gebhart/patrepeval huggingface dataset:
Capsule Structural Heterogeneity and Antigenic Variation in Cryptococcus neoformans (2007)

Cryptococcus neoformans is a human pathogenic fungus with a capsule composed primarily of glucuronoxylomannan (GXM) that is important for virulence. Current views of GXM structure postulate a polymer composed of repeating mannose trisaccharide motifs bearing a single beta(1,2) glucuronic acid with variable xylose and O-acetyl substitutions to form six triads. GXM from different strains is notoriously variable in triad composition, but it is not known if the polymer consists of one or more motif-repeating units. We investigated the polymeric organization of GXM by using mass spectrometry to determine if its compositional motif arrangement was similar to that of bacterial capsular polysaccharides, namely, a polymer of a single repeating unit. The results were consistent with, and confirmatory for, the current view that the basic unit of GXM is a repeating mannose trisaccharide motif, but we also found evidence for the copolymerization of different GXM repeating units in one polysaccharide molecule. Analysis of GXM from isogenic phenotypic switch variants suggested structural differences caused by glucuronic acid positional effects, which implied flexibility in the synthetic pathway. Our results suggest that cryptococcal capsule synthesis is fundamentally different from that observed in prokaryotes and employs a unique eukaryotic approach, which theoretically could synthesize an infinite number of structural combinations. The biological significance of this capsule construction scheme is that it is likely to confer a powerful avoidance strategy for interactions with the immune system and phagocytic environmental predators. Consistent with this premise, the antigenic variation of a capsular epitope recognized by a nonprotective antibody was observed under different growth conditions.
Output Saturation in Electric Motor Systems: Identification and Controller Design (2010)

Input saturation is a well-known nonlinearity in mechanical control systems; it constrains the maximum acceleration, which results in the limitation of the system response time. Input saturation has been considered in controller design in various ways, e.g., antiwindup control. In addition to the input, the state variables of mechanical systems are often subjected to saturation. For example, the maximum angular velocity of electric motor systems is limited by the maximum voltage provided to the motor windings. In the case of electronically commutated motors (i.e., brushless dc motors), the maximum speed is additionally constrained by limitations of the servo amplifier output. If gears are utilized, further constraints are introduced due to resonances in ball bearings and/or velocity dependent friction. Although such factors are significant in practice, they have not been fully considered in controller design. This paper investigates the input and output saturations, and presents how they may be considered in the controller design; a Kalman filter, a PID controller, and a disturbance observer are designed, taking input/output saturations into consideration. A case study is provided to verify the proposed methods.
Leukocytapheresis Therapy by Extracorporeal Circulation Using A Leukocyte Removal Filter (1998)

Leukocytapheresis therapy has been used to try to treat such intractable diseases as autoimmune and neurologic diseases, achieving good results. However, a number of problems have been identified in leukocyte removal by thoracic duct drainage or continuous centrifugal separation; namely the high risk, expensive cost, and complicated operation. Asahi Medical Co. has developed an innovative solution for such conventional problems. Its new leukocyte removal filter (Cellsorba) is capable of removing white blood cells by perfusion of whole blood by means of simple extracorporeal circulation. Leukocytapheresis therapy using the Cellsorba column is being confirmed as extremely effective for many inflammatory diseases, as well as in autoimmune and neurologic diseases. This paper outlines information about the Cellsorba column and introduces several reports on therapeutic results.
Ring resonator with cascaded arrayed waveguide gratings for accurate insertion loss measurement (2016)

A device with two identical arrayed waveguide gratings (AWGs) in a DEMUX-MUX configuration within a ring resonator is proposed and modeled. This allows extracting the insertion loss of a single AWG, independent of the coupling efficiency, with less error than previous methods.
Supplementary Data 4 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome (2023)

Supplementary Data 4 from Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Rac1 and Nuclear Factor-κB and Correlate with Poor Patient Outcome
On kernel support for real-time multimedia applications (2003)

