gebhart/patrepeval huggingface dataset:
Growing a circular economy with fungal biotechnology: a white paper (2020)

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation's sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.
Direct-binary-search algorithm for fabrication-tolerant photonic-crystal-like subwavelength structures and its application to a four-mode waveguide crossing in 2 μ m waveband (2022)

Abstract A novel direct-binary-search algorithm for the design of fabrication-tolerant photonic-crystal-like subwavelength structures is proposed. In the proposed method, structures based on holes with different diameters are considered to enhance the device performance under diameter variation. The usefulness of the proposed method is demonstrated through the design of a fabrication-tolerant four-mode waveguide crossing in the 2 μ m waveband. With the proposed method, the transmission of TE3 mode is increased by 4.9% (for diameter of 130 nm) and 9.5% (for diameter of 150 nm) on average of 15 samples, compared with the conventional direct-binary-search method. The designed device provides insertion losses of &lt;0.87 dB and crosstalks of &lt;−24 dB in spite of diameter variations of ±10 nm from the ideal diameter.
Intelligent image-activated cell sorting: principles and applications (Conference Presentation) (2019)

I present a newly developed machine intelligence technology called “Intelligent Image-Activated Cell Sorting” [Cell 175, 1 (2018)] that achieves real-time fluorescence-image-based intelligent cell sorting at a high throughput of ~100 events per second. This technology builds on a unique integration of high-throughput cell microscopy, focusing, and sorting techniques on a unique software-hardware platform and hence performs fully automated operation for data acquisition, data processing, decision making, and actuation. Also, I introduce the technology’s broad utility to addressing a fundamental biological question that cannot be answered by conventional technologies – how molecular architectures of cells are connected with their physiological functions.
Shape-Selective Deposition and Assembly of Anisotropic Nanoparticles (2014)

We report the large-area assembly of anisotropic gold nanoparticles into lithographically defined templates with control over their angular position using a capillary force-based approach. We elucidate the role of the geometry of the templates in the assembly of anisotropic nanoparticles consisting of different shapes and sizes. These insights allow us to design templates that immobilize individual triangular nanoprisms and concave nanocubes in a shape-selective manner and filter undesired impurity particles from a mixture of triangular prisms and other polyhedra. Furthermore, by studying the assembly of two particles in the same template, we elucidate the importance of interparticle forces in this method. These advances allow for the construction of face-to-face and edge-to-edge nanocube dimers as well as triangular nanoprism bowtie antennas. As an example of the fundamental studies enabled by this assembly method, we investigate the surface-enhanced Raman scattering (SERS) of face-to-face concave cube dimers both experimentally and computationally and reveal a strong polarization dependence of the local field enhancement.
Microsurgical laser resection of brainstem cavernous malformations (2019)

This operative technique video demonstrates laser microsurgery for brainstem cavernous malformations (CMs). In case 1 we demonstrate CO<sub>2</sub> laser microsurgery for a symptomatic pontine CM using far lateral craniotomy and olivary zone entry. Case 2 demonstrates the subtemporal approach and removal of a paratrigeminal CM, and case 3 is a dorsal midbrain CM. We illustrate several advantages of laser microsurgery including improved visualization in narrow corridors, precise cutting with reduced thermal damage, and effective sealing of small vessels. Over the past decade at Stanford University School of Medicine, over 120 brainstem CMs have been removed using laser microsurgery with good results. The video can be found here: https://youtu.be/DwwqWGv_vzo.
Photophysical pore control in an azobenzene-containing metal–organic framework (2013)

