gebhart/patrepeval huggingface dataset:
Subcellular Localizations of RIG-I, TRIM25, and MAVS Complexes (2016)

The first line of defense against viral infections is the innate immune response. Viruses are recognized by pathogen recognition receptors, such as the RIG-I like receptor family, that activate a signaling cascade that induces IFN production. In the present study, we visualized, for the first time in cells, both in overexpression and endogenous levels, complexes formed among key proteins involved in this innate immune signaling pathway. Through different techniques we were able to analyze how these proteins are distributed and reorganized spatially within the cell in order to transmit the signal, leading to an efficient antiviral state. In addition, this work presents a new means by how, when, and where viral proteins can target these pathways and act against the host immune system in order to counteract the activation of the immune response.
Digital redesign and multi-rate control for motion control-a general approach and application to hard disk drive servo system (2000)

This paper is concerned with the digital redesign of continuous time controllers for motion control. Multirate digital control with a high order hold is utilized to better approximate the continuous time controller when the measurement sampling rate is relatively low. The proposed approach is illustrated for track following control of a hard disk drive (HDD) servo system. The HDD controller is first designed in the continuous time domain based on LQG/LTR method. It is redesigned as a single rate digital controller as well as multirate digital controllers with different holds. The redesigned controllers are evaluated by simulation, and the advantage of multirate control is demonstrated.
Synthesis of Unnatural Lipohilic N‐(9H‐Fluoren‐9‐ylmethoxy)carbonyl‐Substituted α‐Amino Acids and Their Incorporation into Cyclic RGD‐Peptides: A structure‐activity study (1997)

Abstract The α v /β 3 integrin is implicated in human tumor metastasis and angiogenesis. It has been shown that structures of the sequence cyclo(‐Arg 1 ‐Gly 2 ‐Asp 3 ‐ D ‐Phe 4 ‐Xaa 5 ‐) ( I ) and cyclo(‐Arg 1 ‐Gly 2 ‐Asp 3 ‐Phe 4 ‐ D ‐Xaa 5 ‐) ( II ) bind with high affinity and the latter with high selectivity to this receptor. The residues Xaa and D ‐Xaa accept a broad variety of amino acids. Here, we report on the synthesis, activities, and conformational analysis of cyclic Arg‐Gly‐Asp (RGD) peptides containing liophilic amino acids Xaa or D ‐Xaa in position 5. For I , these were (2 S )‐2‐aminohexadecanoic acid (Ahd) and N ′‐hexadecylglycine (Hd‐Gly) and in II , D ‐Ahd and Hd‐Gly, and, for control purposes, Ahd were incorporated ( Fig. 1 ). The enantiomerically pure a‐amino acids were obtained by non‐enantioselective synthesis and subsequent enzymatic separation of isomers using acylase I ( Scheme ). Hd‐Gly was prepared in a modified procedure according to Stewart from ethyl bromoacetate and hexadecylamine ( Scheme ). The synthesis and physicochemical properties of the corresponding (9 H ‐fluoren‐9‐ylmethoxy)carbonyl (Fmoc) derivatives, compatible with solid‐phase peptide synthesis, are described. Structure elucidation by NMR reveals that the lipid modification has no significant impact on the template structures when incorporated into them. For peptides I with Xaa = Ahd or Hd‐Gly ( 1 or 2 ), a βII′/γ‐turn‐like arrangement with D ‐Phe in i + 1 position of the β‐turn is found. Peptides II with D ‐Xaa = D ‐Ahd or Hd‐Gly ( 3 or 4 ) exhibit a βII′/γ‐turn conformation with Gly in i + 1 position of the β‐turn, whereas II with Ahd instead of D ‐Xaa, i.e., lacking a D ‐amino acid in position 4 or 5 ( 5 ). adopts no defined conformation. However, in assays of receptor specificity employing human α v v/β 3 integrin, the compounds exhibit IC 50 values ranging from nanomolar to less than millimolar. These results indicate that although the arrangement of the pharmacophoric groups is preserved in the target compounds, the biological activity is highly dependent on spatial requirements of the lipid anchor in the receptor binding pocket. Obviously, only certain positions do not affect the binding.
Prescription and acceptance of durable medical equipment in FORTITUDE-ALS, a study of reldesemtiv in ALS: post hoc analyses of a randomized, double-blind, placebo-controlled clinical trial (2021)

