gebhart/patrepeval huggingface dataset:
Chloroplast bioengineering: the greening of chloroplasts in vitro (1982)

During the first symposium on biotechnology in energy production and conservation we discussed the concept of cell-free agriculture and described its initial implementation via the assembly of an experimental photosynthetic reactor. Transducing photosynthetic membranes capable of converting solar energy, CO/sub 2/, and H/sub 2/O into chemical energy at extremely high efficiencies, approaching the theoretical efficiency of photosynthesis, are very essential components of the reactor. Although such membranes are not presently available, the technology for the bioengineering of such manmade membranes is developing very rapidly. We have been working on this problem for the past several years and as a first step in the right direction, it is now possible to biosynthesize chlorophyll in cell-free systems at rates higher than those observed in intact greening plants. This progress has been made possible by considerable improvements in analytical techniques and instrumentation and in our understanding of the biochemistry of the greening process. 4 figures, 6 tables.
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer (2014)

Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations. A 512-node Anton 2 machine, currently in operation, is up to ten times faster than Anton 1 with the same number of nodes, greatly expanding the reach of all-atom bio molecular simulations. Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 μs/day -- 180 times faster than any commodity hardware platform or general-purpose supercomputer.
GENERATION OF NARROW-BANDWIDTH SINGLE PHOTONS USING ELECTROMAGNETICALLY INDUCED TRANSPARENCY IN ATOMIC ENSEMBLES (2007)

We review recent experiments [M. D. Eisaman et al., Nature438 (2005) 837] demonstrating the generation of narrow-bandwidth single photons using a room-temperature ensemble of 87 Rb atoms. Our method involves creation of an atomic coherence via Raman scattering and projective measurement, followed by the coherent transfer of this atomic coherence onto a single photon using electromagnetically induced transparency (EIT). The single photons generated using this method are shown to have many properties necessary for quantum information protocols, such as narrow bandwidths, directional emission, and controllable pulse shapes. The narrow bandwidths of these single photons (~MHz), resulting from their matching to the EIT resonance (~MHz), allow them to be stored in narrow-bandwidth quantum memories. We demonstrate this by using dynamic EIT to store and retrieve the single photons in a second ensemble for storage times up to a few microseconds. We also describe recent improvements to the single-photon fidelity compared to the work by M. D. Eisaman in Nature438 (2005) 837. These techniques may prove useful in quantum information applications such as quantum repeaters, linear-optics quantum computation, and daytime free-space quantum communication.
Spectral shaping to inhibit sidelobes of point spread function in optical coherence tomography (2003)

Optical coherence tomography [1] (OCT) is an interferometric biomedical imaging technique for high resolution cross-sectional imaging of highly scattering tissue. In OCT, light sources having smooth power spectra are preferred as spectral dips result in sidelobes in the axial point spread function (PSF) that cause ghost images and mask weak axial reflections located near a strong reflection [2,3,4]. Real broadband light sources, however, often present spectral dips in their power spectra.
A new carboxamide compound exerts immuno‐suppressive activity by inhibiting dendritic cell maturation (2005)

The immunosuppressive properties of a benzamide derivative, JM34, previously characterized as an anti-inflammatory compound are described. The immunosuppressive potential of JM34 was evidenced by inhibition of PBMC proliferation in vitro with an IC50 of 20 microM. In contrast with classical immunosuppressive drugs, JM34 affected neither cytokine production nor IL-2R expression from activated T cell clones, and displayed only moderate inhibition of IL-2-induced or anti-CD3/anti-CD28-induced proliferation. We investigated its effects on dendritic cells (DC) in vitro. Addition of JM34 during DC maturation inhibited the expression of some maturation markers: specifically, MHC molecule up-regulation was totally inhibited and CD83 expression was significantly reduced, while up-regulation of CD86, CD80 or CD40 was less affected. Moreover, JM34-treated DC showed impaired IL-12 but not IL-10 secretion, and a markedly reduced ability to present antigens to naive T lymphocytes in vitro. We provide evidence that these JM34-induced alterations of DC were associated with a marked inhibition of NF-kappaB nuclear translocation. Finally, JM34 inhibited delayed type hypersensitivity dose dependently in mice. In conclusion, our data suggest that JM34 inhibited T lymphocyte activation mainly by targeting DC, and thus may represent a new class of therapeutic agents in the fields of transplantation and autoimmune diseases.
Targeted PERK inhibition with biomimetic nanoclusters confers preventative and interventional benefits to elastase-induced abdominal aortic aneurysms (2023)

