gebhart/patrepeval huggingface dataset:
Vaccine targeting ANGPTL3 ameliorates dyslipidemia and associated diseases in mouse models of obese dyslipidemia and familial hypercholesterolemia (2021)

Dyslipidemia is a risk factor for cardiovascular disease (CVD), a major cause of death worldwide. Angiopoietin-like protein 3 (ANGPTL3), recognized as a new therapeutic target for dyslipidemia, regulates the metabolism of low-density lipoprotein-cholesterol (LDL-C) and triglycerides. Here, we design 3 epitopes (E1-E3) for use in development of a peptide vaccine targeting ANGPTL3 and estimate effects of each on obesity-associated dyslipidemia in B6.Cg-<i>Lep</i><sup><i>ob</i></sup> /J (<i>ob/ob</i>) mice. Vaccination with the E3 (<sup>32</sup>EPKSRFAMLD<sup>41</sup>) peptide significantly reduces circulating levels of triglycerides, LDL-C, and small dense (sd)-LDL-C in <i>ob/ob</i> mice and decreases obese-induced fatty liver. Moreover, E3 vaccination does not induce cytotoxicity in <i>ob/ob</i> mice. Interestingly, the effect of E3 vaccination on dyslipidemia attenuates development of atherosclerosis in B6.KOR/StmSlc-<i>Apoe</i><sup><i>shl</i></sup> mice fed a high-cholesterol diet, which represent a model of severe familial hypercholesterolemia (FH) caused by ApoE loss of function. Taken together, ANGPTL3 vaccination could be an effective therapeutic strategy against dyslipidemia and associated diseases.
Evaluation of Hitachi CAD to CD-SEM metrology package for OPC model tuning and product devices OPC verification (2005)

Optical proximity corrections are widely used in semiconductor industry to compensate non-linear effects occurring when printing features smaller than exposure wavelength. Most advanced OPC software packages simulate optical behavior starting from a physical description of illumination and projection optics, while the characterization of resist development and etch loading effects is still performed empirically, with different approaches that, generally, require the collection of a huge amount of experimental data. Due to the wide variety of target patterns, which makes conventional CD-SEM recipe creation impossible, critical dimension (CD) measurements are usually performed manually, requiring long time and, despite the attention paid while measuring, with poor guarantee of repeatability. The introduction of 193nm resists, much more sensitive to SEM e-beam exposure if compared to 248nm materials, required increased attention to be paid on both focusing and measuring phases in order to obtain reliable results. As well as OPC model tuning, the verification of correction effectiveness on product devices is performed almost in the same way leading to the same kind of issues. In order to overcome most of these problems ST is evaluating a new CD metrology package from Hitachi High Technologies; this tool allows fully automatic CD measurements starting from GDS II coordinate input. The exact recognition of measurement locations is obtained through an algorithm, based on the superposition of the drawn GDS II layout to the SEM wafer images, which allows achieving high positioning accuracy. The introduction of the tool significantly reduces measuring time down to the range of normal automated CD measurement times, while guarantying improved repeatability and optimized conditions even with 193nm resists due to the possibility of defining different structures for addressing and focusing before the measurement. This new system opens new perspectives in OPC modeling giving the opportunity of a more accurate model tuning, required by 65 nm technology node, and enables an extensive product devices OPC verification presently impossible due to time and procedure issues.
Programmable Animation Texturing using Motion Stamps (2016)

Abstract Our work on programmable animation texturing enhances the concept of texture mapping by letting artists stylize arbitrary animations using elementary animations, instantiated at the scale of their choice. The core of our workflow resides in two components: we first impose structure and temporal coherence over the animation data using a novel radius‐based animation‐aware clustering. The computed clusters conform to the user‐specified scale, and follow the underlying animation regardless of its topology. Extreme mesh deformations, complex particle simulations, or simulated mesh animations with ever‐changing topology can therefore be handled in a temporally coherent way. Then, in analogy to fragment shaders that specify an output color based on a texture and a collection of properties defined per vertex (position, texture coordinate, etc.), we provide a programmable interface to the user, letting him or her specify an output animation based on the collection of properties we extract per cluster (position, velocity, etc.). We equip elementary animations with a collection of parameters that are exposed in our programmable system and enables users to script the animated textures depending on properties of the input cluster. We demonstrate the power of our system with complex animated textures created with minimal user input.
Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus (2020)