<i>Objective</i>: To evaluate the possible effect of <i>reldesemtiv</i>, a fast skeletal muscle troponin activator, on prescription and acceptance of durable medical equipment (DME) in the FORTITUDE-ALS trial. <i>Methods:</i> Health economic outcome information was collected in FORTITUDE-ALS (NCT03160898); sites recorded if and when DME, specifically manual or power wheelchairs, gastrostomy tubes, noninvasive ventilators, or augmentative language devices, was prescribed by a physician and accepted by the patient (DME-PAP) during the trial. Acceptance was defined as the patient agreeing the item was needed. Cox regression analysis compared time to DME-PAP for each <i>reldesemtiv</i> dose with placebo. Post hoc analyses evaluated all <i>reldesemtiv</i> doses compared with placebo. <i>Results:</i> At least one DME item was prescribed and accepted by 33/114 (28.9%) of placebo patients, 19/112 (17.0%) of patients receiving <i>reldesemtiv</i> 150 mg bid, 24/113 (21.2%) receiving 300 mg bid, and 29/117 (24.8%) receiving 450 mg bid. The proportion of new DME-PAP was significantly lower in patients receiving <i>reldesemtiv</i> 150 mg bid vs placebo (17.0% vs 28.9%, <i>p</i> = 0.032). The hazard ratio versus placebo for accepting at least one DME item for all <i>reldesemtiv</i> doses combined was 0.61 (confidence interval: 0.39, 0.96, <i>p</i> = 0.032). 25% of placebo patients were prescribed and agreed to obtain a DME item by 84 days; this threshold was met for <i>reldesemtiv</i>-treated patients at 120 days. <i>Conclusions:</i> Results suggest ALS patients receiving <i>reldesemtiv</i> may have lower risk of and delayed need for DME related to impaired mobility, breathing, swallowing, or speaking; this delay is consistent with other measures indicating delay in disease progression.
Inference of deformation mechanisms and constitutive response of soft material surrogates of biological tissue by full-field characterization and data-driven variational system identification (2020)

Abstract We present a novel, fully three-dimensional approach to soft material characterization and constitutive modeling with relevance to soft biological tissue. Our approach leverages recent advances in experimental techniques and data-driven computation. The experimental component of this approach involves in situ mechanical loading in a magnetic field (using MRI), yielding the entire deformation tensor field throughout the specimen regardless of the possible irregularities in its three-dimensional shape. Characterization can therefore be accomplished with data at a reduced number of deformation states. We refer to this experimental technique as MR- u . Its combination with powerful approaches to inverse modelling, specifically methods of model inference, would open the door to insightful mechanical characterization for soft materials. In recent computational advances that answer this need, we have developed new, data-driven inverse techniques to infer the model that best explains the physics governing observed phenomena from a spectrum of admissible ones, while maintaining parsimony of representation. This approach is referred to as Variational System Identification (VSI). In this communication, we apply the MR– u approach to characterize soft polymers regarding them as surrogates of soft biological tissue, and using VSI, we infer the physically best-suited and parsimonious mathematical models of their mechanical response. We demonstrate the performance of our methods in the face of noisy data with physical constraints that challenge the identification of mathematical models, while attaining high accuracy in the predicted response of the inferred models.
Constant-Depth and Subcubic-Size Threshold Circuits for Matrix Multiplication (2020)

Boolean circuits of McCulloch-Pitts threshold gates are a classic model of neural computation studied heavily in the late 20th century as a model of general computation. Recent advances in large-scale neural computing hardware has made their practical implementation a near-term possibility. We describe a theoretical approach for multiplying two $N$ by $N$ matrices that integrates threshold gate logic with conventional fast matrix multiplication algorithms, that perform $O(N^ω)$ arithmetic operations for a positive constant $ω&lt; 3$. Our approach converts such a fast matrix multiplication algorithm into a constant-depth threshold circuit with approximately $O(N^ω)$ gates. Prior to our work, it was not known whether the $Θ(N^3)$-gate barrier for matrix multiplication was surmountable by constant-depth threshold circuits. Dense matrix multiplication is a core operation in convolutional neural network training. Performing this work on a neural architecture instead of off-loading it to a GPU may be an appealing option.
Kinetic modelling of batch slurry reactions (2012)

