gebhart/patrepeval huggingface dataset:
Optimisation of Smart Well Completion Design in the Presence of Uncertainty (2013)

Abstract Intelligent/smart completions are widely used to maximize the value of production wells through higher ultimate hydrocarbon recoveries, to promote better clean-up of unconventional wells during ‘flow-back’ and to improve sweep efficiency in case of injector wells. To maximize the economic value of these applications, especially in the presence of uncertainties (geological, reservoir and long term tool reliability) and minimize the economic risk it's vital to optimise the placement and operational settings of the Interval Control Devices (ICDs)/AICDs (Autonomous Inflow Control Devices)/Interval Control Valves (ICVs). The requirement for optimisation could also arise from the limitation imposed by present technology on the maximum number of valves deployable in a single completion string. In this paper an optimisation routine for determining the optimal placement of Interval Control Valves (ICVs), and their inflow settings is presented. The overall optimisation scheme uses the simulated annealing algorithm in conjunction with a commercial reservoir simulator to maximize an objective function that captures the mean and variance in the well's estimated value. Multiple geostatistical realizations are used to incorporate the element of geological/reservoir uncertainty in the optimisation process. The workflow also accounts for the risk of flow control valve failure. A brief description of the screening methodology (to choose the appropriate inflow control technology) and a decision analysis framework for deploying intelligent completion technology, based on utility theory, is also presented herein. The optimisation technique was applied to cooptimise the positions and flow cross-section areas of the ICVs in a horizontal well, completed in an oil reservoir using a composite objective function. Geologic/reservoir and valve-life uncertainties were incorporated in the routine. The improvement in the well's Net Present Value (which is between 55–70% for the cases investigated) obtained through the employment of this technique, is also illustrated. An instance of the decision analysis is carried out to exhibit the suitability of intelligent completions deployment in the given well.
Cell segmentation and classification via unsupervised shape ranking (2013)

As histology patterns vary depending on different tissue types, it is typically necessary to adapt and optimize segmentation algorithms to these tissue type-specific applications. Here we present an unsupervised method that utilizes cell shape cues to achieve this task-specific optimization by introducing a shape ranking function. The proposed algorithm is part of our Layers™ toolkit for image and data analysis for multiplexed immunohistopathology images. To the best of our knowledge, this is the first time that this type of methodology is proposed for segmentation and ranking in cell tissue samples. Our new cell ranking scheme takes into account both shape and scale information and provides information about the quality of the segmentation. First, we introduce cell-shape descriptor that can effectively discriminate the cell-type's morphology. Secondly, we formulate a hierarchical-segmentation as a dynamic optimization problem, where cells are subdivided if they improve a segmentation quality criteria. Third, we propose a numerically efficient algorithm to solve this dynamic optimization problem. Our approach is generic, since we don't assume any particular cell morphology and can be applied to different segmentation problems. We show results in segmenting and ranking thousands of cells from multiplexing images and we compare our method with well established segmentation techniques, obtaining very encouraging results.
Machine learning applications in cancer prognosis and prediction (2014)

Cancer has been characterized as a heterogeneous disease consisting of many different subtypes. The early diagnosis and prognosis of a cancer type have become a necessity in cancer research, as it can facilitate the subsequent clinical management of patients. The importance of classifying cancer patients into high or low risk groups has led many research teams, from the biomedical and the bioinformatics field, to study the application of machine learning (ML) methods. Therefore, these techniques have been utilized as an aim to model the progression and treatment of cancerous conditions. In addition, the ability of ML tools to detect key features from complex datasets reveals their importance. A variety of these techniques, including Artificial Neural Networks (ANNs), Bayesian Networks (BNs), Support Vector Machines (SVMs) and Decision Trees (DTs) have been widely applied in cancer research for the development of predictive models, resulting in effective and accurate decision making. Even though it is evident that the use of ML methods can improve our understanding of cancer progression, an appropriate level of validation is needed in order for these methods to be considered in the everyday clinical practice. In this work, we present a review of recent ML approaches employed in the modeling of cancer progression. The predictive models discussed here are based on various supervised ML techniques as well as on different input features and data samples. Given the growing trend on the application of ML methods in cancer research, we present here the most recent publications that employ these techniques as an aim to model cancer risk or patient outcomes.
A CMOS camera as a tool for process analysis not only for laser beam welding (2001)

