gebhart/patrepeval huggingface dataset:
MG-115 Colorectal cancer patients with BRCA1 and BRCA2 mutations: Preparing for unexpected results (2015)

<h3>Background</h3> A new paradigm in genetic panel testing for hereditary colorectal cancer (CRC) has emerged. CRC association with BRCA1/2 has been suggested, but guidelines do not include CRC in Hereditary Breast and Ovarian Cancer syndrome (HBOC). <h3>Objectives</h3> We describe 6 patients with CRC and germline mutations in BRCA1 or BRCA2, detected by multi-gene panels, to highlight actionable findings that would have been missed by traditional CRC genetic testing. <h3>Design/method</h3> 585 patients with a personal history of CRC and/or gastrointestinal (GI) polyps were tested. Variants were identified using an NGS-based cancer gene panel with CRC genes and BRCA1/2. Germline variants were classified using a point-based system based on ACMG guidelines. Clinical histories from test request forms were de-identified for analysis. <h3>Results</h3> Hereditary cancer panel testing found Pathogenic (P) or Likely Pathogenic (LP) variants in 92 of 585 (15%) patients. Of the 92 mutation carriers, 69 (75%) had a P/LP variant in a CRC gene, while 6 (6%) had a P/LP variant in BRCA1/2. None of the patients with BRCA1/2 mutations reported Ashkenazi Jewish ancestry. The 4 male patients did not meet HBOC testing guidelines. <h3>Conclusions</h3> In this series, a substantial minority of P/LP variants were in non-canonical CRC genes. BRCA1/2 pathogenic variants’ prevalence in the general population is insufficiently elevated to account for these findings. More research is needed to link CRC and BRCA1/2, and clinicians need to prepare themselves and their patients to deal with unexpected, potentially actionable.
Reinforcement with cellulose nanocrystals of poly(vinyl alcohol) hydrogels prepared by cyclic freezing and thawing (2011)

Cellulose nanocrystals (CNCs) were incorporated into polyvinyl alcohol (PVA) hydrogels prepared by repeated freeze–thaw processing. The CNC-loaded hydrogels had improved structural stabilities and distinct microstructures, characterized by ordered domains of CNCs. The water sorption of the gels increased with CNC content due to the hydrophilic nature of the cellulose and the decrease in PVA crystallinity. A reinforcement effect was observed in the CNC-loaded samples upon the application of uniaxial, confined compression, with the elastic moduli of the PVA–CNC samples increased relative to pure PVA hydrogels. Hydraulic permeability values were derived from the stress transients: at strains of ∼15 to 20% and greater, the permeability of all samples approached a plateau value reflective of the hindered flow in soft gels which have been compressed, densified and dehydrated.
Brush/Gold Nanoparticle Hybrids: Effect of Grafting Density on the Particle Uptake and Distribution within Weak Polyelectrolyte Brushes (2014)

The effect of the brush grafting density on the loading of 13 nm gold nanoparticles (AuNPs) into stimuli-responsive poly(N,N-(dimethylamino ethyl) methacrylate) (PDMAEMA) brushes anchored to flat impenetrable substrates is reported. Atom-transfer radical polymerization (ATRP) is used to grow polymer brushes via a "grafting from" approach from a 2-bromo-2-methyl-N-(3-(triethoxysilyl) propyl) propanamide (BTPAm)-covered silicon substrate. The grafting density is varied by using mixtures of initiator and a "dummy" molecule that is not able to initiate polymerization. A systematic study is carried out by varying the brush grafting density while keeping all of the other parameters constant. X-ray reflectivity is a suitable tool for investigating the spatial structure of the hybrid, and it is combined with scanning electron microscopy and UV/vis spectroscopy to study the particle loading and interpenetration of the particles within the polymer brush matrix. The particle uptake increases with decreasing grafting density and is highest for an intermediate grafting density because more space between the polymer chains is available. For very low grafting densities of PDMAEMA brushes, the particle uptake decreases because of a lack of the polymer matrix for the attachment of particles. The structure of the surface-grafted polymer chains changes after particle attachment. More water is incorporated into the brush matrix after particle immobilization, which leads to a swelling of the polymer chains in the hybrid material. Water can be removed from the brush by decreasing the relative humidity, which leads to brush shrinking and forces the AuNPs to get closer to each other.
Cryo-CARE: Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data (2018)

