gebhart/patrepeval huggingface dataset:
An Asymptotic Analysis of Differential Electrical Mobility Classifiers (2011)

An asymptotic analysis of balanced flow operations of differential mobility analyzers (DMAs) and a new class of instruments that includes opposed migration aerosol classifiers (OMACs) and inclined grid mobility analyzers (IGMAs) provides new insights into the similarities and differences between the devices. The characteristic scalings of different instruments found from minimal models are shown to relate the resolving powers, dynamic ranges, and efficiencies of most such devices. The resolving powers of all of the instruments in the nondiffusive regime of high voltage classifications, , is determined by the ratio of the flow rate of the separation gas (sheath or crossflow) to that of the aerosol. At low voltage, when diffusion degrades the classification, the OMAC and the IGMA share an factor advantage in dynamic range of mobilities over the DMA, although the OMAC also suffers greater losses because diffusion immediately deposits particles onto its porous electrodes. On the basis of this analysis, a single master operating diagram is proposed for DMAs, OMACs, and IGMAs. Analysis of this operating diagram and its consequences for the design of differential electrical mobility classifiers suggests that OMACs and IGMAs also have advantages over DMAs in design flexibility and miniaturization. Most importantly, OMACs and IGMAs may outperform DMAs for the currently difficult classification of particles with diameters less than 10 nm. On the other hand, DMAs are more amenable to voltage scanning-mode operation to enable accelerated size distribution measurements, whereas it is most convenient to operate OMACs and IGMAs in voltage stepping-mode operation.
The natural volume method (NVM): Presentation and application to shallow water inviscid flows (2008)

Abstract In this paper a fully Lagrangian formulation is used to simulate 2D shallow water inviscid flows. The natural element method (NEM), which has been used successfully with several solid and fluid mechanics applications, is used to approximate the fluxes over Voronoi cells. This particle‐based method has shown huge potential in terms of handling problems involving large deformations. Its main advantage lies in the interpolant character of its shape function and consequently the ease it allows with respect to the imposition of Dirichlet boundary conditions. In this paper, we use the NEM collocationally, and in a Lagrangian kinematic description, in order to simulate shallow water flows that are boundary moving problems. This formulation is ultimately shown to constitute a finite‐volume methodology requiring a flux computation on Voronoi cells rather than the standard elements, in a triangular or quadrilateral mesh. St Venant equations are used as the mathematical model. These equations have discontinuous solutions that physically represent the existence of shock waves, meaning that stabilization issues have thus been considered. An artificial viscosity deduced from an analogy with Riemann solvers is introduced to upwind the scheme and therefore stabilize the method. Some inviscid bidimensional flows were used as preliminary benchmark tests, which produced decent results, leading to well‐founded hopes for the future of this method in real applications. Copyright © 2008 John Wiley &amp; Sons, Ltd.
LASER-ASSISTED ENDOSCOPIC THIRD VENTRICULOSTOMY (2008)

This study demonstrates that LA-ETV is a safe and effective procedure that is comparable to other techniques for ETV. LA-ETV is most effective in patients aged 1 year and older and in patients with aqueductal stenosis and tumors, with a low major complication rate.
Abstract 1819: Profiling of extracellular matrix proteins in pancreatic ductal adenocarcinoma progression and metastasis (2015)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most common causes of cancer-related death, and is characterized by accumulation of excessive extracellular matrix (ECM). Although the ECM of tumors, such as PDAC, has long been known to have major effects on behavior of both tumor and stromal cells, including invasion, angiogenesis, metastasis, and resistance to therapy, the detailed composition of the ECM in PDAC tumor progression and metastasis are not understood. To study the involvement of ECM proteins in PDAC primary tumor growth and the tissue-specific metastasis program, we modified the comprehensive ECM proteomic approach by Mass Spectrometry (MS) recently developed in our lab to profile the ECM changes during PDAC progression in both the LSL-KrasG12D/+; LSL-Trp53R127H/+; Pdx-1-Cre (KPC) mouse models of PDAC and human patient samples. We will compare ECM profiles from normal pancreas, pancreatitis, early and late pancreatic intraepithelial neoplasia (PanIN) stages, and PDAC. Initial MS identified between 100 and 140 ECM proteins in samples representing each stage. The changes identified include changes previously associated with PDAC (e.g., upregulation of Tnc, Lox) plus novel, previously unreported changes. The combination of mouse models and human samples will allow us to uncover critical ECM changes during PDAC progression and metastasis and, furthermore, to investigate and understand the functional consequences of such changes. The ongoing studies will characterize the ECM of PDAC in detail and provide novel insights into diagnosis, prognosis and treatments of this very difficult disease. Citation Format: Chenxi Tian, Daniel Ohlund, Karl Clauser, Steven A. Carr, David A. Tuveson, Richard O. Hynes. Profiling of extracellular matrix proteins in pancreatic ductal adenocarcinoma progression and metastasis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1819. doi:10.1158/1538-7445.AM2015-1819
Increasing pelletizing extruder output with fluoropolymer alloys (1997)

