gebhart/patrepeval huggingface dataset:
Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden Species (2018)

Gene networks with feedback often involve interactions between multiple species of biomolecules, much more than experiments can actually monitor. Coupled with this is the challenge that experiments often measure gene expression in noisy fluorescence instead of protein numbers. How do we infer biophysical information and characterize the underlying circuits from this limited and convoluted data? We address this by building stochastic models using the principle of Maximum Caliber (MaxCal). MaxCal uses the basic information on synthesis, degradation, and feedback-without invoking any other auxiliary species and ad hoc reactions-to generate stochastic trajectories similar to those typically measured in experiments. MaxCal in conjunction with Maximum Likelihood (ML) can infer parameters of the model using fluctuating trajectories of protein expression over time. We demonstrate the success of the MaxCal + ML methodology using synthetic data generated from known circuits of different genetic switches: (i) a single-gene autoactivating circuit involving five species (including mRNA), (ii) a mutually repressing two-gene circuit (toggle switch) with seven species (including mRNA) considering stochastic time traces of two proteins, and (iii) the same toggle switch circuit considering stochastic time traces of only one of the two proteins. To further challenge the MaxCal + ML inference scheme, we repeat our analysis for the second and third scenario with traces expressed in noisy fluorescence instead of protein number to closely mimic typical experiments. We show that, for all of these models with increasing complexity and obfuscation, the minimal model of MaxCal is still able to capture the fluctuations of the trajectory and infer basic underlying rate parameters when benchmarked against the known values used to generate the synthetic data. Importantly, the model also yields an effective feedback parameter that can be used to quantify interactions within these circuits. These applications show the promise of MaxCal's ability to characterize circuits with limited data, and its utility to better understand evolution and advance design strategies for specific functions.
Targeting Protein-Protein Interactions for Parasite Control (2011)

Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs) offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank). EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite) and B. malayi (H. sapiens parasite), which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly applicable.
A photonic microwave source for optical applications (2005)

Wireless technology is a cost-effective means to bring broadband communications to both mobile users and home consumers; however, deploying next generation, multi-GHz wireless systems is currently too expensive. For these systems, photonic technologies can bring cost reduction as well as an increase in performance, mainly due to the ultra low-loss property of optical fibers. One approach to signal distribution is to capitalise on the vast fibre-optic distribution networks deployed within and between cities. A microwave carrier can be optically deployed from central offices to remote antenna sites using these optical links. This paper will discuss the generation of such a microwave carrier using a dual-wavelength, external-cavity laser (ECL). Two different dual-wavelength ECL's, constructed with fiber-Bragg-gratings (FBG's), have been investigated. One uses a semiconductor gain chip with a dual-FBG acting as an external reflector. The other uses two similar dual-FBG reflectors on each side of a semiconductor optical amplifier (SOA). In both cases the wavelength separation between the gratings is 0.25 nm. We will demonstrate that a dual-wavelength emission can be temporarily stabilized in the gain-chip ECL if a specific phase relation, between the external feedback from the FBG's and the residual feedback from the gain chip, is satisfied at both lasing wavelengths. The power of the RF beat signal generated by the dual-wavelength optical signal was typically 25 dB above the noise floor. The 3-dB linewidth of the RF signal was approximately 2 MHz and it can be tuned over a frequency range of 200 MHz. The physical mechanisms underlying the observed laser instability will be briefly discussed.
The α5β1 Integrin Mediates Elimination of Amyloid-β Peptide and Protects Against Apoptosis (1998)

The amyloid-beta peptide (Abeta) can mediate cell attachment by binding to beta1 integrins through an arg-his-asp sequence. We show here that the alpha5beta1 integrin, a fibronectin receptor, is an efficient binder of Abeta, and mediates cell attachment to nonfibrillar Abeta. Cells engineered to express alpha5beta1 internalized and degraded more added Abeta1-40 than did alpha5beta1-negative control cells. Deposition of an insoluble Abeta1-40 matrix around the alpha5beta1-expressing cells was reduced, and the cells showed less apoptosis than the control cells. Thus, the alpha5beta1 integrin may protect against Abeta deposition and toxicity, which is a course of Alzheimer's disease lesions.
Pulse laser imaging amplifier for advanced ladar systems (2016)

