gebhart/patrepeval huggingface dataset:
Tailored Ahp‐cyclodepsipeptides as Potent Non‐covalent Serine Protease Inhibitors (2017)

The S1 serine protease family is one of the largest and most biologically important protease families. Despite their biomedical significance, generic approaches to generate potent, class-specific, bioactive non-covalent inhibitors for these enzymes are still limited. In this work, we demonstrate that Ahp-cyclodepsipeptides represent a suitable scaffold for generating target-tailored inhibitors of serine proteases. For efficient synthetic access, we developed a practical mixed solid- and solution-phase synthesis that we validated through performing the first chemical synthesis of the two natural products Tasipeptin A and B. The suitability of the Ahp-cyclodepsipeptide scaffold for tailored inhibitor synthesis is showcased by the generation of the most potent human HTRA protease inhibitors to date. We anticipate that our approach may also be applied to other serine proteases, thus opening new avenues for a systematic discovery of serine protease inhibitors.
Development of fiber optical sensor with resonator (2008)

An optical fiber sensor based on evanescent wave sensing and excitation light resonance using a pair of optical reflectors adjacent to two ends of the optical fiber is presented. Excitation light is coupled into the fiber optical sensor through a hole in the first reflector. The excitation light starts to resonate between the reflectors, and results in the amplification of the fluorescent signal, which is generated by the excitation of the analyte binding to the surface of the active fiber sensing area. This device was successfully demonstrated in achieving over 600% amplification in the output signal. This design provides a simple and efficient method in improving the S/N and the sensitivity of the optical fiber evanescent wave sensor over the traditional approach.
Three-dimensional and high-speed swept-source optical coherence tomography for in vivo investigation of human anterior eye segments (2005)

A two- and three-dimensional swept source optical coherence tomography (SS-OCT) system, which uses a ready-to-ship scanning light source, is demonstrated. The light source has a center wavelength of 1.31 mum, -3 dB wavelength range of 110 nm, scanning rate of 20 KHz, and high linearity in frequency scanning. This paper presents a simple calibration method using a fringe analysis technique for spectral rescaling. This SS-OCT system is capable of realtime display of two-dimensional OCT and can obtain three-dimensional OCT with a measurement time of 2 s. In vivo human anterior eye segments are investigated two- and three-dimensionally. The system sensitivity is experimentally determined to be 114 dB. The three-dimensional OCT volumes reveal the structures of the anterior eye segments, which are difficult to observe in two-dimensional OCT images.
A low-frequency model for wedge or pyramid absorber arrays-I: theory (1994)

The interaction of electromagnetic waves with an array of absorbing wedges or pyramid cones is studied in the low-frequency limit; i.e., when the period of the array is small compared with wavelength. A theoretical model is obtained using the method of homogenization, which replaces the transversely periodic structure with a transversely uniform medium possessing a certain (generally anisotropic) effective permittivity and permeability. Plane-wave reflection from such structures can then be modeled using well-known techniques for one-dimensionally inhomogeneous media; a Riccati equation for the reflection coefficient is used in this work. This model is appropriate for use with absorbers found in anechoic chambers used for electromagnetic compatibility and electromagnetic interference (EMC/EMI) measurements over the frequency range of 30-1000 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Liquid chromatography‐mass spectrometry interface–I: The direct introduction of liquid solutions into a chemical ionization mass spectrometer (1973)

Abstract Mass spectra of solutes can be obtained by direct introduction of the solution into a chemical ionization source. This should facilitate direct monitoring of the effluent from liquid chromatography columns with nanogram sensitivity.
0°–360° bistable nematic liquid crystal display with large dΔn and high contrast (2000)

