gebhart/patrepeval huggingface dataset:
Dynamic high throughput screening of chemical libraries using acoustic-wave sensor system (2002)

We report a novel sensor-based high throughput screening (HTS) system for identification and quantitation of volatile substances in combinatorial chemical libraries. The measurement method employs a combination of a periodic introduction of a minute amount of a liquid sample into the HTS system, rapid evaporation of volatile components in the sample at room temperature, and dynamic measurement of a generated vapor pulse. These measurements are performed using an array of four 10 MHz acoustic-wave thickness-shear mode sensors coated with different chemically sensitive films. Developed HTS system is applied for screening of multiple samples such as those created in combinatorial chemical libraries of catalyst candidates in an industrially important arene oxidation process. The temporal modulation of the concentration of analyte vapors and measurement of both the temporal profile and the magnitude of the response improves sensor selectivity and makes possible robust identification and quantitation of arene oxidation components such as cresol and benzoquinone in multicomponent combinatorial mixtures with reduced number of sensors in the array. Different solvents such as water, acetonitrile, benzene, and toluene do not alter the response of sensors to analytes. Depending on the gas flow rate, quantitative measurements are performed 10–150 s after the sample introduction and provide significant throughput advantage over gas-chromatographic instruments. Determinations of mixtures of analytes in a variety of solvents are performed using multivariate locally weighted regression. This data analysis method provides the root mean squared error of prediction of less than 2 μg when measurements of cresol and benzoquinone amounts ranging from 0 to 50 μg are performed in 2 μL samples. This method of dynamic sensor-based measurements allows for instrument miniaturization and increases the usefulness of the instrument in space-limited applications. Upon operation of multiple sensors in parallel, effective analysis of dense combinatorial libraries of materials is possible.
Motion Prediction Using Temporal Inception Module (2020)

Human motion prediction is a necessary component for many applications in robotics and autonomous driving. Recent methods propose using sequence-to-sequence deep learning models to tackle this problem. However, they do not focus on exploiting different temporal scales for different length inputs. We argue that the diverse temporal scales are important as they allow us to look at the past frames with different receptive fields, which can lead to better predictions. In this paper, we propose a Temporal Inception Module (TIM) to encode human motion. Making use of TIM, our framework produces input embeddings using convolutional layers, by using different kernel sizes for different input lengths. The experimental results on standard motion prediction benchmark datasets Human3.6M and CMU motion capture dataset show that our approach consistently outperforms the state of the art methods.
Distributed Sensors in the Oil and Gas Industry (2020)

Specific workshops on distributed optical fibre sensors (DOFS) in the oil and gas industry are organized on a regular basis, such as the Society of Petroleum Engineers Annual Workshop on FibreOptic Sensing Applications for Well, Reservoir, and Asset Management. This chapter starts by providing a primer on the relevant stages in the exploration, development, production, and use of hydrocarbon resources. It discusses the challenges in the deployment of optical fibres in the oilfield environment. The chapter describes common methods of installing sensing fibres in this applicationsdomain. It focuses on the main successful applications of DFOS in the industry. The chapter also describes the processes that the hydrocarbons go through from discovery to consumption. The oil and gas industry may be separated into: upstream operations, midstream operations, and downstream operations. A monograph on the interpretation methods used for applying distributed temperature sensing in the oilfield is recommended.
The Complete Amino‐Acid Sequence of the Sweet Protein Thaumatin I (1979)

The primary structure of the sweet-tasting protein thaumatin has been elucidated. The protein consists of a single polypeptide chain of 207 residues. The sequence of the N-terminal part of the chain was determined by sequenator analysis. As the protein contains only one methionine residue, it was possible to deduce the N-terminal sequence of the C-terminal cyanogen bromide fragment by automatic sequencing of the cyanogen-bromide-cleaved, succinylated protein. To arrive at the sequence of the whole protein tryptic and Staphylococcus protease peptides, together with chymotryptic peptides and a 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole) fragment were also sequenced. Comparing the amino acid sequence of thaumatin with that of the other sweet-tasting protein, monellin, we have located five sets of identical tripeptides. Since immunological cross-reactivity of thaumatin antibodies with monellin has recently been described, one or more of these tripeptides might be part of a common antibody recombination site and possibly be involved in the interaction with the sweet-taste receptor.
The Class I Antigen-processing Pathway for the Membrane Protein Tyrosinase Involves Translation in the Endoplasmic Reticulum and Processing in the Cytosol (1998)

