gebhart/patrepeval huggingface dataset:
Massively multiplexed nucleic acid detection with Cas13 (2020)

The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples<sup>1-3</sup> while simultaneously testing for many pathogens<sup>4-6</sup>. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents<sup>7</sup> self-organize in a microwell array<sup>8</sup> to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health<sup>9-11</sup>.
Ultrafast Surface Inspection using Hybrid Dispersion Laser Scanner (2013)

We report an ultrafast surface inspection method using a hybrid dispersion laser scanner. Using the technique, we demonstrate real-time detection of microparticles on silicon wafer surfaces at 1,000 times higher scan rates than conventional methods.
Time-reversal in an ultrasonic waveguide (1997)

The aim of this letter is to study, by using a time-reversal mirror (TRM), ways to overcome the distortions induced by multipaths in an acoustic transmission. A set of experiments is performed with a TRM made of 96 reversible transducers and results will be presented. One result is related to the high focusing property obtained with a TRM working in a bounded channel. It will be shown that the time-reversed beam is much thinner than the one measured in an unbounded medium. The second result concerns the time compression observed for the time-reversed acoustic pulse. The influence of the number of TRM elements on the time compression is discussed.
Robust Motion Control Method Considering Saturation of Joint Torque and Joint Servo System (1998)

When a robot manipulator performs fast motion control, high joint torque is required. Moreover, additional joint torque is necessary to suppress disturbance. However, as an actuator can not produce very high joint torque, the saturation on joint torque occurs. This paper proposes a strategy to solve the saturation problem stated above. The two algorithms called the torque limiting algorithm and the reference adjusting algorithm are introduced. The torque limiting algorithm is applied in order to prevent the saturation of joint torque. Another algorithm called the path reference adjusting algorithm will suppress the deviation on path tracking caused by the limitation. The effectiveness of the proposed method is confirmed by experimental results of a 2-link planar arm manipulator.
Supplementary Figure 7 from First-in-Human Trial of a STAT3 Decoy Oligonucleotide in Head and Neck Tumors: Implications for Cancer Therapy (2023)

&lt;p&gt;PDF file - 107K, Systemic delivery of cyclic STAT3 decoy does not affect total or pSTAT3 expression levels&lt;/p&gt;
Tunable and Active Metamaterials (2010)

One of the most unique properties of light is that it can package information into a signal of zero mass and propagate it at the ultimate speed. It is, however, a daunting challenge to bring photonic devices to the nanometer scale because of the fundamental diffraction limit. Metamaterials can focus light down to the nanoscale and thus enable a family of new nanophotonic devices. Metamaterials, i.e. artificial materials with rationally designed geometry, composition, and arrangement of nanostructured building blocks are opening a gateway to unprecedented electromagnetic properties and functionalities that are unattainable with naturally occurring materials. We review this exciting field and discuss the recent, significant progress in developing metamaterials for the optical part of the electromagnetic spectrum. Specifically, we report on our recent world’s smallest nanolaser (collaborative work with Norfolk State University and Cornell), describe the phenomena of artificial magnetism across the whole visible and negative refractive indices in the optical range, and demonstrate a broadband cloaking in the visible based on tapered waveguides (collaboration with BAE and Towson University). Loss-free and active negative-index metamaterials will be reviewed. Finally, a new, powerful paradigm of engineering space for light with transformation optics, which can enable a family of new applications including a planar magnifying hyperlens, optical black hole and engineered photonic density of states will be also discussed.
Comparative performance analysis for computer aided lung nodule detection and segmentation on ultra-low-dose vs. standard-dose CT (2006)

The performance of computer aided lung nodule detection (CAD) and computer aided nodule volumetry is compared between standard-dose (70-100 mAs) and ultra-low-dose CT images (5-10 mAs). A direct quantitative performance comparison was possible, since for each patient both an ultra-low-dose and a standard-dose CT scan were acquired within the same examination session. The data sets were recorded with a multi-slice CT scanner at the Charite university hospital Berlin with 1 mm slice thickness. Our computer aided nodule detection and segmentation algorithms were deployed on both ultra-low-dose and standard-dose CT data without any dose-specific fine-tuning or preprocessing. As a reference standard 292 nodules from 20 patients were visually identified, each nodule both in ultra-low-dose and standard-dose data sets. The CAD performance was analyzed by virtue of multiple FROC curves for different lower thresholds of the nodule diameter. For nodules with a volume-equivalent diameter equal or larger than 4 mm (149 nodules pairs), we observed a detection rate of 88% at a median false positive rate of 2 per patient in standard-dose images, and 86% detection rate in ultra-low-dose images, also at 2 FPs per patient. Including even smaller nodules equal or larger than 2 mm (272 nodules pairs), we observed a detection rate of 86% in standard-dose images, and 84% detection rate in ultra-low-dose images, both at a rate of 5 FPs per patient. Moreover, we observed a correlation of 94% between the volume-equivalent nodule diameter as automatically measured on ultra-low-dose versus on standard-dose images, indicating that ultra-low-dose CT is also feasible for growth-rate assessment in follow-up examinations. The comparable performance of lung nodule CAD in ultra-low-dose and standard-dose images is of particular interest with respect to lung cancer screening of asymptomatic patients.
How to Assess Gaming-Induced Benefits on Attention and Working Memory (2012)

