gebhart/patrepeval huggingface dataset:
Substrate and Inhibitor Profile of BACE (β-Secretase) and Comparison with Other Mammalian Aspartic Proteases (2002)

The full-length and ectodomain forms of beta-site APP cleavage enzyme (BACE) have been cloned, expressed in Sf9 cells, and purified to homogeneity. This aspartic protease cleaves the amyloid precursor protein at the beta-secretase site, a critical step in the Alzheimer's disease pathogenesis. Comparison of BACE to other aspartic proteases such as cathepsin D and E, napsin A, pepsin, and renin revealed little similarity with respect to the substrate preference and inhibitor profile. On the other hand, these parameters are all very similar for the homologous enzyme BACE2. Based on a collection of decameric substrates, it was found that BACE has a loose substrate specificity and that the substrate recognition site in BACE extends over several amino acids. In common with the aspartic proteases mentioned above, BACE prefers a leucine residue at position P1. Unlike cathepsin D etc., BACE accepts polar or acidic residues at positions P2'0 and P1 but prefers bulky hydrophobic residues at position P3. BACE displays poor kinetic constants toward its known substrates (wild-type substrate, SEVKM/DAEFR, K(m) = 7 microm, K(cat) = 0.002 s(-1); Swedish mutant, SEVNL/DAEFR, K(m) = 9 microm, K(cat) = 0.02 s(-1)). A new substrate (VVEVDA/AVTP, K(m) = 1 microm, K(cat) = 0.004) was identified by serendipity.
Dopamine imbalance in Huntington's disease: a mechanism for the lack of behavioral flexibility (2013)

Dopamine (DA) plays an essential role in the control of coordinated movements. Alterations in DA balance in the striatum lead to pathological conditions such as Parkinson's and Huntington's diseases (HD). HD is a progressive, invariably fatal neurodegenerative disease caused by a genetic mutation producing an expansion of glutamine repeats and is characterized by abnormal dance-like movements (chorea). The principal pathology is the loss of striatal and cortical projection neurons. Changes in brain DA content and receptor number contribute to abnormal movements and cognitive deficits in HD. In particular, during the early hyperkinetic stage of HD, DA levels are increased whereas expression of DA receptors is reduced. In contrast, in the late akinetic stage, DA levels are significantly decreased and resemble those of a Parkinsonian state. Time-dependent changes in DA transmission parallel biphasic changes in glutamate synaptic transmission and may enhance alterations in glutamate receptor-mediated synaptic activity. In this review, we focus on neuronal electrophysiological mechanisms that may lead to some of the motor and cognitive symptoms of HD and how they relate to dysfunction in DA neurotransmission. Based on clinical and experimental findings, we propose that some of the behavioral alterations in HD, including reduced behavioral flexibility, may be caused by altered DA modulatory function. Thus, restoring DA balance alone or in conjunction with glutamate receptor antagonists could be a viable therapeutic approach.
Government Policies, Residential Mortgage Defaults and the Boom and Bust Cycle of Housing Prices (2014)

We develop a micro‐based macromodel for residential home prices in an economy where defaults on residential mortgages negatively affect housing prices. Our model enables us to study the impact of subprime defaults on prime borrowers and the impact of various government policies on the housing market boom and bust cycle. In this regard, our key conclusions are that (i) there is a contagion effect from subprime defaults to prime defaults due to the negative impact of subprime defaults and (ii) monetary policy is the most effective tool for decreasing mortgage defaults and increasing aggregate home prices in contrast to alternative government fiscal policies designed to loosen mortgage credit.
Risk factors for lacune subtypes in the Atherosclerosis Risk in Communities (ARIC) Study (2011)

Smaller lacunes (even those <3 mm) were associated with diabetes and HbA(1)c, and larger lacunes associated with LDL cholesterol, differences which support long-held theories relating to their underlying pathology. The findings may contribute to broader understanding of cerebral microvascular disease.
Towards a model of agent-assisted team search (2007)

