gebhart/patrepeval huggingface dataset:
Electrical and Mechanical Characterization of Doped and Annealed Polycrystalline 3C-SiC Thin Films (2008)

+Deposition of doped polycrystalline 3C-SiC thin films from the precursors 1,3-disilabutane (DSB) and dichlorosilane (DCS), and the dopant precursor ammonia is investigated in a large-scale low-pressure chemical vapor deposition (LPCVD) reactor for micro- and nanoelectromechanical systems (M/NEMS) applications. Films deposited from only DSB and have residual stresses in excess of tensile and resistivity values of . Addition of DCS yields films that exhibit mechanical and electrical properties more favorable for M/NEMS devices. For films deposited with DCS, electrical resistivity varies between for undoped, as-deposited films to for films doped with nitrogen. Residual stress of films deposited from DSB, DCS, and varies little for as-deposited films with different doping concentrations; however, annealing in an argon ambient shifts residual stress toward, and in some cases, into the compressive regime. The strain gradient, which is less than in magnitude for all as-deposited films from DSB, DCS, and , shifts to large negative values in excess of upon annealing for at in an argon ambient. Two sources of stress shift with annealing are identified, namely oxygen diffusion and a change in N atom bonding.
Janus-Type Dendrimer-like Poly(ethylene oxide)s (2008)

A straightforward and original methodology allowing the synthesis of Janus-type dendrimer-like poly(ethylene oxide)s (PEOs) carrying orthogonal functional groups on their surface is described. The use of 3-allyloxy-1,2-propanediol (1) as a latent AB2-type heterofunctional initiator of anionic ring-opening polymerization (AROP) of ethylene oxide (EO) and of selective branching agents of PEO chain ends served to construct the two dendrons of these dendrimer-like PEOs, following a divergent pathway. Thus, the first PEO generation of the first dendron was grown by AROP from 1 followed by the reaction of the corresponding alpha-allyl,omega,omega'-bishydroxy- heterofunctional PEO derivative with 2-(3'-chloromethybenzyloxymethyl)-2-methyl-5,5-dimethyl-1,3-dioxane (2) used as a branching agent. This afforded the dendron A with four latent peripheral hydroxyls protected in the form of two ketal rings. The remaining alpha-allylic double bond of the PEO thus prepared was transformed into two hydroxyl groups using OsO4 in order to create the first PEO generation of the dendron B by AROP of EO. Allyl chloride (3) was then used as another (latent) branching agent to react with the terminal hydroxyl of the corresponding PEO chains. Deprotection under acidic conditions of the ketal groups of dendron A, followed by AROP of EO, afforded the second PEO generation on this face. This alternate and divergent procedure, combining AROP of EO and selective branching of PEO branches, could be readily iterated, one dendron after the other up to the generation six, leading to a Janus-type dendrimer-like PEO exhibiting a total mass of around 300 kg/mol and possessing 64 peripheral groups on each face. The possibility of orthogonal functionalization of the surfaces of such Janus-type dendritic PEOs was exploited. Indeed, a dendron of generation 4 was functionalized with hydroxyl functions at its periphery, whereas the other was end-capped with either tertiary amino or disulfide groups. In a variant of this strategy, azido groups and acetylene could also be orthogonally introduced at the periphery of the fourth generation Janus-type dendrimer-like PEO and subjected to polycondensation by a 1,3-dipolar cycloaddition reaction. This afforded a necklace-like covalent assembly of dendrimer-like PEOs through the formation of stable [1,2,3]-triazole linkages.
Stereospecific Palladium-Catalyzed C–H Arylation of Pyroglutamic Acid Derivatives at the C3 Position Enabled by 8-Aminoquinoline as a Directing Group (2017)

An efficient and stereospecific Pd-catalyzed protocol for the C-H arylation of pyroglutamic acid derivatives that uses 8-aminoquinoline as a directing group is described. The reaction was shown to proceed efficiently with a variety of aryl and heteroaryl iodides bearing different functional groups, giving C3-arylated cis products in good to high yields. Removal of the 8-aminoquinoline unit from these C-H arylation products enables access to synthetically useful cis and trans pyroglutamic acid-based building blocks.
Using XBDDs and ZBDDs in points‐to analysis (2008)