Formation of major histocompatibility complex class I-associated peptides from membrane proteins has not been thoroughly investigated. We examined the processing of an HLA-A*0201-associated epitope, YMDGTMSQV, that is derived from the membrane protein tyrosinase by posttranslational conversion of the sequence YMNGTMSQV. Only YMDGTMSQV and not YMNGTMSQV was presented by HLA-A*0201 on cells expressing full-length tyrosinase, although both peptides have similar affinities for HLA-A*0201 and are transported by TAP. In contrast, translation of YMNGTMSQV in the cytosol, as a minigene or a larger fragment of tyrosinase, led to the presentation of the unconverted YMNGTMSQV. This was not due to overexpression leading to saturation of the processing/conversion machinery, since presentation of the converted peptide, YMDGTMSQV, was low or undetectable. Thus, presentation of unconverted peptide was associated with translation in the cytosol, suggesting that processing of the full-length tyrosinase occurs after translation in the endoplasmic reticulum. Nevertheless, presentation of YMDGTMSQV in cells expressing full-length tyrosinase was TAP (transporter associated with antigen processing) and proteasome dependent. After inhibition of proteasome activity, tyrosinase species could be detected in the cytosol. We propose that processing of tyrosinase involves translation in the endoplasmic reticulum, export of full-length tyrosinase to the cytosol, and retransport of converted peptides by TAP for association with HLA-A*0201.
Nanocrystalline H‐RTH Zeolite: An Efficient Catalyst for the Low‐Temperature Dehydration of Ethanol to Ethene (2018)

The low-temperature dehydration of bioethanol is an environmentally benign route to ethene production. Here we compare the catalytic properties of a series of cage-based small-pore zeolites with different framework structures, acid strengths, and/or crystallite sizes for ethanol dehydration at 200 °C under wet conditions (H<sub>2</sub> O/EtOH=0.2). Among the zeolites studied here, nanocrystalline H-RTH was found to be considerably more effective than H-mordenite, the best catalyst for this reaction known to date, which can be rationalized by product shape selectivity. Whereas the acidity of this zeolite also plays a crucial role in selectively forming ethene, its nanocrystallinity is primarily responsible for the observed high catalyst durability.
NPC Seven-Level Single-Phase Inverter with DC-Link Voltage Balancing, Input Voltage Boosting, and AC Power Decoupling (2022)

This paper presents a novel concept of the DC-AC system with the input voltage boost ability, seven-level output voltage modulation, and the input AC current reduction at the double frequency of the output voltage. The system integrates the NPC full-bridge inverter which is composed of four-level legs and an active input voltage balancer (AIVB). The DC-link is composed of three capacitors connected in a series. The source of the energy is connected directly to the middle capacitor while the upper and lower capacitors of the DC-link are charged by the AIVB. The operation of the AIVB leads to balancing of the DC-link voltage and a three-fold boosting of the input voltage. The AIVB utilizes a novel switched-capacitor (SC) topology and can be designed as a low-volume quasi-magneticless converter with a simple open-loop control. One of the proposed methods of the control of the AIVB allows for a double frequency reduction in the input current. The application of the AIVB allows for the use of a seven-level NPC full-bridge (FB) inverter with a simple classic carrier-based PWM which is not applicable in the typical DC-link configurations. This paper presents the converter’s concept, its operation, control methods, and the results of simulations and experiments.
Figure S2 from Identification of Membrane-expressed CAPRIN-1 as a Novel and Universal Cancer Target, and Generation of a Therapeutic Anti-CAPRIN-1 Antibody TRK-950 (2023)

&lt;p&gt;CAPRIN-1 correlated to the cell proliferation and viability.&lt;/p&gt;
Effect of disease-modifying therapies on subcortical gray matter atrophy in multiple sclerosis (2019)