Multiple approaches to use deep learning for image restoration have recently been proposed. Training such approaches requires well registered pairs of high and low quality images. While this is easily achievable for many imaging modalities, e.g. fluorescence light microscopy, for others it is not. Cryo-transmission electron microscopy (cryo-TEM) could profoundly benefit from improved denoising methods, unfortunately it is one of the latter. Here we show how recent advances in network training for image restoration tasks, i.e. denoising, can be applied to cryo-TEM data. We describe our proposed method and show how it can be applied to single cryo-TEM projections and whole cryo-tomographic image volumes. Our proposed restoration method dramatically increases contrast in cryo-TEM images, which improves the interpretability of the acquired data. Furthermore we show that automated downstream processing on restored image data, demonstrated on a dense segmentation task, leads to improved results.
Experimental analysis and predictive modelling of Ti6Al4V laser surface texturing for biomedical applications (2022)

Laser surface texturing (LST) is a powerful technique for creating high quality micro-textured patterns with different shapes and sizes on metallic biomaterials. Textured surfaces may improve the interaction between bone and implant by increasing the surface contact area and thus promoting bone regeneration. The goal of this study was to explore Nd:YAG laser potential for texturing micro-scale pillars with pyramid geometry, with dimensions in a selected range, in a reproducible way. First, the design and texture of grooves were addressed, then proceeding to pillars. Two laser machining and marking strategies were investigated, and the consecutive laser processing strategy and continuous marking mode were selected due to the resultant smoother grooves. Then, a cross-hatched pattern was designed to texture a pillar pattern with targeted dimensions. Given the direct effect of the LST drawing and laser parameters on the texture dimensions, three mathematical models, one for each texture dimension (groove width, pillar width and pillar depth) were developed. These models are accurate tools for predicting the texture dimensions in the selected range and this LST approach was effective on creating well-defined, uniform and equally spaced surface textures on Ti6Al4V parts, in a reproducible way. A combination of drawing and laser parameters was selected for the target dimensions, also considering suitable wettability and roughness for biomedical applications.
Abstract 1339: Inhibition of chitinase-3-like-1 protein to suppress angiogenesis and enhance immune response in a mammary tumor model (2010)

Abstract The purpose of this study is to determine whether inhibition of Chitinase-3-like 1 protein reduces the expression of angiogenic chemokines in macrophages while enhancing IFN-γ production in T cells. It is known that tumors can induce the upregulation of angiogenic and extracellular matrix degrading molecules. Tumor growth is often accompanied by immunosuppression. Our previous studies using the DA-3 mammary adenocarcinoma mouse model has shown that with tumor progression there is a profound down-regulation of interferon-gamma (IFN-γ), a crucial molecule involved in anti-tumor response. Additionally, angiogenic chemokines such as Monocyte Chemoattractant Protein-1 (CCL2/MCP-1) and Matrix Metalloproteinase-9 (MMP-9) are upregulated with mammary tumor growth. CCL2/MCP-1 is a known inflammatory chemoattractant for T cells and macrophages, and we have evidence that this molecule downregulates IFN-γ by the T lymphocytes. Recent studies have linked tumor progression with upregulation of Chitinase-3-like-1 protein (CHI3L1) in human breast cancer patients and that macrophages express this molecule during inflammatory processes. Our studies using DA-3 mammary breast cancer model indicate that CHI3L1 is expressed by DA-3 tumor cells. Expression of CHI3L1 in macrophages has been linked with upregulation of angiogenic chemokine, CCL2/MCP-1. Our studies indicate that macrophages from mammary tumor-bearing mice express higher levels of CHI3L1 compared to normal control mice and also secrete CCL2/MCP-1. We hypothesize that inhibition of CHI3L1 will suppress the production of CCL2/MCP-1 and enhance IFN-γ production in mammary tumor-bearing mice. One of the known ligands for CHI3L1 is chitin microparticle. Our in vitro studies of cultured splenocytes from normal and 5-week mammary tumor-bearing mice with chitin micro-particles revealed down-regulation of CHI3L1 and upregulation of IFN-γ. Therefore, it is expected that in vivo blocking of CHI3L1 with chitin microparticles will have a favorable anti-tumor response by inhibiting the production of angiogenic chemokines, metalloproteinase, MMP-9 and enhancing the production of IFN-γ. The results from these studies may provide new avenues for cancer treatment. 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 1339.
Based on Diode with 30GHz Bandwidth Terahertz Amplitude Modulator (2020)