The synthesis and structure of an azobenzene functionalized isoreticular metal–organic framework (azo-IRMOF-74-III) [Mg2(C26H16O6N2)] are described and the ability to controllably release a guest from its pores in response to an external stimulus has been demonstrated. Azo-IRMOF-74-III is an isoreticular expansion of MOF-74 with an etb topology and a 1-D hexagonal pore structure. The structure of azo-IRMOF-74-III is analogous to that of MOF-74, as demonstrated by powder X-ray diffraction, with a surface area of 2410 m2 g−1 BET. Each organic unit within azo-IRMOF-74-III is decorated with a photoswitchable azobenzene unit, which can be toggled between its cis and trans conformation by excitation at 408 nm. When propidium iodide dye was loaded into the MOF, spectroscopic studies showed that no release of the luminescent dye was observed under ambient conditions. Upon irradiation of the MOF at 408 nm, however, the rapid wagging motion inherent to the repetitive isomerization of the azobenzene functionality triggered the release of the dye from the pores. This light-induced release of cargo can be modulated between an on and an off state by controlling the conformation of the azobenzene with the appropriate wavelength of light. This report highlights the ability to capture and release small molecules and demonstrates the utility of self-contained photo-active switches located inside highly porous MOFs.
Femtosecond laser writing of porous capillaries inside fused silica glass (2007)

We demonstrate that within a restricted optical pulse duration-pulse energy parameter space tightly focused femtosecond laser radiation can be used to fabricate porous capillaries in bulk fused silica glass by simply moving the laser focus through the material. We show that the rate of penetration of liquids into the porous capillaries can be controlled by the laser polarization, which determines their morphology. The fluid propagation is measured using the form birefringence of nanocrack/nanovoid structures produced inside the capillaries. We also demonstrate the nanofiltration capabilities of the capillaries by separating the relatively small molecules of Rhodamine 6G dye from their solvent.
Interstitial photodynamic therapy planning with 3D placement optimization (2020)

We present an optimized light diffuser placement algorithm for high-quality interstitial photodynamic therapy planning. We simulate the algorithm on modeled glioblas-toma multiforme cases. Results show damage to organs-at-risk is reduced by 46%-77% on average.
Subconjunctival Injection of XG-102, a c-Jun N-Terminal Kinase Inhibitor Peptide, in the Treatment of Endotoxin-Induced Uveitis in Rats (2014)

These results confirm that XG-102 peptide has potential for treating intraocular inflammation. SCJ injection appears as a good compromise to provide a therapeutic effect while limiting side effects.
Generation of Coherent sub-20 nm XUV Radiation at 78 MHz via Cavity-Based HHG (2013)

We present two major advances of enhancement-cavity-based high-order harmonic generation (HHG). First, the generated extreme ultraviolet (XUV) radiation is coupled out collinearly through an on-axis opening in the mirror following the HHG focus. This minimizes the interaction of both the fundamental and the intracavity generated ra diation with the output coupler while simultaneously enabling a large enhancement and an output coupling efficiency that increases with the harmonic order. Second, we use the nonlinearly compressed pulses of an Yb-based laser to drive intracavity HHG allowing for a unique power regime combining short pulses with high average powers. Together, these advances overcome fundamental limitations of current enhancement cavity setups and extend intracavity HHG towards higher photon energies. In a proof-of-principle experiment we use a 3-kW and 78-MHz train of 54-fs to generate and couple out coherent sub-20 nm radiation.
Characteristics of Silicon Nitride Reaction to Vapor-phase HF Gas Treatment (2006)

Evidence has been presented that the mixed anhydrous hydrogen fluoride (HF) and methanol (CH3OH) gas, which is used for dry etching the sacrificial layer of silicon dioxide film, deteriorates silicon nitride film (SiN). From the results of chemical composition analyses, the alteration product was identified to be ammonium hexafluorosilicate ((NH4)2SiF6). We found that the alteration product can be decomposed and removed by heat-treatment in atmosphere. The deterioration of the SiN by the HF/CH3OH gas treatment is approximately 3 nm/min, and the growth rate of the SiN alteration product is approximately 30 nm/min.
Engineering post-translational proofreading to discriminate non-standard amino acids (2017)