Our daily actions are driven by our goals in the moment, constantly forcing us to choose among various options. Attention and working memory are key enablers of that process. Attention allows for selective processing of goal-relevant information and rejecting task-irrelevant information. Working memory functions to maintain goal-relevant information in memory for brief periods of time for subsequent recall and/or manipulation. Efficient attention and working memory thus support the best extraction and retention of environmental information for optimal task performance. Recent studies have evidenced that attention and working memory abilities can be enhanced by cognitive training games as well as entertainment videogames. Here we review key cognitive paradigms that have been used to evaluate the impact of game-based training on various aspects of attention and working memory. Common use of such methodology within the scientific community will enable direct comparison of the efficacy of different games across age groups and clinical populations. The availability of common assessment tools will ultimately facilitate development of the most effective forms of game-based training for cognitive rehabilitation and education.
Test beam demonstration of silicon microstrip modules with transverse momentum discrimination for the future CMS tracking detector (2018)

A new CMS Tracker is under development for operation at the High Luminosity LHC from 2026 onwards. It includes an outer tracker based on dedicated modules that will reconstruct short track segments, called stubs, using spatially coincident clusters in two closely spaced silicon sensor layers. These modules allow the rejection of low transverse momentum track hits and reduce the data volume before transmission to the first level trigger. The inclusion of tracking information in the trigger decision is essential to limit the first level trigger accept rate. A customized front-end readout chip, the CMS Binary Chip (CBC), containing stub finding logic has been designed for this purpose. A prototype module, equipped with the CBC chip, has been constructed and operated for the first time in a 4 GeV/c positron beam at DESY. The behaviour of the stub finding was studied for different angles of beam incidence on a module, which allows an estimate of the sensitivity to transverse momentum within the future CMS detector. A sharp transverse momentum threshold around 2 GeV/c was demonstrated, which meets the requirement to reject a large fraction of low momentum tracks present in the LHC environment on-detector. This is the first realistic demonstration of a silicon tracking module that is able to select data, based on the particle's transverse momentum, for use in a first level trigger at the LHC . The results from this test are described here.
SHEET ATOMIZATION OF NON-NEWTONIAN LIQUIDS (2003)

An experimental investigation is made of the sheet atomization of dilute concentrations of flexible 9 ґ 106 molecular-weight nonionic polyacrylamide in glycerin-thickened aqueous solutions. These solutions are sprayed through a single fan male at pressures of 1.4-21 MPa. The original molecular weight and extensional viscosity are significantly degraded at all pressures by the strain rates imposed by the spray system and nozzle. In spite of this degradation, however, the sheet breakup features are nonetheless visibly altered by these dilute polymer concentrations. From our results, the physics of polymeric solution sheet breakup appears to be a combination of destabilizing and stabilizing extensional viscosity effects. The destabilizer is the amplification of sheet waves at the nozzle exit, which leads to decreased sheet breakup lengths, whereas the stabilizer is the extensional viscosity-induced increase of wavelength. Implications of these results are considered in terms of rheological instruments and industrial applications, especially "airless" spray painting.
The role of chemical sciences in 21st century cancer drug discovery. (2005)

Extract: The chemical sciences are increasingly overlapping with many aspects of the study of biological molecules at the molecular level. By contrast, the traditional view of chemistry, at least as far as cancer therapeutics is concerned, has been a much narrower one as a tool of the cancer drug discovery process, generally being solely concerned with synthesis. The thesis that we develop in this short review is that the role of the chemical sciences in cancer therapeutics increasingly covers far more than this, and requires the active involvement of many aspects of the subject if the full potential of our knowledge of the cellular, molecular, and genetic basis of cancer is to be translated into clinically useful therapeutics. Effective drug discovery requires an understanding of small molecule and macromolecule physico-chemical properties, mechanism of action, structure and reactivity of individual components (including targets) of pathways, and the ways in which they interact together by means of both covalent and non-covalent recognition and signal transfer. It is no coincidence that several effective clinical agents have been discovered by creative chemists who possess a deep understanding of these topics, especially of the relationships between the structure and reactivity properties of a particular class of molecules, leading to insights into their potential as anticancer agents.
GNC and CGA1 Modulate Chlorophyll Biosynthesis and Glutamate Synthase (GLU1/Fd-GOGAT) Expression in Arabidopsis (2011)