Schottky diodes have switching characteristics, and combined with microstructure can achieve a terahertz modulator with a 30GHz bandwidth which has insertion loss of-5dB and switching ratio of 15dB.
Monitoring MLP's free parameters for generalization (2009)

Generalization is one of major concerns for neural network training. In common practice, the number of weights in a MLP network is assumed to be the number of free parameters. This assumption leads to a conclusion: large MLP networks will generalize poorly if their sizes exceed the necessary capacity. However, individual weight in MLP network may not stay as a free parameter since operational condition for hidden neurons alters during the course of training. There have been studies showing that larger networks appear to generalize as well as smaller networks, sometimes even better. Therefore this paper constructs a new perspective on MLP's free parameters to address the issue of generalization.
Cumulative Live-Birth Rates per Total Number of Embryos Needed to Reach Newborn in Consecutive In Vitro Fertilization Cycles: A New Approach to Measuring the Likelihood of In Vitro Fertilization Success (2011)

The most accurate method for advising couples unable to conceive, who seek assisted reproductive techniques on the likelihood of a live birth with in vitro fertilization (IVF), calculates cumulative live-birth rates (CLBRs) per ovarian stimulation cycle. The authors believe that a better method to help predict the likelihood of IVF success (a live birth) in a given couple would be calculation of CLBR according to the total number of embryos required to achieve a live birth (EmbR). This method would consider each embryo as a single opportunity to obtain a live birth. This is the first study to use this approach. This retrospective study was designed to report IVF success calculating CLBRs according to the EmbR. Data obtained since 1998 were used to calculate CLBRs, considering age, infertility etiology, and day of embryo transfer as key parameters affecting the likelihood of IVF success. The study was conducted at a university-affiliated infertility center in infertile couples undergoing IVF using the mother's own oocytes. Kaplan-Meier methods were used to analyze CLBR for each couple. The primary study outcome measure was CLBR per embryo transferred. A live birth was achieved more frequently with fewer EmbR: transfer of between 1 and 5 embryos resulted in a rapid increase in CLBR, whereas transfer of 5 to 15 produced moderate increases, and additional EmbR resulted in slow increases. Live-birth rates increased more slowly when embryos were transferred on days 2 to 3 compared with days 5 to 6, with little difference in long-term results. Live-birth rates decreased with maternal age: CLBR was lower in women aged 35 to 37 years than younger women, with a marked decrease above the age of 40. Patients with idiopathic infertility and endometriosis produced the worst results. The investigators conclude from these findings that the relationship between CLBR and number of EmbR can provide couples and physicians with realistic and accurate information concerning the likelihood of achieving a live birth with IVF.
Preparation of silica-reinforced styrene–butadiene rubber via co-coagulation process (2012)

Styrene–butadiene rubber (SBR) was reinforced with silica (SiO 2 ) by co-coagulating process. This study investigated the SiO 2 amount, stirring time and pH value affecting the SiO 2 content, curing characteristics and mechanical properties of SBR. Results showed that SiO 2 content and reinforcing behavior were greatly influenced by the amount of SiO 2 and pH value. The torque, tensile strength and elongation at break were optimal when the mass fraction of SiO 2 was 21.5 wt%, stirring time was 6 h and pH value was 6.57. The utilized efficiency of SiO 2 decreased with the increasing amount of SiO 2 but increased with the increasing stirring time. The optimum cure time decreased with the increasing amount of SiO 2 . Both tensile strength and elongation at break decreased with the increasing pH value. Scanning electron microscopy observations showed that the SiO 2 nanoparticles were distributed evenly in the SBR.
Performance of Optical Networks With Limited Reconfigurability (2009)