DMT-H treatment may be associated with slower rates of subcortical GM atrophy, especially of the thalamus and putamen. Thalamic and putaminal volumes are promising imaging biomarkers in MS.
Phosphorylation State-Responsive Lanthanide Peptide Conjugates: A Luminescence Switch Based on Reversible Complex Reorganization (2006)

[reaction: see text] A luminogenic probe for peptide dephosphorylation has been developed. It consists of a serine-/tyrosine-containing peptide modified on the N-terminus with a tryptophan residue and a DTPA chelate capable of binding Tb(3+). We propose a mechanistic model for the luminescence enhancement based on the interconversion of monomeric and dimeric lanthanide species, which is affected by the phosphorylation state of the serine or tyrosine residue. The optical switch reports effectively on phosphatase-catalyzed dephosphorylation in vitro.
Modulation Frequency Analysis of 1-D Semi-Transparent Medium (2004)

Frequency analysis is an interesting alternative to the full transient optical probing due to its relatively simpler frame of investigation. Both frequency analysis and the full transient probing are superior to the steady-state tomography because of more information gathered per measurement point. The study of the systematic response of a semi-transparent slab to a harmonic excitation through a power modulated laser is therefore of interest and is conducted to investigate its optical properties using an accurate algorithm to solve the Radiative Transfer Equation in the frequency domain. It is found that a semi-transparent slab behaves like a low-pass filter for the power modulated light and this behaviour is mainly controlled by the scattering events occurring on the light path (dispersion). The results found are consistent with those in the literature obtained from experiments or simpler analysis models.
Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations (2008)

These findings add IRF5 to the short list of genes shown to be associated with MS in more than one population. Our study adds to the evidence that there might be genes or pathways that are common in multiple autoimmune diseases, and that the type I interferon system is likely to be involved in the development of these diseases.
A shock‐tube study of the kinetics of reaction of hydroxyl radicals with H2, CO, CH4, CF3H, C2H4, and C2H6 (1976)

Abstract Concentration‐time profiles have been measured for hydroxyl radicals generated by the shock‐tube decomposition of hydrogen peroxide in the presence of a variety of additives. At temperatures close to 1300°K the rate constants for the reaction are found to be in the ratio 0.18:0.19:0.59:1.00:2.33:2.88 for the additives CO:CF 3 H:H 2 :CH 4 :C 2 H 4 :C 2 H 6 , respectively.
Characterization and heme oxygenase‐1 content of extracellular vesicles in human biofluids (2020)

Heme oxygenase-1 (HO-1), a highly inducible stress protein that degrades heme to biliverdin, carbon monoxide, and free ferrous iron, is increased in blood and other biofluids of subjects with various systemic and neurological disorders. HO-1 does not contain an N-terminal signal peptide and the mechanism responsible for its secretion remains unknown. Extracellular vesicles (EVs) are membrane-bound inclusions that transport microRNAs, messenger RNAs, lipids, and proteins among diverse cellular and extracellular compartments. The objective of the current study was to determine whether EVs in human biofluids contain HO-1, and whether the latter may be transported in EVs from brain to periphery. Total, L1 cell adhesion molecule protein (L1CAM)-enriched (neuron-derived), and glutamate aspartate transporter 1 (GLAST)-enriched (astrocyte-derived) EVs were purified from five different human biofluids (saliva [n = 40], plasma [n = 14], serum [n = 10], urine [n = 10], and cerebrospinal fluid [n = 11]) using polymer precipitation and immuno-affinity-based capture methods. L1CAM-enriched, GLAST-enriched, and L1CAM/GLAST-depleted (LGD) EV, along with EV-depleted (EVD), fractions were validated by nanoparticle tracking analysis, enzyme-linked immunosorbent assay (ELISA), and western blot. HO-1 was assayed in all fractions using ELISA and western blot. The majority of HO-1 protein was localized to LGD, L1CAM-enriched, and GLAST-enriched EVs of all human biofluids surveyed after adjusting for age and sex, with little HO-1 protein detected in EVD fractions. HO-1 protein in human biofluids is predominantly localized to EV compartments. A substantial proportion of EV HO-1 in peripheral human biofluids is derived from the central nervous system and may contribute to the systemic manifestations of various neurological conditions.
Ultrasensitive and low-volume point-of-care diagnostics on flexible strips – a study with cardiac troponin biomarkers (2016)