Security measures sometimes require persistent surveillance of government, military and public areas Borders, bridges, sport arenas, airports and others are often surveilled with low-cost cameras. Their low-light performance can be enhanced with laser illuminators; however various operational scenarios may require a low-intensity laser illumination with the object-scattered light intensity lower than the sensitivity of the Ladar image detector. This paper discusses a novel type of high-gain optical image amplifier. The approach enables time-synchronization of the incoming and amplifying signals with accuracy &le; 1 ns. The technique allows the incoming signal to be amplified without the need to match the input spectrum to the cavity modes. Instead, the incoming signal is accepted within the spectral band of the amplifier. We have gauged experimentally the performance of the amplifier with a 40 dB gain and an angle of view 20 mrad.
Diastereoselective Borocyclopropanation of Allylic Ethers Using a Boromethylzinc Carbenoid (2017)

A borocyclopropanation of (E)- and (Z)-allylic ethers and styrene derivatives via the Simmons-Smith reaction using a novel boromethylzinc carbenoid is described. The carbenoid precursor is prepared via a 3-step sequence from inexpensive and commercially available starting materials. This methodology allows for the preparation of 1,2,3-substituted borocyclopropanes in high yields and diastereoselectivities. Several postfunctionalization reactions were also performed to illustrate the versatility of these building blocks.
Direct Current Reduces Wound Edema after Full-Thickness Burn Injury in Rats (1996)

Direct electric current has a beneficial effect in reducing wound edema after burn injury.
Achieving Microparticles with Cell‐Instructive Surface Chemistry by Using Tunable Co‐Polymer Surfactants (2020)

Abstract A flow‐focusing microfluidic device is used to produce functionalized monodisperse polymer particles with surface chemistries designed to control bacterial biofilm formation. This is achieved by using molecularly designed bespoke surfactants synthesized via catalytic chain transfer polymerization. This novel approach of using polymeric surfactants, often called surfmers, containing a biofunctional moiety contrasts with the more commonly employed emulsion methods. Typically, the surface chemistry of microparticles are dominated by unwanted surfactants that dilute/mask the desired surface response. Time of flight secondary ion mass spectrometry (ToF‐SIMS) analysis of particles demonstrates that the comb‐graft surfactant is located on the particle surface. Biofilm experiments show how specifically engineered surface chemistries, generated by the surfactants, successfully modulate bacterial attachment to both polymer films, and microparticles. Thus, this paper outlines how the use of designed polymeric surfactants and droplet microfluidics can exert control over both the surface chemistry and size distribution of microparticle materials, demonstrating their critical importance for controlling surface‐cell response.
Grain boundary barrier breakdown in niobium donor doped strontium titanate using in situ electron holography (1999)

The electrical activity of numerous electroceramics originates with space charge potential across internal interfaces. Space charge formation and the resultant potential barrier at interfaces are believed to be responsible for many interesting and useful properties of electroceramics, ranging from nonlinear current–voltage characteristics to enhanced dielectric properties. Direct current electrical measurements of individual grain boundaries in Nb donor doped SrTiO3 bicrystals reveal a highly resistive and nonlinear behavior compared to single crystals. The origin of this nonlinear resistance has been examined with electron holography, observing both static and dynamic attributes of the internal potential. In the static case with no applied current, the grain boundary potential barrier height was measured to be about 0.45 V. During the application of a high current, this potential barrier was suppressed, presenting the first direct real space evidence for breakdown of an internal grain boundary barrier.
The Heat Shock-binding Protein (HspBP1) Protects Cells against the Cytotoxic Action of the Tag7-Hsp70 Complex (2011)

Heat shock-binding protein HspBP1 is a member of the Hsp70 co-chaperone family. The interaction between HspBP1 and the ATPase domain of the major heat shock protein Hsp70 up-regulates nucleotide exchange and reduces the affinity between Hsp70 and the peptide in its peptide-binding site. Previously we have shown that Tag7 (also known as peptidoglycan recognition protein PGRP-S), an innate immunity protein, interacts with Hsp70 to form a stable Tag7-Hsp70 complex with cytotoxic activity against some tumor cell lines. This complex can be produced in cytotoxic lymphocytes and released during interaction with tumor cells. Here the effect of HspBP1 on the cytotoxic activity of the Tag7-Hsp70 complex was examined. HspBP1 could bind not only to Hsp70, but also to Tag7. This interaction eliminated the cytotoxic activity of Tag7-Hsp70 complex and decreased the ATP concentration required to dissociate Tag7 from the peptide-binding site of Hsp70. Moreover, HspBP1 inhibited the cytotoxic activity of the Tag7-Hsp70 complex secreted by lymphocytes. HspBP1 was detected in cytotoxic CD8+ lymphocytes. This protein was released simultaneously with Tag7-Hsp70 during interaction of these lymphocytes with tumor cells. The simultaneous secretion of the cytotoxic complex with its inhibitor could be a mechanism protecting normal cells from the cytotoxic effect of this complex.
Effect of hydrogen dilution on carrier transport in hydrogenated boron-doped nanocrystalline silicon-silicon carbide alloys (2006)

