gebhart/patrepeval huggingface dataset:
Molecular Recognition in Vitamin D-Binding Protein (1996)

Vitamin D-binding protein (DBP) or group-specific component (Gc) is a relatively abundant serum protein with multiple functions, the majority of which are initiated by the highly specific recognition and binding of a ligand by this protein. During the past decade and a half, several structure-functional studies have been carried out to shed light on the physiological significance of the multiple functions of DBP. Results of these studies are discussed.
Subsite mapping of Aspergillus niger glucoamylases I and II with malto‐ and isomaltooligosaccharides (1989)

Glucoamylase, industrially derived from Aspergillus niger, was chromatographically separated into forms I and II and purified to near homogeneity. Preparations were proved to be free of D-glucosyltransferase by electrophoretic and differential inhibition tests. Maximum rates and Michaelis constants were obtained for both glucoamylases I and II with maltooligosaccharides from maltose to maltoheptaose and with isomaltooligosaccharides from isomaltose to isomaltohexaose. Subsite maps were calculated from these kinetic data and were not significantly different for the two forms. Subsites in both forms had lower affinities for D-glucosyl residues contained in isomaltooligosaccharides than for D-glucosyl residues in maltooligosaccharides.
Status of the Intracellular Gate in the Activated-not-open State of Shaker K+ Channels (2005)

Voltage-dependent K+ channels like Shaker use an intracellular gate to control ion flow through the pore. When the membrane voltage becomes more positive, these channels traverse a series of closed conformations before the final opening transition. Does the intracellular gate undergo conformational changes before channel opening? To answer this question we introduced cysteines into the intracellular end of the pore and studied their chemical modification in conditions favoring each of three distinct states, the open state, the resting closed state, and the activated-not-open state (the closed state adjacent to the open state). We used two independent ways to isolate the channels in the activated-not-open state. First, we used mutations in S4 (ILT; Smith-Maxwell, C.J., J.L. Ledwell, and R.W. Aldrich. 1998. J. Gen. Physiol. 111:421-439; Ledwell, J.L., and R.W. Aldrich. 1999. J. Gen. Physiol. 113:389-414) that separate the final opening step from earlier charge-movement steps. Second, we used the open channel blocker 4-aminopyridine (4-AP), which has been proposed to promote closure of the intracellular gate and thus specifically to stabilize the activated-not-open state of the channels. Supporting this proposed mechanism, we found that 4-AP enters channels only after opening, remaining trapped in closed channels, and that in the open state it competes with tetraethylammonium for binding. Using these tools, we found that in the activated-not-open state, a cysteine located at a position considered to form part of the gate (Shaker 478) showed higher reactivity than in either the open or the resting closed states. Additionally, we have found that in this activated state the intracellular gate continued to prevent access to the pore by molecules as small as Cd2+ ions. Our results suggest that the intracellular opening to the pore undergoes some rearrangements in the transition from the resting closed state to the activated-not-open state, but throughout this process the intracellular gate remains an effective barrier to the movement of potassium ions through the pore.
Laser projection photogrammetry and video system for quantification and mensuration (2005)

This paper describes a novel photogrammetric laser/video system suited for a variety of underwater quantification and mensuration applications. The system is comprised of a purpose-built frame to which are mounted a roll/pitch motion reference sensor, video camera, and three microlasers. Orientation of the three lasers provides for optical triangulation, which allows computation of range at specific location in the field-of-view. From this information and that derived from the motion sensor, the spatially variant magnification can be determined over the entire field-of-view using a simple algorithm. A variety of parameters can then be estimated using image-processing techniques, including perspective overlays, range to a point or location, scale in any region of the image, and area measurements. Specialized image processing algorithms can be added to provide object recognition, tracking, and other information. The specification of each component (i.e., laser wavelength and power, camera sensitivity and resolution, and dynamic range) and mounting geometry are determine based on the specific application and needed accuracy. The system can be mounted for use on any subsea vehicle or platform and provides a low cost automated approach for obtaining quantitative information from standard undersea video. Currently, the application software allows for post-processing of the video information but could be modified to process the video information real-time. The first application of this system will be used by Washington State Department of Fish and Wildlife researchers onboard DSV DELTA. The system may prove valuable for estimating the abundance of commercially and recreationally exploited groundfish species within a transect area conducted off the coast of Washington State. This non-intrusive, direct observation technique affords a means to estimate the density of certain benthic fish species in high relief areas that currently cannot be sampled using routine trawl survey techniques. The system may prove useful in other scientific and industrial applications. Laboratory and field data are provided to demonstrate system output and performance, as well as an error analysis summary. Future hardware and software enhancements to provide a means of geocoding or georeferencing the images that would support orthorectification and mosaicking of the transect images are described.
Time-Resolved Fluorescence Spectroscopy of Molecularly Imprinted Nanoprobes as an Ultralow Detection Nanosensing Tool for Protein Contaminants (2023)