Real-time operating system services are required to support multimedia systems that rely heavily on the workstation processor for control of the audio and video processors and movement of audio and video data. The requirements for each service are described, together with the YARTOS kernel, an operating system kernel that provides real-time communication and computation services. The programming model supported by YARTOS is an extension of Wirth's discipline of real-time programming. In essence it is a message-passing system with a semantics of interprocess communication that specifies the real-time response that an operating system must provide to a message receiver. This allows a programmer to assert an upper bound on the time to receipt and processing of each message. The YARTOS kernel supports the notion of guaranteed processing rates. The desired processing rate of each task is made known to the kernel, and the kernel provides a guaranteed response time to each task that is sufficient for ensuring that the required processing rate is achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detection of photoreceptor disruption by adaptive optics fundus imaging and Fourier-domain optical coherence tomography in eyes with occult macular dystrophy (2011)

Structural changes of photoreceptors in OMD patients were detected tangentially by FD-OCT and en face by AO.
Reactions of the propynylium isomer manifold with acetylene and diacetylene in the gas phase (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of the propynylium isomer manifold with acetylene and diacetylene in the gas phaseF. Ozturk, G. Baykut, M. Moini, and J. R. EylerCite this: J. Phys. Chem. 1987, 91, 16, 4360–4364Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/j100300a029https://doi.org/10.1021/j100300a029research-articleACS PublicationsRequest reuse permissionsArticle Views95Altmetric-Citations38LEARN 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 options Get e-Alerts
Biologically Inspired Mechanisms for Burrowing in Undersea Substrates (2011)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2011.
Intoxication Detection using Phonetic, Phonotactic and Prosodic Cues (2011)

In this paper, we investigate multiple approaches for automatically detecting intoxicated speakers given samples of their speech. Intoxicated speech in a given language can be viewed simply as a different accent of this language; therefore we adopt our recent approach to dialect and accent recognition to detect intoxication. The system models phonetic structural differences across sober and intoxicated speakers. This approach employs SVM with a kernel function that computes similarities between adapted phone GMMs which summarize speakers’ phonetic characteristics in their utterances. We also investigate additional cues, such as prosodic events, phonotactics and phonetic durations under intoxicated and sober conditions. We find that our phonetic-based system when combined with phonotactic features provides us with our best result on the official development set, an accuracy of 73% and an equal error rate of 26.3%, significantly higher than the official baseline.
Molecular Portraits and 70-Gene Prognosis Signature Are Preserved throughout the Metastatic Process of Breast Cancer (2005)

Microarray analysis has been shown to improve risk stratification of breast cancer. Breast tumors analyzed by hierarchical clustering of expression patterns of "intrinsic" genes have been reported to subdivide into at least four molecular subtypes that are associated with distinct patient outcomes. Using a supervised method, a 70-gene expression profile has been identified that predicts the later appearance or absence of clinical metastasis in young breast cancer patients. Here, we show that distant metastases display both the same molecular breast cancer subtype as well as the 70-gene prognosis signature as their primary tumors. Our results suggest that the capacity to metastasize is an inherent feature of most breast cancers. Furthermore, our data imply that poor prognosis breast carcinomas classified either by the intrinsic gene set or the 70 prognosis genes represent distinct disease entities that seem sustained throughout the metastatic process.
Unobtrusive Activity Recognition and Position Estimation for Work Surfaces Using RF-Radar Sensing (2019)

Activity recognition is a core component of many intelligent and context-aware systems. We present a solution for discreetly and unobtrusively recognizing common work activities above a work surface without using cameras. We demonstrate our approach, which utilizes an RF-radar sensor mounted under the work surface, in three domains: recognizing work activities at a convenience-store counter, recognizing common office deskwork activities, and estimating the position of customers in a showroom environment. Our examples illustrate potential benefits for both post-hoc business analytics and for real-time applications. Our solution was able to classify seven clerk activities with 94.9% accuracy using data collected in a lab environment and able to recognize six common deskwork activities collected in real offices with 95.3% accuracy. Using two sensors simultaneously, we demonstrate coarse position estimation around a large surface with 95.4% accuracy. We show that using multiple projections of RF signal leads to improved recognition accuracy. Finally, we show how smartwatches worn by users can be used to attribute an activity, recognized with the RF sensor, to a particular user in multi-user scenarios. We believe our solution can mitigate some of users’ privacy concerns associated with cameras and is useful for a wide range of intelligent systems.
The SEANet Project: Toward a Programmable Internet of Underwater Things (2018)

