gebhart/patrepeval huggingface dataset:
Rates and mechanisms of optic contamination in the EUV engineering test stand (2003)

The EUV Engineering Test Stand (ETS) is a full field, alpha class Extreme Ultraviolet Lithography (EUVL) tool that has demonstrated the printing of 70 nm resolution scanned images. The tool employs Mo/Si multilayer optics that reflect EUV radiation (13.4nm / 92.5eV) with ~67% peak reflectance per optic. For good reflectivity, many (greater than or equal to 40)Mo/Si layers must be present. Consequently, processes such as plasma induced multilayer erosion, which reduces the number of bilayer pairs on plasma facing optics, need to be understood. Since most materials readily absorb EUV photons, it is important to prevent contamination of mirror surfaces with EUV absorbing material. Contamination can occur by EUV photons “cracking” hydrocarbons or other species absorbed on the optical surfaces. The first ETS condenser component, referred to as C1, is coated with Mo/Si multilayers. Data collected from Mo/Si witness plates placed at the C1 position indicate erosion, using the Xe Laser Produced Plasma (LPP) spray jet, of 1 bilayer per ~15 million shots. Preliminary experiments with a filament jet yielded a significantly higher erosion rate. In the spray jet studies, erosion was found to depend sensitively on the composition of the residual background environment. Addition of low levels, ~7x10<sup>-7</sup> Torr, of H<sub>2</sub>O to the vacuum background produced oxidation of the Si cap, and significantly slowed spray jet induced erosion. Operation of the plasma changed the environment in the Illuminator Chamber from oxidizing to carbonizing, thereby changing the nature of the contamination found environment at the C3 optic which does not view the plasma directly (and therefore does not erode). The change in environment is attributed to plasma induced outgassing of fluorocarbons in the Illuminator. Due to the non zero conductance between the Illuminator and Main Chambers, fluorocarbons were also found in the Main Chamber during Xe LPP operation. RGA data are presented that document the effect. In the presence of such outgassing, Carbon deposition rates were measured for the C3, and P.O. Box optics. For C3, a C deposition rate of 3 angstrom / 10 million shots was found, while for the PO Box, a C deposition rate of 0.02 angstrom / 10 million shots was found from the data. All data was acquired with no attempt to mitigate C deposition with gas phase additives such as O<sub>2</sub>.
Bacterial viruses as human vaccines? (2004)

Bacteriophages (or phages) are viruses of bacteria, consisting of nucleic acid packaged within a protein coat. In eukaryotic hosts, phages are unable to replicate and in the absence of a suitable prokaryotic host, behave as inert particulate antigens. In recent years, work has shown that whole phage particles can be used to deliver vaccines in the form of immunogenic peptides attached to modified phage coat proteins or as delivery vehicles for DNA vaccines, by incorporating a eukaryotic promoter-driven vaccine gene within their genome. While both approaches are promising by themselves, in future there is also the exciting possibility of creating a hybrid phage combining both components to create phage that are cheap, easy and rapid to produce and that deliver both protein and DNA vaccines via the oral route in the same construct.
Curve-based 2D-3D registration of coronary vessels for image guided procedure (2009)

3D roadmap provided by pre-operative volumetric data that is aligned with fluoroscopy helps visualization and navigation in Interventional Cardiology (IC), especially when contrast agent-injection used to highlight coronary vessels cannot be systematically used during the whole procedure, or when there is low visibility in fluoroscopy for partially or totally occluded vessels. The main contribution of this work is to register pre-operative volumetric data with intraoperative fluoroscopy for specific vessel(s) occurring during the procedure, even without contrast agent injection, to provide a useful 3D roadmap. In addition, this study incorporates automatic ECG gating for cardiac motion. Respiratory motion is identified by rigid body registration of the vessels. The coronary vessels are first segmented from a multislice computed tomography (MSCT) volume and correspondent vessel segments are identified on a single gated 2D fluoroscopic frame. Registration can be explicitly constrained using one or multiple branches of a contrast-enhanced vessel tree or the outline of guide wire used to navigate during the procedure. Finally, the alignment problem is solved by Iterative Closest Point (ICP) algorithm. To be computationally efficient, a distance transform is computed from the 2D identification of each vessel such that distance is zero on the centerline of the vessel and increases away from the centerline. Quantitative results were obtained by comparing the registration of random poses and a ground truth alignment for 5 datasets. We conclude that the proposed method is promising for accurate 2D-3D registration, even for difficult cases of occluded vessel without injection of contrast agent.
Numerical simulation of tetracene light-emitting transistors: A detailed balance of exciton processes (2004)

