gebhart/patrepeval huggingface dataset:
Using i<scp>RT</scp>, a normalized retention time for more targeted measurement of peptides (2012)

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.
A System for new event detection (2003)

We present a new method and system for performing the New Event Detection task, i.e., in one or multiple streams of news stories, all stories on a previously unseen (new) event are marked. The method is based on an incremental TF-IDF model. Our extensions include: generation of source-specific models, similarity score normalization based on document-specific averages, similarity score normalization based on source-pair specific averages, term reweighting based on inverse event frequencies, and segmentation of the documents. We also report on extensions that did not improve results. The system performs very well on TDT3 and TDT4 test data and scored second in the TDT-2002 evaluation.
One-Pot Synthesis of Block Copolymers Containing a Polyolefin Block (2018)

Polyolefin-containing block copolymers were catalytically synthesized using a postpolymerization modification strategy. A traditional olefin polymerization followed by a tandem hydroformylation/hydrogenation of the olefinic terminated polymer was implemented to yield a hydroxyl terminated polyolefin. The hydroxyl terminated polyolefin was then used as a macroinitiator for the ring-opening polymerization of cyclic esters to yield the corresponding diblock copolymer. This methodology was applied to an array of different polyolefins and two cyclic monomers (ε-caprolactone and lactide) showcasing the versatility of the protocol. Most noticeably, isotactic polypropylene was quantitatively incorporated into block copolymers. Additionally, the hydrophobicity of polyethylene films was successfully decreased by the addition of small amounts of a block copolymer.
Abstract 8785: CYT387, a Novel Jak1/Jak2 Inhibitor, Prevents Progression of Pulmonary Arterial Hypertension in the Rat Monocrotaline Model (2010)

Introduction: The JAK/STAT pathway has been implicated in the pathophysiology of pulmonary arterial hypertension (PAH). Hypothesis: This study tested the hypothesis that CYT387 (N-(cyanomethyl)-(4-...
Virtual character performance from speech (2013)

We demonstrate a method for generating a 3D virtual character performance from the audio signal by inferring the acoustic and semantic properties of the utterance. Through a prosodic analysis of the acoustic signal, we perform an analysis for stress and pitch, relate it to the spoken words and identify the agitation state. Our rule-based system performs a shallow analysis of the utterance text to determine its semantic, pragmatic and rhetorical content. Based on these analyses, the system generates facial expressions and behaviors including head movements, eye saccades, gestures, blinks and gazes. Our technique is able to synthesize the performance and generate novel gesture animations based on coarticulation with other closely scheduled animations. Because our method utilizes semantics in addition to prosody, we are able to generate virtual character performances that are more appropriate than methods that use only prosody. We perform a study that shows that our technique outperforms methods that use prosody alone.
Waveguide-based extraction of near-field electromagnetic radiation: a new method for thermal energy conversion? (2016)

Energy in a useful form is a vital resource and hence there is a continuous strive to improve existing technologies and to find new ones that address that basic need. The conversion of thermal energy is the primary source of generating electrical energy from a broad range of sources such as, for example coal, oil, natural gas, solar, geothermal, and nuclear energy. A common need in all cases is the ability to efficiently extract the generated electromagnetic and thermal energy and to convert it to electricity. The current methods of thermal energy extraction are based on heat engines, thermoelectric, and thermophotovoltaic conversion. In this report a method based on the direct extraction of Electromagnetic energy from the thermal near-field through the use of optical waveguides, is presented.
Probabilistic Forecasting with Spline Quantile Function RNNs (2019)

In this paper, we propose a flexible method for probabilistic modeling with conditional quantile functions using monotonic regression splines. The shape of the spline is parameterized by a neural network whose parameters are learned by minimizing the continuous ranked probability score. Within this framework, we propose a method for probabilistic time series forecasting, which combines the modeling capacity of recurrent neural networks with the flexibility of a spline-based representation of the output distribution. Unlike methods based on parametric probability density functions and maximum likelihood estimation, the proposed method can flexibly adapt to different output distributions without manual intervention.
We empirically demonstrate the effectiveness of the approach 
on synthetic and real-world data sets.
Author response: Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia (2016)

High resolution structures of the essential human AAA+ ATPase TorsinA and its disease mutant in complex with an activator reveal details of the interaction that will guide drug design and further functional characterization.
Synthesis and biological evaluation of Tc-99m N,N'-bis(mercaptoacetyl)-2,3-diaminopropanoate: a potential replacement for [131I]o-iodohippurate. (1982)