Microbial coculture to mimic the ecological habitat has been suggested as an approach to elucidate the effect of microbial interaction on secondary metabolite biosynthesis of Streptomyces. However, because of chemical complexity during coculture, underlying mechanisms are largely unknown. Here, we found that iron competition triggered antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus. During coculture, M. xanthus enhanced the production of a siderophore, myxochelin, leading M. xanthus to dominate iron scavenging and S. coelicolor to experience iron-restricted conditions. This chemical competition, but not physical contact, activated the actinorhodin biosynthetic gene cluster and the branched-chain amino acid degradation pathway which imply the potential to produce precursors, along with activation of a novel actinorhodin export system. Furthermore, we found that iron restriction increased the expression of 21 secondary metabolite biosynthetic gene clusters (smBGCs) in other Streptomyces species. These findings suggested that the availability for key ions stimulates specific smBGCs, which had the potential to enhance secondary metabolite biosynthesis in Streptomyces.
Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys (2005)

Eight coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococcal strains were isolated from the gastrointestinal tracts of South American squirrel monkeys (Saimiri sciureus L.). These strains were differentiated from known staphylococcal species on the basis of 16S rRNA gene and hsp60 gene sequencing, and from the most closely related species by using DNA-DNA hybridization, ribotyping, whole-cell protein profiles and biotyping. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that these strains are members of the Staphylococcus aureus species group (99% similarity) but are biochemically similar to Staphylococcus piscifermentans, from which they can be phenotypically distinguished by resistance to polymyxin B, acid production from D-mannitol, the inability to hydrolyse aesculin and DNA and the absence of alpha-glucosidase. On the basis of these analyses, a novel species of the genus Staphylococcus is described, for which the name Staphylococcus simiae sp. nov. is proposed, with CCM 7213(T) (=LMG 22723(T)) as the type strain.
ChemInform Abstract: Synthesis of Oligosaccharide Structures Unique to Pituitary Glycoprotein Hormones. (1987)

Abstract The trisaccharide (VIe) and its sulfate ester (VIf) are synthesized: 1. The component (IVb) is prepared starting from the glucopyranose derivative (Ia) via the intermediates (Ib), (Ic), (IIIa), (IIIb), and (IVa).
A Three-Phase Four-Leg Inverter-Based Active Power Filter for Unbalanced Current Compensation Using a Petri Probabilistic Fuzzy Neural Network (2017)

A three-phase four-leg inverter-based shunt active power filter (APF) is proposed to compensate three-phase unbalanced currents under unbalanced load conditions in grid-connected operation in this study. Since a DC-link capacitor is required on the DC side of the APF to release or absorb the instantaneous apparent power, the regulation control of the DC-link voltage of the APF is important especially under load variation. In order to improve the regulation control of the DC-link voltage of the shunt APF under variation of three-phase unbalanced load and to compensate the three-phase unbalanced currents effectively, a novel Petri probabilistic fuzzy neural network (PPFNN) controller is proposed to replace the traditional proportional-integral (PI) controller in this study. Furthermore, the network structure and online learning algorithms of the proposed PPFNN are represented in detail. Finally, the effectiveness of the three-phase four-leg inverter-based shunt APF with the proposed PPFNN controller for the regulation of the DC-link voltage and compensation of the three-phase unbalanced current has been demonstrated by some experimental results.
Miscible Blends of Poly(siloxane Imide) Segmented Copolymers and Polybenzimidazole as Potential High Performance Aerospace Materials (1990)