Currently, optical sensors based on molecularly imprinted polymers (MIPs) have been attracting significant interest. MIP sensing relies on the combination of the MIP's selective capability, which is conveyed to the polymeric material by a template-assisted synthesis, with optical techniques that offer exquisite sensitivity. In this work, we devised an MIP nanoparticle optical sensor for the ultralow detection of serum albumin through time-resolved fluorescence spectroscopy. The Fluo-nanoMIPs (&empty;~120 nm) were synthetized using fluorescein-O-methacrylate (0.1×, 1×, 10× mol:mol versus template) as an organic fluorescent reporter. The ability of 0.1× and 1×Fluo-nanoMIPs to bind albumin (15 fM-150 nM) was confirmed by fluorescence intensity analyses and isothermal titration calorimetry. The apparent dissociation constant (K<sub>app</sub>) was 30 pM. Conversely, the 10× fluorophore content did not enable monitoring binding. Then, the time-resolved fluorescence spectroscopy of the nanosensors was studied. The 1×Fluo-nanoMIPs showed a decrease in fluorescence lifetime upon binding to albumin (100 fM-150 nM), K<sub>app</sub> = 28 pM, linear dynamic range 3.0-83.5 pM, limit of detection (LOD) 1.26 pM. Selectivity was confirmed testing 1×Fluo-nanoMIPs against competitor proteins. Finally, as a proof of concept, the nanosensors demonstrated detection of the albumin (1.5 nM) spiked in wine samples, suggesting a possible scaling up of the method in monitoring allergens in wines.
Amphiphilic nonlinear optical bis-chromophores and their mixtures with amphotropic copolymers: preparation of monolayers and Langmuir-Blodgett multilayers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmphiphilic nonlinear optical bis-chromophores and their mixtures with amphotropic copolymers: preparation of monolayers and Langmuir-Blodgett multilayersDonald Lupo, Helmut Ringsdorf, Andreas Schuster, and Markus SeitzCite this: J. Am. Chem. Soc. 1994, 116, 23, 10498–10506Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ja00102a017https://doi.org/10.1021/ja00102a017research-articleACS PublicationsRequest reuse permissionsArticle Views216Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Single amino acid resolution of proteolytic fragments generated in individual cells (2010)

The complex nature of enzyme regulation mandates that enzyme activity profiles be measured in the context of the intact cell. Single-cell capillary electrophoresis (CE) coupled with laser-induced fluorescence is a powerful approach for quantitation and separation of analytes present in small samples and single live cells; however, it does not allow for the definitive identification of the reaction products. On the other hand, mass spectrometry (MS) is able to identify analytes but still lacks the requisite sensitivity for most single-cell analysis applications. Thus, it follows that by determining the relative amounts of reaction products generated in single cells using CE and by producing larger quantities of these products using bulk cell populations to identify them using MS, it is possible to determine enzyme activity profiles in single cells. In this study, the applicability of this approach was demonstrated by examining the intracellular fate of a protease substrate derived from the beta-amyloid precursor protein (beta-APP). In single live TF-1 cells, three distinct fragments were generated from the beta-APP peptide, which differed by a single uncharged amino acid. The CE measurements indicated that the proteolytic fragment profiles (i.e., the relative amounts of each fragment) were consistent from cell to cell but that they were different from those obtained in cell lysates. Furthermore, measurements obtained at the single cell level made it possible to observe a modest but statistically significant negative correlation between the total amount of beta-APP peptide loaded in cells and the fraction of peptide that remained intact. This study demonstrates how single-cell CE, MS, and peptide substrates can be combined to identify and measure enzyme activities in single live cells.
Bayesian Active Learning for Classification and Preference Learning (2011)

Information theoretic active learning has been widely studied for probabilistic models. For simple regression an optimal myopic policy is easily tractable. However, for other tasks and with more complex models, such as classification with nonparametric models, the optimal solution is harder to compute. Current approaches make approximations to achieve tractability. We propose an approach that expresses information gain in terms of predictive entropies, and apply this method to the Gaussian Process Classifier (GPC). Our approach makes minimal approximations to the full information theoretic objective. Our experimental performance compares favourably to many popular active learning algorithms, and has equal or lower computational complexity. We compare well to decision theoretic approaches also, which are privy to more information and require much more computational time. Secondly, by developing further a reformulation of binary preference learning to a classification problem, we extend our algorithm to Gaussian Process preference learning.
The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model (2012)