A new technetium-chelating agent based on amide and mercaptide donor groups, N,N'-bis(mercaptoacetyl)-2,3-diaminopropanoate, was synthesized as an analog of previously described N,N'-bis(mercaptoacetyl)ethylenediamine (DADS). Complexation of Tc-99m with the new chelating group resulted in two components that were separable by high-performance liquid chromatography. The component that eluted first demonstrated high specificity for renal excretion, with over 90% in the urine of rabbits at 35 min, 87% in the urine of mice at 2 hr, and 1.6% or less in the intestines of mice. Excretion was rapid, with the first component equaling or exceeding [131I]o-iodohippurate in the urine of rabbits at all times. The second or latter component demonstrated comparable specificity but slightly slower renal excretion kinetics. Clinical trials with the first component are probably warranted.
Miniature Bioreactor System for Long-Term Cell Culture (2010)

A prototype miniature bioreactor system is designed to serve as a laboratory benchtop cell-culturing system that minimizes the need for relatively expensive equipment and reagents and can be operated under computer control, thereby reducing the time and effort required of human investigators and reducing uncertainty in results. The system includes a bioreactor, a fluid-handling subsystem, a chamber wherein the bioreactor is maintained in a controlled atmosphere at a controlled temperature, and associated control subsystems. The system can be used to culture both anchorage-dependent and suspension cells, which can be either prokaryotic or eukaryotic. Cells can be cultured for extended periods of time in this system, and samples of cells can be extracted and analyzed at specified intervals. By integrating this system with one or more microanalytical instrument(s), one can construct a complete automated analytical system that can be tailored to perform one or more of a large variety of assays.
A novel modification of the avidin-biotin complex method for immunohistochemical studies of transgenic mice with murine monoclonal antibodies. (1992)

When mouse tissues are probed with murine monoclonal antibodies (MAb) by indirect immunohistochemistry, the secondary antibody detects tissue-bound MAb and irrelevant, endogenous mouse immunoglobulins. The latter are a source of confounding background, especially in diseased tissues. To circumvent this problem, we generated complexes of primary MAb and biotinylated secondary antibodies in vitro for use as antigen-specific probes. After blocking free binding sites in the complexed secondary antibodies with normal mouse serum, the complexes were applied to mouse tissue sections and tissue-bound complexes were visualized with an avidin-biotin detection system. Complexes formed with 12 different rat or mouse MAb were used to probe sections of normal mice, tumor-bearing transgenic mice, and mice with tumor xenografts. The staining patterns produced by these probes reflected the specificity of the MAb in the complexes, and the labeling of irrelevant, endogenous mouse immunoglobulins was reduced substantially. This novel, indirect immunohistochemical method can be exploited to study normal and diseased mouse tissues using a variety of murine MAb.
First structural characterization of a covalently bonded porphyrin–carborane system (2001)

The first definitive crystal structure of a covalently bonded carborane–porphyrin system is reported; unusual inter- and intra-molecular carborane–porphyrin interactions are observed in the molecular structure and in variable temperature 1H NMR experiments.
Neural Inverse Rendering of an Indoor Scene From a Single Image (2019)

Inverse rendering aims to estimate physical attributes of a scene, e.g., reflectance, geometry, and lighting, from image(s). Inverse rendering has been studied primarily for single objects or with methods that solve for only one of the scene attributes. We propose the first learning based approach that jointly estimates albedo, normals, and lighting of an indoor scene from a single image. Our key contribution is the Residual Appearance Renderer (RAR), which can be trained to synthesize complex appearance effects (e.g., inter-reflection, cast shadows, near-field illumination, and realistic shading), which would be neglected otherwise. This enables us to perform self-supervised learning on real data using a reconstruction loss, based on re-synthesizing the input image from the estimated components. We finetune with real data after pretraining with synthetic data. To this end, we use physically-based rendering to create a large-scale synthetic dataset, named SUNCG-PBR, which is a significant improvement over prior datasets. Experimental results show that our approach outperforms state-of-the-art methods that estimate one or more scene attributes.
Dilute-nitride mid-infrared type-II "W" quantum-well lasers on InP substrates (2004)

It is predicted that InAsN/GaAsSb/InAsN/GaInP strain-compensated type-II W quantum wells grown on InP substrates should emit in the mid-IR (3-5 /spl mu/m) with favorable lasing characteristics.
Multi-material decomposition of spectral CT images (2010)

