gebhart/patrepeval huggingface dataset:
Design of carbon supports for metal-catalyzed acetylene hydrochlorination (2021)

For decades, carbons have been the support of choice in acetylene hydrochlorination, a key industrial process for polyvinyl chloride manufacture. However, no unequivocal design criteria could be established to date, due to the complex interplay between the carbon host and the metal nanostructure. Herein, we disentangle the roles of carbon in determining activity and stability of platinum-, ruthenium-, and gold-based hydrochlorination catalysts and derive descriptors for optimal host design, by systematically varying the porous properties and surface functionalization of carbon, while preserving the active metal sites. The acetylene adsorption capacity is identified as central activity descriptor, while the density of acidic oxygen sites determines the coking tendency and thus catalyst stability. With this understanding, a platinum single-atom catalyst is developed with stable catalytic performance under two-fold accelerated deactivation conditions compared to the state-of-the-art system, marking a step ahead towards sustainable PVC production.
Selenium Compounds and their Effects on Oxidative DNA Damage (2013)

Several transition metals react with H2O2 and produce reactive oxygen species (ROS) responsible for oxidative damage linked to many diseases and disorders, and species that form coordination complexes with these metal ions show promise as antioxidants. The present study demonstrates that metal-mediated radical and non-radical oxidative DNA damage decreases when selenium dioxide (SeO2) and sodium selenite (Na2SeO3) are present. Radical-induced damage is associated with production of 8-hydroxy-2′-deoxyguanosine (8-OH-dG), which arises from ROS generated at or near the guanine base, and the selenium compounds reduce Fe(II)-, Cr(III)- and Cu(II)-mediated radical damage to differing degrees based on the identity of the metal ion and the order in which the metals, selenium compounds and DNA are combined. Radical damage arising from Fe(II) and Cr(III) decreases substantially when they are pre-incubated with the selenium compounds prior to adding DNA. Non-radical damage is associated with oxidation of the adenine base in the presence of high H2O2 concentrations through an ionicmechanism, and this type of damage also decreases significantly when the selenium compounds are allowed to interact with themetal ions before adding DNA. Fluorescence studies using dihydrodichlorofluorescein diacetate (DCF-DA) to probe ROS formation indicate that the majority of the SeO2- and SeO32- - metal systems in combination with H2O2 (no DNA present) produce ROS to the same degree as themetal/H2O2 systems in the absence of the selenium compounds, suggesting that selenium–metal complexes react with H2O2 in a sacrificial manner that protects DNA from oxidative damage.
Advanced machine learning eco-system to address HVM optical metrology requirements (2020)

Machine learning (ML) techniques have been successfully deployed to resolve optical metrology challenges in semiconductor industry during recent years. With more advanced computing technology and algorithms, the ML system can be improved further to address High Volume Manufacturing (HVM) requirements. In this work, an advanced ML eco-system was implemented based on big data architecture to generate fast and user-friendly ML predictive models for metrology purposes. Application work and results completed by using this ML eco-system have revealed its capability to quickly refine solutions to predict both external reference data and to improve the throughput of conventional Optical Critical Dimension (OCD) metrology. The time-to-solution has been significantly improved and human operational time has also been greatly reduced. Results were shown for both front end and back end of line measurement applications, demonstrating good correlations and small errors in comparison with either external reference or conventional OCD results. The incremental retraining from this ML eco-system improved the correlation to external references, and multiple retrained models were analyzed to understand retraining effects and corresponding requirements. Quality Metric (QM) was also shown to have relevance in monitoring recipe performance. It has successfully demonstrated that with this advanced ML eco-system, streamlined ML models can be readily updated for high sensitivity and process development applications in HVM scenarios.
Abstract P404: Membrane Composition Of Cardiac-derived Extracellular Vesicles Changes With Vesicle Origin And Determines Uptake (2021)

