gebhart/patrepeval huggingface dataset:
A 500W high efficiency class-E power amplifier for heating a variable plasma load at 10MHz (2016)

In this contribution, a high efficiency class-E power amplifier is presented, which is optimized with respect to heat a variable plasma load at 10MHz. First of all, the design of the class-E amplifier is demonstrated. Therefore, after the fundamental design equations, the dimensioning of amplifier's lumped elements is presented. Furthermore, simulations and measurements are performed in order to verify the functionality and efficiency. During this, two high power MOSFETs from Microsemi and IXYS are compared. An efficiency of 90.7% at 507W output power and 50Ω load is achieved. The resistance of the plasma load can change between 200Ω and 300Ω. Therefore, an optimized matching network, which provides an almost constant output power of ±1% in the desired load resistance range, is presented.
Abolish runtime systems (2006)

Singularity [1] is a research project in Microsoft Research that started with a question: what would a software platform look like if it was designed from scratch with the primary goal of dependability? Singularity is working to answer this question by building on advances in programming languages and tools to develop a new system architecture and operating system (named Singularity), with the aim of producing a more robust and dependable software platform.Singularity made some design decisions that distinguish it from other systems. First, Singularity is written, for the most part, in safe, managed code and it will only run verifiably safe programs. Second, the system is the runtime; there is no separate JVM or CLR. Third, each process's execution environment is independent, with its own, distinct runtime, garbage collector, and libraries. As a consequence, Singularity uses control of the execution environment as a mechanism to enforce system policy and enhance system dependability.This talk will describe Singularity and then explain why conventional runtime systems, such as the JVM and CLR, should go away, like punch cards, teletypes, time sharing, etc.
Development of VU6019650: A Potent, Highly Selective, and Systemically Active Orthosteric Antagonist of the M5 Muscarinic Acetylcholine Receptor for the Treatment of Opioid Use Disorder (2022)

The muscarinic acetylcholine receptor (mAChR) subtype 5 (M<sub>5</sub>) represents a novel potential target for the treatment of multiple addictive disorders, including opioid use disorder. Through chemical optimization of several functional high-throughput screening hits, <b>VU6019650</b> (<b>27b</b>) was identified as a novel M<sub>5</sub> orthosteric antagonist with high potency (human M<sub>5</sub> IC<sub>50</sub> = 36 nM), M<sub>5</sub> subtype selectivity (>100-fold selectivity against human M<sub>1-4</sub>) and favorable physicochemical properties for systemic dosing in preclinical addiction models. In acute brain slice electrophysiology studies, <b>27b</b> blocked the nonselective muscarinic agonist oxotremorine-M-induced increases in neuronal firing rates of midbrain dopamine neurons in the ventral tegmental area, a part of the mesolimbic dopaminergic reward circuitry. Moreover, <b>27b</b> also inhibited oxycodone self-administration in male Sprague-Dawley rats within a dose range that did not impair general motor output.
Design concepts for a mid-infrared instrument for the Thirty-Meter Telescope (2010)

A mid-infrared imager and spectrometer is under consideration for construction in the first decade of the Thirty- Meter Telescope (TMT) operation (see the companion paper by Okamoto). MIRES, a mid-infrared high-spectral resolution optimized instrument, was previously proposed to provide these capabilities to the TMT community. We have revised the design in order to provide an improved optical design for the high-spectral resolution mode with R=120,000, improved imaging with sky chopping, low-spectral resolution mode with an integral field spectrograph, and polarimetry. In this paper we describe the optical design concepts currently under consideration.
Photoinduced electron transfer from zinc porphyrin to a linked quinone in myoglobin (1995)

Myoglobin reconstituted with the covalently linked zinc porphyrin–peptide–quinone triad 1 is prepared and the singlet electron transfer from zinc porphyrin to quinone within the protein is examined by fluorescence measurements.
ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept (1983)

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.
Enantioselective Synthesis of Antiinfluenza Compound A-315675 (2002)

Drug discovery efforts at Abbott Laboratories have led to the identification of influenza neuraminidase inhibitor A-315675 (1) as a candidate for development as an antiinfluenza drug. A convergent, stereoselective synthesis of this highly functionalized pyrrolidine is reported that utilizes pyrrolinone 2 as the key intermediate. The C5, C6 stereochemistry was established through a diastereoselective condensation of chiral imine compound 3 with silyloxypyrrole 4 to give pyrrolinone 2. The stereochemical outcome of this reaction depended critically on the choice of the imine functional group (FG), with tritylsulfenyl and (R)-toluenesulfinyl providing the desired products in good yields as crystalline intermediates. Conversion of pyrrolinone 2 into 1 was accomplished in seven subsequent steps, including Michael addition of cis-1-propenylcuprate at C4 and introduction of a cyano group as a carboxylic acid equivalent at C2.
MyD88 Signaling Contributes to Early Pulmonary Responses toAspergillus fumigatus (2007)