We assess the possibility to use an ambipolar organic light-emitting transistor structure as gain medium for an electrically pumped laser. Singlet and triplet continuity equations are solved together with Poissons and drift-diffusion equations in two dimensions. The solution allows for a detailed balance between the exciton decay, quenching and generation mechanisms. Simulations of a tetracene light-emitting transistor show that triplets are most dominant in quenching singlets. Singlet–triplet quenching can ultimately prevent pure tetracene crystals or films—when provided with a realistic optical feedback structure, to reach the threshold for stimulated emission.
Hydrogen Silsesquioxane: A Molecular Precursor for Nanocrystalline Si—SiO<sub>2</sub> Composites and Freestanding Hydride‐Surface‐Terminated Silicon Nanoparticles. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Absolute and Precise Terahertz-Wave Radar Based on an Amplitude-Modulated Resonant-Tunneling-Diode Oscillator (2018)

We present the principle of a terahertz-wave radar and its proof-of-concept experimental verification. The radar is based on a 522 GHz resonant-tunneling-diode oscillator, whose terahertz output power can be easily modulated by superimposing the modulation signal on its bias voltage. By using one modulation frequency and measuring the time delay of the returning signal, a relative measurement of the propagation distance is possible; adding a second modulation frequency removes the ambiguity stemming from the periodicity of the modulation sine wave and allows an absolute distance measurement. We verified this measurement method experimentally and obtained a submillimeter precision, as predicted by theory.
Thread-specific heaps for multi-threaded programs (2000)

Garbage collection for a multi-threaded program typically involves either stopping all threads while doing the collection or involves copious amounts of synchronization between threads. However, a lot of data is only ever visible to a single thread, and such data should ideally be collected without involving other threads.
A multispecies enzyme-linked immunosorbent assay for von Willebrand's factor. (1992)

A modified double-sandwich enzyme-linked immunosorbent assay (ELISA), which was developed for human and canine von Willebrand's factor (vWF), was adapted for quantitation of vWF in other species. In addition to human and dog plasmas, 12 other mammalian plasmas that were surveyed exhibited significant cross-species reactivity with antibodies specific for canine vWF or monoclonal antibodies against porcine or bovine vWF. Mixed combinations of monoclonal antibodies and various polyclonal antibodies were also used as sandwich or capture antibodies. The ability of this multispecies ELISA to detect less than 0.002 U of vWF per milliliter of plasma in a large number of species enhances its utility for both research and clinical diagnostic applications. A quantitative assay for rabbit vWF, which exhibits poor cross-species reactivity with most antibodies, was constructed with anti-porcine monoclonal antibody W1-5 and goat-anti-canine vWF as capture and sandwich antibodies, respectively. The same conjugate antibody configuration was used to visualize rabbit vWF multimers by immunoblotting. Specificity of the assay for vWF in human, dog, pig, and horse plasmas was confirmed by use of species-specific vWF-deficient plasmas. In other species, for which vWD plasmas were not available, ELISA specificity for vWF was demonstrated by recovery of greater than 75% of the ELISA-reactive antigen coincident with vWF multimers in the high-molecular-weight (greater than 500 kd) fractions of purified plasmas. This multispecies ELISA permits, for the first time, the measurement of vWF in a variety of mammals for which species-specific immunologic reagents do not currently exist. The results also suggest that certain vWF epitopes have been highly conserved among phylogenetically diverse species.
A distributed approach to precoder selection using factor graphs for wireless communication networks (2013)