Abstract Fluoropolymer processing additives are used by many polyolefin processors. Typical benefits include the reduction of die build‐up and the elimination of shark‐skin melt fracture. Improvements in this technology have led to the fluoropolymer alloy, the most efficient fluoropolymer additive available. This same fluoropolymer additive can be used to increase the output in a pelletizing extruder. The improved efficiency of the fluoropolymer alloy makes the improvement cost effective. This paper will show how this is being done. Results will be shown from polyethylene plants where these improvements have been demonstrated.
Allergen1 regulates polysaccharide structure in Cryptococcus neoformans (2013)

Cryptococcus neoformans is an important human, fungal pathogen that sheds polysaccharide (exo-PS) into host tissues. While shed exo-PS mediates numerous untoward effects (including promoting increased intracranial pressure), little is known about the regulation of this phenomenon. Since downregulation of the Allergen 1 (ALL1) gene is associated with high ICP, we investigated the relationship between ALL1 expression and exo-PS structure using a variety of biophysical techniques. The Δall1 mutants of two serotypes produced a shorter exo-PS with less branching and structural complexity than the parental strains. Consistent with lower branching, these exo-PSs manifested higher intrinsic viscosity than the parental strains. The Δall1 mutant strains manifested differences in epitope expression and significant resistance to phagocytosis. Exo-PS of Δall1 mutant exhibited anti-phagocytic properties. Comparative transcriptome analysis of mutant and parental strain under iron-deprived conditions indicated a role of ALL1 in iron homeostasis, characterized by differential regulation of genes that mediate iron reduction and transport. Together, our results demonstrate a role of ALL1 in regulating conformational aspects of PS structure and iron homeostasis. These findings provide a mechanism to explain how changes in ALL1 expression influence virulence of switch variants and suggest that structural changes and polymer length are epigenetically regulated.
Stochastic Stability of Genetic Networks With Disturbance Attenuation (2007)

Gene regulation is an intrinsically noisy process, which is subject to intracellular and extracellular noise perturbations and environment fluctuations. In this brief, we consider a stochastic nonlinear model for genetic regulatory networks with SUM regulatory functions. Based on the Lyapunov method and the Lur'e system approach, sufficient conditions for the stochastic stability of the genetic networks with disturbance attenuation are derived. The case with time delays owing to the slow processes of transcription, translation, and translocation is also studied. All the results are presented in terms of linear matrix inequalities (LMIs).
Identification of lung regions in chest radiographs using Markov random field modeling (1998)

The authors present an algorithm utilizing Markov random field modeling for identifying lung regions in a digitized chest radiograph (DCR). Let x represent the classifications of each pixel in a DCR as either lung or nonlung. We model x as a realization of a spatially varying Markov random field. This model is developed utilizing spatial and textural information extracted from samples of lung and nonlung region-types in a training set of DCRs. With this model, the technique of Iterated Conditional Modes is used to determine the optimal classification of each pixel in a DCR. The algorithm's ability to identify lung regions is evaluated on a testing set of DCRs. The algorithm performs well yielding a sensitivity of 90.7% +/- 4.4%, a specificity of 97.2% +/- 2.0%, and an accuracy of 94.8% +/- 1.6%. In an attempt to gain insight into the meaning and level of the algorithm's performance numbers, the results are compared to those of some easily implemented classification algorithms.
Direct detection of albumin in human blood plasma by proton NMR spectroscopy. Complexation of nickel2+ (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirect detection of albumin in human blood plasma by proton NMR spectroscopy. Complexation of nickel2+Sunil U. Patel, Peter J. Sadler, Alan Tucker, and John H. VilesCite this: J. Am. Chem. Soc. 1993, 115, 20, 9285–9286Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00073a053https://doi.org/10.1021/ja00073a053research-articleACS PublicationsRequest reuse permissionsArticle Views201Altmetric-Citations33LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Microbioreactor Cultivations of Fab‐Producing Escherichia coli Reveal Genome‐Integrated Systems as Suitable for Prospective Studies on Direct Fab Expression Effects (2019)