Abdominal aortic aneurysm (AAA) is a progressive aortic dilatation, causing ∼80% mortality upon rupture. Currently, there is no approved drug therapy for AAA. Surgical repairs are invasive and risky and thus not recommended to patients with small AAAs which, however, account for ∼90% of the newly diagnosed cases. It is therefore a compelling unmet clinical need to discover effective non-invasive strategies to prevent or slow down AAA progression. We contend that the first AAA drug therapy will only arise through discoveries of both effective drug targets and innovative delivery methods. There is substantial evidence that degenerative smooth muscle cells (SMCs) orchestrate AAA pathogenesis and progression. In this study, we made an exciting finding that PERK, the endoplasmic reticulum (ER) stress Protein Kinase R-like ER Kinase, is a potent driver of SMC degeneration and hence a potential therapeutic target. Indeed, local knockdown of PERK in elastase-challenged aorta significantly attenuated AAA lesions in vivo. In parallel, we also conceived a biomimetic nanocluster (NC) design uniquely tailored to AAA-targeting drug delivery. This NC demonstrated excellent AAA homing via a platelet-derived biomembrane coating; and when loaded with a selective PERK inhibitor (PERKi, GSK2656157), the NC therapy conferred remarkable benefits in both preventing aneurysm development and halting the progression of pre-existing aneurysmal lesions in two distinct rodent models of AAA. In summary, our current study not only establishes a new intervention target for mitigating SMC degeneration and aneurysmal pathogenesis, but also provides a powerful tool to facilitate the development of effective drug therapy of AAA.
Remaining oil thickness and well positioning using 4D at Alba field, North Sea (2009)

High quality 4D seismic shot in 2008 over the Alba field allows us to estimate the remaining oil thickness from 4D amplitudes. This is used to modify planned wells and reduce risk for new production and water injection wells. The 4D allows better vertical positioning of horizontal wells using the areal information of 2008 oil‐water contact (OWC) and top sand. Further, the 4D data also shows time‐shifts across the reservoir that matches injector and producer locations.
Bimodal Fluorescence-Magnetic Resonance Contrast Agent for Apoptosis Imaging (2019)

Effective cancer therapy largely depends on inducing apoptosis in cancer cells via chemotherapy and/or radiation. Monitoring apoptosis in real-time provides invaluable information for evaluating cancer therapy response and screening preclinical anticancer drugs. In this work, we describe the design, synthesis, characterization, and in vitro evaluation of caspase probe 1 (CP1), a bimodal fluorescence-magnetic resonance (FL-MR) probe that exhibits simultaneous FL-MR turn-on response to caspase-3/7. Both caspases exist as inactive zymogens in normal cells but are activated during apoptosis and are unique biomarkers for this process. CP1 has three distinct components: a DOTA-Gd(III) chelate that provides the MR signal enhancement, tetraphenylethylene as the aggregation induced emission luminogen (AIEgen), and DEVD peptide which is a substrate for caspase-3/7. In response to caspase-3/7, the water-soluble peptide DEVD is cleaved and the remaining Gd(III)-AIEgen (Gad-AIE) conjugate aggregates leading to increased FL-MR signals. CP1 exhibited sensitive and selective dual FL-MR turn-on response to caspase-3/7 in vitro and was successfully tested by fluorescence imaging of apoptotic cells. Remarkably, we were able to use the FL response of CP1 to quantify the exact concentrations of inactive and active agents and accurately predict the MR signal in vitro. We have demonstrated that the aggregation-driven FL-MR probe design is a unique method for MR signal quantification. This probe design platform can be adapted for a variety of different imaging targets, opening new and exciting avenues for multimodal molecular imaging.
Addition of Indole to Methyl 2‐Chloro‐2‐cyclopropylideneacetate en Route to Spirocyclopropanated Analogues of Demethoxyfumitremorgine C and Tadalafil (2005)