Toll-like receptors and the beta-glucan receptor, dectin-1, mediate macrophage inflammatory responses to Aspergillus fumigatus through MyD88-dependent and -independent signaling mechanisms; however, pulmonary inflammatory responses in MyD88-deficient mice challenged with A. fumigatus are poorly defined. The role of MyD88 signaling in early pulmonary inflammation and fungal clearance was evaluated in C57BL/6J wild-type (WT) and MyD88-deficient (MyD88-/-) mice. Early (<48 h) after infection, MyD88-/- mice had higher fungal burdens than those of WT mice, although fungal burdens rapidly declined (>72 h) in both. MyD88-/- mice had less consolidated inflammation, with fewer NK cells, in lung tissue early (24 h) after infection than did WT mice. At the latter time point, MyD88-/- mouse lungs were characterized by a large amount of necrotic cellular debris and fibrin, while WT lungs had organized inflammation. Although there were equivalent numbers of macrophages in WT and MyD88-/- mouse lung tissues, MyD88-/- cells demonstrated delayed uptake of green fluorescent protein-expressing A. fumigatus (GFP-Af293); histologically, MyD88-/- mouse lungs had more hyphal invasion of terminal airways and vessels, the appearance of bronchiolar epithelial cell necrosis, and necrotizing vasculitis. MyD88-/- lung homogenates contained comparatively decreased amounts of interleukin-1beta (IL-1beta), IL-6, KC, and gamma interferon and paradoxically increased amounts of tumor necrosis factor alpha and macrophage inflammatory protein 1alpha. These data indicate that the MyD88-dependent pathway mediates acute pulmonary fungal clearance, inflammation, and tissue injury very early after infection. Resolution of abnormalities within a 3-day window demonstrates the importance of redundant signaling pathways in mediating pulmonary inflammatory responses to fungi.
Evaluation of the diagnostic accuracy of cervical biopsy and determination of associated risk factors for positive margin status in recurrent cervical dysplasia after leep or conization. (2014)

5609 Background: Severe dysplasia on a cervical biopsy is often followed by an excisional procedure such as a loop electrosurgical excisional procedure (LEEP) or cone biopsy. The objective of this study was to determine the prevalence and associated risk factors for positive surgical margins on cold knife conization or LEEP as well as the recurrence of dysplasia after these procedures. Secondary objective was to determine the correlation of cervical biopsy revealing CIN II with degree of dysplasia found on final pathology. Methods: This is a descriptive analytical study of 118 patients who underwent a LEEP or cone biopsy during a 12 year period (1999-2011) by trained gynecologic oncologists at our institution. Medical records were reviewed from a prospectively maintained pathology database. Cases were identified through a search performed for all patients in this period with a CIN II diagnosis. All pathology specimens were reviewed by one of four board specialized gynecologic pathologists. The need for cervical biopsy was determined based on pap results according to the ASCCP guidelines. Univariate analysis was performed with the chi-square test and the Student's t-test. Results: Of the 118 patients, 29 cases had a positive cone/LEEP margin (24.6%). Of the patients with positive margins, 48.2 % of these patients were considered to be immuno-compromised due to factors such as chronic steroid use and smoking, chemotherapy or HIV positivity. Recurrence of abnormal pap smears within 2 years of an excisional procedure was 19% in the margin negative group and 31% in the margin positive group (P <0.0001). The positive predictive value of cervical biopsy for determining CIN II on an excisional procedure was 94.1%. Conclusions: Positive surgical margins on LEEP/cone biopsy is not uncommon and increases the risk for abnormal cervical cytology in the subsequent years post-procedure. Cervical biopsies when performed by trained physicians correlate well with final pathology on cone biopsy/LEEP. Risk factor assessment continues to be important in following patients after cervical excisional procedures.
Light trapping for thin silicon solar cells by femtosecond laser texturing (2012)

Femtosecond laser texturing is used to create nano- to micron-scale surface roughness that strongly enhances light-trapping in thin crystalline silicon solar cells. Light trapping is crucial for thin solar cells where a single light-pass through the absorber is insufficient to capture the weakly absorbed red and near-infrared photons, especially with an indirect-gap semiconductor absorber layer such as crystalline Si which is less than 20 μm thick [1-2]. We achieve enhancement of the optical absorption from light-trapping that approaches the Yablonovitch limit [3].
A nationwide cohort study of cigarette smoking and risk of neovascular age-related macular degeneration in East Asian men (2017)

Cigarette smoking is associated with a strong risk of neovascular AMD among Korean men. These data highlight the public health impact of smoking on blindness in Asia.
Abstract 756: Optimization of tetrahydroisoquinoline-based microtubule disruptors as anticancer agents (2010)

