gebhart/patrepeval huggingface dataset:
MO‐C‐17A‐03: A GPU‐Based Method for Validating Deformable Image Registration in Head and Neck Radiotherapy Using Biomechanical Modeling (2014)

Purpose: Deformable image registration (DIR) plays a pivotal role in head and neck adaptive radiotherapy but a systematic validation of DIR algorithms has been limited by a lack of quantitative high‐resolution groundtruth. We address this limitation by developing a GPU‐based framework that provides a systematic DIR validation by generating (a) model‐guided synthetic CTs representing posture and physiological changes, and (b) model‐guided landmark‐based validation. Method: The GPU‐based framework was developed to generate massive mass‐spring biomechanical models from patient simulation CTs and contoured structures. The biomechanical model represented soft tissue deformations for known rigid skeletal motion. Posture changes were simulated by articulating skeletal anatomy, which subsequently applied elastic corrective forces upon the soft tissue. Physiological changes such as tumor regression and weight loss were simulated in a biomechanically precise manner. Synthetic CT data was then generated from the deformed anatomy. The initial and final positions for one hundred randomly‐chosen mass elements inside each of the internal contoured structures were recorded as ground truth data. The process was automated to create 45 synthetic CT datasets for a given patient CT. For instance, the head rotation was varied between +/− 4 degrees along each axis, and tumor volumes were systematically reduced up to 30%. Finally, the original CT and deformed synthetic CT were registered using an optical flow based DIR. Results: Each synthetic data creation took approximately 28 seconds of computation time. The number of landmarks per data set varied between two and three thousand. The validation method is able to perform sub‐voxel analysis of the DIR, and report the results by structure, giving a much more in depth investigation of the error. Conclusions: We presented a GPU based high‐resolution biomechanical head and neck model to validate DIR algorithms by generating CT equivalent 3D volumes with simulated posture changes and physiological regression.
Expression and delivery of an endolysin to combat Clostridium perfringens (2013)

Clostridium perfringens is a cause for increasing concern due to its responsibility for severe infections both in humans and animals, especially poultry. To find new control strategies to treat C. perfringens infection, we investigated the activity and delivery of a bacteriophage endolysin. We identified a new endolysin, designated CP25L, which shows similarity to an N-acetylmuramoyl-L-alanine amidase domain and is distinct from other C. perfringens endolysins whose activity has been demonstrated in vitro. The cp25l gene was cloned and expressed in Escherichia coli, and the gene product demonstrated lytic activity against all 25 C. perfringens strains tested. The probiotic strain Lactobacillus johnsonii FI9785 was engineered to deliver the endolysin to the gastrointestinal tract. The integration of the nisRK two-component regulatory system from the Lactococcus lactis nisin A biosynthesis operon into the chromosome of L. johnsonii allowed constitutive expression of the endolysin under the control of the nisA promoter (P nisA ), while the use of a signal peptide (SLPmod) led to successful secretion of the active endolysin to the surrounding media. The high specificity and activity of the endolysin suggest that it may be developed as an effective tool to enhance the control of C. perfringens by L. johnsonii in the gastrointestinal tract.
Wide field-of-view imaging system using a liquid crystal spatial light modulator (2005)

This paper presents the optical design and experimental demonstration of a compact, foveated, wide field-of-view (FOV) imaging system using two lenses and a liquid crystal spatial light modulator (SLM). The FOV of this simple doublet system is dramatically improved by the SLM, which can be programmed to correct all the geometrical aberrations at any particular field angle. The SLM creates a variation in the image quality across the entire FOV, with a diffraction-limited performance at the field angle of interest (similar to the foveated human vision). The region of interest can be changed dynamically, such that any area within the FOV of the system can be highly resolved within milliseconds. The wide FOV, compactness, and absence of moving parts make this system a good candidate for tracking and surveillance applications. We designed an f/7.7 system, with a 60° full FOV, and a 27 mm effective focal length. Only two lenses and a beam splitter cube were used along with a reflective SLM. The theoretical wavefront aberration coefficients were used to program the SLM, which was placed in the pupil plane of the system. A prototype was built and the system was experimentally demonstrated using monochromatic light and a CCD camera.
Effect of thickness and carrier density on the optical polarization of Al0.44Ga0.56N/Al0.55Ga0.45N quantum well layers (2014)