A new mode of 0°–360° bistable twisted nematic (BTN) liquid crystal display is developed by using a parameter space method. This new mode possesses a large dΔn value that provides a possibility of using a 4.8–7 μm cell gap and a 6.5 V operating voltage for the new 0°–360° BTN cells. The high-contrast ratios above 80 within −80°–80° viewing-angle ranges are obtained experimentally in a horizontal direction, and the highest contrast ratio achieved is up to 250. In the contrast ratio, the experiment’s results concur with the simulation results.
Low complexity adaptive code tracking with improved multipath resolution for DS-CDMA communications over fading channels (2002)

A new adaptive timing error detector (TED) embedded in a code-tracking loop for RAKE reception of direct sequence-CDMA signals is presented. The loop consists of a digital coherent TED and a loop filter with lowpass characteristic. In a multipath fading environment, one such loop can be allocated for each finger in a RAKE receiver and the interference from adjacent paths can be mitigated by adaptively prefiltering the signal prior to the correlation process. The filter coefficients are computed online in order to minimize an interference cost function. Multipaths whose delays differ by as little as one chip duration become resolvable and can be tracked, resulting in significant performance gains of the overall system, especially if the channel delay spread is small. The tracking performance of the proposed loop is assessed by computer simulation.
Erythromycin a oxime 11,12-carbonate and its oxime ethers. (1989)

Erythromycin A oxime 11,12-carbonate (5a) and its oxime ethers 5b approximately 5p have been prepared and their antibacterial activities compared with those of erythromycin A (1) and its 11,12-carbonate 2. The oxime 5a and many of its oxime ether derivatives showed good activity in vitro against Gram-positive and the more permeable Gram-negative organisms, in some cases being even more active than the carbonate 2.
A novel target-field method for finite-length magnetic resonance shim coils: I. Zonal shims (2001)

This paper presents a new approach for the design of genuinely finite-length shim and gradient coils, intended for use in magnetic resonance imaging equipment. A cylindrical target region is located asymmetrically, at an arbitrary position within a coil of finite length. A desired target field is specified on the surface of that region, and a method is given that enables winding patterns on the surface of the coil to be designed, to produce the desired field at the inner target region. The method uses a minimization technique combined with regularization, to find the current density on the surface of the coil. The method is illustrated for linear, quadratic and cubic magnetic target fields located asymmetrically within a finite-length coil.
Apparatus for removing organic contaminants from inorganic-rich mineral solids. [Removing oil from oil-contaminated drill cuttings] (1984)

Method and apparatus for removing oil and other organic constituents from particulate, inorganic-rich mineral solids. The method and apparatus are particularly suitable for removing oil from oil-contaminated drill cuttings. The solids to be treated are transferred into pressure vessel means wherein they are contacted with an extractant which is normally a gas but is under conditions of pressure and temperature to provide the extractant in a fluidic solvent state for the constituents to be removed, whereby the constituents are transferred to the extractant. The extractant containing the constituents is withdrawn from the pressure vessel and depressurized to render it a nonsolvent for the constituents and to form a two-phase system which can then be separated into extractant for repressurizing and recycling with proper handling of the constituents removed. In the case of removing oil from drill cuttings, the essentially oil-free cuttings can be disposed of in any suitable manner including dumping overboard from an offshore drilling rig.
Endoglycosidase S enables a highly simplified clinical chemistry assay procedure for direct assessment of serum IgG undergalactosylation in chronic inflammatory disease (2018)

Abstract Over the past 30 years, it has been firmly established that a wide spectrum of (autoimmune) diseases such as rheumatoid arthritis, Crohn’s and lupus, but also other pathologies like alcoholic and non-alcoholic steatohepatitis (ASH and NASH) are driven by chronic inflammation and are hallmarked by a reduced level of serum IgG galactosylation. IgG (under)galactosylation is a promising biomarker to assess disease severity, and monitor and adjust therapy. However, this biomarker has not been implemented in routine clinical chemistry due to a complex analytical procedure that necessitates IgG purification, which is difficult to perform and validate at high throughput. We addressed this issue by using endo-β-N-acetylglucosaminidase from Streptococcus pyogenes (endoS) to specifically release Fc N-glycans in whole serum. The entire assay can be completed in a few hours and only entails adding endoS and labeling the glycans with APTS. Glycans are then readily analyzed through capillary electrophoresis. We demonstrate in two independent patient cohorts that IgG undergalactosylation levels obtained with this assay correlate very well with scores calculated from PNGaseF-released glycans of purified antibodies. Our new assay allows to directly and specifically measure the degree of IgG galactosylation in serum through a fast and completely liquid phase protocol, without the requirement for antibody purification. This should help advancing this biomarker towards clinical implementation.
Estimation of contour motion and deformation for nonrigid object tracking (2007)