Introduction: Myocardial infarction (MI) is a leading cause of mortality worldwide. The potency of cell-based therapies for MI is increasingly attributed to the release of extracellular vesicles (EVs) which consist of a lipid/protein membrane and encapsulate RNA cargo. Specifically, EVs from ckit+ progenitor cells (CPCs) and mesenchymal stromal cells (MSCs) are shown to be pro-reparative, with clinical trials ongoing. Despite copious research into EV cargo, the role of donor cell type on EV membrane composition and its effects on EV uptake mechanism by recipient cells remain unclear. This is crucial for designing EV-based therapeutics as uptake mechanism dictates the functionality of the cargo. Thus, we hypothesized that (1) EV membrane composition varies by donor cell type and (2) this variation covaries with the mechanism of uptake. Methods: EVs were isolated using differential ultracentrifugation from four cardiac cell types: CPCs, MSCs, cardiac endothelial cells (CECs) and rat cardiac fibroblasts (RCFs) grown in normoxia (18% O 2 ) or hypoxia (1% O 2 ) to mimic ischemic conditions. EVs were characterized for size and concentration. EV lipid membrane profile was assessed through LC/MS/MS. Donor cell’s role on EV uptake mechanism was determined by inhibiting known uptake pathways (clathrin, dynamin, macropinocytosis and caveolae/lipid raft) with small molecules and quantifying CEC/RCF endocytosis of EVs with flow cytometry. Finally, partial least squares regression was used to determine the most important lipids involved in EV uptake mechanism. Results: EVs were successfully isolated and characterized. The EV membrane lipid profiles clustered by donor cell type. Uptake mechanism of EVs varied based on both donor and recipient cell type with dynamin mediated endocytosis being the most common. Further, the uptake mechanism was independent of normoxic/hypoxic conditioning. Finally, supervised learning methods revealed specific lipid classes (sphingolipids and glycerophospholipids) covaried with EV uptake mechanism. Conclusion: This work highlights the importance of the understudied EV membrane and its role in delivering therapeutic cargo. Active donor cell selection for efficient EV uptake will allow for more potent EV-based MI therapies.
Optimizing 3-mode fibers for Mode Division Multiplexing (2011)

3-mode fibers with large Aeff of 150 µm2 (LP01 mode), and >200 µm2 (LP11 and LP21 modes) were successfully designed and fabricated. The optical properties were measured for center Gaussian mode and outside ring modes.
Synthesis and Conformational Analysis of a Locked Analogue of Carbovir Built on a Bicyclo[3.1.0]-hex-2-enyl Template (2003)

The synthesis and biological evaluation of a carbovir analogue (5) built on a bicyclo[3.1.0]hex-2-enyl template is described. A conformational analysis using density functional theory at the B3LYP/6-31G* level has been carried out on the rigid pseudosugar template of 5, the cyclopentene moiety of carbovir and the bicyclo[3.1.0]hex-2-yl pseudosugars of two isomeric carbonucleosides (12 and 13) containing exo- and endo-fused cyclopropane rings. The results show that while the planar configuration of the fused cyclopentane ring of compound 5 helps retain weak anti-HIV activity, the ability of the cyclopentene ring of carbovir to easily adopt a planar or puckered conformation with little energy penalty may prove to be a crucial advantage. The bicyclo[3.1.0]hex-2-yl nucleosides 12 and 13 that were inactive against HIV exhibited stiffer resistance to having a planar, fused cyclopentane moiety.
Saliva as a useful tool for evaluating upper mucosal antibody response to influenza (2022)