This paper addresses distributed parameter coordination methods for wireless communication systems. This proposes a method based on a message-passing algorithm, namely min-sum algorithm, on factor graphs for the application of precoder selection. Two particular examples of precoder selection are considered: transmit antenna selection and beam selection. Evaluations on the potential of such an approach in a wireless communication network are provided, and its performance and convergence properties are compared with those of a baseline selfish/greedy approach. Simulation results for the precoder selection examples are presented and discussed, which show that the graph-based technique generally obtains gain in sum rate over the greedy approach at the cost of a larger message size. Besides, the proposed method usually reaches the global optima in an efficient manner. Methods of improving the rate of convergence of the graph-based distributed coordination technique and reducing its associated message size are therefore important topics for wireless communication networks.
Dome-shaped piezopolymer electroacoustic transducers (1983)

Piezopolymer dome-shaped diaphragmsare studied for their use as telephone transducers. The earphone efficiency is shown to be limited by the piezoelectric coupling factor. Microphones using thick PVF2 diaphragms are described and exhibit a well fitted response with excellent stability.
Production of 5-(chloromethyl)furan-2-carbonyl chloride and furan-2,5-dicarbonyl chloride from biomass-derived 5-(chloromethyl)furfural (CMF) (2015)

Biomass-derived CMF is oxidized to the acid chloride CMFCC in a single step using inexpensive t -butyl hypochlorite. Likewise, DFF, also a CMF derivative, is oxidized directly to the diacid chloride FDCC. The products are platforms for a variety of chemical derivatives of carbohydrates.
Photonic crystals and their potential applications (1996)

A new class of composite materials has emerged which provides a means to control and manipulate light. These materials, known as photonic crystals, are periodic arrays of dielectric scatterers in homogeneous dielectric matrices. They affect the properties of photons in much the same way semiconductors affect the properties of electrons. As a result, photons display similar features such as band structures, localized defect states, and surface states. The ability to design the properties of electromagnetic states will lead to many applications in the control of spontaneous emission and in the fabrication of novel optoelectronic devices.
Blockade of <scp>CD</scp>40–<scp>TRAF</scp>2,3 or <scp>CD</scp>40–<scp>TRAF</scp>6 is sufficient to inhibit pro‐inflammatory responses in non‐haematopoietic cells (2014)

Inhibition of the CD40-CD154 pathway controls inflammatory disorders. Unfortunately, administration of anti-CD154 monoclonal antibodies causes thromboembolism. Blockade of signalling downstream of CD40 may represent an approach to treat CD40-driven inflammatory disorders. Blocking tumour necrosis factor receptor-associated factor 6 (TRAF6) signalling downstream of CD40 in MHC II(+) cells diminishes inflammation. However, CD40-TRAF6 blockade may cause immunosuppression. We examined the role of CD40-TRAF2,3 and CD40-TRAF6 signalling in the development of pro-inflammatory responses in human non-haematopoietic and monocytic cells. Human aortic endothelial cells, aortic smooth muscle cells, renal proximal tubule epithelial cells, renal mesangial cells and monocytic cells were transduced with retroviral vectors that encode wild-type CD40, CD40 with a mutation that prevents TRAF2,3 recruitment (ΔT2,3), TRAF6 recruitment (ΔT6) or both TRAF2,3 plus TRAF6 recruitment (ΔT2,3,6). Non-haematopoietic cells that expressed CD40 ΔT2,3 exhibited marked inhibition in CD154-induced up-regulation of vascular cell adhesion molecule 1, intercellular adhesion molecule 1 (ICAM-1), monocyte chemotactic protein 1 (MCP-1), tissue factor and matrix metalloproteinase 9. Similar results were obtained with cells that expressed CD40 ΔT6. Although both mutations impaired ICAM-1 up-regulation in monocytic cells, only expression of CD40 ΔT6 reduced MCP-1 and tissue factor up-regulation in these cells. Treatment of endothelial and smooth muscle cells with cell-permeable peptides that block CD40-TRAF2,3 or CD40-TRAF6 signalling impaired pro-inflammatory responses. In contrast, while the CD40-TRAF2,3 blocking peptide did not reduce CD154-induced dendritic cell maturation, the CD40-TRAF6 blocking peptide impaired this response. Hence, preventing CD40-TRAF2,3 or CD40-TRAF6 interaction inhibits pro-inflammatory responses in human non-haematopoietic cells. In contrast to inhibition of CD40-TRAF6 signalling, inhibition of CD40-TRAF2,3 signalling did not impair dendritic cell maturation. Blocking CD40-TRAF2,3 signalling may control CD40-CD154-dependent inflammatory disorders.
Testability analysis and test-point insertion in RTL VHDL specifications for scan-based BIST (1999)