The thickness and carrier density of AlGaN quantum well (QW) layers have a strong influence on the valence subband structure, and the resulting optical polarization and light extraction of ultraviolet light-emitting diodes. An ultraviolet-emitting (270–280 nm) multiple quantum well heterostructure consisting of 3 periods of Al0.44Ga0.56N/Al0.55Ga0.45N with individual layer thicknesses between 2–3.2 nm is studied both experimentally and theoretically. The optical polarization changes to preferentially polarized perpendicular to the QW plane as the QW thickness increases or the carrier density increases. Calculations show these trends are due to (a) a larger decrease in overlap of conduction band to light and heavy hole envelope functions compared to crystal-field split-off envelope functions, and (b) coupling between the valence subbands where higher heavy hole subbands couple to lower light hole and crystal-field split-off subbands. These changes in the valence band have a profound effect on the optical polarization, emission patterns, and eventual light extraction for ultraviolet emitters at these compositions and thicknesses, and need to be controlled to ensure high device efficiency.
Novel highly efficient in-band pump wavelengths for Ho-doped fiber amplifiers (2021)

We report the design and performance of Holmium-doped fiber amplifiers (HDFAs) with novel alternative in-band pump wavelengths in the 1720—2000 nm spectral region. We demonstrate through simulations that pump wavelengths of 1840—1860 nm can yield significantly improved output power (3—6 dB), gain (8—10 dB) , and optical-optical conversion efficiency compared to the previous technical and industry standard pump wavelength of 1940 nm. Experimental results fully confirm our simulations.
Effect of Chemical Permeation Enhancers on Skin Permeability: In silico screening using Molecular Dynamics simulations (2019)

Breaching of the skin barrier is essential for delivering active pharmaceutical ingredients (APIs) for pharmaceutical, dermatological and aesthetic applications. Chemical permeation enhancers (CPEs) are molecules that interact with the constituents of skin's outermost and rate limiting layer stratum corneum (SC), and increase its permeability. Designing and testing of new CPEs is a resource intensive task, thus limiting the rate of discovery of new CPEs. In-silico screening of CPEs in a rigorous skin model could speed up the design of CPEs. In this study, we performed coarse grained (CG) molecule dynamics (MD) simulations of a multilayer skin lipid matrix in the presence of CPEs. The CPEs are chosen from different chemical functionalities including fatty acids, esters, and alcohols. A multi-layer in-silico skin model was developed. The CG parameters of permeation enhancers were also developed. Interactions of CPEs with SC lipids was studied in silico at three different CPE concentrations namely, 1% w/v, 3% w/v and 5% w/v. The partitioning and diffusion coefficients of CPEs in the SC lipids were found to be highly size- and structure-dependent and these dependencies are explained in terms of structural properties such as radial distribution function, area per lipid and order parameter. Finally, experimentally reported effects of CPEs on skin from the literature are compared with the simulation results. The trends obtained using simulations are in good agreement with the experimental measurements. The studies presented here validate the utility of in-silico models for designing, screening and testing of novel and effective CPEs.
Use of piezoelectric actuators as elements of intelligent structures (1987)

This work presents the analytic and experimental development of piezoelectric actuators as elements of intelligent structures, i.e., structures with highly distributed actuators, sensors, and processing networks. Static and dynamic analytic models are derived for segmented piezoelectric actuators that are either bonded to an elastic substructure or embedded in a laminated composite. These models lead to the ability to predict, a priori, the response of the structural member to a command voltage applied to the piezoelectric and give guidance as to the optimal location for actuator placement. A scaling analysis is performed to demonstrate that the effectiveness of piezoelectric actuators is independent of the size of the structure and to evaluate various piezoelectric materials based on their effectiveness in transmitting strain to the substructure. Three test specimens of cantilevered beams were constructed: an aluminum beam with surface-bonded actuators, a glass/epoxy beam with embedded actuators, and a graphite/epoxy beam with embedded actuators. The actuators were used to excite steady-state resonant vibrations in the cantilevered beams. The response of the specimens compared well with those predicted by the analytic models. Static tensile tests performed on glass/epoxy laminates indicated that the embedded actuator reduced the ultimate strength of the laminate by 20%, while not significantly affecting the global elastic modulus of the specimen.
A polarization technique for mitigating low-grazing-angle radar sea clutter (2017)