The mathematical model provides a new tool for studying the effects of various doses of acetaminophen on the liver metabolism of acetaminophen and glutathione. It can be used to study how the metabolism of acetaminophen depends on the expression level of liver enzymes. Finally, it can be used to predict patient metabolic and physiological responses to APAP doses and different NAC dosing strategies.
AQUIFER THERMAL ENERGY STORAGEuRECENT PARAMETER AND SITE-SPECIFIC STUDIES (1981)

The concept of Aquifer Thermal Enerqy storaqe (ATES) has been studied extensively for the past six years at the Lawrence Berkeley Laboratory (LBL).In particular, parameter and Site-specific studies have been emphasized.In our parameter studies, characterization techniques have been developed for the hydrothermal behavior of ATES systems.These characterization schemes allow production temperatures and enerqy recovery factors for a ranqe of cases to be read from qraphs showinq these variables in terms of a few dimensionless parameters.For site-specific studies, a detailed numerical simulation of the Auburn University three-cycle doublet well heat storaqe experiment has been done in order to demonstrate the predictive ability of the numerical model CCC, as well as to provide quidance in carryinq out the second and third cycles of the experiment.The experimental injection temperatures and flowrates were used.Recovery factors and production temperatures were predicted prior to receivinq the temperature data from the field.Subsequently, a series of parameter sensitivity studies were done to examine the differences between the predicted and observed results.
Density-functional approximation for the correlation energy of the inhomogeneous electron gas (1986)

Langreth and Mehl (LM) and co-workers have developed a useful spin-density functional for the correlation energy of an electronic system. Here the LM functional is improved in two ways: (1) The natural separation between exchange and correlation is made, so that the density-gradient expansion of each is recovered in the slowly varying limit. (2) Uniform-gas and inhomogeneity effects beyond the randomphase approximation are built in. Numerical results for atoms, positive ions, and surfaces are close to the exact correlation energies, with major improvements over the original LM approximation for the ions and surfaces.
Immunohistochemical Localization of Phosphodiesterase 2A in Multiple Mammalian Species (2009)

Phosphodiesterases (PDEs) comprise a family of enzymes that regulate the levels of cyclic nucleotides, key second messengers that mediate a diverse array of functions. PDE2A is an evolutionarily conserved cGMP-stimulated cAMP and cGMP PDE. In the present study, the regional and cellular distribution of PDE2A in tissues of rats, mice, cynomolgus monkeys, dogs, and humans was evaluated by immunohistochemistry. A polyclonal antibody directed to the C-terminal portion of PDE2A specifically detected PDE2A by Western blotting and by immunohistochemistry. The pattern of PDE2A immunoreactivity (ir) was consistent across all species. Western blot analysis demonstrated that PDE2A was most abundant in the brain relative to peripheral tissues. PDE2A ir was heterogeneously distributed within brain and was selectively expressed in particular peripheral tissues. In the brain, prominent immunoreactivity was apparent in components of the limbic system, including the isocortex, hippocampus, amygdala, habenula, basal ganglia, and interpeduncular nucleus. Cytoplasmic PDE2A staining was prominent in several peripheral tissues, including the adrenal zona glomerulosa, neurons of enteric ganglia, endothelial cells in all organs, lymphocytes of spleen and lymph nodes, and pituitary. These studies suggest that PDE2A is evolutionarily conserved across mammalian species and support the hypothesis that the enzyme plays a fundamental role in signal transduction.
Experimental investigation of a 250-kW turbine organic Rankine cycle system for low-grade waste heat recovery (2016)

An organic Rankine cycle (ORC) is generally used for converting low-grade heat into electricity. In this study, an extensive literature survey was conducted to identify current research gaps on experimental ORC systems. Specifically, there is limited experimental data and limited details on thermal and expander efficiencies of ORC systems. In order to address these gaps, the objective of this study included developing a turbine ORC with a power output exceeding 50 kW and thermal efficiency exceeding 8% for a heat source temperature < 120°C. The experimental results indicated that the system achieved a net power output of 242.5 kW and a thermal efficiency of 8.3% (the highest value for a turbine ORC system for the heat source temperature below 120°C). Thus, the study addressed the gaps identified in the research area of ORCs.
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case (2009)

The collected data, prioritized candidate genes, and gene prioritization tools are freely available at http://bioinfo.mc.vanderbilt.edu/SZGR/.
Decentralized Offloading Strategies Based on Reinforcement Learning for Multi-Access Edge Computing (2021)

Using reinforcement learning technologies to learn offloading strategies for multi-access edge computing systems has been developed by researchers. However, large-scale systems are unsuitable for reinforcement learning, due to their huge state spaces and offloading behaviors. For this reason, this work introduces the centralized training and decentralized execution mechanism, designing a decentralized reinforcement learning model for multi-access edge computing systems. Considering a cloud server and several edge servers, we separate the training and execution in the reinforcement learning model. The execution happens in edge devices of the system, and edge servers need no communication. Conversely, the training process occurs at the cloud device, which causes a lower transmission latency. The developed method uses a deep deterministic policy gradient algorithm to optimize offloading strategies. The simulated experiment shows that our method can learn the offloading strategy for each edge device efficiently.
Abstract 1470: Detection of circulating tumor cells harboring a unique ALK rearrangement in ALK-positive non-small cell lung cancer. (2013)