This paper proposes a new testability analysis and test-point insertion method at the register transfer level (RTL), assuming a full scan and a pseudorandom built-in self-test design environment. The method is based on analyzing the RTL synchronous specification in synthesizable very high speed integrated circuit hardware descriptive language (VHDL). A VHDL intermediate form representation is first obtained from the VHDL specification and then converted to a directed acyclic graph (DAG) that represents all data dependencies and flow of control in the VHDL specification. Testability measures (TMs) are computed on this graph. The considered TMs are controllability and observability for each bit of each signal/variable that is declared or may be implied in the VHDL specification. Internal signals of functional modules (FMs) such as adders and comparators are also analyzed to compute their controllability and observability values. The internal signals are obtained by decomposing at the RTL large FMs into smaller ones. The calculation of TMs is carried out at a functional level rather than the gate level, to reduce or eliminate errors introduced by ignoring reconvergent fanouts in the gate network, and to reduce the complexity of the DAG construction. Based on the controllability/observability values, test-point insertion is performed to improve the testability for each bit of each signal/variable. This insertion is carried out in the original VHDL specification and thus becomes a part of it unlike in other existing methods. This allows full application of RTL synthesis optimization on both the functional and the test logic concurrently within the designer constraints such as area and delay. A number of benchmark circuits were used to show the applicability and the effectiveness of our method in terms of the resulting testability, area, and delay.
Timing and Biosynthetic Potential for Carotenoid Accumulation in Genetically Diverse Germplasm of Maize    (2009)

Enhancement of the carotenoid biosynthetic pathway in food crops benefits human health and adds commercial value of natural food colorants. However, predictable metabolic engineering or breeding is limited by the incomplete understanding of endogenous pathway regulation, including rate-controlling steps and timing of expression in carotenogenic tissues. The grass family (Poaceae) contains major crop staples, including maize (Zea mays), wheat (Triticum aestivum), rice (Oryza sativa), sorghum (Sorghum bicolor), and millet (Pennisetum glaucum). Maize carotenogenesis was investigated using a novel approach to discover genes encoding limiting biosynthetic steps in the nutritionally targeted seed endosperm. A combination of bioinformatics and cloning were first used to identify and map gene families encoding enzymes in maize and other grasses. These enzymes represented upstream pathways for isopentenyl diphosphate and geranylgeranyl diphosphate synthesis and the downstream carotenoid biosynthetic pathway, including conversion to abscisic acid. A maize germplasm collection was used for statistical testing of the correlation between carotenoid content and candidate gene transcript levels. Multiple pathway bottlenecks for isoprenoid biosynthesis and carotenoid biosynthesis were discovered in specific temporal windows of endosperm development. Transcript levels of paralogs encoding isoprenoid isopentenyl diphosphate and geranylgeranyl diphosphate-producing enzymes, DXS3, DXR, HDR, and GGPPS1, were found to positively correlate with endosperm carotenoid content. For carotenoid pathway enzymes, transcript levels for CrtISO inversely correlated with seed carotenoid content, as compared with positive correlation of PSY1 transcripts. Since zeaxanthin epoxidase (ZEP) depletes the carotenoid pool in subsequent conversion to abscisic acid, ZEP transcripts were examined. Carotenoid accumulation was found to be inversely associated with ZEP1 and ZEP2 transcript levels. Extension of the maize results using phylogenetic analysis identified orthologs in other grass species that may serve as potential metabolic engineering targets.
A novel intra-cavity for efficient cascaded Raman generation using WDM couplers (2001)

A novel intra-cavity with a broadband spectral response is designed and demonstrated to deliver a 4th order Stokes cascaded Raman generation. Large transmission bandwidth of 295 nm is realized using the two WDM couplers. The results applied to Raman fiber laser operating at 1706 nm wavelength using 1313 nm pump source are reported.
Abstract 1754: Identification of BAY 94-9343, a mesothelin antibody-drug conjugate (ADC): Characterization and anti-tumor activity in mesothelin-positive preclinical tumor models (2011)