We investigate the blocking performance of all-optical reconfigurable networks with constraints on reconfiguration brought by reconfigurable optical add/drop multiplexers (ROADMs) and tunable transponders. Considering a fully reconfigurable ROADM and limited tunable transponders at each ROADM port, we develop an analytical model to calculate call blocking probability in a network of arbitrary topology for two different models for transponder sharing within a node: share-per-link (SPL) and share-per-node (SPN). In such a configuration, limited tunable transponders determine the set of wavelengths that can be added/dropped at a reconfigurable node. A lightpath can only be established if a transponder on both ends can tune to the same available wavelength along the route. We call this wavelength termination constraint. The number of transponders (as many as ports) and the waveband size (the range of wavelengths over which a transponder is tunable) are the key parameters of the model, assuming that wavebands are randomly assigned to transponders. We also present a heuristic algorithm for assigning wavebands to transponders at each node and modify the analytical model to approximate the performance of the algorithm. We present simulation results to validate our model and also show results for share-per-link and share-per-node models with various sets of parameters. We show that limited tunable transponders give the same performance with widely tunable transponders in terms of blocking. We also show that transponder waveband assignment to limited tunable transponders is an important factor determining the blocking.
A Disintegrin and Metalloproteinase with Thrombospondin Motifs-5 (ADAMTS-5) Forms Catalytically Active Oligomers (2015)

The metalloproteinase ADAMTS-5 (A disintegrin and metalloproteinase with thrombospondin motifs) degrades aggrecan, a proteoglycan essential for cartilage structure and function. ADAMTS-5 is the major aggrecanase in mouse cartilage, and is also likely to be the major aggrecanase in humans. ADAMTS-5 is a multidomain enzyme, but the function of the C-terminal ancillary domains is poorly understood. We show that mutant ADAMTS-5 lacking the catalytic domain, but with a full suite of ancillary domains inhibits wild type ADAMTS activity, in vitro and in vivo, in a dominant-negative manner. The data suggest that mutant ADAMTS-5 binds to wild type ADAMTS-5; thus we tested the hypothesis that ADAMTS-5 associates to form oligomers. Co-elution, competition, and in situ PLA experiments using full-length and truncated recombinant ADAMTS-5 confirmed that ADAMTS-5 molecules interact, and showed that the catalytic and disintegrin-like domains support these intermolecular interactions. Cross-linking experiments revealed that recombinant ADAMTS-5 formed large, reduction-sensitive oligomers with a nominal molecular mass of ∼ 400 kDa. The oligomers were unimolecular and proteolytically active. ADAMTS-5 truncates comprising the disintegrin and/or catalytic domains were able to competitively block full-length ADAMTS-5-mediated aggrecan cleavage, measured by production of the G1-EGE(373) neoepitope. These results show that ADAMTS-5 oligomerization is required for full aggrecanase activity, and they provide evidence that blocking oligomerization inhibits ADAMTS-5 activity. The data identify the surface provided by the catalytic and disintegrin-like domains of ADAMTS-5 as a legitimate target for the design of aggrecanase inhibitors.
Networked agents for scientific computing (1999)

Ideally, a designer would change some aspect of the engine and then run a simulation to see how the change affects the performance, cost, durability, and so forth. Such a simple approach will be infeasible for the foreseeable future because the complete simulation of an engine design requires days, weeks or even years on petaflops class computing systems. Thus the design process and simulation software must be configurable so that a simulation can focus on particular aspects of the engine. For example, in designing a new turbine blade (they do not all have the same shape) one might (a) model the blade itself very accurately, (b) model the air flow field and structure near the blade with moderate accuracy, (c) roughly model the air flow fields and structures further away from the blade, and (d) model the remainder of the engine by fixed boundary conditions surrounding the focal area of this particular simulation. Step (d), of course, removes over 99% of the parts and phenomena from this particular simulation, making it feasible to explore many design parameter effects quickly. As a new engine design evolves and matures, the focus of such simulations is enlarged, first bringing several new parts together, then dozens or hundreds of parts, then complete subassemblies, 48
A bi-directional Interface enabling cross-disciplinary Engineering with RAMI 4.0 and AutomationML (2022)

