gebhart/patrepeval huggingface dataset:
Sensing Matrix Design via Mutual Coherence Minimization for Electromagnetic Compressive Imaging Applications (2017)

Compressive sensing (CS) theory states that sparse signals can be recovered from a small number of linear measurements y = Ax using l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm minimization techniques, provided that the sensing matrix satisfies a restricted isometry property (RIP). Unfortunately, the RIP is difficult to verify in electromagnetic imaging applications, where the sensing matrix is computed deterministically. Although it provides weaker reconstruction guarantees than the RIP, the mutual coherence is a more practical metric for assessing the CS recovery properties of deterministic matrices. In this paper, we describe a method for minimizing the mutual coherence of sensing matrices in electromagnetic imaging applications. Numerical results for the design method are presented for a simple multiple monostatic imaging application, in which the sensor positions for each measurement serve as the design variables. These results demonstrate the algorithm's ability to both decrease the coherence and to generate sensing matrices with improved CS recovery capabilities.
Optimal Drug Cocktail Design: Methods for Targeting Molecular Ensembles and Insights from Theoretical Model Systems (2008)

Drug resistance is a significant obstacle in the effective treatment of diseases with rapidly mutating targets, such as AIDS, malaria, and certain forms of cancer. Such targets are remarkably efficient at exploring the space of functional mutants and at evolving to evade drug binding while still maintaining their biological role. To overcome this challenge, drug regimens must be active against potential target variants. Such a goal may be accomplished by one drug molecule that recognizes multiple variants or by a drug "cocktail"--a small collection of drug molecules that collectively binds all desired variants. Ideally, one wants the smallest cocktail possible due to the potential for increased toxicity with each additional drug. Therefore, the task of designing a regimen for multiple target variants can be framed as an optimization problem--find the smallest collection of molecules that together "covers" the relevant target variants. In this work, we formulate and apply this optimization framework to theoretical model target ensembles. These results are analyzed to develop an understanding of how the physical properties of a target ensemble relate to the properties of the optimal cocktail. We focus on electrostatic variation within target ensembles, as it is one important mechanism by which drug resistance is achieved. Using integer programming, we systematically designed optimal cocktails to cover model target ensembles. We found that certain drug molecules covered much larger regions of target space than others, a phenomenon explained by theory grounded in continuum electrostatics. Molecules within optimal cocktails were often dissimilar, such that each drug was responsible for binding variants with a certain electrostatic property in common. On average, the number of molecules in the optimal cocktails correlated with the number of variants, the differences in the variants' electrostatic properties at the binding interface, and the level of binding affinity required. We also treated cases in which a subset of target variants was to be avoided, modeling the common challenge of closely related host molecules that may be implicated in drug toxicity. Such decoys generally increased the size of the required cocktail and more often resulted in infeasible optimizations. Taken together, this work provides practical optimization methods for the design of drug cocktails and a theoretical, physics-based framework through which useful insights can be achieved.
P1‐139: TESTS OF DISEASE RISK VERSUS AGE AT ONSET: A POWER COMPARISON (2019)

Genetic tests for risk typically compare genotype (or allele) frequencies between affected and unaffected individuals. Genetic variants showing significant differences with such a case-control test may directly or indirectly influence one's risk of developing disease. Some genes may instead control the timing of disease, or age at onset (AAO). We can test for AAO effects by looking for association between genotypes and AAO as a quantitative variable in a group of cases. APOE is an example of a gene that shows both risk and AAO effects in Alzheimer disease (AD). With large enough samples, this effect should be detectable with both risk and AAO tests, but the tests may have different power. Here, we compare the power of the case-control risk test and a case-only AAO test under a variety of genetic models. We propose a genetic model for AAO and use this to analytically compute the required sample size for 80% power for the Cochran-Armitage trend case-control test for risk and a linear regression model (with additive genotypic values) case-only test for AAO. We also compare power of a joint test for risk and AAO. APOE genotypes are used as an example in an AD dataset of 467 cases and 640 controls. We find that neither risk nor AAO test is most powerful in all situations. In general, when there is little heterogeneity, the risk test has more power than the AAO test (with equivalent sample sizes), but when the model is complex (e.g., with heterogeneity or reduced penetrance), this pattern reverses. We find that the joint test tends to have more power than either test individually. The results for APOE show the expected trend, given the established strong effect of APOE on AD: The joint test is the most significant (p=6.36 x 10−51), followed by the risk test (p=4.46 x 10−42), followed by the AAO test (p=9.55 x 10−12). A test for risk will be most powerful for variants with strong, homogeneous effects. With heterogeneity, AAO tests can be more powerful. Joint tests for risk and AAO may be preferred in general situations.
Executive Function Predicting Longitudinal Change in Type 1 Diabetes Management During the Transition to Emerging Adulthood (2018)