Chloroplast development is an important determinant of plant productivity and is controlled by environmental factors including amounts of light and nitrogen as well as internal phytohormones including cytokinins and gibberellins (GA). The paralog GATA transcription factors GNC and CGA1/GNL up-regulated by light, nitrogen and cytokinin while also being repressed by GA signaling. Modifying the expression of these genes has previously been shown to influence chlorophyll content in Arabidopsis while also altering aspects of germination, elongation growth and flowering time. In this work, we also use transgenic lines to demonstrate that GNC and CGA1 exhibit a partially redundant control over chlorophyll biosynthesis. We provide novel evidence that GNC and CGA1 influence both chloroplast number and leaf starch in proportion to their transcript level. GNC and CGA1 were found to modify the expression of chloroplast localized GLUTAMATE SYNTHASE (GLU1/Fd-GOGAT), which is the primary factor controlling nitrogen assimilation in green tissue. Altering GNC and CGA1 expression was also found to modulate the expression of important chlorophyll biosynthesis genes (GUN4, HEMA1, PORB, and PORC). As previously demonstrated, the CGA1 transgenic plants demonstrated significantly altered timing to a number of developmental events including germination, leaf production, flowering time and senescence. In contrast, the GNC transgenic lines we analyzed maintain relatively normal growth phenotypes outside of differences in chloroplast development. Despite some evidence for partial divergence, results indicate that regulation of both GNC and CGA1 by light, nitrogen, cytokinin, and GA acts to modulate nitrogen assimilation, chloroplast development and starch production. Understanding the mechanisms controlling these processes is important for agricultural biotechnology.
Expression of active spinach glycolate oxidase in Aspergillus nidulans (1996)

The biocatalytic production of glyoxylic acid from glycolic acid requires two enzymes: glycolate oxidase, which catalyzes the oxidation of glycolic acid by oxygen to produce glyoxylic acid and hydrogen peroxide, and catalase, which decomposes the byproduct hydrogen peroxide. As an alternative to isolation from the leaf peroxisomes of spinach, glycolate oxidase has now been cloned and expressed in transformants of Aspergillus nidulans T580 at levels ranging from 1.7 to 36 IU/g dry wt. cells. The glycolate oxidase of transformant strain T17 comprises ca. 1.9% of total cell protein and is expressed at near 100% activity.
Broadband Dielectric Investigation of Amorphous and Semicrystalline l-Lactide/meso-Lactide Copolymers (2004)

The dynamics of crystalline and amorphous samples of poly(l-lactide) and three l-lactide/meso-lactide random copolymers were investigated in the frequency domain using broadband dielectric spectroscopy (DRS). Two relaxations, the segmental (α) and subglass (β) processes, were observed in the temperature range between −100 and 105 °C. Modification of the characteristics of the α process, i.e., the relaxation strength (Δε), mean relaxation time (τm), and shape parameters, as a function of crystal content was investigated on “fully crystallized” samples as well as in real-time crystallization experiments. As expected, the strength of the α relaxation was smaller and its distribution broader for materials with higher degrees of crystallinity. The relaxation strength of the α process of the amorphous samples increased with temperature, while that of the crystalline materials changed very little or in the opposite direction with temperature. This behavior can be explained by the existence of a rigid amorphous component. Changes in τm and T0 (the Vogel temperature) for the copolymers crystallized at various Tc are influenced by crystalline microstructure as well as by crystalline content. A relaxation is also observed in higher temperature (125−155 °C) experiments on amorphous and crystalline materials. The evidence at hand suggests that these processes are associated with the normal mode and αc process, respectively.
Isolated amyloidosis presenting with lumbosacral radiculoplexopathy: description of two cases and pathogenic review (2006)

In this study, we present two cases of infiltrative, localized amyloidosis involving lumbosacral root and plexus, e.g., isolated amyloidomas. Rare and poorly understood amyloidomas may occur in both neurologic and non-neurologic tissues. The described cases emphasize potential for localized peripheral amyloidomas: (1) potential for associated lambda light chain lymphoplasmacytic lymphoma association; (2) e isolated amyloidosis without evidence for systemic plasma cell dyscrasia; (3) features suggestive of potential pathogenesis; and (4) discussion of treatment options including immunotherapy and resection. The limited literature and experience among other cases is described.
Crystallography of excimer laser-crystallized In-Ga-Zn-O film (2013)