Traditional detection schemes in conventional maritime surveillance radars may suffer serious performance degradation due to sea clutter, particularly in low-grazing-angle (LGA) geometries. In such geometries, typical statistical assumptions regarding sea clutter backscatter do not hold. Trackers can be overwhelmed by false alarms, while objects of interest can be challenging to detect. Despite several decades of attempts to devise a means of mitigating the effects of LGA sea clutter on traditional detection schemes, minimal progress has been made in developing an approach that is both robust and practical. To supplement work exploring whether polarization information might offer an effective means of enhancing target detection in sea clutter, MIT Lincoln Laboratory (MIT LL) collected a fully polarimetric X-band radar dataset on the Atlantic coast of Massachusetts Cape Ann in October 2015. Leveraging this dataset, MIT LL developed Polarimetric Co-location Layering (PCL), an algorithm that uses a fundamental polarimetric characteristic of sea clutter to retain detections on objects of interest while reducing the number of false alarms in a conventional single-polarization radar by as many as two orders of magnitude. PCL is robust across waveform bandwidths, pulse repetition frequencies, and sea states. Moreover, PCL is practical: It can plug directly into the standard radar signal processing chain.
On‐Demand Control of the Photochromic Properties of Naphthopyrans (2018)

Photofunctional compounds have emerged as critically important materials for both fundamental studies and industrial applications. Control of the thermal decoloration speed to within several seconds while sustaining satisfactory photochromic colorability is an important challenge for the application of such materials to photochromic lenses and smart windows. Photochromic naphthopyran derivatives are utilized for photochromic lenses because of their high durability and easily controllable colorability. However, the residual color imparted by the long-lived transient species upon ceasing light irradiation remains a hindrance to practical applications. In this study, a strategy is demonstrated for on-demand control of the thermal decoloration speed of the transient colored species of naphthopyran derivatives. The increase in the ring-size of the alkylenedioxy moiety on the naphthopyrans accelerates the thermal back-reaction independently of the maximum-absorption wavelength of the colored isomer, leading to the realization of yellow-, red-, and blue-photochromic naphthopyrans with similar thermal fading speeds. This novel molecular design provides a strategy for the future development of advanced photoresponsive materials.
Automatic scheme selection for toolkit hex meshing (2000)

Current hexahedral mesh generation techniques rely on a set of meshing tools, which when combined with geometry decomposition leads to an adequate mesh generation process. Of these tools, sweeping tends to be the workhorse algorithm, accounting for at least 50 per cent of most meshing applications. Constraints which must be met for a volume to be sweepable are derived, and it is proven that these constraints are necessary but not sufficient conditions for sweepability. This paper also describes a new algorithm for detecting extruded or sweepable geometries. This algorithm, based on these constraints, uses topological and local geometric information, and is more robust than feature recognition-based algorithms. A method for computing sweep dependencies in volume assemblies is also given. The auto sweep detect and sweep grouping algorithms have been used to reduce interactive user time required to generate all-hexahedral meshes by filtering out non-sweepable volumes needing further decomposition and by allowing concurrent meshing of independent sweep groups. Parts of the auto sweep detect algorithm have also been used to identify independent sweep paths, for use in volume-based interval assignment. Published in 2000 by John Wiley & Sons, Ltd.
Adhesion of normal and Plasmodium falciparum ring–infected erythrocytes to endothelial cells and the placenta involves the rhoptry-derived ring surface protein-2 (2003)

Recent findings have challenged the current view of Plasmodium falciparum (P falciparum) blood-stage biology by demonstrating the cytoadhesion of early ring-stage-infected erythrocytes (rIEs) to host endothelial cells and placental syncytiotrophoblasts. The adhesion of rIEs was observed only in parasites that bind to the placenta via chondroitin sulfate A (CSA). In this work, a panel of mouse monoclonal antibodies (mAbs) that specifically inhibit cytoadhesion of rIEs but not of mature IEs was generated The previously described ring surface protein 2 (RSP-2), a 42-kDa protein, was identified as the target of the ring-stage-specific mAbs. Time course surface fluorescence experiments revealed a short overlap (approximately 4 hours) of expression between RSP-2 and P falciparum erythrocyte membrane protein 1 (PfEMP1). Their consecutive expression enables IEs to adhere to endothelial cells during the entire blood-stage cycle. During this study, a new phenotype was detected in parasite cultures, the adhesion of normal erythrocytes (nEs) to endothelial cells. All adherent nEs were coated with RSP-2. Immunolocalization studies show that RSP-2 is a rhoptry-derived protein that is discharged onto the erythrocyte membrane during contact with merozoites. Our results identify RSP-2 as a key molecule in sequestration of young blood-stage forms and nEs to endothelial cells.
Light-scattering method combined with production of fine particles by photochemical reaction for determination of silane in air (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLight-scattering method combined with production of fine particles by photochemical reaction for determination of silane in airHiroaki. Tao, Akira. Miyazaki, and Kenji. BanshoCite this: Anal. Chem. 1986, 58, 6, 1148–1152Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/ac00297a038https://doi.org/10.1021/ac00297a038research-articleACS PublicationsRequest reuse permissionsArticle Views44Altmetric-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
Comparison of PHOX2B Testing Methods in the Diagnosis of Congenital Central Hypoventilation Syndrome and Mosaic Carriers (2010)

