gebhart/patrepeval huggingface dataset:
Comparison of linear and nonlinear models for coherent hemodynamics spectroscopy (CHS) (2015)

A recently proposed linear time-invariant hemodynamic model for coherent hemodynamics spectroscopy1 (CHS) relates the tissue concentrations of oxy- and deoxy-hemoglobin (outputs of the system) to given dynamics of the tissue blood volume, blood flow and rate constant of oxygen diffusion (inputs of the system). This linear model was derived in the limit of “small” perturbations in blood flow velocity. We have extended this model to a more general model (which will be referred to as the nonlinear extension to the original model) that yields the time-dependent changes of oxy and deoxy-hemoglobin concentrations in response to arbitrary dynamic changes in capillary blood flow velocity. The nonlinear extension to the model relies on a general solution of the partial differential equation that governs the spatio-temporal behavior of oxygen saturation of hemoglobin in capillaries and venules on the basis of dynamic (or time resolved) blood transit time. We show preliminary results where the CHS spectra obtained from the linear and nonlinear models are compared to quantify the limits of applicability of the linear model.
Exploration of Sulfur‐Containing Analogues for Imaging Vesicular Acetylcholine Transporter in the Brain (2018)

Sixteen new sulfur-containing compounds targeting the vesicular acetylcholine transporter (VAChT) were synthesized and assessed for in vitro binding affinities. Enantiomers (-)-(1-(3-hydroxy-1,2,3,4-tetrahydronaphthalen-2-yl)piperidin-4-yl)(4-(methylthio)phenyl)methanone [(-)-8] and (-)-(4-((2-fluoroethyl)thio)phenyl)(1-(3-hydroxy-1,2,3,4-tetrahydronaph-thalen-2-yl)piperidin-4-yl)methanone [(-)-14 a] displayed high binding affinities, with respective K<sub>i</sub> values of 1.4 and 2.2 nm for human VAChT, moderate and high selectivity for human VAChT over σ<sub>1</sub> (≈13-fold) and σ<sub>2</sub> receptors (>420-fold). Radiosyntheses of (-)-[<sup>11</sup> C]8 and (-)-[<sup>18</sup> F]14 a were achieved using conventional methods. Ex vivo autoradiography and biodistribution studies in Sprague-Dawley rats indicated that both radiotracers have the capacity to penetrate the blood-brain barrier, with high initial brain uptake at 5 min and rapid washout. The striatal region had the highest accumulation for both radiotracers. Pretreating the rats with the VAChT ligand (-)-vesamicol decreased brain uptake for both radiotracers. Pretreating the rats with the σ<sub>1</sub> ligand YUN-122 (N-(4-benzylcyclohexyl)-2-(2-fluorophenyl)acetamide) also decreased brain uptake, suggesting these two radiotracers also bind to the σ<sub>1</sub> receptor in vivo. The microPET study of (-)-[<sup>11</sup> C]8 in the brain of a non-human primate showed high striatal accumulation that peaked quickly and washed out rapidly. Although preliminary results indicated these two sulfur-containing radiotracers have high binding affinities for VAChT with rapid washout kinetics from the striatum, their σ<sub>1</sub> receptor binding properties limit their potential as radiotracers for quantifying VAChT in vivo.
Turbo-Detection for Multilayer Magnetic Recording Using Deep Neural Network-Based Equalizer and Media Noise Predictor (2021)

This article considers deep neural network (DNN)-based turbo-detection for multilayer magnetic recording (MLMR), an emerging hard disk drive (HDD) technology that uses vertically stacked magnetic media layers with readers above the top-most layer. The proposed system uses two layers with two upper layer tracks and one lower layer track. The reader signals are processed by convolutional neural networks (CNNs) to separate the upper and lower layer signals and equalize them to 2-D and 1-D partial response (PR) targets, respectively. The upper and lower layer signals feed 2-D and 1-D Bahl–Cocke–Jelinek–Raviv (BCJR) detectors, respectively. The detectors’ soft outputs feed a multilayer CNN-based media noise predictor whose predicted noise outputs are fed back to the BCJR equalizers to reduce their bit error rates (BERs). The BCJR equalizers also interface with low-density parity-check (LDPC) decoders. Additional BER reductions are achieved by sending soft-information from the upper layer BCJR to the lower layer BCJR. Simulations of this turbo-detection system on a two-layer MLMR signal generated by a grain-switching-probabilistic (GSP) media model show density gains of 11.32% over a comparable system with no lower layer and achieve an overall density of 2.6551 terabits per square inch (Tb/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ).
A counting sensor for inbound and outbound people using IR-UWB radar sensors (2016)