Abstract—This paper is the first step in our research plan towards addressing the fundamental question of how software agents can best aid distributed human teams performing timestressed critical tasks in uncertain and dynamic environments. Based on prior work, we hypothesize that to improve the performance of human teams, agents must do some combination of the following: (1) reduce the cost of the humans ’ information processing; (2) decrease uncertainty in the task; (3) improve coordination between team members; (4) directly assist in task completion. In order to (a) establish an experimental baseline of the performance of human-only teams for some particular task domain, and (b) best understand where agents can provide best utility in supporting human teamwork, we designed scenarios and performed experiments with human teams performing a time-stressed, collaborative search task in a multi-player gaming environment. The collaborative search task recreates some of the challenges faced by human teams during search and rescue operations, such as the one described in the Holistan scenario. In our experiments, we analyze (1) verbal communication between team members and (2) the effects of presenting or omitting task progress information. By ascertaining the information processing and coordination requirements of this team task, we expect to identify “insertion points ” for agent assistance to human teams. Agent assistance will be particularly critical to military teams as their operations become more agile and situation specific. As unfamiliar forces are brought together for different coalition missions, agent support of teamwork becomes crucial. I.
Seen in a New Light: Evaluation of Light Quality From LED Fittings (2022)

This paper discusses a new method of evaluating light quality in relation to specific light fixtures. All existing studies of light quality have taken place in laboratory settings and the qualitative aspect of the participant’s experience is limited. In order to address these limitations a two-stage process for evaluation of the artefacts was developed. The first stage used an already established technique from the lighting area and the second stage used technique from Computer Human Interface (CHI), a technique that was adapted to fit with this study. This evaluation process is part of a wider study that involves the design of light fittings suitable for LED sources. The paper reports on how the each stage of the evaluation process was carried out, the nature of data elicited, and the themes that emerged from the data. The paper concludes with an analysis of the value of this mixed method approach to the evaluation of light quality.
Affect and the medium of digital data (2012)

This paper attempts a technical analysis of the medium of digital data to establish how affect may emerge in that medium. Two central questions here are, first, whether it is possible for two immanently digital entities to establish an affect cycle with each other, and, second, how this relates to affect cycles established between digital data and non-digital entities? It should be possible to build artworks that can test certain of their own intrinsic properties in both these respects. The author had a hand in creating some such artworks, and these are examined later in this paper.
BRAIN INJURY SCREENING DIAGNOSTICS FOR EMERGENCY MEDICINE: QUANTITATION OF CEREBROSPINAL FLUID SPECIFIC PROTEINS IN HUMAN NASAL DISCHARGE (2011)

A microfluidic device with integrated sample preparation is introduced for the detection of cerebrospinal fluid rhinorrhea—a condition resulting in leakage of CSF from the nose due to head trauma. While CSF rhinorrhea is a serious condition, current state-of-the-art diagnostics are expensive or slow (MRI, CT scan or ELISA). We show the capability of a microfluidic immunoassay to accept and processes raw biological fluids with integrated sample preparation steps prior to characterizing biomarker content via immunosubtraction PAGE. Results indicate the ability to rapidly identify and differentiate CSF from nasal mucus based on their biomarker profile in less than 5 minutes.
Shared Nearest-Neighbor Quantum Game-Based Attribute Reduction With Hierarchical Coevolutionary Spark and Its Application in Consistent Segmentation of Neonatal Cerebral Cortical Surfaces (2018)