Clinical diagnostic testing for congenital central hypoventilation syndrome (CCHS) usually involves amplification and detection by (1) targeted mutation analysis or (2) sequence analysis. Test method performance differences are more pronounced when studying difficult templates [eg, guanine-cytosine (GC)-rich regions] or samples with abnormal allele ratios (eg, mosaicism). CCHS, an autosomal dominant disorder with identified mosaic carriers, is caused by expansion mutations of the GC-rich polyalanine-coding region of the PHOX2B gene in greater than 90% of patients (and other PHOX2B mutations in remaining patients). The combination of a GC-rich testing region and known mosaicism in CCHS necessitates the determination of the limit of detection for diagnostic tests. This study compared the limit of detection in CCHS-PHOX2B testing for both targeted mutation analysis and sequence analysis. Test samples included 6 differentially sized PHOX2B expansion mutations and 1 PHOX2B deletion mutation, all diluted over a range of concentrations; and 2 mosaic dyads. The limit of detection for PHOX2B expansion mutations was 1% and 20% mutant allele concentration with targeted mutation analysis and sequence analysis, respectively. These results indicate that PHOX2B testing using targeted mutation analysis is more likely to identify even low-level mosaicism for polyalanine expansion and deletion mutations. However, sequencing of PHOX2B is required to detect single base-pair mutations that cause the remaining small subset of CCHS cases. A combination of both the tests may be required in cases in which 1 test fails to identify the disease-causing mutation. These results can help guide clinicians when choosing a CCHS/PHOX2B clinical diagnostic testing method and interpreting results.
Transforming growth factor-beta and suppression of carcinogenesis. (1989)

Transforming growth factor-beta (TGF-beta) plays an important role in controlling proliferation or differentiation in almost all epithelial tissues. The pathophysiology of TGF-beta during carcinogenesis is now an important area of investigation, since it appears that as the process of carcinogenesis progresses, epithelial cells often become refractory to the growth-regulatory actions of TGF-beta. In this article we consider the possible cellular and molecular bases for this phenomenon, and then discuss some pharmacological approaches to enhancing the synthesis or activity of TGF-beta. These approaches may provide new modalities for prevention of carcinogenesis, if they can be applied during the early stages of the disease process, before cells become refractory. We give particular attention to tamoxifen and retinoic acid, since it has been shown that these agents, which are of known efficacy for prevention of cancer, can markedly enhance the secretion of specific isotypes of TGF-beta by several types of cells.
Secondary Porosity and Permeability of Coal vs. Gas Composition and Pressure (2006)

Summary We have been investigating the sequestration of atmospheric pollutants by injection into coal seams while at the same time enhancing hydrocarbon productivity by displacement of methane with pollutants. Our effort is one of several field-based research efforts into CO2 storage in coal seams that are currently operating in Canada (Mavor et al. 2004), China (Robinson et al. 2004), Japan (Nago and Komaki 2004), and Poland (Van Bergen et al. 2004). During the course of our field measurements, we have been using single-well injection, soak, and production tests to collect data required to understand and predict enhanced coalbed methane (ECBM) recovery potential and sequestration capacity. We found that changing the composition of the gas sorbed into the coal changes the porosity and permeability of the coal natural-fracture system owing to gas-content changes, which cause matrix swelling or shrinkage due to relative adsorption of different gases. We collected sufficient information to develop a method for predicting the permeability and porosity of a coalbed as a function of the secondary porosity system (SPS) pressure and the gas content and composition of the primary porosity system (PPS). The method uses data from injection/falloff tests with water and/or a weaker adsorbing gas (WAG) than CH4 and a stronger adsorbing gas (SAG) than CH4. Estimates of effective permeability to gas and water obtained from these tests are used with an iterative computation procedure subject to constraints to solve for equivalent SPS porosity and absolute permeability at atmospheric pressure. Once calibrated, the model can be used to predict a coalbed's permeability and porosity as a function of injection pressure and injected-fluid composition, which in turn are used to predict injection performance. The model is applicable to production forecasts to account for SPS permeability and porosity changes as reservoir pressure declines with changes in gas composition. This paper describes the new model and discusses well-test procedures to obtain the data required for model calibration. Also included are coal property estimates resulting from Alberta Medicine River (Manville) coal core and test data and an example model calibration.