Abilities involved in performance on EF tests may be one resource for maintaining better glycemic control during the transition to emerging adulthood. Assessment of such EF abilities may allow for the identification of individuals who are most at risk for deterioration of glycemic control during this transition.
Helicopter Noise Source Separation Using an Order Tracking Filter (2022)

Due to the importance of understanding the aeroacoustics of rotorcraft with continually changing noise sources, this paper presents a new technique for source separation from ground-based acoustic measurements. The source separation process is based on combining a time-domain de-Dopplerization method with the Vold-Kalman (VK) order tracking filter approach. This process can extract rotor harmonic noise even when the sources are continuously changing with time, including impulsive events such as Blade Vortex Interaction (BVI) noise. The advantage of this approach over traditional methods such as harmonic averaging is that the phase and amplitude relationship of acoustic signals is preserved throughout the extraction process. The approach is applied to the measured acoustic data from a Bell 430 helicopter. The measured data were separated into main rotor harmonic, tail rotor harmonic, and broadband residual components. For steady-state conditions, the extracted components could be de-propagated to form acoustic spheres showing the directivity of the separated main and tail rotor components. The source separation process was also applied to a maneuvering flight condition. Each component has different pulse shapes and directivity trends, consistent with aeroacoustic theory.
Mortandad Canyon seismic modeling (Progress Report) (2016)

The goal of this project is to assess site amplification for LANL through modeling of site and topography effects. Such assessment is difficult due to the lack of data documenting site effects for large normal faulting earthquakes such as the Pajarito Fault System that was found to be governing the seismic hazard at LANL. LANL site is also characterized by unique geologic settings, a series of mesa at the edge of the huge volcanic complex of the Jemez caldera. The latter has produced a series of successive and intertwined deposits of volcanic flow and sedimentary layer. Such layering of material with different elastic properties is expected to create large amplification effects magnified further by the presence at the surface of tuff materials. In 2014, a seismic campaign was performed in the Mortandad Canyon with a network of sensors on and near a local mesa. That campaign was designed to provide experimental data to estimation and prediction of amplification and site effects at LANL. An analysis on the seismic noise records of that campaign shows evidence of amplification of the seismic amplitude for the stations on the top of the mesa. Our goal is to reproduce the effect observed (both retrieving the resonance frequencies and amplification levels). We also plan to test if amplification effects observed for seismic noise can be extended to shaking produced by earthquakes. We are using a 3D modeling tool based on the Spectral Element Method (SEM) that is a particular type of high-order finite element modeling. Two types of seismic sources will be considered: (1) earthquakes for purpose of seismic hazard evaluation, (2) ambient noise. We show 2 series of numerical computations: (1) seismic waves are generated by random sources to simulate ambient noise. (2) seismic waves are planar waves to simulate a distant earthquake. We plan in the future to model rupture scenario on the Pajarito Fault System.
Distillation (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDistillationArthur. RoseCite this: Anal. Chem. 1950, 22, 1, 59–61Publication Date (Print):January 18, 1950Publication History Published online1 May 2002Published inissue 18 January 1950https://pubs.acs.org/doi/10.1021/ac60037a015https://doi.org/10.1021/ac60037a015research-articleACS PublicationsRequest reuse permissionsArticle Views242Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
E-036 New in vitro AVM model with realistic nidus for simulation and flow analysis (2020)