Abstract Indole readily added across the double bond of the highly reactive Michael acceptor methyl 2‐chloro‐2‐cyclopropylideneacetate ( 4 ) to yield 2‐chloro‐2‐(3′‐indolylcyclopropyl)acetate 5 (85%) which was converted in two steps into the racemic tryptophan analogue 7 in 90% yield. This in turn was transformed by a condensation and Pictet−Spengler sequence into the spirocyclopropane analogues, 11 , 13 and 15 , of both the natural product (demethoxy)fumitremorgine C ( 3b , 3 steps, 11% yield) and the potent PDE‐5 inhibitor Tadalafil ( 2 , 3 steps, 71% yield) as well as the original lead structure with a hydantoin backbone ( 1 , 2 steps, 79% yield). (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Characteristics of Boron Diffusion in Polysilicon/Silicon Systems with a Thin Si‐B Layer as Diffusion Source (1995)

A new material, Si‐B layer, as boron diffusion source for polysilicon/silicon systems, has been investigated. The Si‐B layer was deposited on polysilicon in an ultrahigh vacuum chemical vapor deposition (UHV/CVD) system at 550°C. The characteristics of boron diffusion in Si‐B layer/polysilicon/silicon systems have been investigated by using secondary ion mass spectroscopy (SIMS) and cross‐sectional transmission electron microscopy (XTEM). To remove the Si‐B layer after the drive‐in step, the Si‐B layer was oxidized completely during thermal drive‐in stage and removed with a diluted hydrofluoric acid. The effects of thermal oxidation of Si‐B layer on boron diffusion profiles and polysilicon structures were analyzed. It was found that the boron profiles within the polysilicon are slightly dependent on the oxidation of Si‐B layer. Moreover, the polysilicon grain size for Si‐B layer source were enlarged, as compared with conventional polysilicon source. It is attributed to the effects of the gettering of oxygen impurity by the Si‐B layer and secondary grain growth during Si‐B layer oxidation. In addition, the boron diffusion profiles in the silicon substrate for Si‐B layer source exhibited a more shallow junction depth and less sensitivity to the thermal budget, as compared with polysilicon source. This is considered to be the effect of the smaller surface concentration, , in the silicon substrate for Si‐B layer source.
Stronger Material for Cold-Formed Coil Springs Used in Automotive Suspensions (2002)

&lt;div class="htmlview paragraph"&gt;Hot-formed coil spring material (SUP 190) has been developed in order to achieve weight reduction and corrosion fatigue strength and is currently used from the viewpoint of environmental protections&lt;sup&gt;(&lt;span class="xref"&gt;1&lt;/span&gt;)&lt;/sup&gt;. In the meanwhile, we have further developed a means of applying a high frequency induction heat treatment to the hot-formed coil spring material to create cold-formed coil spring material with features such as excellent formability and high shape freedom, as well as corrosion fatigue strength.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Consequently, a weight reduction of approximately 20% can be achieved in comparison with cold-formed coil springs using SAE &lt;a href="http://www.sae.org/technical/papers/9254" target="_blank"&gt;9254&lt;/a&gt;, which has been used up to this point.&lt;/div&gt;
Niobium carbide for wear protection – tailoring its properties by processing and stoichiometry (2016)

Niobium carbide is a hardly explored carbide but its functional profile shows a high potential for wear protection and tribological applications, which are currently dominated by tungsten carbide. Surprisingly little information is available on niobium carbide (NbC). Niobium carbide can be either synthesized by carbothermal conversion of Nb2O5 or be metallurgically grown and leached out. Furthermore NbC hardmetal grades can be bonded by all known metallic binders and processed and sintered in exactly the same way as WC-based hardmetals. Niobium is today largely available. NbC can be efficiently produced, provides comparably low friction in many relevant tribo-contacts and displays low wear. NbC and Nb2O5 have so far no REACH classification related to human toxicology and are not listed as substances of very high concern contrary to WO3 and Co3O4. This contribution demonstrates the key characteristics of NbC and discusses its sustainability and reliable value chain.
Reconstitution in vitro of MSP‐based filopodium extension in nematode sperm (2006)