Abstract Binary decision diagrams (BDDs) have recently become widely accepted as a space‐efficient method of representing relations in points‐to or reference analyses. When BDDs are used to represent relations, each element of a domain is assigned a bit pattern to represent it, but not every bit pattern represents an element. The circuit design, model checking, and verification communities have achieved significant reductions in BDD sizes using several techniques to reduce the overhead of these don't‐care bit patterns. We adapt these techniques to BDD‐based program analysis, and we study their effect on the BDD size in this context. Specifically, we compare the effectiveness of Coudert and Madre's restrict operation and the use of zero‐suppressed BDDs (ZBDDs) to represent relations. Using don't‐care BDDs (XBDDs) and ZBDDs to reduce the size of the relations allows a compiler or other software analysis tools to analyze larger programs with greater precision. Our experimental evaluation considers both context‐insensitive and context‐sensitive program analyses. We also provide a metric that can be used to estimate whether ZBDDs will be more compact than BDDs for a given analysis. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Innate immune response of human pluripotent stem cell-derived airway epithelium (2014)

The acquisition of innate immune response is requisite to having bona fide differentiation of airway epithelium. Procedures developed to differentiate lung airway from human pluripotent stem cells (hPSCs) have demonstrated anecdotal evidence for innate immune response, but an in-depth exploration of response levels is lacking. Herein, using an established method of airway epithelial generation from hPSCs, we show that hPSC-derived epithelial cells are able to up-regulate expression of TNFα, IL8 and IL1β in response to challenge with bacterial endotoxin LPS, but lack response from genes associated with innate immune response in other cell types. Further, stimulation of cells with TNF-α resulted in auto-induction of TNFα transcript, as well as cytokine responses of IL8 and IL1β. The demonstration of innate immune induction in hPSC-derived airway epithelia gives further strength to the functionality of in vitro protocols aimed at generating differentiated airway cells that can potentially be used in a translational setting. Finally, we propose that innate immune challenge of airway epithelium from human pluripotent stem cell sources be used as a robust validation of functional in vitro differentiation.
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing (2022)

CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against incoming RNA and DNA phages by binding to complementary target phage transcripts followed by general, non-specific RNA degradation. Here we analysed the defensive capabilities of LbuCas13a from Leptotrichia buccalis and found it to have robust antiviral activity unaffected by target phage gene essentiality, gene expression timing or target sequence location. Furthermore, we find LbuCas13a antiviral activity to be broadly effective against a wide range of phages by challenging LbuCas13a against nine E. coli phages from diverse phylogenetic groups. Leveraging the versatility and potency enabled by LbuCas13a targeting, we applied LbuCas13a towards broad-spectrum phage editing. Using a two-step phage-editing and enrichment method, we achieved seven markerless genome edits in three diverse phages with 100% efficiency, including edits as large as multi-gene deletions and as small as replacing a single codon. Cas13a can be applied as a generalizable tool for editing the most abundant and diverse biological entities on Earth.
Single Degree-of-Freedom Rigidly Foldable Cut Origami Flashers (2015)

We present the design for a family of deployable structures based on the origami flasher, which are rigidly foldable, i.e., foldable with revolute joints at the creases and planar rigid faces. By appropriate choice of sector angles and introduction of a cut, a single degree-of-freedom (DOF) mechanism is obtained. These structures may be used to realize highly compact deployable mechanisms.
Methods of using a laser to spall and drill holes in rocks (2023)