In this paper, a new algorithm and structure are proposed to count the number of inbound and outbound people using the impulse radio ultra-wideband (IR-UWB) radar sensors. Two IR-UWB radar sensors are used which are equipped with the narrow beam antenna. Two radar sensors make two adjacent thin layers vertically with the moving direction of the people. Using the system, we propose a new algorithm to count the number of people. Basically the magnitude information of each radar's received signal is used and the mutual information between the two adjacent radars is used to improve the performance of the algorithm. To prove the performance, two kinds of tests are implemented. The one of the experiments is implemented in the laboratory environment, and the other test is implemented in the real world, subway station for the ordinary people.
Demand Charge and Response with Energy Storage (2018)

Commercial and industry (C& I) customers incur two types of electricity charges on their bills: one for the amount of energy usage and another one for the maximum demand during certain billing periods. The second charge type is known as Demand Charge (DC), which could account for over half of a customers' electricity bill. Those C& I customers often sign up for Demand Response (DR) programs to contribute to peak demand reduction as well as to receive incentives and rewards from participating in the programs. The critical factor of achieving both DR and DC reduction is to recognize the nature of these two types of problems and create an effective strategy that can handle them at the same time by which the benefits from DR incentives and DC reduction are maximized. This paper discusses the possible DR scenarios with DC reduction framework for C& I customers who use a Behind-the-Meter (BTM) energy storage and proposes a consistent real-time procedure of deciding battery's charging and discharging set points to solve the problem of maximizing the rewards by conducting DRs as well as the savings by reducing DC costs.
Programmable Integrated Photonics: State of the Art and Future Trends (2018)

Here we review past, present and future work in the next photonic ICs generation aiming the integration of multi-functional software-defined systems for signal processing operations.
Soliton propagation with up- and down-sliding-frequency guiding filters (1995)

We analyze the effect of the third-order guiding filter term on soliton transmission in optical fibers. We find that this term causes a significant difference between the regimes of up- and down-sliding of filter frequency. In particular, the use of up-sliding requires less additional amplifier gain than down-sliding does, which is preferable in real systems.
Rate-Based Contractive Model Predictive Control of Diesel Air Path (2013)

A model predictive control (MPC) strategy is developed for the diesel engine air path. The objective is to regulate the intake manifold pressure (MAP) and exhaust gas recirculation rate (EGR rate) to the specified set-points by coordinated control of the Variable Geometry Turbine (VGT), and EGR valve. The approach taken enforces a decay in a flexible Lyapunov function so that a computationally simple MPC controller can be constructed using a single-step prediction and control horizon. A rate-based framework is also utilized to achieve zero-steady state tracking in the presence of model and plant mismatch. Closed-loop simulation results are reported.
Nanostructured Biosensor for Measuring Neuropathy Target Esterase Activity (2007)

Neuropathy target esterase (NTE) is a membrane protein found in human neurons and other cells, including lymphocytes. Binding of certain organophosphorus (OP) compounds to NTE is believed to cause OP-induced delayed neuropathy (OPIDN), a type of paralysis for which there is no effective treatment. Mutations in NTE have also been linked with serious neurological diseases, such as motor neuron disease. This paper describes development of the first nanostructured biosensor interface containing a catalytically active fragment of NTE known as NEST. The biosensor was fabricated using the layer-by-layer assembly approach, by immobilizing a layer of NEST on top of multilayers consisting of a polyelectrolyte (poly-L-lysine) and an enzyme (tyrosinase). The biosensor has a response time on the order of seconds and gives a concentration-dependent decrease in sensor output in response to a known NEST (and NTE) inhibitor. Potential applications of the biosensor include screening OP compounds for NTE inhibition and investigating the enzymology of wild-type and mutant forms of NTE. Although the development of a NEST biosensor was the primary purpose of this study, we found that the approach developed for NEST could also be extended to measure the activity of other esterases involved in neural processes, such as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). On the basis of measured sensitivities, phenyl valerate was the preferred substrate for NEST and BChE, whereas phenyl acetate was better for AChE.
Ligninolytic enzyme production by<i>Phanerochaete chrysosporium</i>under conditions of nitrogen sufficiency (1984)