The major sperm protein (MSP) motility system in nematode sperm is best known for propelling the movement of mature sperm, where it has taken over the role usually played by actin in amoeboid cell motility. However, MSP filaments also drive the extension of filopodia, transient organelles composed of a core bundle of MSP filaments, that form in the late in sperm development but are not found on crawling cells. We have reconstituted filopodial extension in vitro whereby thin bundles of MSP filaments, each enveloped by a membrane sheath at their growing end, elongated at rates up to 17 microm/min. These bundles often exceeded 500 microm in length but were comprised of filaments only 1 microm long. The reconstituted filopodia assembled in the same cell-free sperm extracts that produced MSP fibers, robust meshworks of filaments that exhibit the same organization and dynamics as the lamellipodial filament system that propels sperm movement. The filopodia and fibers that assembled in vitro both had a membranous structure at their growing end, shared four MSP accessory proteins, and responded identically to agents that alter MSP-based motility by modulating protein phosphorylation. However, filopodia grew three- to four-fold faster than fibers. The reconstitution of filopodial extension shows that, like the actin cytoskeleton, MSP filaments can adopt two architectures, bundles and meshworks, each capable of pushing against membranes to generate protrusion. The reconstitution of both forms of motility in the same in vitro system provides a promising avenue for understanding how the forces for membrane protrusion are produced.
A Qualitative Study of Affordability: Virginia and San Antonio Class Programs (2014)

Abstract : During the mid-1990s, the U.S. Navy initiated a wide-ranging series of Department of Defense acquisition reforms. Amid this environment of DOD acquisition reform, the U.S. Navy started the Virginia-class submarine program and San Antonio-class amphibious transport dock ship program. Both of these programs sought to reduce ownership costs of these new vessels. This study compares the Virginia-class submarine and San Antonio-class ship across platforms and across time in order to find those factors that appear to affect cost. This study isolates those key metrics and relationships that demonstrate an apparently significant impact on affordability. The purpose of this study is to find the programmatic decisions, environmental circumstances, or managerial tools that benefit or jeopardize affordability in a consistent manner, and to recommend further study in those areas most likely to promote the development of better practices for affordability throughout a program's life cycle. The results of this study indicated that the interpretation of affordability changes across the life-cycle phases of an acquisition program; however, the factors that affected cost between the Virginia-class submarine and the San Antonio-class ship were comparable across time. The overall findings of affordability across time and between these two acquisition programs were mixed. During the pre-acquisition stage, key elements, which accept a high degree of cost-growth risk, do not appear to be sufficiently responsive to cost-growth mitigation initiatives. The findings suggest that, in the acquisition stage, it is possible to reverse cost growth by setting a non-negotiable cost target and establishing all other factors as flexible. For the sustainment stage, analysis of the cost effectiveness of an acquisition system's design is limited by the degree of consistency between operational events and program assumptions and the percentage of life-cycle completion that are supported by actual cost.
Pyrazole Chemistry in Crop Protection (2007)

An overview is given of the significance of pyrazole derivatives in crop protection chemistry.The main herbicidally, fungicidally and insecticidally active pyrazole classes are presented, together with their synthetic routes, their modes-of-action and their biological efficacies.Indazoles and other bicyclic pyrazole derivatives are also covered.
A Robust Dynamic State Estimation Method for Power Systems Using Exponential Absolute Value-Based Estimator (2022)