A new system for process monitoring of laser beam welding based on a CMOS-camera was presented in former presentations [1,2,3]. The system observes the welding process online and coaxial to the laser beam. Until now we got some new experiences with this system in industrial applications. On the basis of these experiences we found, that this system can be a useful tool for the inspection of the interaction zone during materials processing using a laser beam. The recorded films can be analyzed by the software of our system. The resulting curves are presented directly during the process. The data streams can be stored as an ASCII file and read in by another software. The possibilities of our methods are illustrated by one example for a welding process with a ND-YAG laser beam. The resulting images are interpreted as the absorption front. From the recorded images it is possible to conclude on the gradient of the front.
An optimal wavelet function based on wavelet denoising for multifunction myoelectric control (2009)

The aim of this study was to investigate and select the wavelet function that is optimum to denoise the surface electromyography (sEMG) signal for multifunction myoelectric control. Wavelet denoising algorithm has been used to find the optimal wavelet function for removing white Gaussian noise (WGN) at various signal-to-noise ratios (SNRs) from sEMG signals. A total of 53 wavelet functions were used in evaluation of the denoised performance. The wavelets are Daubechies, Symlets, Coiflet, BiorSplines, ReverseBior, and Discrete Meyer. Universal thresholding method has been used to estimate threshold value. Soft, hard, hyperbolic, and garrote thresholding are applied. Evaluations of the performance of these algorithms are mean squared error (MSE). The results show that the best wavelet functions for denoising are the first order of Daubechies, BioSplines, and ReverseBior wavelets (db1, bior1.1, rbio1.1). Various families can be used except the third order of decomposition of BiorSplines (bior3.1, bior3.3, bior3.5, bior3.7, bior3.9) and Discrete Meyer (dmey) are not recommended to use in wavelet denoising of sEMG signal. In addition, performance of soft thresholding is better than the others modified thresholding.
Monoclonal Antibody to Rat α-CGRP: Production, Characterization, and In Vivo Immunoneutralization Activity (1993)

Spleen cells from a Robertsonian mouse immunized with rat alpha-CGRP were fused with FOX-NY cells to induce hybridoma cells. Antibody activities were screened by radioimmunoassay, and hybridomas producing high affinity antibodies were cloned by limiting dilutions. Ascites were produced from the highest affinity clone in pristine-primed Balb/c mice. Ascites fluid contained approximately 20 mg/ml IgG which was of subclass IgG2a as determined by immunodiffusion analysis. The titer of this IgG2a antibody titled #4901, was 1:2,000,000 and the ID50 for rat alpha-CGRP, rat beta-CGRP and human alpha-CGRP were 350, 4000, and 4500 pg/ml respectively. Protein A purified CGRP antibody #4901 (5-10 mg/kg) completely abolished the portal release of somatostatin and the inhibition of gastric acid secretion induced by intravenous infusion of rat alpha CGRP (15-20 micrograms/kg/h) in anesthetized rats. The unpurified antibody (25 mg/kg) also prevented the fall in mean arterial blood pressure and the increase in heart rate caused by intravenous injection of rat alpha-CGRP. Immunohistochemistry showed that CGRP monoclonal antibody stains nerve fibers and endocrine-like cells in the pancreas, and neuronal elements in the gastrointestinal tract. These results show that CGRP monoclonal antibody #4901, which is relatively specific for rat alpha-CGRP, is useful for in vivo immunoneutralization of CGRP and is also an excellent reagent for immunohistochemical localization of alpha- and beta-CGRP in mammals.
3′-Deoxy-3′-[18F]Fluorothymidine Positron Emission Tomography Is a Sensitive Method for Imaging the Response of BRAF-Dependent Tumors to MEK Inhibition (2007)