The unprecedented increase in data volume has become a severe challenge for conventional patterns of data mining and learning systems tasked with handling big data. The recently introduced Spark platform is a new processing method for big data analysis and related learning systems, which has attracted increasing attention from both the scientific community and industry. In this paper, we propose a shared nearest-neighbor quantum game-based attribute reduction (SNNQGAR) algorithm that incorporates the hierarchical coevolutionary Spark model. We first present a shared coevolutionary nearest-neighbor hierarchy with self-evolving compensation that considers the features of nearest-neighborhood attribute subsets and calculates the similarity between attribute subsets according to the shared neighbor information of attribute sample points. We then present a novel attribute weight tensor model to generate ranking vectors of attributes and apply them to balance the relative contributions of different neighborhood attribute subsets. To optimize the model, we propose an embedded quantum equilibrium game paradigm (QEGP) to ensure that noisy attributes do not degrade the big data reduction results. A combination of the hierarchical coevolutionary Spark model and an improved MapReduce framework is then constructed that it can better parallelize the SNNQGAR to efficiently determine the preferred reduction solutions of the distributed attribute subsets. The experimental comparisons demonstrate the superior performance of the SNNQGAR, which outperforms most of the state-of-the-art attribute reduction algorithms. Moreover, the results indicate that the SNNQGAR can be successfully applied to segment overlapping and interdependent fuzzy cerebral tissues, and it exhibits a stable and consistent segmentation performance for neonatal cerebral cortical surfaces.
Room-temperature capsule-shaped wavelength-scale metal-clad laser operating at 1550 nm (2017)

We fabricate a capsule-shaped metal-clad wavelength-scale cavities on InP and demonstrate room-temperature lasing at 1550-nm wavelength. By introducing an optimized curvature to the sidewalls of a conventional rectangular metal-clad laser, we effectively reduce the optical loss of transverse-electric (TE) mode and experimentally confirm, for the first time, clear improvement in side mode suppression ratio and slope efficiency of the laser under pulsed optical pumping.
A mixed-signal correlator for acoustic transient classification (2002)

Correlation computations are widely used in template-based temporal pattern recognition, but are expensive to compute in real time on DSP systems. We have designed and fabricated a low-power chip which uses current-mode analog circuits to compute the correlation between an auditory input signal in the time-frequency domain and a stored binary template. We use a bucket-brigade device (BED) to accumulate partial column sums over time at rates consistent with the auditory-band input. Experimental results of the correlator demonstrate its correct operation over a wide range of operating frequencies.
Hospital Resource Utilization for Primary and Revision Total Hip Arthroplasty (2005)

At one institution, hospital resource utilization for revision total hip arthroplasty was found to be significantly higher than that for primary arthroplasty. This information is not reflected by current United States Medicare hospital reimbursement, which is the same for all lower-extremity arthroplasty procedures, regardless of the diagnosis, the complexity of the procedure, or the patient's baseline medical health. If these findings are generalizable to other institutions, appropriate reimbursement formulas should be developed to accurately reflect the true costs of caring for patients with a failed total hip arthroplasty.
Observation of n = 2–3 and n = 3–4 transitions in Li-like ions of P, S, Cl, and K in plasmas produced by line-focus laser irradiation (1989)

Transitions of the type n = 2–3 and n = 3–4 in P xiii, S xiv, Cl xv, and K xvii were observed in the spectra from linear plasmas. The 3d–4f transitions were observed in all four ions and are of potential interest for x-ray lasers. The wavelengths of the transitions were determined with an uncertainty of ±0.010 Å, and the observed wavelengths are compared with predicted and calculated values.
Structural and electrical properties of metastable defects in hydrogenated amorphous silicon (2015)

The structural and electrical properties of metastable defects in various types of hydrogenated amorphous silicon have been studied using a powerful combination of continuous wave electron-paramagnetic resonance spectroscopy, electron spin echo (ESE) decay measurements, and Doppler broadening positron annihilation spectroscopy. The observed dependence of the paramagnetic defect density on the Doppler $S$ parameter indicates that porous, nanosized void-rich materials exhibit higher spin densities, while dense, divacancy-dominated materials show smaller spin densities. However, after light soaking more similar spin densities are observed, indicating a long-term defect creation process in the Staebler-Wronski effect that does not depend on the a-Si:H nanostructure. From ESE decays it appears that there are fast and slowly relaxing defect types, which are linked to various defect configurations in small and large open volume deficiencies. A nanoscopic model for the creation of light-induced defects in the a-Si:H nanostructure is proposed.
Protective Effects of Anthocyanins in Obesity‐Associated Inflammation and Changes in Gut Microbiome (2019)