Even though the noise model applied in power system dynamic state estimation is usually assumed to be Gaussian, this is not the case due to the unknown system inputs, influence from the communication channel noise and the outliers generated by phasor measurement units (PMUs). In this paper a robust power system dynamic state estimation (DSE) method combining a robust exponential absolute value based estimator and the unscented Kalman filter together is proposed under non-Gaussian noise. Based on the quadratic function and the exponential absolute value function, robust exponential absolute value based estimator is derived, further mitigating the effects of bad data or outliers. The influence function is utilized to calculate the state estimation error covariance of the proposed robust DSE method. The simulation results on the IEEE 39-bus system verify the robustness and effectiveness of the proposed dynamic state estimation method.
Surface emitting photonic crystal mid-infrared quantum cascade lasers (2009)

We demonstrate spectrally single-mode, low-divergence surface-emission from photonic-crystal quantum cascade lasers operating in the mid-infrared spectral range (λ~7.2μm). The photonic-crystal resonator is defined by the sole top metallization. No semiconductor etch is employed. The effective index contrast is induced by the different profiles of surface plasmon and air-confined modes. Numerical electromagnetic simulations show that the resonator Q-factor depends strongly on the r/a ratio. The devices – which operate up to 220 K - exhibit single mode emission with a side mode suppression ratio ≥20/25dB. The far-field emission pattern is doughnut-shaped, with a full divergence angle of ~12 degrees.
Architected materials and structures to control shock output characteristics (2023)

A system that provides control of the output shockwave properties of energetic material wherein the system includes an energetic material having a first portion and a second portion. An additive manufacturing system combines the first portion and the second portion of the energetic material wherein the first portion and the second portion are positioned relative to each other to provide control of the output shockwave properties of the energetic material.
Effervescent paracetamol poisoning: a case report (2002)

Severe poisoning with effervescent paracetamol tablets has never been described in the literature. Indeed, the effervescent formulation contains high amounts of sodium and bicarbonate, both responsible for important emetic properties in the case of massive ingestion. Moreover, dissolving more than 6-8 tablets in the same glass appears to be difficult. We report a well-documented case of a patient with potentially hepatotoxic serum levels after the ingestion of 16 g effervescent paracetamol, apparently without vomiting. We show that the difficulties of a massive oral intake may be overcome by a slow intake. Nevertheless, this case report does not modify the important assertion that effervescent paracetamol use could limit the risk of life-threatening intoxication by a single massive acute overdose.
WNT5AExhibits Tumor-Suppressive Activity through Antagonizing the Wnt/β-Catenin Signaling, and Is Frequently Methylated in Colorectal Cancer (2008)

WNT5A is frequently inactivated in CRC by tumor-specific methylation, and thus, is a potential biomarker. WNT5A could act as a tumor suppressor for CRC by antagonizing the Wnt/beta-catenin signaling.
Multiple species implants with pulsed and DC plasma immersion ion implantation (2002)

Plasma Immersion Ion Implantation (PIII) is an emerging implant technology for high dose and low energy applications. Since PIII does not contain mass separation, all ion species in the plasma are implanted into the wafer. By utilizing an effective mass and an effective Bohm velocity for the plasma, the single species PIII model has been extended to multiple species. This model includes two components of ion current, the ions uncovered by the expanding sheath, and ions that diffuse across the sheath boundary. This new model calculates the dose rates for all the ion species in the plasma, and is valid for pulsed and DC PIII. Calculation and simulation show that the percentage of each ion implanted is a function of the pulse width. For a plasma containing 10% He/sup +/ and 90% PH/sub 3//sup +/, the implant is 90% PH/sub 3//sup +/ for short pulses, and only 76% PH/sub 3//sup +/ for longer pulses. For proper calibration and dosimetry it is imperative to understand that changing the pulse width will alter the implant ratios.
Exploring Applications of Random Walks on Spiking Neural Algorithms (2018)

Neuromorphic computing has many promises in the future of computing due to its energy efficient and scalable implementation. Here we extend a neural algorithm that is able to solve the diffusion equation PDE by implementing random walks on neuromorphic hardware. Additionally, we introduce four random walk applications that use this spiking neural algorithm. The four applications currently implemented are: generating a random walk to replicate an image, finding a path between two nodes, finding triangles in a graph, and partitioning a graph into two sections. We then made these four applications available to be implemented on software using a graphical user interface (GUI).