A lignin-degrading enzyme has been detected in culture supernatants of Phanerochaete chrysosporium strain INA-12 grown under non-limiting nitrogen conditions. Highest levels of enzyme activity were observed when glycerol served as carbon source. Veratryl alcohol, a known secondary metabolite of P. chrysosporium, was also produced in high nitrogen/glycerol cultures of strain INA-12 and closely followed the development of the ‘ligninase’ activity. Evolution of 14CO2 from 14C-ring-DHP was readily observed when a hydrogen peroxide-generating system was added to 5-day-old high nitrogen/glycerol cultures which contained high amounts of enzyme.
Determinants of angiotensin II generation during converting enzyme inhibition. (1990)

The reaction of the renin-angiotensin system to acute angiotensin converting enzyme inhibition was investigated in a single-blind, crossover study in nine normal volunteers receiving two out of three regimens in random order: the new converting enzyme inhibitor benazepril (20 mg once or 5 mg four times at 6-hour intervals) or enalapril (20 mg). Plasma converting enzyme activity, drug levels, angiotensin I and angiotensin II, active renin, and aldosterone were measured before and 1-4 hours and 14-30 hours after drug intake. Baseline in vitro plasma converting enzyme activity was 97 +/- 15 nmol/ml/min (mean +/- SD) when Hip-Gly-Gly was used as substrate, but with carbobenzoxy-Phe-His-Leu (Z-Phe-His-Leu) or angiotensin I as substrate it was only 20 +/- 4 and 1.7 +/- 0.3 nmol/ml/min, respectively. Discriminating power at peak converting enzyme inhibition was enhanced with the two latter substrates. In vivo converting enzyme activity was estimated by the plasma angiotensin II/angiotensin I ratio, which correlated well with in vitro converting enzyme activity using Z-Phe-His-Leu as substrate (r = 0.76, n = 252). Angiotensin II levels returned to baseline less than 24 hours after drug administration, whereas in vitro and in vivo converting enzyme activity remained considerably inhibited and active renin together with angiotensin I levels were still elevated. A close linear relation was found between plasma angiotensin II and the angiotensin I/drug level ratio (r = 0.91 for benazeprilat and r = 0.88 for enalaprilat, p less than 0.001). Thus, plasma angiotensin II truly reflects the resetting of the renin-angiotensin system at any degree of converting enzyme inhibition. The ratio of plasma angiotensin II to angiotensin I represents converting enzyme inhibition more accurately than in vitro assays, which vary considerably depending on substrates and assay conditions used.
Universal Optical Gain in Strongly Confined Semiconductor Quantum Dots (2008)

Using state-selective excitation to tailor multi-exciton interactions, we have demonstrated that optical gain in strongly confined semiconductor quantum dots is a completely universal, size independent, and intrinsic property of these materials.
Reliable Performance Data Collection for Streaming Media Services. (2006)

The recent proliferation of streaming media systems in both wired and wireless networks challenges the network operators to provide cost-effective streaming solutions that maximize the usage of their infrastructure while maintaining adequate service quality. Some of these goals conflict and motivate the development of precise and accurate models that predict the system states under extremely diverse workloads on-the-fly. However, many earlier studies have derived models and subsequent simulations that are well-suited only for a controlled environment, and hence explain a limited sets of behavioral singularities observed from software component profiles. In this study, we describe a systematic performance evaluation methodology for streaming media systems that starts with the reliable collection of performance data, presents a mechanism to calibrate the data for later use during the modeling phase, and finally examines the prediction power and the limitations of the calibrated data itself. We validate our method with two widely used streaming media systems and the results indicate an excellent match of the modelled data with the actual system measurements.
Surface-patterned microgel-tethered molecular beacons (2012)

We use focused electron beams to create surface-patterned biotinylated poly(ethylene glycol) microgels to which molecular beacon probes are immobilized viabiotin–streptavidin binding. We hypothesize that immobilizing molecular beacon probes to highly hydrated microgels will maintain the high performance typical of untethered molecular beacon probes free in solution. Monte Carlo simulations show that the microgel mesh size resulting from focused radiation crosslinking is highly non-uniform and approaches infinity at the microgel–water interface. This structure is important because the extremely liquid-like environment at the diffuse microgel surface reduces the compromising effects that hard surfaces can exert on molecular beacon secondary conformation, accessibility of nucleic acid targets to the molecular beacons, and the efficiency of energy transfer between the molecular beacon fluorophore and quencher. We assess the performance of microgel-tethered molecular beacons using molecular beacons designed to distinguish between methicillin-sensitive and methicillin-resistant Staphylococcus aureus. We show that each microgel presents approximately 11 800 such molecular beacons and that each molecular beacon on average occupies an area of microgel surface corresponding to an individual streptavidin molecule. The signal-to-background ratio we measure ranges from 40–50, substantially higher than many other surface-tethering approaches. Furthermore, this platform exhibits both low non-specific background and high specific fluorescence when the microgel-tethered molecular beacons are exposed to multiple targets, and it thus promises to lend itself well to high-sensitivity, self-reporting oligonucleotide based assays.
Fabrication of high aspect ratio structures for microchannel plates (1995)