It is found by nanobeam electron diffraction that the excimer laser crystallization of In-Ga-Zn-O films which are not c-axis-aligned can lead to formation of polycrystalline In-Ga-Zn-O thin films having spinel structures. The crystal structure of ZnInxGa2-xO4 in which Ga site of ZnGa2O4 is substituted by In was obtained by first-principle calculation. It has been revealed that the unitcell constants and out-of-plane XRD peak angles (2θ) which are calculated from electron diffraction are reproduced in x = 0.5-1. In contrast, in the case of performing laser crystallization on a CAAC-IGZO film as a precursor, although polycrystalline In-Ga-Zn-O thin films having homologous structures are formed, formation of spinel structures is not observed.
Conduction Type Control of Ge-on-Insulator: Combination of Smart-Cut™ and Defect Elimination (2019)

We electrically characterized Ge-on-Insulator (GOI) fabricated by Smart-Cut™ method. Annealing improved electrical characteristics of the p-GOI. On the other hand, conduction type of the n-GOI changed to p-type after annealing. Structural analysis showed many defects were introduced near the bottom interface and it cannot be recovered by annealing. We suggest alternative ways to avoid defects for n-GOI fabrication.
Synthesis, characterization, and humidity-responsiveness of guar gum xanthate and its nanocomposite with copper sulfide covellite (2022)

A novel conjugation of guar gum with xanthate groups via facile aqueous xanthation reaction has been reported. Density of grafted xanthate on guar gum product (GG-X) is as high as 4.4%, thus GG-X is conceivably characterized and confirmed by various spectrometric, electrochemical, thermogravimetric, and microscopic methods. Complexation of GG-X with numerous borderline and soft metal ions (e.g. Fe<sup>2+</sup>, Co<sup>2+</sup>, Ni<sup>2+</sup>, Cu<sup>2+</sup>, Pb<sup>2+</sup>, Pt<sup>2+</sup> and Cd<sup>2+</sup>) yields hydrophilic gel-like materials and shows good agreement with hard and soft acid and base (HSAB) theory. This indicates tremendous potential of GG-X in metal ion extraction, removal and hydrogel cross-linking. GG-X is also employed to formulate an aqueous colloidal dispersion of copper sulfide covellite (GG-X/CuS) nanocomposites. GG-X therefore behaves as a surfactant, allowing formation of electronically conductive nanocomposites. XRD indicates apparent beneficial effects of GG-X in the synthesis of CuS with a crystallite size of 15.6 nm. This novel nanocomposite is a promising material for humidity sensing, showing reversible linear responses to relative humidity changes within 10 to 80% range. The interaction between GG-X and water might cause changes in electrical permittivity of GG-X/CuS nanocomposite and/or electrical hopping conductivity between CuS nanoparticles.
Rapid dissonant grunting, or, but why does music sound the way it does? (2021)

Each target article contributes important proto-musical building blocks that constrain music as-we-know-it. However, neither the credible signaling nor social bonding accounts elucidate the central mystery of why music sounds the way it does. Getting there requires working out how proto-musical building blocks combine and interact to create the complex, rich, and affecting music humans create and enjoy.
Mechanical Behavior of 980MPa NANOHITEN<sup>TM</sup> at Elevated Temperatures and its Effect on Springback in Warm Forming (2014)

High tensile strength steel sheets have large springback after being formend at room temperature. Warm forming can be a solution to reduce springback of high tensile strength steel parts. NANOHITEN TM is a high strength ferritic steel precipitation-strengthened by nanometer-sized carbides developed by JFE Steel Corporation. Tensile strength of the steel at room temperature does not change before and after deformation at elevated temperatures up to 873K since the carbides in the steel are stable at high temperatures less than 973K. Therefore, the steel is suitable for warm forming. Springback of 980MPa NANOHITEN TM parts warm formed at 873K is the same level of that of cold formed conventional 590MPa steel parts. In this study, two kinds of material testing at room temperature and at elevated temperatures between 573K and 937K were performed to understand the mechanical behavior of 980MPa NANOHITEN TM : uniaxial tensile tests and bending tests. The steels flow stress depends on not only material temperature but also strain rate in uniaxial tensile tests. After a bending test, the specimen shows springback measured by the change of an angle between the two sides. Stress relaxation happens while a test specimen is held at the bottom dead point after bending. And the stress relaxation could be used to reduce springback of warm formed parts.
Roles of RecBC Enzyme and Chi Sites in Homologous Recombination (1984)

Advances in our understanding of the molecular mechanisms of homologous recombination have come from a variety of experimental approaches. Genetic analyses of mutants defective in recombination have identified genes whose functions are required for recombination and have led to the concept of alternative pathways of recombination. Biochemical analyses of wild-type and mutant cells have identified enzymatic activities associated with some of these genes and therefore necessary for recombination. Studies on the transfer of genetic information and material from parental DNA molecules to recombinant DNA molecules have shown recombination in some cases to be a breakage and reunion reaction with production of hybrid DNA and have led to the proposal of models of recombination. These genetic studies have also shown that homologous recombination is sometimes controlled by special DNA sites that act either negatively or positively in their vicinity. Collectively, these approaches promise to lead to a more complete molecular description...