<h3>Background</h3> In vitro vascular models for brain aneurysms and acute stroke have been used for training, simulation and research purpose. However, the use of realistic in vitro models for arteriovenous malformation (AVM) have not been reported. Current in vitro AVM models analyzing the efficacy of embolic materials or flow conditions are limited due to a lack of realistic anatomical and dynamic features of complex nidus. <h3>Materials and Methods</h3> 3D AVM nidus images were extracted and segmented from 3D rotational angiography from a patient. Additional artificial feeders and drainers were attached to the AVM nidus. The inner vascular mold was printed using a plastic 3D printer. The inner mold was coated with silicone and then removed with acetone, leaving a hollow AVM model. Injections of liuid embolic material and 4D flow MRI were performed using the 3D in vitro AVM model. Computational fluid dynamics (CFD) analysis was also performed to compare the flow volume and velocity to 4D flow MRI <h3>Results</h3> The created in vitro AVM models had realistic representation of nidus vasculature and complexity derived from patients. The injection of liquid embolic material performed in this model replicated real-life treatment conditions. The plug and push technique was successfully simulated to penetratreliquid embolic material into the AVM nidus. The flow data from 4D flow MRI were comparable to CFD analysis. <h3>Conclusions</h3> An in vitro human brain AVM model with realistic complexities of nidus was successfully manufactured using 3D printing technology. The model demonstrated realistic pliability during the liquid embolic material injection and also feasibility of flow analysis. This in vitro AVM model may represent a valuable tool for simulation, flow research and development of new materials or technique. <h3>Disclosures</h3> <b>N. Kaneko:</b> None. <b>H. Ullman:</b> None. <b>F. Ali:</b> None. <b>P. Berg:</b> 1; C; German Research Foundation, Federal Ministry of Education and Research within the Forschungscampus STIMULATE. <b>Y. Ooi:</b> None. <b>S. Tateshima:</b> 2; C; Cerenovus, Medtronic, Stryker. <b>G. Colby:</b> 2; C; Medtronic, Microvention, Stryker. <b>Y. Komuro:</b> None. <b>P. Hu:</b> None. <b>V. Szeder:</b> None. <b>M. Nour:</b> None. <b>L. Guo:</b> None. <b>A. Chien:</b> None. <b>F. Vinuela:</b> None. <b>S. Nemoto:</b> None. <b>J. Hinman:</b> None. <b>G. Duckwiler:</b> 1; C; Tarsadia Foundation. 2; C; Medtronic. <b>R. Jahan:</b> None.
Language Muse: Automated Linguistic Activity Generation for English Language Learners (2016)

Current education standards in the U.S. require school students to read and understand complex texts from different subject areas (e.g., social studies). However, such texts usually contain figurative language, complex phrases and sentences, as well as unfamiliar discourse relations. This may present an obstacle to students whose native language is not English — a growing sub-population in the US. 1 One way to help such students is to create classroom activities centered around linguistic elements found in subject area texts (DelliCarpini, 2008). We present a web-based tool that uses NLP algorithms to automatically generate customizable linguistic activities that are grounded in language learning research.
Optical Encoding by Plasmon-Based Patterning: Hard and Inorganic Materials Become Photosensitive (2011)

The photosensitivity of nanocomposite AlN films with embedded silver nanospheres is reported. It stems from localized surface plasmon resonances (LSPR) whose modulation is photoinduced by laser annealing that induces a combined effect of metallic nanoparticle enlargement and dielectric matrix recrystallization; the photoindunced changes of the refractive index of the matrix result in strong spectral shift of LSPR. We demonstrate the utilization of this process for spectrally selective optical encoding into hard, durable, and chemically inert films.
NANO HIGHLIGHT Clusters to Nanoparticles: Implications for Atmospheric Nucleation (2005)

It is known that new particles formed by nucleation are observed in the atmospheric on about 20% of days [1], and that these particles can grow to sizes large enough to serve as cloud condensation nuclei during the course of a day. Proposed nucleation mechanisms include ion induced nucleation and multicomponent nucleation of electrically neutral species. Existing theories, however, do not accurately predict rates of particle production that are observed in the atmosphere. Because of the likely impact of nucleated particles on cloud cover (and therefore on the earth’s radiative energy balance), it is important to have nucleation models that are sufficiently accurate to be used in climate models. This project is designed to provide information that can be used to develop such models. We plan to measure the distributions of electrically neutral clusters and nanoparticles in nucleating systems. The measured cluster masses will also provide information about species contained in the nucleated clusters. These measurements will be used to infer kinetic information on rates of forward and reverse reactions on molecular clusters that ultimately determine nucleation rates. The work involves developing a chemical ionization mass spectrometer for measuring cluster distributions, and using it in laboratory and atmospheric measurements. We also plan to extend aerosol instrumentation to sizes smaller than 3 nm with the eventual goal of bridging the gap between measurements of molecules, clusters and nanoparticles.
Outer membrane protein composition of Yersinia pestis at different growth stages and incubation temperatures (1980)

The protein composition of the outer membrane of Yersinia pestis grown at 26 and at 37 degrees C was examined. The outer membrane was isolated by isopycnic sucrose density centrifugation, and its degree of purity was determined with known inner and outer membrane components. Using two-dimensional gel electrophoresis, we identified a large number of heat-modifiable proteins in the outer membrane of cells grown at either incubation temperature. One-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of heated preparations indicated five proteins in the outer membrane of 37 degrees C-grown cells not evident in 26 degrees C-grown cells. Differences in the protein composition of the outer membrane due to the stage of growth were evident at both 26 degrees C and 37 degrees C, although different changes were found at each temperature. When cell envelopes were examined for the presence of peptidoglycan-associated proteins, no differences were seen as a result of stage of growth. Envelopes from 26 degrees C-grown cells yielded two peptidoglycan-associated proteins, E and J. Cells grown at 37 degrees C, however, also contained an additional protein (F) which was not found in either the bound or free form 26 degrees C. The changes in outer membrane protein composition in response to incubation temperature may relate to known nutritional and antigenic changes which occur under the same conditions.
Power density improvement of the power conditioning circuit for combined piezoelectric and electrodynamic generators (2016)