Mucosal immunity plays a crucial role in controlling upper respiratory infections, including influenza. We established a quantitative ELISA to measure the amount of influenza virus-specific salivery IgA (sIgA) and salivary IgG (sIgG) antibodies using a standard antibody broadly reactive to the influenza A virus. We then analyzed saliva and serum samples from seven individuals infected with the A(H1N1)pdm09 influenza virus during the 2019-2020 flu seasons. We detected an early (6-10 days post-infection) increase of sIgA in five of the seven samples and a later (3-5 weeks) increase of sIgG in six of the seven saliva samples. Although the conventional parenteral influenza vaccine did not induce IgA production in saliva, vaccinated individuals with a history of influenza infection had higher basal levels of sIgA than those without a history. Interestingly, we observed sIgA and sIgG in an asymptomatic individual who had close contact with two influenza cases. Both early mucosal sIgA secretion and late systemically induced sIgG in the mucosal surface may protect against virus infection. Despite the small sample size, our results indicate that the saliva test system can be useful for analyzing upper mucosal immunity in influenza.
Supplementary Table S5 from COVID-19 Outcomes by Cancer Status, Site, Treatment, and Vaccination (2023)

&lt;p&gt;Logistic regression odds ratios (95% CI) for COVID-19 outcomes by cancer treatment type using restricted electronic health record for cancer recency analysis.&lt;/p&gt;
Molecular Electronic Study of Spiro-[cyclopenta[1,2-<i>b</i>:5,4-<i>b</i>′]dithiophene-4,9′-fluorene] Derivatives: Route to Decent Hole-Transporting Materials (2022)

Spiro-type molecules have been extensively explored as hole-transporting materials (HTMs) in perovskite solar cells (PSCs). However, a closer look at the rule of design of such molecules is missing, and a combined experimental and theoretical study is needed. In this work, three spiro-[cyclopenta[1,2-b:5,4-b′]dithiophene-4,9′-fluorene] (SDTF) derivatives decorated with triphenylamine have been designed and synthesized. The thermal and optoelectronic properties, single-crystal structures, and charge-transport properties have been extensively investigated to reveal the impact of the linkage position of triphenylamine groups by combining experimental and theoretical methods, and the results are consistent with each other. Moreover, transfer integrals and reorganization energies in these molecules are also calculated to predict hole mobility. Our comprehensive studies show that SDTF-2 with a suitable energy alignment, good hole injection/transportability, and high theoretical hole mobility can be employed for efficient perovskite solar cells, achieving a high power conversion efficiency of 19.3%. In addition, first-principle calculations reveal that the strong interactions between SDTF-2 and the perovskite surface can facilitate fast hole extraction. Our way of study has provided useful information as part of the Materials Genome Initiative. We hope our investigation will offer a reliable path to predict or find the potential of novel spiro-type HTMs to become the alternative choice of spiro-OMeTAD.
Who's in, who's out? Re‐evaluation of lipid raft residents (2021)

Lipid rafts, membrane microdomains enriched with (glyco)sphingolipids, cholesterol, and select proteins, act as cellular signalosomes. Various methods have been used to separate lipid rafts from bulk (non-raft) membranes, but most often, non-ionic detergent Triton X-100 has been used in their isolation. However, Triton X-100 is a reported disruptor of lipid rafts. Histological evidence confirmed raft disruption by Triton X-100, but remarkably revealed raft stability to treatment with a related polyethylene oxide detergent, Brij O20. We report isolation of detergent-resistant membranes from mouse brain using Brij O20 and its use to determine the distribution of major mammalian brain gangliosides, GM1, GD1a, GD1b and GT1b. A different distribution of gangliosides-classically used as a raft marker-was discovered using Brij O20 versus Triton X-100. Immunohistochemistry and imaging mass spectrometry confirm the results. Use of Brij O20 results in a distinctive membrane distribution of gangliosides that is not all lipid raft associated, but depends on the ganglioside structure. This is the first report of a significant proportion of gangliosides outside raft domains. We also determined the distribution of proteins functionally related to neuroplasticity and known to be affected by ganglioside environment, glutamate receptor subunit 2, amyloid precursor protein and neuroplastin and report the lipid raft populations of these proteins in mouse brain tissue. This work will enable more accurate lipid raft analysis with respect to glycosphingolipid and membrane protein composition and lead to improved resolution of lipid-protein interactions within biological membranes.
GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology (2021)