Obesity is a complex disease and a major public health epidemic. Chronic, low-grade inflammation is a common underlying feature of obesity and associated metabolic diseases; adipose tissue is a major contributor to this systemic inflammation. Evidence shows that obesity-associated inflammation may originate from gut dysfunction, including changes in intestinal bacteria or microbiome profiles. Increasingly, food and plant bioactive compounds with antioxidant and anti-inflammatory properties are proposed to ameliorate obesity-associated inflammation. Among these, the health-promoting effects of anthocyanin-rich foods are of interest here. Specifically, this review summarizes the reported benefits of anthocyanins in obesity-associated inflammation and underlying molecular mechanisms, including the role of gut microbiome and cell signaling pathways regulated by anthocyanins both in vivo and in vitro.
Turning bubbles on and off during boiling using charged surfactants (2015)

Boiling--a process that has powered industries since the steam age--is governed by bubble formation. State-of-the-art boiling surfaces often increase bubble nucleation via roughness and/or wettability modification to increase performance. However, without active in situ control of bubbles, temperature or steam generation cannot be adjusted for a given heat input. Here we report the ability to turn bubbles 'on and off' independent of heat input during boiling both temporally and spatially via molecular manipulation of the boiling surface. As a result, we can rapidly and reversibly alter heat transfer performance up to an order of magnitude. Our experiments show that this active control is achieved by electrostatically adsorbing and desorbing charged surfactants to alter the wettability of the surface, thereby affecting nucleation. This approach can improve performance and flexibility in existing boiling technologies as well as enable emerging or unprecedented energy applications.
Collagen type II is downregulated in the degenerative nucleus pulposus and contributes to the degeneration and apoptosis of human nucleus pulposus cells (2017)

Degenerative disc disease (DDD) is a common degenerative condition initiated mainly within the nucleus pulposus (NP). To date, the etiopathogenesis of DDD remains unclear, and because no effective therapeutic strategies are available to target its pathological processes, DDD is still treated with symptomatic interventions that are far from adequate. Collagen type II is one of the major matrix components of the NP, and is considered to be essential to NP homeostasis. However, the specific mechanisms by which collagen type II influences NP cells remain unknown. In the present study, collagen type II expression was detected using immunohistochemistry analysis and quantitative polymerase chain reaction, and it was demonstrated to be significantly downregulated in NP tissues from patients with DDD compared with nondegenerative controls. To further explore the mechanism in vitro, interleukin (IL)‑1β stimulation was used to induce degeneration of a human NP cell line. IL‑1β stimulation upregulated both the mRNA and protein levels of the catabolic markers matrix metalloproteinase 13 (MMP13) and a disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4), while it downregulated the anabolic makers aggrecan and collagen type II. However, addition of purified collagen type II prevented this IL‑1β‑induced metabolic disturbance of the NP cells. Furthermore, IL‑1β stimulation significantly promoted apoptosis in NP cells, while collagen type II treatment decreased the apoptotic rate and the protein levels of cleaved caspase‑3. In conclusion, collagen type II exhibited protective effects in suppressing NP cell degeneration through its anticatabolic, proanabolic and antiapoptotic effects, suggesting that it may be a promising therapeutic agent for the prevention and treatment of DDD.
Dynamic and composable trust for indirect interactions (2006)

The diversity of the kinds of interactions between principals in distributed computing systems has expanded rapidly in recent years. However, the state of the art in trust management is not yet sufficient to support this diversity of interactions. This dissertation presents a rationale and design for much richer trust management than it is possible today. To do so, it presents a set of requirements for more generalized trust management, an analysis of why they are needed, and how the state of the art in trust management to date does not meet them. It then presents the design of Hestia, our trust management framework. Hestia supports dynamic trust, which enables the specification and management of trust relationships which can be re-evaluated over the lifetime of a relationship. Hestia also supports the composition of trust relationships, which supports indirect interactions between principals as is the case with publish-subscribe systems. Finally, Hestia handles trust for both access control purposes and for reasoning about the quality of (possibly aggregated) data provided by a set of principals. This dissertation also presents formalisms for dynamic and composable trust.
Architectured Interfaces and Electrochemical Modeling in an Anode Supported SOFC (2017)