Abstract We outline the discovery and optimisation of new microtubule disruptors with in vivo anti-tumor activity. Translation of the SAR from a steroidal series of microtubule disruptors led us to identify a series of tetrahydroisoquinoline (THIQ) based systems which exhibit a similar activity profile. Of this new series, 2-(3′,4′,5′-Trimethoxybenzyl)-7-methoxy-6-O-sulfamoyl THIQ 1 proved especially potent in both in vitro (GI50 [DU-145] 297 nM) and in vivo experiments. Herein, we describe the results of optimisation at C-6 and C-7 of the THIQ core and assessment of other polymethoxylated N-benzyl systems. Variations at the N-2 and C-6 positions were achieved by alkylation, esterification and etherification. Friedel Crafts acylation of C-7 and functional group interconversion allowed access to various C-7 alkyl and alkoxy derivatives. The various dimethoxybenzyl compounds proved similar in activity to the lead compound 2 (GI50 2.1 μM) in the N-mono-methoxybenzyl series while, apart from the 3′,4′,5′-trimethoxybenzyl compound 1, only 2′,4′,5′-trimethoxybenzyl substitution delivered sub-micromolar activity. Investigations of the effect of C-6 substitution proved more fruitful. In contrast to the SAR observed for 2 where the sulfamate group is essential for activity, the 6-OH, with the 6-O-acyl and 6-O-mesyl derivatives of 1 displayed similar or improved activity to the parent compound (GI50s range from 650 to 220 nM). The 6-O-methyl derivative, in contrast, proved completely inactive, highlighting the importance of a H-bond donor directly attached to C-6 or a H-bond acceptor projecting further out from this position. The most pronounced improvement in activity was obtained from exploration of C-7 substitution. In the 3′,4′,5′-trimethoxybenzyl series isosteric replacement of methoxy with ethyl delivered a 7-fold improvement in activity (3 GI50 41 nM). Intriguingly, the corresponding phenol proved significantly active suggesting different binding modes operate for the phenol and sulfamate derivatives since the H-bond acceptor properties of the C-7 substituent of the former are clearly important. Incorporation of a C-7 ethoxy group meanwhile proved detrimental for both sulfamate and phenol derivatives. The same transformations were made to 2, though no improvement in activity was obtained. In order to establish the potential of these compounds as anti-tumor agents their activity in the RPMI-8226 multiple myeloma xenograft model was assessed. The &amp;gt;75% inhibition of tumor growth observed (3 p.o. 40 mg/kg, 28d) in this preliminary study augers well for the development of this class of anti-cancer agents. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 756.
Regenerative Medicine, Resource and Regulation: Lessons Learned from the Remedi Project (2011)

The successful commercialization of regenerative medicine products provides a unique challenge to the manufacturer owing to a lack of suitable investment/business models and a constantly evolving regulatory framework. The resultant slow translation of scientific discovery into safe and clinically efficacious therapies is preventing many potential products from reaching the market. This is despite of the need for new therapies that may reduce the burden on the world's healthcare systems and address the desperate need for replacement tissues and organs. The collaborative Engineering and Physical Sciences Research Council (EPSRC)-funded remedi project was devised to take a holistic but manufacturing-led approach to the challenge of translational regenerative medicine in the UK. Through strategic collaborations and discussions with industry and other academic partners, many of the positive and negative issues surrounding business and regulatory success have been documented to provide a remedi-led perspective on the management of risk in business and the elucidation of the regulatory pathways, and how the two are inherently linked. This article represents the findings from these discussions with key stakeholders and the research into best business and regulatory practices.
AFM force spectroscopy reveals how subtle structural differences affect the interaction strength betweenCandida albicansand DC-SIGN (2015)

The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C-type lectin dendritic cell-specific intracellular cell adhesion molecule-3 (ICAM-3)-grabbing non-integrin (DC-SIGN), because a detailed characterization at the structural level is lacking. DC-SIGN recognizes specific Candida-associated molecular patterns, that is, mannan structures present in the cell wall of Candida. The molecular recognition mechanism is however poorly understood. We postulated that small differences in mannan-branching may result in considerable differences in the binding affinity. Here, we exploit atomic force microscope-based dynamic force spectroscopy with single Candida cells to gain better insight in the carbohydrate recognition capacity of DC-SIGN. We demonstrate that slight differences in the N-mannan structure of Candida, that is, the absence or presence of a phosphomannan side chain, results in differences in the recognition by DC-SIGN as follows: (i) it contributes to the compliance of the outer cell wall of Candida, and (ii) its presence results in a higher binding energy of 1.6 kB T. The single-bond affinity of tetrameric DC-SIGN for wild-type C. albicans is ~10.7 kB T and a dissociation constant kD of 23 μM, which is relatively strong compared with other carbohydrate-protein interactions described in the literature. In conclusion, this study shows that DC-SIGN specifically recognizes mannan patterns on C. albicans with high affinity. Knowledge on the binding pocket of DC-SIGN and its pathogenic ligands will lead to a better understanding of how fungal-associated carbohydrate structures are recognized by receptors of the immune system and can ultimately contribute to the development of new anti-fungal drugs.
Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses (2019)