The Reference Architecture Model Industrie 4.0 (RAMI 4.0) has been proposed to faciliate the discussion and contribute to the standardization of future industrial systems, especially in the area of basic engineering. In order to provide the resulting system model to the heterogeneous detailed engineering disciplines, AutomationML appears to be one of the technology drivers, giving the possibility to exchange respective engineering artifacts. Concluding, the utilization of this standard after applying the theoretical engineering concepts of RAMI 4.0 would strongly enhance the interoperability between industrial systems aligned to the reference architecture on the one hand and provide a practical implementation of its theoretical concepts on the other hand. Therefore, this work-in-progress Paper introduces the first implementation of a bi-directional interface, which interconnects basic engineering with detailed engineering of such systems. As model-based systems engineering (MBSE) with either RAMI 4.0 or AutomationML is currently under broad investigation, already established approaches are used to verify the application of the developed interface. An initial real-world example is taken for use to validate the research goals or challenges of the resulting engineering tool-chain, which can strongly contribute to engineering practitioners of flexible production systems by maxing out the heterogeneous tool-landscape.
Cobalt(III) Diazabutadiene Precursors for Metal Deposition: Nanoparticle and Thin Film Growth (2013)

We report the synthesis and characterization of a family of cobalt(III) metal precursors, based around cyclopentadienyl and diazabutadiene ligands. The molecular structure of the complexes cyclopentadienyl-Cobalt(III)(N,N'-dicyclohexyl-diazabutadiene) (2c) and cyclopentadienyl-Cobalt(III)(N,N'-dimesityl-diazabutadiene) (2d) are described, as determined by single crystal X-ray diffraction analysis. Thermogravimetric analysis of the complexes highlighted the isopropyl derivative CpCo((i)Pr2-dab) (2a) as a possible cobalt metal chemical vapor deposition (CVD) precursor. Atmospheric pressure CVD (AP-CVD) was employed using precursor 2a to synthesize thin films of metallic cobalt on silicon substrates under an atmosphere of hydrogen (H2). Analysis of the thin films deposited at substrate temperatures of 250 °C, 275 °C, 300 °C, 325 °C, and 350 °C, respectively, by scanning electron microscopy (SEM) and atomic force microscopy (AFM) reveal temperature dependent growth features: films grown at 325 and 350 °C are continuous and pinhole free, whereas those films grown at substrate temperatures of 250 °C, 275 °C, and 300 °C consist of crystalline nanoparticles. Powder X-ray diffraction (PXRD) and X-ray photoelectron spectroscopy (XPS) all show the films to be high purity metallic cobalt. Raman spectroscopy has also been used to prove the absence of cobalt silicides at the substrate/thin film interface.
Frequency-based nonlinear controller design for regulating systems subjected to time-domain constraints (2000)

Presented is a nonlinear controller design methodology for a class of linear regulating systems subjected to quantitative time-domain constraints. The design objective is to satisfy an output time-domain tolerance given an actuator saturation constraint despite an external step disturbance. The goal is to increase the allowable magnitude of the external disturbance beyond that achievable via linear control subject to the time-domain specifications. The controller design process is comprised of two phases. In the first phase, a linear controller is designed that balances the trade-off between output regulation and required actuation. To realize the linear design, the time-domain performance specifications are mapped into amplitude and phase constraints which are in turn imposed on the frequency response of the linear open-loop transfer function. In the second phase, the linear controller is then augmented with an odd nonlinearity. The coefficient for the nonlinear term is designed such that the gain and phase distortions (in the sense of describing functions) meet the frequency-domain constraints. The describing function calculation is automated by a recursive Volterra Series relationship. The nonlinear controller design methodology is experimentally verified on the idle speed control of a Ford 4.6L V-8 fuel injected engine. Copyright © 2000 John Wiley & Sons, Ltd.
Remote Spectroscopy over Optical Fibers for In Situ Measurement of Contaminants in Soil (1996)

Fiber optic-based sensor probes have been developed that can be pushed up to 50 meters into the soil for remote, real-time detection of petroleum hydrocarbons using laser-induced fluorescence (LIF) and metals via laser-induced breakdown spectroscopy (LIBS).