Compatible blends of high performance engineering thermoplastics have been investigated for aerospace applications, where stability in an aggressive atomic oxygen environment is of significant concern. The blends were comprised of polyimide homopolymers and poly(siloxane imide) segmented copolymers based upon benzophe-none tetracarboxylic dianhydride (BTDA) and m-diaminodiphenyl sulfone, and polybenzimidazole (PBI). The blends exhibited glass transition temperatures in excess of 300°C, and significantly reduced water sorption relative to PBI. Conversion of the siloxane surface to an inorganic, oxidation resistant silicate in the presence of atomic oxygen accounted for the enhanced stability of siloxane-containing blends to a simulated low earth orbit environment.
Innate Immune Responses to Danger Signals in Systemic Inflammatory Response Syndrome and Sepsis (2009)

The systemic immune response induced by non-infectious agents is called systemic inflammatory response syndrome (SIRS) and infection-induced systemic immune response is called sepsis. The host inflammatory response in SIRS and sepsis is similar and may lead to multiple organ dysfunction syndrome (MODS) and ultimately death. The mortality and morbidity in SIRS and sepsis (i.e. critical illness) remain high despite advances in diagnostic and organ supporting possibilities in intensive care units. In critical illness, the acute immune response is organized and executed by innate immunity influenced by the neuroendocrine system. This response starts with sensing of danger by pattern-recognition receptors on the immune competent cells and endothelium. The sensed danger signals, through specific signalling pathways, activate nuclear transcription factor kappaB and other transcription factors and gene regulatory systems which up-regulate the expression of pro-inflammatory mediators. The plasma cascades are also activated which together with the produced pro-inflammatory mediators stimulate further the production of inflammatory biomarkers. The acute inflammatory response underlies the pathophysiological mechanisms involved in the development of MODS. The inflammatory mediators directly affect organ function and cause a decline in remote organ function by mediating the production of nitric oxide leading to mitochondrial anergy and cytopathic hypoxia, a condition of cellular inability to use oxygen. Understanding the mechanisms of acute immune responses in critical illness is necessary for the development of urgently needed therapeutics. The aim of this review is to provide a description of the key components and mechanisms involved in the immune response in SIRS and sepsis.
A Performance Prediction Model for Low-Speed Centrifugal Fans (2014)

A generalized model for mapping the trend of the performance characteristics of a double-discharge centrifugal fan is developed based on the work by Casey and Robinson (C&amp;R) which formulated compressor performance maps for tip-speed Mach numbers ranging from 0.4 to 2 using test data obtained from turbochargers with vaneless diffusers. The current paper focuses on low-speed applications for Mach number below 0.4. The C&amp;R model uses four non-dimensional parameters at the design condition including the flow coefficient, the work input coefficient, the tip-speed Mach number and the polytropic efficiency, in developing a prediction model that requires limited geometrical knowledge of the centrifugal turbomachine. For the low-speed fan case, the C&amp;R formulas are further extended to a low-speed, incompressible analysis. The effort described in this paper begins by comparing generalized results using efficiency data obtained from a series of fan measurements to that using the C&amp;R model. For the efficiency map, the C&amp;R model is found to heavily depend on the ratio of the flow coefficient at peak efficiency to that at the choke flow condition. Since choke flow is generally not applicable in the low-speed centrifugal fan operational environment, an alternate, but accurate estimation method based on fan free delivery derived from the fan test data is presented. Using this new estimation procedure, the modified C&amp;R model predicts reasonably well using the double-discharge centrifugal fan data for high flow coefficients, but fails to correlate with the data for low flow coefficients. To address this undesirable characteristic, additional modifications to the C&amp;R model are also presented for the fan application at low flow conditions. A Reynolds number correction is implemented in the work input prediction of the C&amp;R model to account for low-speed test conditions. The new model provides reasonable prediction with the current fan data in both work input and pressure rise coefficients. Along with the developments for the efficiency and work input coefficient maps, the use of fan shut-off and free delivery conditions are also discussed for low-speed applications.
A facile method for preparing molecularly imprinted polymer spheres using spherical silica templates (2002)