Activating mutations of BRAF occur in approximately 7% of all human tumors and in the majority of melanomas. These tumors are very sensitive to pharmacologic inhibition of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase (MEK), which causes loss of D-cyclin expression, hypophosphorylation of Rb, and G(1) arrest. Growth arrest is followed by differentiation or senescence and, in a subset of BRAF mutant tumors, by apoptosis. The former effects result in so-called "stable disease" and, in patients with cancer, can be difficult to distinguish from indolent tumor growth. The profound G(1) arrest induced by MEK inhibition in BRAF mutant tumors is associated with a marked decline in thymidine uptake and is therefore potentially detectable in vivo by noninvasive 3'-deoxy-3'-[(18)F]fluorothymidine ([(18)F]FLT) positron emission tomography (PET) imaging. In SKMEL-28 tumor xenografts, MEK inhibition completely inhibited tumor growth and induced differentiation with only modest tumor regression. MEK inhibition also resulted in a rapid decline in the [(18)F]FLT signal in V600E BRAF mutant SKMEL-28 xenografts but not in BRAF wild-type BT-474 xenografts. The data suggest that [(18)F]FLT PET can effectively image induction of G(1) arrest by MEK inhibitors in mutant BRAF tumors and may be a useful noninvasive method for assessing the early biological response to this class of drugs.
Combined Effects of Metal and Ligand Capable of Accepting a Proton or Hydrogen Bond Catalyze Anti-Markovnikov Hydration of Terminal Alkynes (2001)

Eine Bindungstasche für ein Wassermolekül wird von den Imidazolylphosphan-Liganden und dem RuII-Zentrum in 1 gebildet. Dieser Komplex erweist sich als ausgezeichneter Katalysator für eine hochselektive Anti-Markownikow-Hydratisierung terminaler Alkine, durch die unter nahezu neutralen Reaktionsbedingungen Aldehyde in großem Überschuss gegenüber den isomeren Ketonen gebildet werden (Verhältnis Aldehyd/Keton bis zu 1000:1). Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Parainfluenza Virus Type 3 Expressing the Native or Soluble Fusion (F) Protein of Respiratory Syncytial Virus (RSV) Confers Protection from RSV Infection in African Green Monkeys (2004)

Respiratory syncytial virus (RSV) causes respiratory disease in young children, the elderly, and immunocompromised individuals, often resulting in hospitalization and/or death. After more than 40 years of research, a Food and Drug Administration-approved vaccine for RSV is still not available. In this study, a chimeric bovine/human (b/h) parainfluenza virus type 3 (PIV3) expressing the human PIV3 (hPIV3) fusion (F) and hemagglutinin-neuraminidase (HN) proteins from an otherwise bovine PIV3 (bPIV3) genome was employed as a vector for RSV antigen expression with the aim of generating novel RSV vaccines. b/h PIV3 vaccine candidates expressing native or soluble RSV F proteins were evaluated for efficacy and immunogenicity in a nonhuman primate model. b/h PIV3 is suited for development of pediatric vaccines since bPIV3 had already been evaluated in clinical studies in 1- and 2-month-old infants and was found to be safe, immunogenic, and nontransmissible in a day care setting (Karron et al., Pediatr. Infect. Dis. J. 15:650-654, 1996; Lee et al., J. Infect. Dis. 184:909-913, 2001). African green monkeys immunized with b/h PIV3 expressing either the native or soluble RSV F protein were protected from challenge with wild-type RSV and produced RSV neutralizing and RSV F-protein specific immunoglobulin G serum antibodies. The PIV3-vectored RSV vaccines evaluated here further underscore the utility of this vector system for developing safe and immunogenic pediatric respiratory virus vaccines.
Mib-Jag1-Notch signalling regulates patterning and structural roles of the notochord by controlling cell-fate decisions (2010)