The effect of the hydrogen dilution ratio on characteristics of hydrogenated boron-doped nanocrystalline silicon-silicon carbide alloy (p-nc-Si–SiC:H) films is investigated. Hydrogen coverage near the growing surface causes nanocrystallization by retarding the reactions of the precursors. It was found that p-nc-Si–SiC:H alloys have two different kinds of carrier transport mechanisms: one is the thermally activated hopping conduction between neighboring crystallites near room temperature and the other is the band tail hopping conduction below 150K. However, the film at the onset of the nanocrystalline growth exhibits a different behavior due to a large band tail disorder.
Error analysis of 3Dc-based normal map compression and its application to optimized quantization (2008)

Normal mapping is one of the most essential technologies for realistic three-dimensional computer graphics. In conventional normal map compression such as 3Dc, only the x and y components are encoded and the z components are restored based on the normalizing condition. In this paper, we present an intuitively comprehensive error analysis for this approach. As a result, we reveal in what condition compression error becomes larger. We also present a non-linear quantization algorithm based on the formula for better compression performance than the conventional approaches. Experimental results using 300 normal map demonstrate that the PSNR is improved by 0.29 dB on average. Our algorithm is compatible with random access and highly-parallel processing on GPU.
5G NetMobil: Pathways Towards Tactile Connected Driving (2019)

Vehicular communications is not only a major opportunity to improve road safety and traffic efficiency but also a key enabler for connected and automated driving. The analysis of future automotive applications and their needs performed in the project 5G NetMobil has brought up various technical challenges that need to be solved in order to support advanced use cases such as High Density Truck Platooning. In this regard, we provide a description of several technical solutions developed within the project to respond to these arising communications demands in terms of reliability and latency. This includes a holistic E2E architecture comprising the concept of hybrid communications to achieve stringent reliability requirements, concepts for monitoring and controlling of QoS as well as network slicing and agile edge cloud concepts to shift parts of the vehicular functionality into the cloud. In addition to an overview of the activities within 5G NetMobil, this paper gives first interim results and insights.
Invited: Confinement Effects on the Structure and Transport of Nafion Ultrathin Films (2014)

Polymer electrolyte membrane (PEM)-based fuel cells are being aggressively targeted as an alternative energy source for transportation and stationary power due to their high charge density and low operating temperatures. While the structure, transport and mechanical properties of bulk PEMs have been extensively studied, there is increasing interest on the behavior of these materials at interfaces and under confinement, since there exist many heterogeneous interfaces within an actual fuel cell assembly. One could argue that the performance and ultimate failure of the membrane electrode assembly is greatly impacted by the structure and transport of ionomers confined to extremely small length-scales. Using a combination of neutron and x-ray reflectivity, grazing-incidence small-angle x-ray scattering (GISAXS), quartz crystal microbalance (QCM), polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS), as well as measurements capable of measuring thin-film mechanics we have studied the water transport and mechanical behavior as a function of humidity and initial film thickness (&lt; 220 nm). Our previous work has shown that when the polyelectrolyte is confined to thin films there is suppression in both swelling and water diffusivity in addition to considerable changes in the nano-scale structure. More recently, we have developed methods to measure the mechanical properties of these systems, as well as extended our PM-IRRAS method to attempt to answer questions about the roles interfacial mass transport and polymer chain relaxations. The mechanical methods reveal an effect of confinement on the measured stiffness of the material. Specifically, we observe an increase in the modulus with decreasing film thickness and, in the beginning of the hydration process, a visco-plastic response due to swelling. These results lend some explanation to the observed decrease in water uptake with decreasing film thickness. Moreover, we have extended our use of PM-IRRAS to include in-situ vapor switching between H 2 O and D 2 O. In this approach, we measure the time-resolved diffusion of H 2 O into the film (swelling), followed by the diffusive exchange of D 2 O for H 2 O (switch), and then then loss of H 2 O upon drying (deswelling). The experiments enable us to (1) eliminate contributions of swelling and relaxation to the measured transport of water and (2) measure the transport in a pseudo-steady state manner. This method shows promise in answering questions about the dominant mechanism for transport in confined thin films. Collectively, our program aims to provide a comprehensive understanding of the effect of confinement on the structure and transport of ionomer-based materials, and how these effects manifest themselves in the performance and mechanical response of such membranes.
Cycloadditions. 26. Regio- and stereochemistry of the cycloadditions of dichloroketene to 2-methyl- and 3-methyl-2-cholestene (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloadditions. 26. Regio- and stereochemistry of the cycloadditions of dichloroketene to 2-methyl- and 3-methyl-2-cholesteneAlfred Hassner and Larry R. KrepskiCite this: J. Org. Chem. 1979, 44, 9, 1376–1379Publication Date (Print):April 1, 1979Publication History Published online1 May 2002Published inissue 1 April 1979https://pubs.acs.org/doi/10.1021/jo01323a003https://doi.org/10.1021/jo01323a003research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Understanding the Effect of Solid Electrolyte Structure on Properties through 3D-Printing (2017)