Spectral Computed Tomography (Spectral CT), and in particular fast kVp switching dual-energy computed tomography, is an imaging modality that extends the capabilities of conventional computed tomography (CT). Spectral CT enables the estimation of the full linear attenuation curve of the imaged subject at each voxel in the CT volume, instead of a scalar image in Hounsfield units. Because the space of linear attenuation curves in the energy ranges of medical applications can be accurately described through a two-dimensional manifold, this decomposition procedure would be, in principle, limited to two materials. This paper describes an algorithm that overcomes this limitation, allowing for the estimation of N-tuples of material-decomposed images. The algorithm works by assuming that the mixing of substances and tissue types in the human body has the physicochemical properties of an ideal solution, which yields a model for the density of the imaged material mix. Under this model the mass attenuation curve of each voxel in the image can be estimated, immediately resulting in a material-decomposed image triplet. Decomposition into an arbitrary number of pre-selected materials can be achieved by automatically selecting adequate triplets from an application-specific material library. The decomposition is expressed in terms of the volume fractions of each constituent material in the mix; this provides for a straightforward, physically meaningful interpretation of the data. One important application of this technique is in the digital removal of contrast agent from a dual-energy exam, producing a virtual nonenhanced image, as well as in the quantification of the concentration of contrast observed in a targeted region, thus providing an accurate measure of tissue perfusion.
Invasive differences among <i>Porphyromonas gingivalis</i> strains from healthy and diseased periodontal sites (2008)

The increased invasion noted with P. gingivalis isolates from diseased sites vs. healthy sites, and the increased invasive capabilities with increasing probing depth, indicate that P. gingivalis isolates have a varying ability to invade host cells in the periodontal pocket.
Direct Phase Measurement Of Aspheric Surface Contours (1986)

Two-wavelength holography and phase-shifting interferometry are combined to measure aspheric surface contours with a variable sensitivity. In this technique, the surface is effectively tested at a synthesized longer equivalent wavelength <sup>λ</sup>eq = <sup>λ</sup>a<sup>λ</sup>b|<sup>λ</sup>a - <sup>λ</sup>b| using measurements made at wavelengths <sup>λ</sup>a and <sup>λ</sup>b where the difference of the phases measured for <sup>λ</sup>a and <sup>λ</sup>b yields the modulo 2π phase at <sup>λ</sup><sub>eq</sub>. A mask of point apertures is placed over the detector array in order to resolve closely spaced fringes. This technique has an rms repeatability of <sup>λ</sup><sub>eq</sub>/100. Limits to this technique are discussed and results are shown.
Pose-assisted Active Visual Recognition in Mobile Augmented Reality (2018)

While existing visual recognition approaches, which rely on 2D images to train their underlying models, work well for object classification, recognizing the changing state of a 3D object requires addressing several additional challenges. This paper proposes an active visual recognition approach to this problem, leveraging camera pose data available on mobile devices. With this approach, the state of a 3D object, which captures its appearance changes, can be recognized in real time. Our novel approach selects informative video frames filtered by 6-DOF camera poses to train a deep learning model to recognize object state. We validate our approach through a prototype for Augmented Reality-assisted hardware maintenance.
Low-voltage operated AC plasma-display panels (1979)

AC plasma-display panels (AC-PDP) with protective coatings of alkaline earth oxides are shown to have lower firing voltage (V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</inf> ) than panels with standard MgO coatings. In particular, a mixture of CaO and SrO leads to a V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</inf> of 65 V, about 30 V less than V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</inf> for MgO coatings. Life in excess of 10 000 h is indicated, but memory margins of only 4 V have been achieved so far.
Demonstration, using sliding-frequency guiding filters, of error-free soliton transmission over more than 20,000 km at 10 Gbit/s, single-channel, and over more than 13,000 km at 20 Gbit/s in a two-channel WDM (1993)

In ultralong distance soliton transmission, the limit to single-channel bit rate is set by jitter in pulse arrival times. That jitter can be reduced through the use of narrow-band frequency-guiding filters, periodically distributed along the transmission line1,2. Because extra gain must be employed to offset the loss the solitons experience from passage through the filters, however, with fixed-frequency filters, amplifier spontaneous emission noise rises exponentially with distance. This tends to put a limit on the maximum useable filter strength, and hence on the practically attainable reduction in jitter. In earlier transmission experiments3, for example, the filter producing the minimum error rate was just strong enough to reduce the standard deviation in the timing jitter by about a half, in the trans-Pacific distance of ~10 Mm (10,000 km). In a recent paper4, however, we have shown how that limitation can be overcome by gradually translating the peak frequency of the filters with distance along the transmission line. That is, with such "sliding- frequency guiding filters," we create a transmission line that is opaque to noise for all but a small final fraction of its length, yet remains transparent to solitons. In this paper, we report the first experimental demonstration of high bit rate transmission using such strong, sliding-frequency filters.
Nitrite reductase activity of sulphate‐reducing bacteria prevents their inhibition by nitrate‐reducing, sulphide‐oxidizing bacteria (2003)