Summary Different regions of the gastrointestinal tract have distinct digestive and absorptive functions, which may be locally disrupted by infection or autoimmune disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. Here, we used mouse models, transcriptomics, and immune profiling to show that regional epithelial expression of the transcription factor GATA4 prevented adherent bacterial colonization and inflammation in the proximal small intestine by regulating retinol metabolism and luminal IgA. Loss of epithelial GATA4 expression increased mortality in mice infected with Citrobacter rodentium . In active celiac patients with villous atrophy, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus , and increased IL-17 immunity. This study reveals broad impacts of GATA4-regulated intestinal regionalization and highlights an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease. One-sentence summary Epithelial GATA4 regulates intestinal regionalization of bacterial colonization, metabolic pathways, and tissue immunity.
SU‐FF‐T‐58: Dosimetric Study of a New Surface Applicator for the Xoft Axxent System (2009)

Purpose: To determine the dosimetric properties of a new surface applicator designed for the Xoft 50 kVp x‐ray system Method and Materials: A 35mm conical stainless steel applicator with Al flattening filter interfaces to the Xoft 50 kVp x‐ray source to provide therapeutic radiation to surfaces such as skin. Measurements of the dose profile at the surface and at depths to 20 mm were performed using a PTW ionization chamber in a water phantom. The chamber was controlled by a stepper motor and linear stage, and data was read into a controlling computer. In addition, film data was taken both parallel and perpendicular to the surface. Results: Nominal dose profiles and depth dose characteristics were determined from an average of ten sources. Dose profiles across at least 80% of the applicator width were flat to within ± 10% for all sources, and to within 5% on average. Depth dose characteristics are very similar to those published for HDR based surface applicators, with the percent depth dose at 5 and 10 mm at 58% and 36%. Such data can be used for treatment planning purposes. The variation seen among sources determines an error band representative of what will be experienced in clinical use. Conclusion: The FDA approved surface applicator delivers a dose profile that is flat to within ± 10% over a span of 80% of the defined width of the device. It can be used for treatment of skin lesions in lightly shielded rooms due to the low energies employed. There are also intriguing possibilities for use intra‐operatively, since the system can be used in an operating room. Conflict of Interest: Research supported by Xoft, Inc.
Chromosome 21-derived MicroRNAs Provide an Etiological Basis for Aberrant Protein Expression in Human Down Syndrome Brains (2009)

Down syndrome (DS), or Trisomy 21, is the most common genetic cause of cognitive impairment and congenital heart defects in the human population. Bioinformatic annotation has established that human chromosome 21 (Hsa21) harbors five microRNA (miRNAs) genes: miR-99a, let-7c, miR-125b-2, miR-155, and miR-802. Our laboratory recently demonstrated that Hsa21-derived miRNAs are overexpressed in DS brain and heart specimens. The aim of this study was to identify important Hsa21-derived miRNA/mRNA target pairs that may play a role, in part, in mediating the DS phenotype. We demonstrate by luciferase/target mRNA 3'-untranslated region reporter assays, and gain- and loss-of-function experiments that miR-155 and -802 can regulate the expression of the predicted mRNA target, the methyl-CpG-binding protein (MeCP2). We also demonstrate that MeCP2 is underexpressed in DS brain specimens isolated from either humans or mice. We further demonstrate that, as a consequence of attenuated MeCP2 expression, transcriptionally activated and silenced MeCP2 target genes, CREB1/Creb1 and MEF2C/Mef2c, are also aberrantly expressed in these DS brain specimens. Finally, in vivo silencing of endogenous miR-155 or -802, by antagomir intra-ventricular injection, resulted in the normalization of MeCP2 and MeCP2 target gene expression. Taken together, these results suggest that improper repression of MeCP2, secondary to trisomic overexpression of Hsa21-derived miRNAs, may contribute, in part, to the abnormalities in the neurochemistry observed in the brains of DS individuals. Finally these results suggest that selective inactivation of Hsa21-derived miRNAs may provide a novel therapeutic tool in the treatment of DS.
The meaning of Beta: background and applicability of the target reliability index for normal conditions to structural fire engineering (2017)