Wirelessly networked systems of underwater devices are becoming the basis of many commercial, scientific, and military applications. In spite of increased attention in the last few years, underwater wireless networking technology still suffers from major limitations, including severe hardware dependence. In this paper, we introduce the SEANet Project, an NSF-funded effort that aims at developing a new generation of programmable platforms and a networking testbed to enable the vision of a programmable Internet of Underwater Things (IoUT). SEANet will be based on new software-defined platforms based on an open architecture to enable the flexibility to define, add, update, and swap new components in both hardware and software. SEANet is designed to support data rates at least one order of magnitude higher than existing commercial platforms over short and moderate range links. Moreover, the SEANet project will explore the design of new custom-designed ultra-wide band Microelectromechanical systems (MEMS) transducers that allow operating over much wider acoustic bandwidth (i.e., 0.01.-2 MHz) than possible with bulk piezoelectric transducers. We present a set of preliminary experiments showing that SEANet can outperform existing software-defined radio SDR-based acoustic modems based on a commercial off-the-shelf (COTS) SDR platforms. We also demonstrate the real-time reconfiguration capability of SEANet and preliminary performance of the MEMS transducers.
Simulating 3-D Lung Dynamics Using a Programmable Graphics Processing Unit (2007)

Medical simulations of lung dynamics promise to be effective tools for teaching and training clinical and surgical procedures related to lungs. Their effectiveness may be greatly enhanced when visualized in an augmented reality (AR) environment. However, the computational requirements of AR environments limit the availability of the central processing unit (CPU) for the lung dynamics simulation for different breathing conditions. In this paper, we present a method for computing lung deformations in real time by taking advantage of the programmable graphics processing unit (GPU). This will save the CPU time for other AR-associated tasks such as tracking, communication, and interaction management. An approach for the simulations of the three-dimensional (3-D) lung dynamics using Green's formulation in the case of upright position is taken into consideration. We extend this approach to other orientations as well as the subsequent changes in breathing. Specifically, the proposed extension presents a computational optimization and its implementation in a GPU. Results show that the computational requirements for simulating the deformation of a 3-D lung model are significantly reduced for point-based rendering.
Long-Term Safety and Efficacy of the Anti-Mucosal Addressin Cell Adhesion Molecule-1 Monoclonal Antibody Ontamalimab (SHP647) for the Treatment of Crohn’s Disease: The OPERA II Study (2021)

Ontamalimab was well tolerated; treatment responses appeared to be sustained over 72 weeks.ClinicalTrials.gov ID: NCT01298492.
Osteogenic protein-1 regulates L1 and neural cell adhesion molecule gene expression in neural cells. (1993)

Osteogenic protein-1 (OP-1) is a member of the TGF-beta superfamily that is expressed in the nervous system. We recently showed that human recombinant osteogenic protein-1 (hOP-1) strongly promotes the aggregation of dividing neuroblastoma x glioma hybrid NG108-15 cells, in part by inducing the major isoforms of the neural cell adhesion molecule (N-CAM) (Perides, G., Safran, R. M., Rueger, D. C., and Charness, M. E. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 10326-10330). Here we show that hOP-1 induces L1 expression approximately 6-fold in NG108-15 cells without changing the levels of N-cadherin, neurofilament 200, Thy-1, tau, and G alpha s. OP-1 induction of L1 and N-CAM was unassociated with changes in cell proliferation and was not reproduced by cellular differentiation. The increased adhesiveness of hOP-1-treated NG108-15 cells could be inhibited in part by Fab fragments of an anti-L1 polyclonal antiserum. L1 and N-CAM expression first increased 12-18 h after hOP-1 treatment, reached a maximum after 2-3 days, persisted for up to 5 days, and returned to control levels 3 days after hOP-1 withdrawal. The increases in L1 and N-CAM protein levels were preceded or accompanied by large increases in the abundance of L1 and all detectable N-CAM mRNAs. Actinomycin D prevented the induction by hOP-1 of L1 and N-CAM mRNAs, suggesting that hOP-1 regulates immunoglobulin CAM gene transcription. OP-1 is the first described growth factor that regulates both N-CAM and L1 gene expression.
Theoretical and Experimental Circular Dichroic Spectra of the Novel Helical Foldamer Poly[(1R,2R)-trans-2-aminocyclopentanecarboxylic acid] (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTheoretical and Experimental Circular Dichroic Spectra of the Novel Helical Foldamer Poly[(1R,2R)-trans-2-aminocyclopentanecarboxylic acid]Jon Applequist, Kimberly A. Bode, Daniel H. Appella, Laurie A. Christianson, and Samuel H. GellmanView Author Information Department of Biochemistry and Biophysics Iowa State University, Ames, Iowa 50011 Department of Chemistry, University of Wisconsin Madison, Wisconsin 53706 Cite this: J. Am. Chem. Soc. 1998, 120, 19, 4891–4892Publication Date (Web):April 29, 1998Publication History Received15 December 1997Published online29 April 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ja9742186https://doi.org/10.1021/ja9742186rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views490Altmetric-Citations92LEARN 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 SUBJECTS:Chemical calculations,Chemical structure,Circular dichroism spectroscopy,Conformation,Mathematical methods Get e-Alerts
O-band excited state quantum dot bilayer lasers (2011)