Influenza A viruses (IAVs) have a remarkable tropism in their ability to circulate in both mammalian and avian species. The IAV NS1 protein is a multifunctional virulence factor that inhibits the type I interferon host response through a myriad of mechanisms. How NS1 has evolved to enable this remarkable property across species and its specific impact in the overall replication, pathogenicity, and host preference remain unknown. Here we analyze the NS1 evolutionary landscape and host tropism using a barcoded library of recombinant IAVs. Results show a surprisingly great variety of NS1 phenotypes according to their ability to replicate in different hosts. The IAV NS1 genes appear to have taken diverse and random evolutionary pathways within their multiple phylogenetic lineages. In summary, the high evolutionary plasticity of this viral protein underscores the ability of IAVs to adapt to multiple hosts and aids in our understanding of its global prevalence.
Asymmetrical effects of unilateral cortical suction lesions: Behavioral characterization. (1984)

Behavioral effects of unilateral frontocortical suction lesions in the right and left hemisphere were characterized by a computerized activity monitoring system. Lesions of the right frontal cortex produced postoperative hyperactivity consisting of increases in the total distance traveled, average distance per movement, and average speed of movement. Vertical, rotational, and stereotypic measures were not changed. Animals receiving left hemisphere lesions did not differ from sham-operated controls on any behavioral variable. The lateralized hyperactivity resulting from lesions of the right frontal cortex was confined to increased length and speed of horizontal movement and did not appear to represent a generalized increase in all components of spontaneous activity.
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency (2021)

These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.
Three Sides of the Same Coin: Combining Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources (2022)

Abstract All catalysts have unique abilities. This is especially true for microbial, enzymatic, and organometallic catalysis, which are often seen as competitive approaches preventing the exploitation of their complementarity. An increasing number of examples show, how using the complete catalytic spectrum can open roads from new substrates to new products. C1‐compounds such as formate, formaldehyde, methanol, or methane from CO 2 in combination with green H 2 are likely to be future sources of carbon feedstock. This short review highlights how combinations of different catalyst types can facilitate integrated reaction sequences with biogenic substrates to form “bio‐hybrid” fuels and products.
Long-wavelength VCSELs with InP/air-gap DBRs (2004)

We demonstrate novel electrically pumped 1300 nm and 1550 nm VCSELs with two InP/air-gap DBRs. The active regions comprise conventional InGaAsP multiple quantum wells. A tunnel junction is placed between the active region and top DBR to convert electrons into holes, thus minimizing the use of p-type material in the structure to reduce the free-carrier loss and achieve current confinement. The whole structure was grown in a single growth run by low pressure MOCVD. For both 1300 and 1550 nm emission wavelengths, air-gap DBR VCSELs exhibit roomtemperature, CW threshold current density as low as 1.1 kA/cm<sup>2</sup>, differential quantum efficiency greater than 30%, and CW operation up to 85°C. The single-mode output power was 1.6 mW from a 1300 nm VCSEL with a 6.3 &mu;m aperture; and 1.1 mW from a 1550 nm VCSEL with a 5.7 &mu;m aperture under room temperature CW operation
F4F (2011)

This paper presents F4F (Framework For Frameworks), a system for effective taint analysis of framework-based web applications. Most modern web applications utilize one or more web frameworks, which provide useful abstractions for common functionality. Due to extensive use of reflective language constructs in framework implementations, existing static taint analyses are often ineffective when applied to framework-based applications. While previous work has included ad hoc support for certain framework constructs, adding support for a large number of frameworks in this manner does not scale from an engineering standpoint. F4F employs an initial analysis pass in which both application code and configuration files are processed to generate a specification of framework-related behaviors. A taint analysis engine can leverage these specifications to perform a much deeper, more precise analysis of framework-based applications. Our specification language has only a small number of simple but powerful constructs, easing analysis engine integration. With this architecture, new frameworks can be handled with no changes to the core analysis engine, yielding significant engineering benefits. We implemented specification generators for several web frameworks and added F4F support to a state-of-the-art taint-analysis engine. In an experimental evaluation, the taint analysis enhanced with F4F discovered 525 new issues across nine benchmarks, a harmonic mean of 2.10X more issues per benchmark. Furthermore, manual inspection of a subset of the new issues showed that many were exploitable or reflected bad security practice.