We demonstrate a flexible, mechanically stable, and disposable electrochemical sensor platform for monitoring cardiac troponins through the detection and quantification of cardiac Troponin-T (cTnT). We designed and fabricated nanostructured zinc oxide (ZnO) sensing electrodes on flexible porous polyimide substrates. We demonstrate ultrasensitive detection is capable at very low sample volumes due to the confinement phenomenon of target species within the ZnO nanostructures leading to enhancement of biomolecular binding on the sensor electrode surface. The performance of the ZnO nanostructured sensor electrode was evaluated against gold and nanotextured ZnO electrodes. The electrochemical sensor functions on affinity based immunoassay principles whereby monoclonal antibodies for cTnT were immobilized on the sensor electrodes using thiol based chemistry. Detection of cTnT in phosphate buffered saline (PBS) and human serum (HS) buffers was achieved at low sample volumes of 20 μL using non-faradaic electrochemical impedance spectroscopy (EIS). Limit of detection (LOD) of 1E-4 ng/mL (i.e. 1 pg/mL) at 7% CV (coefficient of variation) for cTnT in HS was demonstrated on nanostructured ZnO electrodes. The mechanical integrity of the flexible biosensor platform was demonstrated with cyclic bending tests. The sensor performed within 12% CV after 100 bending cycles demonstrating the robustness of the nanostructured ZnO electrochemical sensor platform.
Data from Direct Detection and Quantification of Neoantigens (2023)

&lt;div&gt;Abstract&lt;p&gt;Many immunotherapeutic approaches under development rely on T-cell recognition of cancer-derived peptides bound to human leukocyte antigen molecules on the cell surface. Direct experimental demonstration that such peptides are processed and bound is currently challenging. Here, we describe a method that meets this challenge. The method entailed an optimized immunoprecipitation protocol coupled with two-dimensional chromatography and mass spectrometry. The ability to detect and quantify minute amounts of predefined antigens should be useful both for basic research in tumor immunology and for the development of rationally designed cancer vaccines.&lt;/p&gt;&lt;/div&gt;
Role of senescence marker p16INK4a measured in peripheral blood T-lymphocytes in predicting length of hospital stay after coronary artery bypass surgery in older adults (2020)

Adults older than 65 years undergo more than 120,000 coronary artery bypass (CAB) procedures each year in the United States. Chronological age alone, though commonly used in prediction models of outcomes after CAB, does not alone reflect variability in aging process; thus, the risk of complications in older adults. We performed a prospective study to evaluate a relationship between senescence marker p16INK4a expression in peripheral blood T-lymphocytes (p16 levels in PBTLs) with aging and with perioperative outcomes in older CAB patients. We included 55 patients age 55 and older, who underwent CAB in Johns Hopkins Hospital between September 1st, 2010 and March 25th, 2013. Demographic, clinical and laboratory data following outline of the Society of Thoracic Surgeons data collection form was collected, and p16 mRNA levels in PBTLs were measured using Taqman® qRT-PCR. Associations between p16 mRNA levels in PBTLs with length of hospital stay, frailty status, p16 protein levels in the aortic and left internal mammary artery tissue, cerebral oxygen saturation, and augmentation index as a measure of vascular stiffness were measured using regression analyses. Length of hospital stay was the primary outcome of interest, and major organ morbidity, mortality, and discharge to a skilled nursing facility were secondary outcomes. In secondary analysis, we evaluated associations between p16 mRNA levels in PBTLs and interleukin-6 levels using regression analyses. Median age of enrolled patients was 63.5 years (range 56-81 years), they were predominantly male (74.55%), of Caucasian descent (85.45%). Median log2(p16 levels in PBTLs) were 4.71 (range 1.10-6.82). P16 levels in PBTLs were significantly associated with chronological age (mean difference 0.06 for each year increase in age, 95% CI 0.01-0.11) and interleukin 6 levels (mean difference 0.09 for each pg/ml increase in IL-6 levels, 95% CI 0.01-0.18). There were no significant associations with frailty status, augmentation index, cerebral oxygenation and p16 protein levels in blood vessels. Increasing p16 levels in PBTLs did not predict length of stay in the hospital (HR 1.10, 95% CI 0.87-1.40) or intensive care unit (HR 1.02, 95% CI 0.79-1.32). Additional evaluation of p16 levels in PBTLs as predictor of perioperative outcomes is required and should include additional markers of immune system aging as well as different outcomes after CAB in addition to length of hospital stay.
ChemInform Abstract: CYCLIZATIONS OF ENOLATES ONTO AROMATIC RINGS VIA THE PHOTO‐SRN1 REACTION. PREPARATIVE AND MECHANISTIC ASPECTS (1977)