Slurries are widely used in important chemical and pharmaceutical manufacturing processes. In this presentation we report chemical monitoring and modeling of batch slurry reactions using optical and calorimetric measurement where key analytes are present in both the solid and liquid phases. Experimental studies were performed to:&lt;br&gt; (1) Generate supersaturated solutions for the development of kinetic models of seeded crystallization, crystal growth, and dissolution;&lt;br&gt; (2) Generate unseeded crystallization from homogeneous reaction mixtures for the development of kinetic models of reacting systems, including crystal growth as well as measurement of crystallization driven by cooling of reaction mixtures including the necessary corresponding solubility curves as a function of temperature; &lt;br&gt; (3) Reproduce at laboratory scale, a commercially relevant slurry reaction starting with heterogeneous reaction mixture, producing a product slurry.&lt;br&gt;&lt;br&gt; Simultaneous UV/visible attenuated total reflectance (ATR) and NIR reflectance measurements enabled reliable characterization of reaction mixtures and detection of the onset of crystallization. Kinetic models for dissolution, seeded crystallization, unseeded crystallization, homogeneous reaction and crystallization driven by cooling were successfully developed relating the mass of substance in the solution phase and solid phase to UV/Vis ATR and NIR reflectance measurements. Reactive crystallization experiments with kinetic modeling demonstrated that simultaneous measurements of slurries with UV/Vis ATR and NIR reflectance is an effective means of characterizing the dissolved fraction and the onset of nucleation and crystallization. &lt;br&gt;&lt;br&gt; Work with research partner DuPont Crop Protection Science included development of a 4 L glass reactor with a recirculation loop and sampling system for off-line HPLC analysis. Several different sampling strategies were tested to develop a robust, reproducible method for off-line HPLC analysis. NIR reflectance measurements of slurry reactions at DuPont were demonstrated to be relevant to the property of interest. Kinetic models were obtained for product and reactant from NIR reflectance measurements. Reaction progression was followed by depletion of triazine heterocycle, as indicated by N-H overtone band dissipation. Spectroscopic evidence of a precipitation event was also observed and confirmed by focused beam reflectance measurements (FBRM). Kinetic models of reaction measurements provided clear resolution of two components, the solid phase reactant and solid phase product. Initial product appearance in the kinetic model concentration profile estimates corresponded temporally with the spectroscopic evidence of precipitation. Estimation of spectral profiles from kinetic models include an N-H overtone band observed around 2010nm.
Endovascular Catheter for Magnetic Navigation under MR Imaging Guidance: Evaluation of Safety In Vivo at 1.5T (2013)

Activations of copper coils at the tip of microcatheters at low currents in 1.5T MR scanners can be achieved without significant damage to blood vessel walls in a controlled experimental setting. Further optimization of catheter design and procedure protocols is necessary for safe remote control magnetic catheter guidance.
Endogenous cytokinin dynamics in micropropagated tulips during bulb formation process influenced by TDZ and iP pretreatment (2014)