Sulphate-reducing bacteria (SRB) can be inhibited by nitrate-reducing, sulphide-oxidizing bacteria (NR-SOB), despite the fact that these two groups are interdependent in many anaerobic environments. Practical applications of this inhibition include the reduction of sulphide concentrations in oil fields by nitrate injection. The NR-SOB Thiomicrospira sp. strain CVO was found to oxidize up to 15 mM sulphide, considerably more than three other NR-SOB strains that were tested. Sulphide oxidation increased the environmental redox potential (Eh) from -400 to +100 mV and gave 0.6 nitrite per nitrate reduced. Within the genus Desulfovibrio, strains Lac3 and Lac6 were inhibited by strain CVO and nitrate for the duration of the experiment, whereas inhibition of strains Lac15 and D. vulgaris Hildenborough was transient. The latter had very high nitrite reductase (Nrf) activity. Southern blotting with D. vulgaris nrf genes as a probe indicated the absence of homologous nrf genes from strains Lac3 and Lac6 and their presence in strain Lac15. With respect to SRB from other genera, inhibition of the known nitrite reducer Desulfobulbus propionicus by strain CVO and nitrate was transient, whereas inhibition of Desulfobacterium autotrophicum and Desulfobacter postgatei was long-lasting. The results indicate that inhibition of SRB by NR-SOB is caused by nitrite production. Nrf-containing SRB can overcome this inhibition by further reducing nitrite to ammonia, preventing a stalling of the favourable metabolic interactions between these two bacterial groups. Nrf, which is widely distributed in SRB, can thus be regarded as a resistance factor that prevents the inhibition of dissimilatory sulphate reduction by nitrite.
Colorectal cancer biomarkers: To be or not to be? Cautionary tales from a road well travelled (2014)

Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide and places a major economic burden on the global health care system. The time frame for development from premalignant to malignant disease typically spans 10-15 years, and this latent period provides an ideal opportunity for early detection and intervention to improve patient outcomes. Currently, early diagnosis of CRC is hampered by a lack of suitable non-invasive biomarkers that are clinically or economically acceptable for population-based screening. New blood-based protein biomarkers for early detection of CRC are therefore urgently required. The success of clinical biomarker discovery and validation studies is critically dependent on understanding and adjusting for potential experimental, analytical, and biological factors that can interfere with the robust interpretation of results. In this review we outline some important considerations for research groups undertaking biomarker research with exemplars from our studies. Implementation of experimental strategies to minimise the potential effects of these problems will facilitate the identification of panels of biomarkers with the sensitivity and specificity required for the development of successful tests for the early detection and surveillance of CRC.
Cottonseed extraction with a new solvent system: Isohexane and alcohol mixtures (1998)

Abstract A solvent system, consisting of isohexane and 5 to 25% alcohol, either ethanol (EtOH) or isopropyl alcohol (IPA), was tested for extracting gossypol and oil from cottonseed. The test results indicate that this new solvent system not only is effective in removing free and total gossypol but also is as efficient as n ‐hexane when extracting oil. The amino acid analysis of cottonseed meal, produced by the new solvent system, is similar to that produced by commercial n ‐hexane. Present commercial cottonseed extraction and downstream processing of cottonseed oil refining may need little change to adopt this new solvent system. This new solvent system may lead to a solution to the gossypol problem of cottonseed extraction.
Shoulder and Elbow Joint Angle Tracking With Inertial Sensors (2012)

Wearable inertial systems have recently been used to track human movement in and outside of the laboratory. Continuous monitoring of human movement can provide valuable information relevant to individuals' level of physical activity and functional ability. Traditionally, orientation has been calculated by integrating the angular velocity from gyroscopes. However, a small drift in the measured velocity leads to increasing integration error over time. To compensate that drift, complementary data from accelerometers are normally fused into tracking systems using the Kalman or extended Kalman filter. In this study, we combine kinematic models designed for control of robotic arms with state-space methods to continuously estimate the angles of human shoulder and elbow using two wearable inertial measurement units. We use the unscented Kalman filter to implement the nonlinear state-space inertial tracker. Shoulder and elbow joint angles obtained from 8 subjects using our inertial tracker were compared to the angles obtained from an optical-tracking reference system. On average, there was an RMS angle error of less than 8° for all shoulder and elbow angles. The average correlation coefficient for all movement tasks among all subjects was r ≥ 0.95 . This agreement between our inertial tracker and the optical reference system was obtained for both regular and fast-speed movement of the arm. The same method can be used to track movement of other joints.
Imdazole systems. I. Imidzo[2,1‐<i>b</i>][1,3,5]benzothiadiazepine derivatives as potential antipsychotic agents (1983)

Abstract Imidazo[2,1‐ b ][1,3,5]benzothiadiazepine 3 constitutes a novel ring system, and its analogs 3a‐i were synthesized to investigate their potential antipsychotic activity. The synthesis of the ring system was achieved by reaction of 2‐aminophenylthioimidazoles 7 with phosgene or thiophosgene and by ring closure of the 1‐[2‐(2‐imidazolyl)thiophenyliminocarbonyl]‐1‐piperazines 13 . An efficient method for the conversion of thioureas 8, 12 to guanidine 3a via the corresponding cyanothioamidines 11, 14 was developed.