Abstract Progress in genetic code expansion requires accurate, selective, and high-throughput detection of non-standard amino acid (NSAA) incorporation into proteins. Here, we discover how the N-end rule pathway of protein degradation applies to commonly used NSAAs. We show that several NSAAs are N-end stabilizing and demonstrate that other NSAAs can be made stabilizing by rationally engineering the N-end rule adaptor protein ClpS. We use these insights to engineer a synthetic quality control method, termed “Post-Translational Proofreading” (PTP). By implementing PTP, false positive proteins resulting from misincorporation of structurally similar standard amino acids or undesired NSAAs rapidly degrade, enabling high-accuracy discrimination of desired NSAA incorporation. We illustrate the utility of PTP during evolution of the biphenylalanine orthogonal translation system used for synthetic biocontainment. Our new OTS is more selective and confers lower escape frequencies and greater fitness in all tested biocontained strains. Our approach presents a new paradigm for molecular recognition of amino acids in target proteins.
Differential Effects of a Saturated and a Monounsaturated Fatty Acid on MHC Class I Antigen Presentation (2008)

Lipid overload, associated with metabolic disorders, occurs when fatty acids accumulate in non-adipose tissues. Cells of these tissues use major histocompatibility complex (MHC) class I molecules to present antigen to T cells in order to eliminate pathogens. As obesity is associated with impaired immune responses, we tested the hypothesis that the early stages of lipid overload with saturated fatty acids (SFA) alters MHC class I antigen presentation. Antigen presenting cells (APC) were treated with either the saturated palmitic acid (PA), abundant in the high fat Western diet, or the monounsaturated oleic acid (OA), a component of the Mediterranean diet. PA-treatment lowered APC lysis by activated cytotoxic T lymphocytes and inhibited APC ability to stimulate naïve T cells. Inhibition of immune responses with PA was due to a significant reduction in MHC class I surface expression, inhibition in the rate of APC-T-cell conjugation, and lowering of plasma membrane F-actin levels. OA-treatment had no effect on antigen presentation and upon exposure with PA, prevented the phenotypic effects of PA. OA-treatment conferred protection against changes in antigen presentation by accumulating fatty acids into triglyceride-rich lipid droplets of APC. Our findings establish for the first time a link between the early stages of lipid overload and antigen presentation and suggest that dietary SFA could impair immunity by affecting MHC I-mediated antigen presentation; this could be prevented, paradoxically, by accumulation of triglycerides rich in monounsaturated fatty acids.
Low-cost microbolometer with nano-scaled plasmonic absorbers for far infrared thermal imaging applications (2014)

We present a scalable low-cost microbolometer technology platform which is based on separate fabrication of MEMS and read-out ASIC CMOS wafers. Mechanical, electrical and hermetical connection is achieved by Cu-based thermocompression bonding. The performance loss due to the resulting backside illumination of the sensor is compensated by an optimized microbolometer design including nano-scaled plasmonic absorbers, a dedicated pixel geometry and the use of highly temperature sensitive devices. The low-cost approach features CMOS compatible MEMS processes, wafer level packaging and uncooled operation of the sensor.
Oxidation of glycerol using gold–palladium alloy-supported nanocrystals (2009)

The use of bio-renewable resources for the generation of materials and chemicals continues to attract significant research attention. Glycerol, a by-product from biodiesel manufacture, is a highly functionalised renewable raw material, and in this paper the oxidation of glycerol in the presence of base using supported gold, palladium and gold-palladium alloys is described and discussed. Two supports, TiO(2) and carbon, and two preparation methods, wet impregnation and sol-immobilisation, are compared and contrasted. For the monometallic catalysts prepared by impregnation similar activities are observed for Au and Pd, but the carbon-supported monometallic catalysts are more active than those on TiO(2). Glycerate is the major product and lesser amounts of tartronate, glycolate, oxalate and formate are observed, suggesting a sequential oxidation pathway. Combining the gold and palladium as supported alloy nanocrystals leads to a significant enhancement in catalyst activity and the TiO(2)-supported catalysts are significantly more active for the impregnated catalysts. The use of a sol-immobilisation preparation method as compared to impregnation leads to the highest activity alloy catalysts and the origins of these activity trends are discussed.
Impact of PDMS-Based Microfluidics on Belousov–Zhabotinsky Chemical Oscillators (2020)