There are substantial variations in bulbing (bulb formation) efficiency among micropropagated tulip cultivars. The mechanisms involved are poorly understood, but presumably involve cytokinins (CKs) for several reasons. Therefore, we explored CK profiles and dynamics in ‘Blue Parrot’ and ‘Prominence’ cultivars (which have low and high bulbing efficiency, respectively) during the in vitro propagation stages: the last shoot multiplication subculture extended to 14 weeks (S1–S2), the shoot cooling at 5 °C for induction of bulb formation (S3–S4) and the bulb growth initiation after the end of cooling (S5–S6). The CK thidiazuron (TDZ) is routinely used in tulip micropropagation at the shoot multiplication stage, but replacing it with isopentenyladenine (iP) during the last multiplication subculture substantially changed CK dynamics in later stages, and significantly increased bulb formation rates in both cultivars. Generally, the most abundant CKs in both cultivars were the isoprenoid CK types, trans-zeatin (tZ), iP, cis-zeatin and dihydrozeatin. However, ‘Prominence’ shoots had much lower cis- to trans-Z-type CK ratios than ‘Blue Parrot’ shoots, and generally higher levels of physiologically active CKs (free bases tZ, iP and their ribosides) until the last phase of bulb formation, S6 (bulb growth initiation, i.e. swelling of shoot bases), 6 weeks after the end of cold treatment. In this phase total active CK and O-glucoside contents sharply declined in ‘Prominence’ shoots, but not in ‘Blue Parrot’ shoots pretreated with iP. In contrast, the low bulbing ability observed in ‘Prominence’ shoots pretreated with TDZ and ‘Blue Parrot’ shoots pretreated with either TDZ or iP was associated with a gradual rise in active CK and O-glucoside contents after the end of cooling. The results suggest that low bulbing efficiency may be related to down-regulation of tZ biosynthesis, and high bulbing efficiency to a transient increase in active CK forms (mainly tZs) in response to cold treatment during the bulb induction phase, S4 (at the end of cold treatment), followed by a rapid decrease during bulb formation, S6 (6 weeks after the end of cooling).
Signal recovery from wavelet transform maxima (1994)

The paper presents an iterative algorithm for signal recovery from discrete-time wavelet transform maxima. The signal recovery algorithm is developed by using the method of projections onto convex sets. Convergence of the algorithm is assured.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of an automated analyzer for TEM diffraction patterns (1993)

An application of self-adaptive algorithms to TEM is presented. Analysis of diffraction patterns is an integral part of an experiment because of the need to control contrast conditions. Obtaining two-beam conditions or locating a zone axis can be time consuming or not possible, because of restrictions in the tilt ranges of the holder being used. The present approach is to manually search reciprocal space in the instrument to find zones of interest and that are accessible, visually identify the zone axis, or, analyze the patterns and plot on a stereogram the locations of major zones. Once the experimenter has plotted the orientation, then locating desired zone axes is accomplished by manually tilting. This process can be relatively easy, as in the case of a cubic crystal, or very difficult as in the the cases of hexagonal, trigonal, triclinic, monoclinic or orthorhombic crystals, particularly when the crystalline region is a few microns or less in size.
Lack of correlation between the costs of anticancer drugs and clinical benefits in Japan (2018)

Both overall survival (OS) and progression-free survival (PFS) are primary endpoints of phase III studies of new anticancer drugs. Medical care expenditures, especially oncology drug prices, are rapidly increasing; however, the impact of oncology drug prices on OS and PFS is unclear. We analyzed the relationship between oncology drug prices and clinical outcomes in Japan. The costs of a full course or 1 year of treatment were estimated on the basis of the latest National Health Insurance Drug Price Standards, and the relationship between costs and improvements in OS or PFS obtained with each drug were analyzed. Cost-effectiveness was compared between new-class drugs and next-in-class drugs. We then developed a simple model for estimating the costs required to prolong OS and PFS by 1 day and used this model to compare cost-effectiveness. Drug costs were not significantly related to treatment outcomes in terms of PFS or OS. There was no significant difference in the median cost between novel drugs and the next-in-class drugs (P = 0.39). The oncology drug cost required to prolong PFS by 1 day was more expensive than the drug cost required for prolong OS by 1 day. Prices of oncology drugs should be decided on the basis of actual clinical benefits for cancer patients, and the drug price evaluation process should be disclosed in Japan.
Conceptual design of a high gain antenna system with wide range beam steering capability for broadband radar applications (2014)

In this contribution, an antenna positioning system is presented that combines a high bandwidth, high gain and a wide steering range. The mechanical part of the positioning system is based on a uniaxially driven planetary gear which generates a hypocycloidical shaped, slanting movement. Advantages and disadvantages of the mechanically steering system are discussed and compared to a common electric-steerable patch antenna array. Moreover, two basic applications, i.e. radar based ground level reconstruction and target direction finding are introduced. Fundamentals concerning the theoretical position calculation as well as signal processing algorithms are presented. Furthermore, measurements that were performed for both applications are essential part of this contribution.
A Novel Class of Human Cardiac Stem Cells (2015)