Abstract Monoclonal antibodies have proven to be very effective in the treatment of various cancers, including solid tumors. For example, HERCEPTIN® and Erbitux® are successfully used to treat HER2-positive breast cancer and EGFR-positive colorectal cancer, respectively. Conjugation of cytotoxic drugs to antibodies represents a promising approach to improve cancer therapy. Antibody-drug conjugates (ADCs) are able to deliver highly potent toxophores to tumors while at the same time reducing systemic toxicity. Promising efficacy and tolerability profiles of ADCs have been observed in clinical trials including Hodgkin lymphoma (brentuximab vedotin) and breast cancer (trastuzumab-DM1), thus, development of new ADCs targeting tumor- associated antigens has potential to identifiy novel cancer therapeutics. Mesothelin, a glycoprotein expressed in mesothelial cells found in the membrane lining of the peritoneal and pleural cavities, is overexpressed in all mesotheliomas as well as many ovarian and pancreatic cancers. Due to its limited expression on normal tissues and higher expression in a number of tumor types, mesothelin represents an attractive ADC target. BAY 94-9343 consists of a fully human anti-mesothelin IgG1 antibody conjugated to the potent tubulin-binding drug DM4 with an average of 3.2 drug molecules per antibody. The resulting ADC bound to human recombinant mesothelin with high affinity (Kd = 15nM) leading to antigen-dependent internalization and potent cytotoxicity (nanomolar range in vitro IC50) in tumor cells that express mesothelin either endogenously or exogenously, but not in mesothelin-negative cells. In vivo, BAY 94-9343 demonstrated dose-dependent, mesothelin-specific anti-tumor efficacy in subcutaneous and orthotopic xenograft models at doses between 2.5 and 10 mg/kg using a Q3Dx3 schedule. Endogenously expressing mesothelin tumor models included sc and orthotopic OVCAR3 (ovarian), sc BxPC-3 (pancreatic) and sc NCI-H226 (mesothelioma). Furthermore, in mesothelin-positive patient-derived preclinical tumor models of both platinum-resistant ovarian cancer and gemcitabine-resistant pancreatic cancer, BAY 94-9343 exhibited high anti-tumor efficacy leading to partial and complete tumor regressions with a 10mg/kg Q3Dx3 dosing schedule. This ADC was well tolerated in mice at 10mg/kg (Q3Dx3) without any evidence of body weight loss, compared to either cisplatin or gemcitabine treatments. In summary, BAY 94-9343 is a mesothelin-targeted ADC with promising preclinical anti-tumor activity for mesothelin-positive tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1754. doi:10.1158/1538-7445.AM2011-1754
Site-Specific Incorporation of the Mucin-Type <i>N</i>-Acetylgalactosamine-α-<i>O</i>-threonine into Protein in <i>Escherichia </i><i>c</i><i>oli</i> (2004)

Glycosylation is a prevalent posttranslational process capable of augmenting and modulating protein function. Efficient synthesis of high-purity, homogeneous glycoproteins is essential for the study of unique protein glycoforms and for the manufacture of therapeutically relevant forms. A promising new strategy for controlled in vivo synthesis of glycoproteins was recently established using suppressor tRNA technology. Using an evolved tRNA aminoacyl synthetase-tRNA pair from Methanococcus jannaschii, the glycosyl amino acid, N-acetylglucosamine-beta-O-serine (GlcNAc-beta-Ser), was site-specifically introduced into proteins cotranslationally in Escherichia coli. Herein, we report the evolution of a new tRNA aminoacyl synthetase-tRNA pair that has expanded the repertoire of glycoproteins that can be expressed in E. coli to contain the other major O-linked glycan, N-acetylgalactosamine-alpha-O-threonine (GalNAc-a-Thr).
Continuous Glucose Monitoring and Insulin Informed Advisory System with Automated Titration and Dosing of Insulin Reduces Glucose Variability in Type 1 Diabetes Mellitus (2018)

A CGM/insulin informed advisory system proved to be safe and feasible in a cohort of 24 T1DM subjects. Use of the system may result in reduced GV and improved protection against hypoglycemia.