Sub-nanoliter volumes of the Belousov-Zhabotinsky (BZ) reaction are sealed in microfluidic devices made from polydimethylsiloxane (PDMS). Bromine, which is a BZ reaction intermediate that participates in the inhibitory pathway of the reaction, is known to permeate into PDMS, and it has been suggested that PDMS and bromine can react ( <i>J. Phys. Chem. A</i>. 108, 2004, 1325-1332). We characterize the extent to which PDMS affects BZ oscillations by varying the volume of the PDMS surrounding the BZ reactors. We measure how the oscillation period varies with PDMS volume and compare with a theoretical reaction-diffusion model, concluding that bromine reacts with PDMS. We demonstrate that minimizing the amount of PDMS by making the samples as thin as possible maximizes the number of oscillations before the BZ reaction reaches equilibrium and ceases to oscillate. We also demonstrate that the deleterious effects of the PDMS-BZ interactions are somewhat mitigated by imposing constant chemical boundary conditions through using a light-sensitive catalyst, ruthenium, in combination with patterned illumination. Furthermore, we show that light can modulate the frequency and phase of the BZ oscillators contained in a PDMS matrix by 20-30%.
Fe₂O₃/Cu₂O heterostructured nanocrystals (2014)

We report the synthesis of colloidal γ-Fe₂O₃/Cu₂O hetero-nanocrystals (HNCs) using a solution-phase seeded-growth approach. γ-Fe₂O₃ nanocrystals were used as seeds for the nucleation of metallic Cu followed by oxidation of the Cu domain to Cu₂O upon exposure to air. The resulting dimer, trimer, and oligomer HNCs were characterized by high resolution electron microscopy, energy dispersive X-ray spectroscopy, and powder X-ray diffraction. The iron oxide component was found to be mainly γ-Fe₂O₃ using a combination of Raman and X-ray photoelectron spectroscopy. A maximal HNC yield of 72% was achieved by reducing particle growth time to a lower growth temperature with respect to the individual component particles. Size-selective precipitation was used to enrich the nanoparticle mixture in γ-Fe₂O₃/Cu₂O dimers by removing the larger aggregates. Ultraviolet photoelectron spectroscopy was used to determine that γ-Fe₂O₃ and Cu₂O are n-doped and p-doped respectively and form a staggered, type II band alignment. As such, γ-Fe₂O₃/Cu₂O HNCs may be attractive candidates for applications in solar energy conversion and represent a valuable addition to the growing library of oxide–oxide hetero-nanocrystals.
A gypsum-based artificial stone for shock wave lithotripsy research (2002)

Natural kidney stones are heterogeneous in structure, composition, material properties and fragility, and as such are problematic for use in determining the mechanisms of SW-action in SWL. A variety of model stones have been developed. We have adopted Ultracal-30 gypsum [Dahake and Gracewski, J. Acoust. Soc. Am. 102, 2138 (1997)] for in-vitro and in-vivo studies. U-30 stones (7.5×6.5 mm) cast in polystyrene molds were liberated with chloroform and stored in water. Drop-impact testing of dry stones showed a linear relationship between increase in surface area of fragments and energy applied. Breakage of hydrated stones in a research-electrohydraulic lithotripter, likewise showed a linear increase in fragment area with increased SW-number and SW-voltage. The density (1800 kg/m3) and transverse (1520 m/s) and longitudinal (3100 m/s) wave speeds of U-30 stones place them in the range determined for natural stones. U-30 stones implanted in pig kidneys exhibited cavitation erosion and spall fracture similar to stones in-vitro, and U-30 stones in-vitro and in-vivo showed equivalent response to SW-rate (200% higher fragmentation at 0.5 Hz compared to 2 Hz). U-30 stones softened with prolonged exposure to water and degraded during long-term implantation in-vivo. With these cavaets U-30 stones provide a useful model for SWL research. [Work supported by NIH P01-DK43881.]
Hydrogen peroxide vapour treatment inactivates norovirus but has limited effect on post-treatment viral RNA levels (2019)

Inactivation of murine norovirus viability by hydrogen peroxide vapour was not reflected in qPCR levels. This finding might be extrapolated to the related human norovirus genogroups. We further found that cellular minus strand murine norovirus PCR was an observer-independent marker to study reduction of murine norovirus viability.
Footstep Planning for Autonomous Walking Over Rough Terrain (2019)