A novel and facile preparation method for spherical molecularly imprinted polymer (MIP) beads is presented. Two types of beads were synthesized and investigated: (i) silica–MIP composites were obtained by filling spherical, porous C4-coated silica beads with print molecule and monomers followed by polymerisation; (ii) spherical molecularly imprinted polymer beads were acquired mirroring the silica particles in size, shape and pore structure by removing the silica matrix from the silica–MIP composites. With regard to their chromatographic properties and yield of the materials both types of particle were more advantageous compared to irregularly shaped traditional MIPs. Also the work-up time to obtain imprinted spherical particles is greatly reduced compared to traditional methods using polymer monoliths, which have to be ground, sieved and sedimented. Generally, the described method may open new possibilities for synthesis of novel types of imprinted polymer formats such as membranes, bulk polymers, films or in-situ columns using appropriate support or sacrificial materials.
Signal Averaging in Wolff‐Parkinson‐White Syndrome: Evidence That Fractionated Activation Is Not Necessary for Body Surface High Frequency Potentials (2000)

It is commonly assumed that the presence of high frequency components in body surface potentials implies that fractionated activation fronts, caused by heterogeneously viable tissue, are present in the heart. However, it is possible that non-fractionated activation fronts can also give rise to high frequency surface potentials and that the relative amount of high frequency power is related to the complexity of the activation sequence. In a test of this idea, averaged body surface potentials were recorded during the entire QRS complex of nine Wolff-Parkinson-White (WPW) patients in situations in which fractionated activation fronts should not have been present, but which represent increasing degrees of complexity of ventricular activation: (1) postoperative ectopic pacing from subepicardial wires placed during surgery, when a single coherent activation front was present throughout most of the QRS; (2) Preoperative preexcited rhythm, when a single coherent activation front was present for one portion of the QRS (the delta wave); and (3) postoperative normal rhythm, when two or more activation fronts were present in the ventricles throughout most of the QRS. For comparison, averaged body surface potentials were also analyzed during the last 40 ms of the QRS complex and the ST segment of 14 postinfarction patients with chronic ventricular tachycardia. In the patients with WPW syndrome, relatively high frequency content increased (attenuation -36.7 vs -27.2 vs -18.3 dB) and QRS width decreased (160.7 vs 125.9 vs 94.1 ms) significantly from paced to preoperative to postoperative beats. Significant high frequency content was present in all cases, showing that coherent activation fronts can give rise to high frequencies. Interestingly, the postoperative QRS of WPW patients contained a larger proportion of high frequency power than did the late potentials of the patients with ventricular tachycardia. Thus, while the presence of late fractionated body surface potentials may be a marker for ventricular tachycardia, these potentials by themselves do not necessarily signify that the underlying cardiac activation giving rise to these signals is fractionated.
Diffusive MASS NMR Studies of Transport in Porous Materials (2001)

NMR methods are widely used to probe the structure and fluid dynamics of porous materials including such diverse materials as cheese and chocolate, cosmetics and pharmaceuticals, solvents in resins and soft matter, biological tissue, and for oil exploration. NMR measurements are uniquely suited to these studies since it records the correlation of changing local magnetic fields over a time scale of ms to seconds. The local magnetic fields are established by local variations in the bulk magnetic susceptibility of the sample (and so are directly tied to the sample’s local structure). The fluctuation in field that a spin sees is due to molecular transport (including molecular diffusion) through these local fields, and so reports on the length scales of structures and impediments to transport. In the past this information has primarily been employed via empirical relations that relate bulk measurements of relaxation times or diffusion to some microscopic property (pore size, throat size, S/V, and surface relaxivity, etc.). These empirical relationships, while useful, hide the underlying complexity of spin dynamics in confining geometries. We have developed a new set of methods to provide a means of systematically varying the effective time scale of the measurement and thus the effective length scale. This new handle permits a detailed, microscopic picture of the structure and dynamics.
The SEE Study: Safety, Efficacy, and Equity of Implementing Autonomous Artificial Intelligence for Diagnosing Diabetic Retinopathy in Youth (2021)