Abstract Purpose: The diagnostic test of ALK rearrangement in non-small-cell lung cancer (NSCLC) for crizotinib treatment is currently done on tumor biopsies or fine needle aspirations. The present study was designed to evaluate -1) whether ALK-rearrangement diagnosis could be performed using circulating tumor cells (CTCs), -2) whether CTCs harboring ALK-rearrangement could be monitored in ALK-positive patients treated by crizotinib. Patients and Methods: CTCs were isolated in 18 ALK-positive and 14 ALK-negative patients by blood filtration using ISET (Isolation by Size Epithelial Tumor cells) and tested by filter adapted-fluorescence in situ hybridization (FA-FISH), a FISH method optimized for filters. Numbers of ALK-rearranged cells and patterns of ALK-rearrangement were determined in CTCs and compared to those present in tumor biopsies. ALK-rearranged CTCs and tumor specimens were characterized for epithelial (cytokeratin, E-cadherin) and mesenchymal (vimentin, N-cadherin) markers expression. ALK-rearranged CTCs were monitored in ALK-positive patients treated by crizotinib. Results: ALK-rearranged CTCs [ranging from 4 to 34 CTCs /1mL] were detected in all ALK-positive patients, while no or only one ALK-rearranged CTCs was detected in blood samples obtained from ALK-negative patients. ALK-rearranged CTCs harboured a unique (3’ 5’) split pattern while heterogeneous patterns (3’ 5’, only 3’) of splits were present in tumors. ALK-rearranged CTCs exclusively expressed a mesenchymal phenotype and contrasted with heterogeneous epithelial and mesenchymal marker expressions in tumors. Variations in levels of ALK-rearranged CTCs and in CTCs harboring a gain of ALK native copies were detected under crizotinib treatment. Conclusion: We report that ALK-rearrangement can be detected in CTCs of ALK-positive NSCLC patients using ISET and FA-FISH, enabling diagnostic testing for crizotinib treatment. Our results suggest that CTCs harboring a unique ALK-rearrangement and mesenchymal phenotype may arise from the clonal selection of tumor cells that have acquired the potential to drive metastatic progression of ALK-positive NSCLC. The molecular characterization of CTCs in patients undergoing crizotinib treatment might provide new insights into mechanism of resistance to ALK tyrosine kinase inhibitors, and possible strategies to overcome this resistance. Citation Format: Emma Pailler, Julien Adam, Amélie Barthelemy, Marianne Oulhen, Nathalie Auger, Alexander Valent, David Planchard, Melissa Taylor, Isabelle Borget, Fabrice Andre, Jean-Charles Soria, Philippe Vielh, Benjamin Besse, Françoise Farace. Detection of circulating tumor cells harboring a unique ALK rearrangement in ALK-positive non-small cell lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1470. doi:10.1158/1538-7445.AM2013-1470
Processing of natural language queries to a relational database (2003)

The method, based on a semantic approach, interprets grammatical and lexical units of a natural language into concepts of subject domain, which are given in a conceptual scheme. The conceptual scheme is mapped formally onto the logical scheme. We applied the method to query the FlyEx database in natural language. FlyEx contains information on the expression of segmentation genes in Drosophila melanogaster. The method allows formulation of queries in various natural languages simultaneously, and is adaptive to changes in the knowledge domain and user's views. It provides optimal transformation of queries from natural language to SQL, as well as visualization of information as a hyperscheme. The method does not require specification of all possible language constructions as well as a standard grammar accuracy in formulation of NL queries.
Resonance, a step towards a fluency for complexity: The science, language, and epistemology of Gregory Bateson (2020)

This thesis confronts the urgency with which new language and vocabulary is required to move beyond linear assumptions in mainstream science and humanities, as well as global policy making. I examine Gregory Bateson’s body of work in history and philosophy of science, psychiatry and psychotherapy, anthropology, biology and ecology designed to communicate the necessarily interdisciplinary consideration for a nonlinear and recursive investigation of the self, other, and environment. Such intellectual forays cannot be dismissed as non-scientific. I offer definitions and contextualizations of key terms derived from cybernetics, new materialisms, and posthumanism (such as emergence, process, paradox, metaphor, fractality) to speak about the ramifying intricacies and pathologies in processes of knowing at various different scales. I conclude with a theory of resonance that may offer the epistemological groundwork with which to construct a metaphor of precarious intervention and to model a critical relationship between epistemology and ethics.