We present an algorithm for nonrigid contour tracking in heavily cluttered background scenes. Based on the properties of nonrigid contour movements, a sequential framework for estimating contour motion and deformation is proposed. We solve the nonrigid contour tracking problem by decomposing it into three subproblems: motion estimation, deformation estimation, and shape regulation. First, we employ a particle filter to estimate the global motion parameters of the affine transform between successive frames. Then we generate a probabilistic deformation map to deform the contour. To improve robustness, multiple cues are used for deformation probability estimation. Finally, we use a shape prior model to constrain the deformed contour. This enables us to retrieve the occluded parts of the contours and accurately track them while allowing shape changes specific to the given object types. Our experiments show that the proposed algorithm significantly improves the tracker performance.
A Fuzzy Logic Method for Improved Moment Estimation from Doppler Spectra (1998)

A new method for estimating moments from wind measurement devices that measure Doppler spectra as a function of range is presented. Quite often the spectra are contaminated by a wide variety of sources, including (but not limited to) birds, aircraft, velocity and range folding, radio frequency interference, and ground clutter. These contamination sources can vary in space, time, and even in their basic characteristics. Human experts analyzing Doppler spectra can often identify the desired atmospheric signal among the contamination. However, it is quite difficult to build automated algorithms that can approach the skill of the human expert. The method described here relies on mathematical analyses, fuzzy logic synthesis, and global image processing algorithms to mimic the human expert. Fuzzy logic is a very simple, robust, and efficient technique that is well suited to this type of feature extraction problem. These new moment estimation algorithms were originally designed for boundary layer wind profilers; however, they are quite general and have wide applicability to any device that measures Doppler spectra as a function of range (e.g., lidars, sodars, and weather radars).
Prospects for magnetic field communications and location using quantum sensors (2017)

Signal attenuation limits the operating range in wireless communications and location. To solve the reduced range problem, we can use low-frequency signals in combination with magnetic sensing. We propose the use of an optically pumped magnetometer as a sensor and realize a proof-of-principle detection of binary phase shift keying (BPSK) modulated signals. We demonstrate a ranging enhancement by exploiting both the magnetometer's intrinsic sensitivity of below 1 pT/Hz<sup>1/2</sup> and its 1 kHz operating bandwidth through the use of BPSK signals.
Protection against Brucella abortus in mice with O-polysaccharide-specific monoclonal antibodies (1986)

Mice injected with either of two monoclonal antibodies specific for the O polysaccharide of Brucella abortus prior to challenge infection had viable counts in spleens and livers significantly below those in control groups 1 and 4 weeks later. Two monoclonal antibodies specific for the porin of B. abortus failed to confer protection.
Erroneous automated optical platelet counts in 1‐hour post‐transfusion blood samples (2008)