&lt;b&gt;Objective: &lt;/b&gt;Diabetic retinopathy (DR) is a leading cause of vision loss worldwide. Screening for DR is recommended in children and adolescents but adherence is poor.&lt;b&gt; &lt;/b&gt;Recently, autonomous artificial intelligence (AI) systems have been developed for early detection of DR, and have been included in the American Diabetes Association’s guidelines for screening in adults. We sought&lt;b&gt; &lt;/b&gt;to determine the diagnostic efficacy of autonomous AI for the diabetic eye exam in youth with diabetes. &lt;p&gt;&lt;b&gt; &lt;/b&gt;&lt;/p&gt; &lt;p&gt;&lt;b&gt;Research Design and Methods: &lt;/b&gt;In this prospective study, point-of-care diabetic eye exam was implemented using a non-mydriatic fundus camera with an autonomous AI system for detection of DR in a multidisciplinary pediatric diabetes center. Sensitivity, specificity, and diagnosability of AI was compared with consensus grading by retinal specialists, who were masked to AI output. Adherence to screening guidelines was measured before and after AI implementation.&lt;/p&gt; &lt;p&gt;&lt;b&gt; &lt;/b&gt;&lt;/p&gt; &lt;p&gt;&lt;b&gt;Results: &lt;/b&gt;310 youth aged 5-21 with diabetes were included, of whom 4.2% had DR. Diagnosability of AI was 97.5% (302/310). The sensitivity and specificity of AI to detect more than mild DR was 85.7% (95% CI: 42.1%- 99.6%) and 79.3 % (95% CI: 74.3%-83.8%) compared to the reference standard as defined by retina specialists. Adherence improved from 49% to 95% after AI implementation. &lt;/p&gt; &lt;p&gt;&lt;b&gt; &lt;/b&gt;&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions: &lt;/b&gt;&lt;/p&gt; &lt;p&gt;Use of a non-mydriatic fundus camera with autonomous AI was safe and effective for the diabetic eye exam in youth in our study. Adherence to screening guidelines improved with AI implementation. As the prevalence of diabetes increases in youth, and adherence to screening guidelines remains suboptimal, effective strategies for diabetic eye exams in this population are needed.&lt;b&gt; &lt;/b&gt;&lt;/p&gt;
Highly Efficient Synthesis of a Phosphoramidite Building Block of C8-Deoxyguanosine Adducts of Aromatic Amines (2002)

The synthesis of 5′-O-DMTr-3′-O-phosphoramidite-C8-arylamine-dG adducts 11 and 12 is described. The compounds are potential building blocks for the automated synthesis of site-specifically modified oligonucleotides. The C8-adducts were synthesized by a palladium-catalyzed cross-coupling reaction.
Investigation of a Molecular Morphology Effect on Polyphenylazomethine Dendrimers; Physical Properties and Metal‐Assembling Processes (2006)

A series of novel dendritic polyphenylazomethines (DPA) with asymmetric morphologies was synthesized. Their physical properties, such as encapsulating effect, molecular dynamics, and metal assembly, are strongly dependent on the entire conformation of the molecules. The most important property is layer-by-layer metal assembly in the dendrimer structure from the core to the outside. Bis- and tris-substituted DPAs of the fourth generation also act as frameworks for stepwise assembly of a metal component (SnCl2), like the fully substituted symmetric DPA. However, extensive investigation of metal assembly in specific DPAs revealed that they do not follow the stepwise process. The molecular density calculated from the experimental hydrodynamic volume indicated that bis- and tris-substituted DPAs with asymmetric morphology still retain a free space similar to that of fully substituted symmetric DPA. The monosubstituted DPA, however, displayed a slightly higher density (smaller space) than the other DPAs. The experimental results suggest a bent conformation of the dendrimer in which the core moiety is folded into the dendron structure. In addition, the molecular dynamics were probed by means of the 1H NMR signals of the porphyrin core. It was demonstrated that the conformation is not fixed at room temperature in solvated DPAs, especially in monosubstituted DPA. A similar observation was for the smaller DPAs (third generations) with asymmetric morphologies. These dendrimers do not follow the stepwise complexation process. The structures of bis- and tris-substituted dendrimers which accurately follow the stepwise process are fixed. These observations provide a new insight into the finely controlled metal-assembly chemistry of dendritic macromolecules, and a rigid and fixed conformation is one of important factors for their unique properties.