Substrates for microchannel plates have been fabricated using Si micromachining techniques. High aspect ratio pores are constructed using reactive ion etching and streaming electron cyclotron resonance etching, and low-pressure chemical vapor deposition (LPCVD). In one process, 40 μm deep pores with 2 μm openings on 4 μm centers are directly etched in Si. Alternatively, pores with aspect ratios of 30:1 are constructed in a low-stress SiNx membrane using a sacrificial template process whereby pillars of Si are etched and then subsequently backfilled with a dielectric using LPCVD.
ChemInform Abstract: Enzymatic Methods for Glyco(diversification/Randomization) of Drugs and Small Molecules (2012)

Abstract Review: 377 refs.
Reagent-free, Simultaneous Determination of Serum Cholesterol in HDL and LDL by Infrared Spectroscopy (2002)

IR spectroscopy has the potential to become the clinical method of choice for quick and simultaneous determinations of LDL-C and HDL-C.
Generation of tunable, pulsed vortex beams using an image rotating optical parametric oscillator (2003)

Figure 1 shows the image-rotating optical cavity of our singly resonant, nanosecond optical parametric oscillator [1]. The proper choice of mirror orientations gives a 90° rotation of the circulating signal beam on each round trip of the cavity. This rotation separates the resonant frequencies of beams with differing vortex charge, making it possible to select the charge of the signal beam by controlling its frequency through injection seeding with a cw laser.
Comparison of distributed gain in two dual-wavelength pumping schemes for thulium-doped fibre amplifiers (2003)

Using the coherent optical frequency domain reflectometry technique, a non-invasive study has been made of the distributed gain in two pumping schemes for thulium-doped fibre amplifiers. The compared schemes employed 800+1050 nm or 800+1400 nm pump wavelengths, and it was concluded that the former is advantageous over the later primarily due to the ground-state absorption and pumping mechanism.
Inhibitory effect of Angelica gigas extract powder on induced inflammatory cytokines in rats osteoarthritis (2015)