This work is dedicated to the development of a numerical model to optimize the anodeelectrolyte interface geometry for improving the electrochemical performance of a SOFC cell in a 3- Dimensional SOFC simulation process. A SOFC repeated unit composed of anode, electrolyte and cathode is taken as a modeling target. The model is implemented by considering electron and ions conservation, gas transport and electrochemical reaction kinetics in FEM (finite element method) software COMSOL Multiphysics. Four different interface geometriesâ€”flat, pyramid, ellipsoid and cube, which are predicted to show better electrochemical performance due to increased TPBs and less activation resistance, are investigated to find the best morphology according to their simulated performance. Results reveal that the cubic interface case achieves the highest current density at fixed 0.7V cell operating voltage, 63.55% higher than the flat reference interface. Distribution of different electrochemical variables is also obtained in each condition, giving valuable information for further optimization.
Systems identification with fuzzy spline wavelets (2002)

This paper describes the use of a nonlinear modeling procedure-building a fuzzy spline wavelets (FSW) model. FSW models are produced with a two step process: in the first step, the data set is compressed and denoised with the use of the fast wavelet transform; and in the second stage, the results of the first stage are presented as a fuzzy rule base with the use of linguistic variables. The hybrid model enjoys the excellent numerical and computational characteristics of the fast wavelet transform, combined with the ability to describe the accumulated knowledge in a human like way, in the form of simple IF...THEN rules using linguistic variables. The method is demonstrated for a truck backing problem.
Effect of Plasma Osmolality on Resistance to Blood Flow through Skeletal Muscle (1968)

SummaryThe gastrocnemious-plantaris muscle group of the dog was pump-perfused at constant flow with fresh plasma from a donor dog. When the osmolality of the perfusing plasma was increased by adding sodium chloride, glucose, sucrose, mannitol, dextran, or urea, the resistance to flow through the muscle decreased. The decrease in resistance was proportional to the increase in plasma osmolality. When distilled water was added to the plasma to decrease the osmolality, the resistance to flow through the muscle increased in proportion to the decrease in osmolality. The response to most test substances persisted for at least 20 min. These data suggest a mechanism regulating blood flow in resting muscle that is sensitive to osmolar concentration differences.
Mileage Traveled, Driving Time, and Speeding Behavior as Predictors for Hazmat Transportation Risk Assessment Using Naturalistic Driving Data (2019)

The crashes involving HAZMAT vehicles can easily lead to serious social impact. The results from many researches have proved that risk assessment of transportation procedure was one effective approach for safety improvement. As a result, quantitative risk modeling methods like driving scale, driving rating, usage based insurance model have been popularly developed, but all the above mentioned methods were mainly implemented in passenger vehicles. Therefore, the present study attempt to investigate the HAZMAT transportation risk modeling by integrating three factors as mileage traveled, driving time and speeding behavior using the naturalistic transportation vehicle driving data. Thirty-nine HAZMAT transportation vehicles were installed with on-board diagnostic (OBD) vehicle data recording systems and Advanced Driving Assistance Systems (ADAS) with function delivering driving data to vehicle monitoring center through the cellular network. Two months of driving data including the variable of the mileage, time, and speeding were processed for risk assessment modeling. Analytic Hierarchy Process (AHP) method and Entropy Weight (EW) method was adopted to determine the weight of each variable. Comparison of the rating results for each vehicle driver indicated that, their rated risk level was consistent for different months. The frequency of safety-related events was significantly negative correlated with the rating scores. All these findings have demonstrated that the model proposed in this study was reliable for risk prediction for HAZMAT commercial transportation. The operation of commercial transportation could reduce the high-risk by adjusting the mileage traveled, driving time and enhance enforcement on speeding behavior.