In this study, we report a power management circuit for a combined piezoelectric- electrodynamic generator. A piezoelectric element is bonded to a spring steel cantilever beam and a magnet, used as tip mass, oscillates through a coil. This principle creates the combined generator. A test setup has been created to automate the characterization of the piezoelectric generator and its power management circuit. Three different power management circuits for the piezoelectric part of the combined generator have been analysed: a bridge rectifier, an SSHI circuit with an external inductance and an SSHI circuit which utilizes the coil of the electrodynamic generator as circuit element. The three circuits are compared in terms of their output power, efficiency and power density. The SSHI circuit with an external inductance has the highest output power and efficiency, followed by the SSHI circuit with the electrodynamic generator coil. The power density of the bridge rectifier is t he highest but for higher efficiency the power density of the SSHI circuit with the coil of the electromagnetic generator reaches the best results.
Cloning and characterization of a novel functional organic anion transporting polypeptide 3A1 isoform highly expressed in the human brain and testis (2022)

Organic anion transporting polypeptide 3A1 (OATP3A1, encoded by the <i>SLCO3A1</i> gene) is a prostaglandin, oligopeptide, and steroid/thyroid hormone transporter with wide tissue distribution, expressed, e.g., in the human brain and testis. Although the physiological importance of OATP3A1 has not yet been clarified, based on its expression pattern, substrate recognition, and evolutionary conservation, OATP3A1 is a potential pharmacological target. Previously, two isoforms of OATP3A1, termed as V1 and V2, have been characterized. Here, we describe the cloning and functional characterization of a third isoform, OATP3A1_V3. The mRNA of isoform V3 is formed by alternative splicing and results in an OATP3A1 protein with an altered C-terminus compared to isoforms V1 and V2. Based on quantitative PCR, we demonstrate the widespread expression of SLCO3A1_V3 mRNA in human organs, with the highest expression in the brain and testis. By generation of an isoform V3-specific antibody and immunostaining, we show that the encoded protein is expressed in the human choroid plexus, neurons, and both germ and Sertoli cells of the testis. Moreover, we demonstrate that in contrast to isoform V1, OATP3A1_V3 localizes to the apical membrane of polarized MDCKII cells. Using HEK-293 cells engineered to overexpress OATP3A1_V3, we verify the protein's functionality and identify dehydroepiandrosterone sulfate as a novel OATP3A1 substrate. Based on their distinct expression patterns but overlapping functions, OATP3A1 isoforms may contribute to transcellular (neuro)steroid transport in the central nervous system.
Use and interpretation of on/off diaries in Parkinson's disease (2004)

The data provide support for the overall accuracy and validity of the four category CAPSIT-PD on/off diary, but suggest that a three category diary format may improve accuracy and validity. Interpretation of diary data beyond the assessed time frame should be made with caution unless diaries have been kept for sufficiently long periods.
Two-Time Scale Stabilization of a Flexible Arm With Output Feedback (1989)

This paper presents an approach to designing a control system with output feedback for a lightweight flexible arm. A two-time scale dynamic model is obtained, which allows the adoption of a composite control strategy. First a slow control can be designed for the slow (rigid) subsystem, then a fast stabilising control for the fast (flexible) subsystem. The problem of the lack of full state measurements concerned with the fast control design is solved. An output feedback low order dynamic compensator is designed, whose optimal gains are computed via a convergent numerical algorithm. Also, a more robust design can be achieved if a loop transfer recovery procedure is introduced. The design procedure is finally tested by means of nonlinear simulation results for the flexible arm.
Producing and evaluating a novel lentiviral vector for β-thalassaemia gene therapy (2012)

The β-haemoglobinopathies are of the most prevalent inherited disorders worldwide. β-thalassaemia is a single gene disorder affecting the β-globin gene, thus resulting in a lack or depleted availability of β -globin for formation of haemoglobin. β-thalassaemia has become a target for gene therapy based treatments in hope of a cure, or significant phenotype amelioration. The technique aims to treat the haematopoietic stem cells (HSC) of patients with the viral vectors ex vivo, in the hope of significant β -globin mRNA transcript production on HSC erythroid differentiation post re-transplantation. Numerous investigations have been conducted in the use of Lentiviral vectors harbouring human β-globin transcription units, only one of which has proceeded into clinical trials (Cavazzana-Calvo, Payen et al. 2010). The ultimate aim of all 'construct' designs is to present significant phenotype amelioration with an average of one vector copy number (VCN) per HSC.