골관절염에 대한 참당귀 추출분말의 치료효과를 검토하고자 흰쥐의 monosodium iodoacetate(MIA)로 유발된 골관절염 부위에서 시료를 채취하여 염증관련 효소 및 염증성 cytokines의 발현에 대하여 참당귀 추출분말의 억제효능을 검토하였다. 고농도의 참당귀 추출분말 (50 μg/mL) 투여에서도 독성이 관찰되지 않았으며, 동일조건하에서 interleukin-1α (IL-1α)로 유발된 nitric oxide (NO)의 생성을 효과적으로 억제하였다. 특히, 관절연골 조직의 inducible nitric oxide synthase (iNOS) 및 cyclooxygenase-2(COX-2)의 발현을 농도 의존적으로 억제하였다. 따라서 참당귀 추출분말은 항염증 효능을 나타내는 농도에서 독성 없이 사용할 수 있으며, iNOS발현을 억제하여 방출되는 신호전달 물질인 NO의 생성을 억제하였다. 또한 참당귀 추출분말의 처리로 염증유발 부위에서 염증성 cytokines으로 알려진 tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) 및 interleukin-6 (IL-6)의 발현이 억제됨을 확인하였다. 참당귀 추출분말의 항 염증효과는 TNF-α, IL-1β 및 IL-6의 혈중농도를 낮추어 염증부위뿐만 아니라 전체적으로 항염증효과를 나타내었다. 본 실험결과, 참당귀 추출분말의 투여는 MIA 또는 IL-1α로 유발되는 골관절염 동물모델에서 염증인자, 관련 효소의 발현 및 관련 신호전달 물질의 생성을 효과적으로 억제하여, 슬관절의 활액 내 glycosaminoglycan (GAG) 및 관절연골의 proteoglycan (PG)의 분해를 방지하여 골관절염의 발생을 억제할 것으로 추정되었다. 한편, 참당귀 추출분말의 주성분인 decursin은 혈중에서 2시간이내에 decursinol로 전환되어 8시간이상 LC-MS/MS로 검출되었다, 따라서 참당귀 추출분말에 의한 염증성 사이토카인 TNF-α, IL-1β 및 IL-6의 억제활성은 항염증활성이 큰 decursinol에 의한 것으로 추정된다. The protective effects of extract powder of Angelica gigas on the degeneration of the articular cartilage in rats was investigated with monosodium iodoacetate (MIA)-induced osteoarthritis, The treatment of high concentration (50 μg/mL) of Angelica gigas effectively inhibited nitric oxide (NO) production induced by interleukin-1α (IL-1α) without any cytotoxicity. Specifically, mRNA and protein expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) were dose dependently reduced by extract powder of Angelica gigas. Importantly, mRNA expression in articular cartilage of inflammatory cytokines, tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6) were clearly reduced. The inflammatory cytokines in blood were also reduced as well. These results suggested that the protective effects on the degeneration of the articular cartilage was derived from the inhibitory effects of mRNA and protein expression of tested inflammatory cytokines which is linked to prevent the degradation of proteoglycan (PG), the main matrix content in articular cartilage. Meanwhile, the 2 hrs incubation of decursin, a major compound of extract powder in rat whole blood rapidely converted decursin into decursinol which shows string anti-inflammatory activity. The coverted decursinol was detected after 8 hrs in whole blood by LC-MS/MS. Conclusively, the inhibitory effects of inflammatory cytokines production in osteoarthritis may be derived from the production of decursinol, which performs against inflammatroy cytokines like TNF-α, IL-1β, and IL-6.
Successful Protein Extraction from Over-Fixed and Long-Term Stored Formalin-Fixed Tissues (2011)

One of the major breakthroughs in molecular pathology during the last decade was the successful extraction of full-length proteins from formalin-fixed and paraffin-embedded (FFPE) clinical tissues. However, only limited data are available for the protein extraction efficiency of over-fixed tissues and FFPE blocks that had been stored for more than 15 years in pathology archives. In this study we evaluated the protein extraction efficiency of FFPE tissues which had been formalin-fixed for up to 144 hours and tissue blocks that were stored for 20 years, comparing an established and a new commercial buffer system. Although there is a decrease in protein yield with increasing fixation time, the new buffer system allows a protein recovery of 66% from 144 hours fixed tissues compared to tissues that were fixed for 6 hours. Using the established extraction procedure, less than 50% protein recovery was seen. Similarly, the protein extraction efficiency decreases with longer storage times of the paraffin blocks. Comparing the two buffer systems, we found that 50% more proteins can be extracted from FFPE blocks that were stored for 20 years when the new buffer system is used. Taken together, our data show that the new buffer system is superior compared to the established one. Because tissue fixation times vary in the routine clinical setting and pathology archives contain billions of FFPE tissues blocks, our data are highly relevant for research, diagnosis, and treatment of disease.
Modulation of autoreactive responses of peripheral blood lymphocytes of patients with systemic lupus erythematosus by peptides based on human and murine anti-DNA autoantibodies (2003)

Two peptides, based on the sequences of the complementarity-determining regions (CDR) 1 and 3 of a pathogenic murine monoclonal anti-DNA autoatibody that bears the 16/6 idiotype (Id), were shown to either prevent or treat an already established systemic lupus erythematosus (SLE) in two murine models of lupus. Two additional peptides based on the human monoclonal anti-DNA, 16/6 Id were synthesized. This study was undertaken in order to investigate the ability of the CDR-based peptides to immunomodulate SLE-associated responses of peripheral blood lymphocytes (PBL) of SLE patients. PBL of 24 of the 62 SLE patients tested proliferated in vitro following stimulation with the human 16/6 Id. Peptides based on the CDRs of both the human and murine anti-DNA autoantibodies inhibited efficiently and specifically the 16/6 Id-induced proliferation and IL-2 production. The latter inhibitions correlated with an up-regulated production (by 2.5-3.5-fold) of the immunosuppressive cytokine, TGF-beta. Overall, the results of our study demonstrate that the CDR-based peptides are capable of down-regulating in vitro autoreactive T cell responses of PBL of SLE patients. Thus, these peptides are potential candidates for a novel specific treatment of SLE patients.