Apparatus and methods of using lasers are provided for spalling and drilling holes into rocks. A rock removal process is provided that utilizes a combination of laser-induced thermal stress and laser induced superheated steam explosions just below the surface of the laser/rock interaction to spall the rock into small fragments that can then be easily removed by a purging flow. Single laser beams of given irradiance spall rock and create holes having diameter and depth approximately equal to the beam spot size. A group of the single laser beams are steered in a controllable manner by an electro-optic laser beam switch to locations on the surface of the rock, creating multiple overlapping spalled holes thereby removing a layer of rock of a desired diameter. Drilling of a deep hole is achieved by spalling consecutive layers with an intermittent feed motion of the laser head perpendicular to the rock surface.
Bridging microcombs and silicon photonic engines for optoelectronics systems (2021)

Microcombs have sparked a surge of applications over the last decade, ranging from optical communications to metrology. Despite their diverse deployment, most microcomb-based systems rely on a tremendous amount of bulk equipment to fulfill their desired functions, which is rather complicated, expensive and power-consuming. On the other hand, foundry-based silicon photonics (SiPh) has had remarkable success in providing versatile functionality in a scalable and low-cost manner, but its available chip-based light sources lack the capacity for parallelization, which limits the scope of SiPh applications. Here, we bridge these two technologies by using a power-efficient and operationally-simple AlGaAs on insulator microcomb source to drive CMOS SiPh engines. We present two important chip-scale photonic systems for optical data transmissions and microwave photonics respectively: The first microcomb-based integrated photonic data link is demonstrated, based on a pulse-amplitude 4-level modulation scheme with 2 Tbps aggregate rate, and a highly reconfigurable microwave photonic filter with unprecedented integration level is constructed, using a time stretch scheme. Such synergy of microcomb and SiPh integrated components is an essential step towards the next generation of fully integrated photonic systems.
Plasmin therapy enhances mobilization of HPCs after G-CSF (2008)

The role of proteinases in the mobilization of hematopoietic progenitor cells (HPCs) after granulocyte colony-stimulating factor (G-CSF) remains unclear. Here we report that genetic loss of the plasminogen activator inhibitor Pai-1 or of the plasmin inhibitor alpha2-antiplasmin increases HPC mobilization in response to G-CSF. Moreover, thrombolytic agents, such as tenecteplase and microplasmin, enhance HPC mobilization in mice and humans. Taken together, these findings identify a novel role for plasmin in augmenting HPC mobilization in response to G-CSF.
A Novel RNA In Situ Hybridization Assay for the Long Noncoding RNA SChLAP1 Predicts Poor Clinical Outcome After Radical Prostatectomy in Clinically Localized Prostate Cancer (2014)

Long noncoding RNAs (lncRNAs) are an emerging class of oncogenic molecules implicated in a diverse range of human malignancies. We recently identified SChLAP1 as a novel lncRNA that demonstrates outlier expression in a subset of prostate cancers, promotes tumor cell invasion and metastasis, and associates with lethal disease. Based on these findings, we sought to develop an RNA in situ hybridization (ISH) assay for SChLAP1 to 1) investigate the spectrum of SChLAP1 expression from benign prostatic tissue to metastatic castration-resistant prostate cancer and 2) to determine whether SChLAP1 expression by ISH is associated with outcome after radical prostatectomy in patients with clinically localized disease. The results from our current study demonstrate that SChLAP1 expression increases with prostate cancer progression, and high SChLAP1 expression by ISH is associated with poor outcome after radical prostatectomy in patients with clinically localized prostate cancer by both univariate (hazard ratio = 2.343, P = .005) and multivariate (hazard ratio = 1.99, P = .032) Cox regression analyses. This study highlights a potential clinical utility for SChLAP1 ISH as a novel tissue-based biomarker assay for outcome prognostication after radical prostatectomy.
Single-frequency microchip Nd lasers (1989)

Optically pumped, single-frequency, Nd-doped, solid-state lasers have been constructed using flat-flat cavities, which were diced from large dielectrically coated wafers of various crystals. For example, a Nd:YAG laser with a cavity length of 730 microm has operated at room temperature in a single longitudinal mode from a threshold of less than 1 mW to greater than 40 times the threshold. Theslope efficiency was greater than 30%. Heterodyne measurements showed an instrument-limited linewidth of 5 kHz. The microchip lasers demonstrate ways to reduce greatly the cost and complexity offabricating small lasers and electro-optic devices.
Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water (2018)