Bilayer InAs/GaAs quantum dot (QD) lasers operating in the excited state at wavelengths that span the O-band are demonstrated. The higher saturated gain and lower scattering time of the excited states of the ensemble of QDs offers the opportunity for fast direct-modulation lasers. We predict an increase in K-factor limited modulation bandwidth from QD lasers operating in the excited state due to a reduction in carrier transport and scattering times whilst maintaining high peak modal gain.
Spiro 1,3,4,6-Tetrathiapentalene-2-thiones (1993)

Reaction of the geminal a,a-dichloroketones (3) and (5) with the 4,5dimercapto-1,3-dithiole-2-thionedianion (2) yields the spim 1,3,4,6-temthiapentalene-2-thiones ( 4) and (6).The stmcture of 1,3,4,6-teuathiapentalene-2-thione-5- spiro-3'-benzo[c]furan-1'-(3H)-one (4) was determined by X-ray crystallography.A prerequisite for the preparation of new and unusual tetrathiafulvalenes is the availability of the appropriate 1,3-dithiole-2-tbiones.Numerous modifications have been introduced in tetrathiafulvalene systems ( T F - systems) in order to maintain or improve the metallic conductivity.'The majority of these materials have been based on planer TIFsystems; however, there has been a growing interest in non-planer ~~derivativesz as well as functionalized and macnxyclic ?TF-system^.^A spiro TIFsystem has to the best of our knowledge only been reported oncq4 this system was prepared from the spirobis-uithiocarbonate (1).
ChemInform Abstract: SYNTHESIS OF SPIROHETEROCYCLES BY OXIDATIVE COUPLING OF PHENOLIC SULFONAMIDES (1981)

Abstract Durch Oxidation der Sulfonamide (I) und (III) erhält man die Spiroverbindungen (II) bzw. (IV), von denen letzteres auch aus dem Sulfonamid (V) zugänglich ist.
Initial Study on Implementation of Smoothing Filters for the Purpose of Bioimpedance Spectroscopy Parameters Classification (2022)

Bioimpedance is a commonly used method for various conditions monitoring. In this paper, the authors carried out some research where they implemented various smoothing filters to enable identification of the bioimpedance spectroscopy parameters. The proposed filtering methods may also be used for application on embedded systems, which have smaller computing power but have become recently very popular. The obtained results with the implementation of smoothing filters were promising, however, some of the obtained results were unsatisfactory. This work also contains a brief introduction to bioimpedance spectroscopy and smoothing filters.
Localized detection of speech recognition errors (2012)

We address the problem of localized error detection in Automatic Speech Recognition (ASR) output. Localized error detection seeks to identify which particular words in a user's utterance have been misrecognized. Identifying misrecognized words permits one to create targeted clarification strategies for spoken dialogue systems, allowing the system to ask clarification questions targeting the particular type of misrecognition, in contrast to the “please repeat/rephrase” strategies used in most current dialogue systems. We present results of machine learning experiments using ASR confidence scores together with prosodic and syntactic features to predict whether 1) an utterance contains an error, and 2) whether a word in a misrecognized utterance is misrecognized. We show that by adding syntactic features to the ASR features when predicting misrecognized utterances the F-measure improves by 13.3% compared to using ASR features alone. By adding syntactic and prosodic features when predicting misrecognized words F-measure improves by 40%.