Uncommon structural fire engineering designs must demonstrate adequate safety, in principle, through a balancing of the uncertain future costs and benefits of safety investments. In structural design for normal load conditions (‘ambient design’) this level of detail is commonly avoided through the application of reliability targets. In order to inform the development of reliability targets for structural fire design, the background of the ambient reliability targets is discussed. It is found that different common ambient reliability targets are broadly comparable when taking into account differences in assumptions and applications. As recent reliability targets have been informed by simplified cost-optimizations, the derivation of such a model is presented. The derivation allows identification of possible pitfalls when extending ambient reliability targets to structural fire design. It is concluded that ambient safety targets cannot readily be scaled as a function of the fire occurrence rate for application to structural fire engineering problems. The underlying cost-optimization model is, however, applicable as a concept. A number of issues requiring further attention are identified.
Observation of charged particle bursts from deuterium loaded thin titanium foils (1991)

Intense bursts of energetic charged particles from deuterium gas loaded thin foils of Ti 662 subject to fairly high D.C. electric currents and non‐equilibrium thermal conditions have been observed. The energies of the particles range from less than 1 MeV to greater than 10 MeV. By observing energy shifts through thin foils of Al, the particles are tentatively identified as tritons, 3He, and possibly alpha particles. Control measurements carried out with comparably prepared Ti‐H samples evinced no particle bursts.
Fast high-resolution 3D total internal reflection fluorescence microscopy by incidence angle scanning and azimuthal averaging (2014)

Significance Recent progress has pushed forward the resolving capacity of optical microscopy at the expense of a low acquisition rate and use of specific probes. Such limitations make these techniques incompatible with dynamics localization of multiple elements in single cell. We report here a method to recover 3D volumes from images obtained using several total internal reflection fluorescence (TIRF) incidence angles at dense regime of acquisition. This approach allows investigating several dynamical processes occurring in depth of the cell up to 800 nm from the plasma membrane such as actin remodeling. The study of time-correlated molecular behaviors at the very late steps of vesicle docking–fusion during exocytosis of two distinct recycling transport intermediates, in 3D and at high axial resolution, is also accessible.
Ultrashort Pulsed-Laser Fabrication of Silicon Moth-Eye Structures for Terahertz Anti-Reflection (2018)

We fabricate moth-eye anti-reflection structures for the terahertz region on high-resistivity silicon substrates by ultrashort pulsed-laser ablation. We demonstrate 1.4 times increased THz yield from Mg:LN by using the moth-eye structure as an output coupler.
Computational ligand design. (1999)

A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug-like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative structure-activity relationships (QSAR) are presented. These have gained significantly from recent developments of experimental techniques for combinatorial synthesis and high-throughput screening as well as the use of powerful computational procedures like genetic algorithms and neural networks for the derivation of models. Secondly, empirical energy functions are shown to lead to more general models than standard QSAR, since they are fitted to a variety of complexes. They have been used recently with considerable success. Thirdly, we briefly outline free energy calculations based on molecular dynamics simulations, the method with the most sound theoretical foundation. Recent developments are reestablishing the interest in this approach. In the last part of this review structure-based ligand design programs are described. These are closely related to docking, with the difference that in design, unlike in most docking procedures, ligands are built on a fragment-by-fragment basis. Finally, a short description of our approach to computational combinatorial ligand design is given.
Technologies for reducing power (2010)

With power and cooling becoming an increasingly costly part of the operating cost of a server, the old trend of striving for higher performance with little regard for power is over. Emerging semiconductor process technologies, multicore architectures, and new interconnect technology provide an avenue for future servers to become low power, compact, and possibly mobile. In our talk we examine three techniques for achieving low power: 1) Near threshold operation; 2) 3D die stacking; and 3) replacing DRAM with Flash memory.