To increase the speed of operation and reduce operator burden, humanoid robots must be able to function autonomously, even in complex, cluttered environments. For this to be possible, they must be able to quickly and efficiently compute desired footsteps to reach a goal. In this work, we present a new A * footstep planner that utilizes a planar region representation of the environment enable footstep planning over rough terrain. To increase the number of available footholds, we present an approach to allow the use of partial footholds during the planning process. The footstep plan solutions are then post-processed to capture better solutions that lie between the lattice discretization of the footstep graph. We then demonstrate this planner over a variety of virtual and real world environments, including some that require partial footholds and rough terrain using the Atlas and Valkyrie humanoid robots.
Data Management in the Worldwide Sensor Web (2007)

Harvesting the benefits of a sensor-rich world presents many data management challenges. Recent advances in research and industry aim to address these challenges. With the rapidly increasing number of large-scale sensor network deployments, the vision of a worldwide sensor Web is close to becoming a reality.
Hierarchical Structures: Programmable Building Blocks via Internal Stress Engineering for 3D Collective Assembly (Adv. Mater. Technol. 12/2020) (2020)

In article number 2000758, Jeong Jae Wie and co-workers present a nature-inspired collective assembly of precisely designed 3D building blocks for scaled-up hierarchical 3D architectures. The precise dimension control of 3D building blocks is successfully progressed by controlling the spatio-temporal effect composed of fractal elements throughout the stages of fabrication. The concept of collective assembly extends the morphological diversity of the 3D structures and presents a construction of creatively assembled structures.
Temperature Dependence of Interactions Between Stable Piperidine‐1‐yloxyl Derivatives and a Semicrystalline Ionic Liquid (2010)

The stable 2,2,6,6-tetramethylpiperidine-1-yloxyl and its derivatives with hydrogen-bond-forming (-OH, -OSO(3)H), anionic (-OSO(3) (-) bearing K(+) or [K(18-crown-6)](+) as counter ion), or cationic (-N(+)(CH(3))(3) bearing I(-), BF(4) (-), PF(6) (-) or N(-)(SO(2)CF(3))(2) as counter ion) substituents are investigated in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide over a wide temperature range. The temperature dependence of the viscosity of the ionic liquid is well described by the Vogel-Fulcher-Tammann equation. Interestingly, the temperature dependence of the rotational correlation time of the spin probes substituted with either a hydrogen-bond-forming group or an ionic substituent can be described using the Stokes-Einstein equation. In contrast, the temperature dependence of the rotational correlation time of the spin probe without an additional substituent at the 4-position to the nitroxyl group does not follow this trend. The activation energy for the mobility of the unsubstituted spin probe, determined from an Arrhenius plot of the spin-probe mobility in the ionic liquid above the melting temperature, is comparable with the activation energy for the viscous flow of the ionic liquid, but is higher for spin probes bearing an additional substituent at the 4-position. Quantum chemical calculations of the spin probes using the 6-31G+d method give information about the rotational volume of the spin probes and the spin density at the nitrogen atom of the radical structure as a function of the substituent at the spin probes in the presence and absence of a counter ion. The results of these calculations help in understanding the effect of the additional substituent on the experimentally determined isotropic hyperfine coupling constant.
Supplementary Figure S1 from Radiotherapy Induces Innate Immune Responses in Patients Treated for Prostate Cancers (2023)

&lt;p&gt;Volcano plot showing significant dysregulation of plasma metabolites at 24 hours (Panel A), one month (Panel B), 3 months (Panel C) and six months (Panel D) as compared to baseline (pre-RT).&lt;/p&gt;
Keynote lecture: Twenty-five years of intelligent computer communication - a personal perspective (2016)

During the last 25 years, the field of intelligent computer communication has advanced in leaps and bounds. During this talk, I will review the main drivers of change, while grounding my review in lessons learned while advancing the state of the art and bringing to market several AI technologies. I will also highlight some of the most prominent current trends.