In the developing embryo, cell-cell signalling is necessary for tissue patterning and structural organization. During midline development, the notochord plays roles in the patterning of its surrounding tissues while forming the axial structure; however, how these patterning and structural roles are coordinated remains elusive. Here, we identify a mechanism by which Notch signalling regulates the patterning activities and structural integrity of the notochord. We found that Mind bomb (Mib) ubiquitylates Jagged 1 (Jag1) and is essential in the signal-emitting cells for Jag1 to activate Notch signalling. In zebrafish, loss- and gain-of-function analyses showed that Mib-Jag1-Notch signalling favours the development of non-vacuolated cells at the expense of vacuolated cells in the notochord. This leads to changes in the peri-notochordal basement membrane formation and patterning surrounding the muscle pioneer cells. These data reveal a previously unrecognized mechanism regulating the patterning and structural roles of the notochord by Mib-Jag1-Notch signalling-mediated cell-fate determination.
In vitro evaluation of ap53-expressing adenovirus as an anti-cancer drug (1996)

Deficiency in p53-mediated cell death is common in human cancer, contributing to both tumorigenesis and chemoresistance. In an attempt to restore p53, we evaluated in vitro infectivity and cytotoxicity of a wild type (w.t.) p53-expressing adenovirus (Ad-p53) toward a panel of human cancer cell lines (n = 19). At a multiplicity of infection of 30, both Ad-p53 and adenovirus expressing beta-galactosidase (Ad-LacZ) infected greater than 99% of cells derived from brain, lung, breast, ovarian, colon, and prostate cancer, but failed to infect leukemia or lymphoma cells. Ad-p53, but not Ad-LacZ, infection of cancer cells was followed by nuclear accumulation of the CDK inhibitor p21WAFI/CIPI, cell cycle arrest and loss of viability. Ad-p53 induced apoptotic death in cancer cells that express mutant p53, including multi-drug resistant cells, but fewer deaths were observed in some w.t. p53 expressing cells. Ad-p53-infected SKBr3 breast cancer cells were more sensitive to cytotoxicity of the DNA damaging drugs mitomycin C or Adriamycin, but not the M-phase specific drug vincristine. Our results suggest that Ad-p53 is capable of infecting and killing cancer cells of diverse tissue origins (including multi-drug resistant cancer cells), that p21WAFI/CIPI may be a useful marker of p53 infectivity and that there may be synergy between Ad-p53 and either mitomycin C or Adriamycin induced cell death in tumors with p53 mutations.
Goal-directed stepping with momentum control (2010)

This paper proposes a technique for animating simulated characters to perform controlled steps. The desired step is controlled by high-level goals, namely step position and step duration. These stepping goals guide the desired time-varying values for the center of mass and the stepping foot which in turn lead to objectives dictating the desired changes in momentum and joint angles over the duration of the step. Our approach employs a multiobjective optimization to solve for joint accelerations from the objectives and uses inverse dynamics to compute joint torques. Our approach can guide a character with purposeful, directable steps for controlling careful navigation of the character's position and orientation. In addition, the same system can be used to create protective steps to prevent falling as a reaction to a disturbance. A novel supervisory routine automatically chooses when and where to step based on an analysis of the momentum conditions for the character. We contrast this approach to previous methods for step recovery using the inverted pendulum.
Surface functional group dependence on apatite formation on self‐assembled monolayers in a simulated body fluid (1997)

Self-assembled monolayers (SAMs) of alkanethiols having CH3, PO4H2, COOH, CONH2, OH, and NH2 terminal groups formed on a gold surface via sulfur attachment were soaked in a simulated body fluid (SBF), whose ion concentrations were nearly equal to those of human blood plasma, at 37°C for up to 40 days. The effect of their terminal functional groups on apatite formation was assessed using X-ray photo-electron spectroscopic (XPS) measurement and a quartz crystal microbalance (QCM) technique. The Ca and P atoms were detected, of which element intensities increased with time, on SAMs except for the alkanethiol having the methyl terminal group. The Ca/P atomic ratios of the apatites formed on the SAMs ranged from around 1.0 to around 1.3. The most potent inducer for apatite formation, judged from the growth rate (micrometers per day) calculated from the weight change during QCM measurement, was the SAM of the alkanethiol with the PO4H2 group, followed by that of the alkanethiol with the COOH group. The SAMs of the alkanethiols with the CONH2, OH, and NH2 groups possessed much weaker inducing powers than the former two SAMs. Little weight change was observed for the methyl-group-terminated alkanethiol SAM. The growth rates increased with time, irrespective of the terminal group species among apatite formation-inducing groups. During the experimental observation period, the following relationship held. The growth rate decreased in the order PO4H2 > COOH ≫ CONH2 ≃ OH > NH2 ≫ CH3 ≃ 0. Since negatively charged groups strongly induced apatite formation but the positively charged group did not, it can be said that the apatite formation initiated via calcium ion-adsorption upon complexation with a negative surface-charged group may be dominant in biomaterial calcification where ionic species directly contact the biomaterial surface in body fluids. © 1997 John Wiley & Sons, Inc.
A Modeling and Experimental Investigation of the Effects of Antigen Density, Binding Affinity, and Antigen Expression Ratio on Bispecific Antibody Binding to Cell Surface Targets (2016)