Thrombocytopenic patients with acute leukemia may show high post-transfusion count increments that significantly exceed the number of transfused platelets. This study demonstrates that the automated hematology analyzer Sysmex XE-2100 reports erroneously high optical platelet counts when the blood sample contains particles in the size range of platelets or smaller. Thrombocytopenic or low-normal whole blood samples were spiked with 1 mum latex beads (n = 14) to mimic contaminants under controlled conditions. Optical and impedance measurements of spiked and control samples with the Sysmex XE-2100 were compared with the Advia 120 and the manual counts. The added beads unexpectedly increased the automated optical platelet counts in the Sysmex XE-2100 and, to a lesser extent, the Advia 120 (Wilcoxon signed ranks test, P < 0.05), while the beads were not included in the impedance or the manual microscopic platelet counts. Differential interference contrast microscopy was used to investigate samples from platelet concentrates for transfusion. Platelet concentrates (32/128) were identified as possible sources for particles that were microscopically distinct from platelets but would be included in the automated optical count. Transfusion of platelet concentrates containing contaminating particles can lead to unexpectedly high post-transfusion platelet counts and misdiagnosis of thrombocytopenic patients.
Calculation of shear stiffness in noise dominated magnetic resonance elastography data based on principal frequency estimation (2011)

Magnetic resonance elastography (MRE) is a non-invasive phase-contrast-based method for quantifying the shear stiffness of biological tissues. Synchronous application of a shear wave source and motion encoding gradient waveforms within the MRE pulse sequence enable visualization of the propagating shear wave throughout the medium under investigation. Encoded shear wave-induced displacements are then processed to calculate the local shear stiffness of each voxel. An important consideration in local shear stiffness estimates is that the algorithms employed typically calculate shear stiffness using relatively high signal-to-noise ratio (SNR) MRE images and have difficulties at an extremely low SNR. A new method of estimating shear stiffness based on the principal spatial frequency of the shear wave displacement map is presented. Finite element simulations were performed to assess the relative insensitivity of this approach to decreases in SNR. Additionally, ex vivo experiments were conducted on normal rat lungs to assess the robustness of this approach in low SNR biological tissue. Simulation and experimental results indicate that calculation of shear stiffness by the principal frequency method is less sensitive to extremely low SNR than previously reported MRE inversion methods but at the expense of loss of spatial information within the region of interest from which the principal frequency estimate is derived.
Driver State Monitor from DELPHI (2005)

We present an automotive-grade, real-time, vision-based driver state monitor. Upon detecting and tracking the driver's facial features, the system analyzes eye-closures and head pose to infer his/her fatigue or distraction. This information is used to warn the driver and to modulate the actions of other safety systems. The purpose of this monitor is to increase road safety by preventing drivers from falling asleep or from being overly distracted, and to improve the effectiveness of other safety systems.
Generation of Nyquist sinc pulses using intensity modulators (2013)

Optical sinc-shaped Nyquist pulses are produced based on the generation of an ideal frequency comb using cascaded intensity modulators. Nyquist pulses with 9.8-ps temporal width, 82-fs jitter and more than 40 dB SNR are achieved.
Vaporized Hydrogen Peroxide (VHP) Decontamination of VX, GD, and HD (2003)

Vaporized Hydrogen Peroxide (VHP) has been utilized for more than a decade to sterilize clean rooms and pharmaceutical processing equipment and, quite recently, to decontaminate anthrax-ridden buildings. VHP is also suitable for the decontamination of VX and HD, which readily converts these agents to ethyl methylphosphonic acid and bis(2-chloroethyl) sulfoxide, respectively. However, GD is quite stable in the presence of VHP. The simple addition of low-levels of ammonia gas renders VHP reactive towards GD, converting it pinacolyl methylphosphonic acid. Thus, with suitable activation via ammonia gas, VHP affords the broad-spectrum decontamination of VX, GD, and HD. Potential decontamination applications for this gaseous reactant system include: buildings, vehicle and aircraft interiors, and sensitive equipment.
α-Tocopherol Transfer Protein Is Important for the Normal Development of Placental Labyrinthine Trophoblasts in Mice (2001)