Following the recognition that hematopoietic stem cells improve the outcome of myocardial infarction in animal models, bone marrow mononuclear cells, CD34-positive cells, and mesenchymal stromal cells have been introduced clinically. The intracoronary or intramyocardial injection of these cell classes has been shown to be safe and to produce a modest but significant enhancement in systolic function. However, the identification of resident cardiac stem cells in the human heart (hCSCs) has created great expectation concerning the potential implementation of this category of autologous cells for the management of the human disease. Although phase 1 clinical trials have been conducted with encouraging results, the search for the most powerful hCSC for myocardial regeneration is in its infancy. This manuscript discusses the efforts performed in our laboratory to characterize the critical biological variables that define the growth reserve of hCSCs. Based on the theory of the immortal DNA template, we propose that stem cells retaining the old DNA represent 1 of the most powerful cells for myocardial regeneration. Similarly, the expression of insulin-like growth factor-1 receptors in hCSCs recognizes a cell phenotype with superior replicating reserve. However, the impressive recovery in ventricular hemodynamics and anatomy mediated by clonal hCSCs carrying the "mother" DNA underscores the clinical relevance of this hCSC class for the treatment of human heart failure.
Advanced Switch Design Principles (2010)

This chapter presents some advance switch design principles to further alleviate packet contention problem. It shows that despite these advanced switch designs, switch dimensions continue to be severely limited by both technological and physical constraints. The chapter provides some key principles to construct large switches out of modest-size switches, without sacrificing overall switch performance. It focuses on switch scalability, and presents a modular architecture, which does so by equally partitioning all inputs into multiple subsets and performing switching based on them. One way to solve the packet contention problem without having to buffer the losing packets is to use deflection routing. The chapter concentrates on packet switching in the space domain. A simple extension, called shared-buffer memory switching, removes the partitioning of buffering space and allows it to be shared by all outputs. Controlled Vocabulary Terms computer network performance evaluation; network routing; packet switching; telecommunication buffers
Coupled van der Pol oscillators as a simplified model for generation of neural patterns for jellyfish locomotion (2005)

In this paper, we present a simple system of coupled oscillators as a model of pattern generation for jellyfish locomotion. Coupled oscillator models have been successfully applied to model pattern generation in numerous biological systems including jellyfish locomotion, but the previous jellyfish models have required complicated oscillators or variation of coupling topology to produce gait variations. Here we show that a simple model consisting of identical van der Pol oscillators with fixed coupling topology suffices to produce dynamics corresponding to essential jellyfish gaits (co-ordinated bout swimming, hovering, and turning) solely by uniform adjustment of coupling strengths. Thus, a simple coupled oscillator model succeeds in producing a range of dynamic behaviour analogous to the essential neural dynamics for locomotion control of a simple animal. Copyright © 2005 John Wiley & Sons, Ltd.
IoT-Based Personalized Health and Fitness Monitoring System (2022)

In the developing era of digital, technology plays a vital role in our daily lives. Most of the things are connected digitally on the internet—from searching for information, to security, to space travelling. Nowadays, gadgets, cars, vehicles, and equipment, which work on internet connectivity, are in development stage, while some are in use in certain industries. The Indian pharmaceutical industry has been anticipated to develop globally in the coming years. It is a larger supplier of medical facilities to the entire world and is a leading nation in pharmaceutical manufacturing. The Internet of Things provides the pharma industry with a selection of new personalized market opportunities, better controlled environment of pharma manufacturing, preventative maintenance of equipment, and improved diversified supply chain management system. Owing to the deficiencies in transparency, pharmaceutical manufacturing has been unable to warrant safe medicinal production and circulation. Adoption of the Internet of Things could represent a new competitive advantage for pharma companies. This conceptual explorative research demonstrates the future of Indian pharma, which is on the verge to become self-reliant industry. The use of Internet of Things, artificial intelligence, big data analytics, and the tracking of customers carrying internet-connected digital devices and sensors implanted in wearables would help to locate the customer medical history with health monitoring. This would also alert both the clinical manufacturers and users, resulting in designing personalized healthcare and a better future for Indian pharma industry. Future Pharma would see the business link of IoT-based devices across development and dispersal by using better, more reliable larger volumes of data to revolutionize manufacturing.