark speech recognition task. In spite of the differences with classical reservoir models, the performance of our photonic reservoir is comparable to that of conventional implementations and sometimes slightly better. As our implementation uses coherent light for information processing, we find that phase tuning is crucial to obtain high performance. In parallel we investigate the use of a network of photonic crystal cavities. The coupled mode theory (CMT) is used to investigate these resonators. A new framework is designed to model networks of resonators and SOAs. The same network topologies are used, but feedback is added to control the internal dynamics of the system. By adjusting the readout weights of the network in a controlled manner, we can generate arbitrary periodic patterns.
MPEG-DASH MPD for Tile-based Hybrid Stereoscopic 360-degree Video Streaming (2018)

In this paper, we propose tile-based hybrid stereoscopic 360° video streaming service, in which low-quality 2D, high-quality 2D and 3D services can be provided by a single scalable HEVC (SHVC) en/decoder. In addition to this, its associated MPEG-DASH media presentation description (MPD) signaling is also presented as an example.
Unmanned Aircraft System Traffic Management (UTM) Concept of Operations (2016)

Many applications of small Unmanned Aircraft System (sUAS) have been envisioned. These include surveillance of key assets such as pipelines, rail, or electric wires, deliveries, search and rescue, traffic monitoring, videography, and precision agriculture. These operations are likely to occur in the same airspace in presence of many static and dynamic constraints such as airports, and high wind areas. Therefore, small UAS, typically 55 pounds and below, operations need to be managed to ensure safety and efficiency of operations is maintained. This paper will describe the Concept of Operations (ConOps) for NASA's UAS Traffic Management (UTM) research initiative. The UTM ConOps is focused on safely enabling large-scale small UAS (sUAS) operations in low altitude airspace. The UTM construct supports large-scale visual line of sight and beyond visual line of sight operations. It is based on two primary mantras: (1) flexibility where possible and structure where necessary (2) a risk-based approach where geographical needs and use case indicate the airspace performance requirements. Preliminary stakeholder feedback and initial UTM tests conducted by NASA show promise of UTM to enable large-scale low altitude UAS operations safely.