Prediction of compound properties from structure via quantitative structure-activity relationship and machine-learning approaches is an important computational chemistry task in small-molecule drug research. Though many such properties are dependent on three-dimensional structures or even conformer ensembles, the majority of models are based on descriptors derived from two-dimensional structures. Here we present results from a thorough benchmark study of force field, semiempirical, and density functional methods for the calculation of conformer energies in the gas phase and water solvation as a foundation for the correct identification of relevant low-energy conformers. We find that the tight-binding ansatz GFN-xTB shows the lowest error metrics and highest correlation to the benchmark PBE0-D3(BJ)/def2-TZVP in the gas phase for the computationally fast methods and that in solvent OPLS3 becomes comparable in performance. MMFF94, AM1, and DFTB+ perform worse, whereas the performance-optimized but far more expensive functional PBEh-3c yields energies almost perfectly correlated to the benchmark and should be used whenever affordable. On the basis of our findings, we have implemented a reliable and fast protocol for the identification of low-energy conformers of drug-like molecules in water that can be used for the quantification of strain energy and entropy contributions to target binding as well as for the derivation of conformer-ensemble-dependent molecular descriptors.
Process sensitivities in exemplary chemo-epitaxy directed self-assembly integration (2013)

Directed Self Assembly (DSA) using block copolymers (BCP) has received considerable attention over the past few years as a potential complementary lithographic technique. While many are focused on adapting DSA integrations to high volume manufacturing, the key to the technology’s success lies in its ability to generate low defect patterns. The best way to drive the technology toward a zero defect solution is to understand the fundamentals of the block copolymer assembly, the interactions of the block copolymer with the underlying chemical pattern, and the evaluation of process parameters to obtain a high degree of order of the BCP morphologies. To this end, recent research has investigated numerous material, structural, and process sensitivities of an exemplary chemo-epitaxy line/space integration. Using the DSA flow implemented at imec, substrate properties, such as the geometry and chemistry, were studied and provided the first results regarding the dimensions of the nano-patterns and the energetic conditions necessary to obtain good alignment of the BCP. Additional parameters that have been explored include BCP film thickness and the bake conditions used to execute various steps of the flow. With this work, the key parameters that drive the assembly process have been identified. This will allow the definition of an optimized process window and materials for defect minimization.
Role of Calcium-Sensitive K + Channels and Nitric Oxide in In Vivo Coronary Vasodilation From Enhanced Perfusion Pulsatility (2001)

K(+)(Ca) activation and NO comodulate in vivo pulsatility-stimulated coronary flow, supporting an important role of a hyperpolarization pathway in enhanced mechanovascular signaling. Small- and intermediate-conductance K(+)(Ca) channels are the dominant species involved in modulating both pulse pressure- and bradykinin-induced in vivo coronary dilation.
Bioluminescence Method for In Vitro Screening of Plasmodium Transmission-Blocking Compounds (2017)

The sporogonic stage of the life cycle of <i>Plasmodium</i> spp., the causative agents of malaria, occurs inside the parasite's mosquito vector, where a process of fertilization, meiosis, and mitotic divisions culminates in the generation of large numbers of mammalian-infective sporozoites. Efforts to cultivate <i>Plasmodium</i> mosquito stages <i>in vitro</i> have proved challenging and yielded only moderate success. Here, we describe a methodology that simplifies the <i>in vitro</i> screening of much-needed transmission-blocking (TB) compounds employing a bioluminescence-based method to monitor the <i>in vitro</i> development of sporogonic stages of the rodent malaria parasite <i>Plasmodium berghei</i> Our proof-of-principle assessment of the <i>in vitro</i> TB activity of several commonly used antimalarial compounds identified cycloheximide, thiostrepton, and atovaquone as the most active compounds against the parasite's sporogonic stages. The TB activity of these compounds was further confirmed by <i>in vivo</i> studies that validated our newly developed <i>in vitro</i> approach to TB compound screening.
DefAT: Dependable Connection Setup for Network Capabilities (2011)