Despite the increasing number of multivalent antibodies, bispecific antibodies, fusion proteins, and targeted nanoparticles that have been generated and studied, the mechanism of multivalent binding to cell surface targets is not well understood. Here, we describe a conceptual and mathematical model of multivalent antibody binding to cell surface antigens. Our model predicts that properties beyond 1:1 antibody:antigen affinity to target antigens have a strong influence on multivalent binding. Predicted crucial properties include the structure and flexibility of the antibody construct, the target antigen(s) and binding epitope(s), and the density of antigens on the cell surface. For bispecific antibodies, the ratio of the expression levels of the two target antigens is predicted to be critical to target binding, particularly for the lower expressed of the antigens. Using bispecific antibodies of different valencies to cell surface antigens including MET and EGF receptor, we have experimentally validated our modeling approach and its predictions and observed several nonintuitive effects of avidity related to antigen density, target ratio, and antibody affinity. In some biological circumstances, the effect we have predicted and measured varied from the monovalent binding interaction by several orders of magnitude. Moreover, our mathematical framework affords us a mechanistic interpretation of our observations and suggests strategies to achieve the desired antibody-antigen binding goals. These mechanistic insights have implications in antibody engineering and structure/activity relationship determination in a variety of biological contexts.
Router plugins: a software architecture for next generation routers (1998)

Present day routers typically employ monolithic operating systems which are not easily upgradable and extensible. With the rapid rate of protocol development it is becoming increasingly important to dynamically upgrade router software in an incremental fashion. We have designed and implemented a high performance, modular, extended integrated services router software architecture in the NetBSD operating system kernel. This architecture allows code modules, called plugins, to be dynamically added and configured at run time. One of the novel features of our design is the ability to bind different plugins to individual flows; this allows for distinct plugin implementations to seamlessly coexist in the same runtime environment. High performance is achieved through a carefully designed modular architecture; an innovative packet classification algorithm that is both powerful and highly efficient; and by caching that exploits the flow-like characteristics of Internet traffic. Compared to a monolithic best-effort kernel, our implementation requires an average increase in packet processing overhead of only 8%, or 500 cycles/2.1ms per packet when running on a P6/233.
Interconversion Between Intestinal Stem Cell Populations in Distinct Niches (2011)

Intestinal epithelial stem cell identity and location have been the subject of substantial research. Cells in the +4 niche are slow-cycling and label-retaining, whereas a different stem cell niche located at the crypt base is occupied by crypt base columnar (CBC) cells. CBCs are distinct from +4 cells, and the relationship between them is unknown, though both give rise to all intestinal epithelial lineages. We demonstrate that Hopx, an atypical homeobox protein, is a specific marker of +4 cells. Hopx-expressing cells give rise to CBCs and all mature intestinal epithelial lineages. Conversely, CBCs can give rise to +4 Hopx-positive cells. These findings demonstrate a bidirectional lineage relationship between active and quiescent stem cells in their niches.
Fibrinogen Activates PAK1/Cofilin Signaling Pathway to Protect Endothelial Barrier Integrity (2020)

We have identified a novel pathway by which fibrinogen activates PAK1 signaling to stimulate/dephosphorylate cofilin, leading to disassembly of stress fibers and reduction of endothelial permeability.