Alpha-tocopherol transfer protein (alpha-TTP), a cytosolic protein that specifically binds alpha-tocopherol, is known as a product of the causative gene in patients with ataxia that is associated with vitamin E deficiency. Targeted disruption of the alpha-TTP gene revealed that alpha-tocopherol concentration in the circulation was regulated by alpha-TTP expression levels. Male alpha-TTP(-/-) mice were fertile; however, placentas of pregnant alpha-TTP(-/-) females were severely impaired with marked reduction of labyrinthine trophoblasts, and the embryos died at mid-gestation even when fertilized eggs of alpha-TTP(+/+) mice were transferred into alpha-TTP(-/-) recipients. The use of excess alpha-tocopherol or a synthetic antioxidant (BO-653) dietary supplement by alpha-TTP(-/-) females prevented placental failure and allowed full-term pregnancies. In alpha-TTP(+/+) animals, alpha-TTP gene expression was observed in the uterus, and its level transiently increased after implantation (4.5 days postcoitum). Our results suggest that oxidative stress in the labyrinth region of the placenta is protected by vitamin E during development and that in addition to the hepatic alpha-TTP, which governs plasma alpha-tocopherol level, the uterine alpha-TTP may also play an important role in supplying this vitamin.
Mapping of magnetic resonance imaging’s transverse relaxation time at low signal‐to‐noise ratio using Bloch simulations and principal component analysis image denoising (2022)

High-resolution mapping of magnetic resonance imaging (MRI)'s transverse relaxation time (T<sub>2</sub> ) can benefit many clinical applications by offering improved anatomic details, enhancing the ability to probe tissues' microarchitecture, and facilitating the identification of early pathology. Increasing spatial resolutions, however, decreases data's signal-to-noise ratio (SNR), particularly at clinical scan times. This impairs imaging quality, and the accuracy of subsequent radiological interpretation. Recently, principal component analysis (PCA) was employed for denoising diffusion-weighted MR images and was shown to be effective for improving parameter estimation in multiexponential relaxometry. This study combines the Marchenko-Pastur PCA (MP-PCA) signal model with the echo modulation curve (EMC) algorithm for denoising multiecho spin-echo (MESE) MRI data and improving the precision of EMC-generated single T<sub>2</sub> relaxation maps. The denoising technique was validated on simulations, phantom scans, and in vivo brain and knee data. MESE scans were performed on a 3-T Siemens scanner. The acquired images were denoised using the MP-PCA algorithm and were then provided as input for the EMC T<sub>2</sub> -fitting algorithm. Quantitative analysis of the denoising quality included comparing the standard deviation and coefficient of variation of T<sub>2</sub> values, along with gold standard SNR estimation of the phantom scans. The presented denoising technique shows an increase in T<sub>2</sub> maps' precision and SNR, while successfully preserving the morphological features of the tissue. Employing MP-PCA denoising as a preprocessing step decreases the noise-related variability of T<sub>2</sub> maps produced by the EMC algorithm and thus increases their precision. The proposed method can be useful for a wide range of clinical applications by facilitating earlier detection of pathologies and improving the accuracy of patients' follow-up.
Light extraction efficiency enhancement of InGaN quantum wells light-emitting diodes with polydimethylsiloxane concave microstructures (2009)

Improvement of light extraction efficiency of InGaN light emitting diodes (LEDs) using polydimethylsiloxane (PDMS) concave microstructures arrays was demonstrated. The size effect of the concave microstructures on the light extraction efficiency of III-Nitride LEDs was studied. Depending on the size of the concave microstructures, ray tracing simulations show that the use of PDMS concave microstructures arrays can lead to increase in light extraction efficiency of InGaN LEDs by 1.5 to 2.0 times. Experiments utilizing 2.0 micron thick PDMS with 1.0 micron diameter of the PDMS concave microstructures arrays demonstrated 1.70 times improvement in light extraction efficiency, which is consistent with improvement of 1.77 times predicted from simulation. The enhancement in light extraction efficiency is attributed to increase in effective photon escape cone due to PDMS concave microstructures arrays.
ChemInform Abstract: Silylation of C—H Bonds in Aromatic Heterocycles by an Earth‐Abundant Metal Catalyst. (2015)

Abstract This is a simple method for the C—H silylation of heteroaromatic compounds using potassium tert‐butoxide as a readily available and inexpensive catalyst.