Abstract : Network-layer capabilities offer strong protection against link flooding by authorizing individual flows with unforgeable credentials (i.e., capabilities). However, the capability-setup channel is vulnerable to flooding attacks that prevent legitimate clients from acquiring capabilities; i.e., in Denial of Capability (DoC) attacks. Based on the observation that the distribution of attack sources in the current Internet is highly non-uniform, we provide a router-level scheme, named DefAT (Defense via Aggregating Traffic), that confines the effects of DoC attacks to specified locales or neighborhoods (e.g., one or more administrative domains of the Internet). DefAT provides precise access guarantees for capability schemes, even in the face of flooding attacks. The effectiveness of DefAT is shown in two ways. First, we illustrate the precise link-access guarantees provided by DefAT via ns2 simulations. Second, we show the effectiveness of DefAT in the current Internet via Internet-scale simulations using real Internet topologies and attack distribution.
Physico-chemistry of energy-dense Li1.2Mn0.52Co0.13Ni0.13Al0.02O2 cathode material for lithium-ion batteries obtained from urea and ethylene glycol fuels (2019)

Copyright: 2019 IOP Publishing LTD. Due to copyright restrictions, the attached PDF file only contains the abstract of the full text item. For access to the full text item, please consult the publisher's website. The definitive version of the work is published in Materials Research Express, vol. 6, no. 11, pp. 1-10
Dietary Fatty Acids and Blood Cholesterol (1991)

A series of studies in monkeys and hamsters, and reevaluation of published human data, indicate that dietary saturated fatty acids exert a dissimilar metabolic impact on cholesterol metabolism. Myristic acid(14 : 0) appears to have a major cholesterol-raising effect by means of decreasing LDL receptor activity and by increasing the direct production of LDL (from sources other than VLDL-catabolism) Palmitic acid (16 : 0) appears neutral in most cases (plasma cholesterol
Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality (2021)

SARS-CoV-2 (CoV2) antibody therapies, including COVID-19 convalescent plasma (CCP), monoclonal antibodies, and hyperimmune globulin, are among the leading treatments for individuals with early COVID-19 infection. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the 4 endemic human coronavirus (HCoV) genomes in 126 CCP donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies against CoV2. We also found that plasma preferentially reactive to the CoV2 spike receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a 2-peptide serosignature that identifies plasma donations with high anti-spike titer, but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting desired therapeutics and understanding the complex immune responses elicited by CoV2 infection.
Impact of wave propagation delay on latency in optical communication systems (2012)

Latency is an important figure to describe performance of transmission systems for particular applications, such as data
transfer for earthquake early warning, transaction for financial businesses, interactive services such as online games, etc.
Latency consists of delay due to signal processing at nodes and transmitters, and of signal propagation delay due to
propagation of electromagnetic waves. The lower limit of the latency in transmission systems using conventional single
mode fibers (SMFs) depends on wave propagation speed in the SMFs which is slower than c. Photonic crystal fibers,
holly fibers and large core fibers can have low effective refractive indices, and can transfer light faster than in SMFs. In
free-space optical systems, signals propagate with the speed c, so that the latency could be smaller than in optical fibers.
For example, LEO satellites would transmit data faster than optical submarine cables, when the transmission distance is
longer than a few thousand kilometers. This paper will discuss combination of various transmission media to reduce
negative impact of the latency, as well as applications of low-latency systems.
Randomized Comparison of Allogeneic Versus Autologous Mesenchymal Stem Cells for Nonischemic Dilated Cardiomyopathy (2016)

These findings demonstrated safety and clinically meaningful efficacy of allo-hMSC versus auto-hMSC in NIDCM patients. Pivotal trials of allo-hMSCs are warranted based on these results. (Percutaneous Stem Cell Injection Delivery Effects on Neomyogenesis in Dilated Cardiomyopathy [PoseidonDCM]; NCT01392625).