Over the last decade there has been a sizeable effort within the battery community to improve upon the safety and performance of conventional Li-ion batteries to satisfy market demand. A large fraction of that effort has been devoted to solid-state garnet-type Li-conducting electrolytes, due to their inherent nonflammability, relatively high Li + conductivity (~1 mS/cm), and stability to both lithium metal anodes and high voltage cathodes. Recently, improved materials properties and a paradigm shift in electrolyte microstructure have begun to make solid-state electrolytes competitive with liquid electrolyte counterparts in terms of performance [1,2]. Specifically, researchers have demonstrated 3 mA/cm 2 current density in Li|LLZ|Li symmetric cells and successfully cycled full cells using a porous-dense-porous multilayered LLZ solid electrolyte framework which dramatically reduces the bulk and interfacial impedance of the battery and increases the energy density by reducing excess electrolyte materials [2]. It is clear then that the solid electrolyte microstructure can have a substantial impact on cell electrochemical performance. However, the effect of the electrolyte microstructure on the cell properties has yet to be investigated, properties which are critical to ensuring high battery performance, long-lifetime of the battery and tolerance to abuse. An optimized solid electrolyte microstructure will need to balance electrochemical and mechanical properties for a marketable battery design. In this work, we utilize 3D-printing to rapidly explore the relationship between solid electrolyte microstructure and resulting electrolyte and cell properties (e.g. mechanical strength). Specifically, we 3D-print a variety of different solid electrolyte geometries, including columns (Figure 1), grids, and stacked geometries using recently developed LLZ inks, and correlate the structure type and characteristics (e.g., aspect ratio) with properties of the electrolyte. First, we investigate the properties of the 3D-printed solid electrolyte itself, followed by a study including infiltration of electrode materials which is more representative of the final battery design. This study will help inform the best solid electrolyte microstructure, ensuring the structure of solid-state batteries will be suitable for a wide variety of real-world applications. [1] J. van den Broek, S. Afyon, J. L. M. Rupp, Adv. Energy Mater. , 2016 , 6 , 1600736. [2] G. T. Hitz, D. W. McOwen, Y. Wen, Y. Gong, J. Dai, X. Han, T. R. Hamann, A. L. Ruth, P. C. Latorre, L. Hu, E. D. Wachsman, submitted. Figure 1. 3D-printed LLZ columns. Figure 1
High-speed 4 ${\times}$ 4 silicon photonic electro-optic switch, operating at the 2 μm waveband (2023)

The escalating need for expansive data bandwidth, and the resulting capacity constraints of the single mode fiber (SMF) have positioned the 2-$μ$m waveband as a prospective window for emerging applications in optical communication. This has initiated an ecosystem of silicon photonic components in the region driven by CMOS compatibility, low cost, high efficiency and potential for large-scale integration. In this study, we demonstrate a plasma dispersive, 4 ${\times}$ 4 electro-optic switch operating at the 2-$μ$m waveband with the shortest switching times. The demonstrated switch operates across a 45-nm bandwidth, with 10-90% rise and 90-10% fall time of 1.78 ns and 3.02 ns respectively. In a 4 ${\times}$ 4 implementation, crosstalk below -15 dB and power consumption below 19.15 mW across all 16 ports are indicated. The result brings high-speed optical switching to the portfolio of devices at the promising waveband.