Abstract Aus den J od‐ketonen (I) entstehen bei der Photocyclisierung in sehr unterschiedlichen Ausbeuten die cyclischen Ketone (II).
Ionic Liquid Control Crystal Growth to Enhance Planar Perovskite Solar Cells Efficiency (2016)

Ionic liquids can retard the perovskite crystallization with the aim to form compact films with larger and more uniformly distributed grain size. The ionic liquid driven crystallization is exploited to prepared a record planar perovskite solar cell with stabilized power output of 19.5%. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Measurement of nano-antenna array active impedance using scattered fields (2015)

Modern nanotechnology allows us to fabricate nano-antenna arrays operating at optical frequencies. Due to the fabrication tolerances, inhomogeneity of the materials, and complex behavior of metals at optical frequencies there is a need to measure the nano-antennas' properties. Optical nano-antennas are characterized, like in the RF regime, by the fundamental parameters of antennas such as: directivity, gain, input impedance, polarization, etc. Parameters such as directivity and polarization can be measured by using near-field imaging methods (R. Esteban, R. Vogelgesang, J. Dorfmuller, A. Dmitriev, C. Rockstuhl, C. Etrich, and K. Kern, Nano Letters, 8, 3155–3159, 2008) or by an even more efficient far-field measurement scheme, using coherent scattering from nano-antenna arrays as has been demonstrated experimentally in (Y. Yifat, Z. Iluz, M. Eitan, I. Friedler, Y. Hanein, A. Boag, and J. Scheuer, Appl. Phys. Lett. 100, 111113 (1–4), 2012). Nevertheless, the above measurement techniques cannot measure nano-antenna impedances, which are required for the integration between antennas and loads. Due to the extremely small dimensions, it is impossible to measure the nanoantenna impedance directly by connecting probes or transmission lines to the antenna terminals. For this purpose, we propose a different approach, based on external illumination of an antenna array and measurements of the scattered fields. This technique can be further extended to characterize unknown nano-load properties for new optical sensor applications.
Rapid Learning or Feature Reuse? Towards Understanding the Effectiveness of MAML (2019)

An important research direction in machine learning has centered around developing meta-learning algorithms to tackle few-shot learning. An especially successful algorithm has been Model Agnostic Meta-Learning (MAML), a method that consists of two optimization loops, with the outer loop finding a meta-initialization, from which the inner loop can efficiently learn new tasks. Despite MAML's popularity, a fundamental open question remains -- is the effectiveness of MAML due to the meta-initialization being primed for rapid learning (large, efficient changes in the representations) or due to feature reuse, with the meta initialization already containing high quality features? We investigate this question, via ablation studies and analysis of the latent representations, finding that feature reuse is the dominant factor. This leads to the ANIL (Almost No Inner Loop) algorithm, a simplification of MAML where we remove the inner loop for all but the (task-specific) head of a MAML-trained network. ANIL matches MAML's performance on benchmark few-shot image classification and RL and offers computational improvements over MAML. We further study the precise contributions of the head and body of the network, showing that performance on the test tasks is entirely determined by the quality of the learned features, and we can remove even the head of the network (the NIL algorithm). We conclude with a discussion of the rapid learning vs feature reuse question for meta-learning algorithms more broadly.
Slowly eroding lesions in multiple sclerosis (2016)

We noted sustained radiological contraction of MS lesions, a surprising result given that fresh myelin breakdown products within chronic active lesions are observed relatively frequently at autopsy. Therefore, the primary pathological process in chronic lesions, even those described as "slowly expanding," is likely to be tissue loss.