Despite efforts to develop concepts for efficient antibody fragment (Fab) production in Escherichia coli (E. coli) and the high degree of similarity within this protein class, a generic platform technology is still not available. Indeed, feasible production of new Fab candidates remains challenging. In this study, a setup that enables direct characterization of host cell response to Fab expression by utilizing genome-integrated (GI) systems is established. Among the multitude of factors that influence Fab expression, the variable domain, the translocation mechanism, the host strain, as well as the copy number of the gene of interest (GOI) are varied. The resulting 32 production clones are characterized in carbon-limited microbioreactor cultivations with yields of 0-7.4 mg Fab per gram of cell dry mass. Antigen-binding region variations have the greatest effect on Fab yield. In most cases, the E. coli HMS174(DE3) strain performs better than the BL21(DE3) strain. Translocation mechanism variations mainly influence leader peptide cleavage efficiency. Plasmid-free systems, with a single copy of the GOI integrated into the chromosome, reach Fab yields in the range of 80-300% of plasmid-based counterparts. Consequently, the GI Fab production clones could greatly facilitate direct analyses of systems response to different impact factors under varying production conditions.
Processing and fatty acid acylation of RAS1 and RAS2 proteins in Saccharomyces cerevisiae. (1986)

We demonstrate the pathway for the biosynthesis of RAS1 and RAS2 gene products of Saccharomyces cerevisiae leading to their localization in membranes. The primary translation products of these genes are detected in a soluble fraction. Shortly after synthesis, these precursor molecules are converted to forms that migrate slightly faster than the precursor forms on a NaDodSO4/polyacrylamide gel. These processed proteins are further modified by fatty acid acylation, which is detected by [3H]palmitic acid labeling. The acylated derivatives are found exclusively in cell membranes, indicating the translocation of the RAS proteins from cytosol to membranes during maturation process. The attached fatty acids can be released by mild alkaline hydrolysis, suggesting that the linkage between the fatty acid and the protein is an ester bond. The site of the modification by fatty acid is presumably localized to the COOH-terminal portion of the RAS proteins. Fractionation of the membranes by sucrose gradient demonstrates that a majority of the fatty-acylated RAS proteins are localized in plasma membrane.
The Calcium-Binding Protein EFhd2 Modulates Synapse Formation In Vitro and Is Linked to Human Dementia (2014)

EFhd2 is a calcium-binding adaptor protein that has been found to be associated with pathologically aggregated tau in the brain in Alzheimer disease and in a mouse model of frontotemporal dementia. EFhd2 has cell type-specific functions, including the modulation of intracellular calcium responses, actin dynamics, and microtubule transport. Here we report that EFhd2 protein and mRNA levels are reduced in human frontal cortex tissue affected by different types of dementia with and without tau pathology. We show that EFhd2 is mainly a neuronal protein in the brain and is abundant in the forebrain. Using short hairpin RNA-mediated knockdown of EFhd2 expression in cultured cortical neurons, we demonstrate that loss of EFhd2 affects the number of synapses developed in vitro whereas it does not alter neurite outgrowth per se. Our data suggest that EFhd2 is involved in the control of synapse development and maintenance through means other than affecting neurite development. The changes in expression levels observed in human dementias might, therefore, play a significant role in disease onset and progression of dementia, which is characterized by the loss of synapses.
Advanced Mobile Phone Service: Control Architecture (1979)

The cellular concept used in the Advanced Mobile Phone Service (amps) system to achieve spectrum efficiency requires a complex and flexible distributed system control architecture. Three major subsystems serve as the control elements: the mobile unit, the cell site, and the switching office. System control functions are partitioned among these subsystems to handle the following amps control challenges: interfacing with the nationwide switched telephone network, dialing from mobile units, supervising calls from mobile subscribers in the presence of noise and co-channel interference, performing call setup functions including paging and access, and locating and handing off mobiles between cell sites. This paper explains the techniques used to achieve the control functions of the three major subsystems and the ways they in turn participate in control of the total amps system.
An adaptive routing algorithm for Cognitive Packet Network infrastructure based on neural networks (2011)

This paper examines the possibility of introducing an intelligent routing protocol to the Internet, based on the Cognitive Packet Network (CPN) architecture with respect to the Quality of Service (QoS) delivered to the end users. In the present with increasing populations of countries it is clear that present infrastructure does not hold the sufficient capacity to deliver the expected level of service to the end users. Since there is an eminent need for a solution for improving the QoS in the Internet, this research focuses to provide a new network architecture which would improve the QoS, provide reliable and efficient service which can fulfill the ever growing Internet usage demand. This is achieved through a new network architecture known as CPN which is based on the basis of providing the best and user desired QoS. The main underlying technology behind the CPN will be a neural network. The neural network will be learning the changes in the network and adapt to the situation through the knowledge gathered. The packets will collectively learn about the network thus the load on the routers will be minimized. This mechanism completely replaces the need of a routing table thus making routing far more efficient when comparing to current routing protocols like Open Shortest Path First (OSPF). Final outcome of the research is coming to the conclusion that the future of the Internet is with the neural network based intelligent, dynamically adapting and learning CPN infrastructure instead of current packet switched network.
Experimental Infection of Dogs with Leishmania and Saliva as a Model to Study Canine Visceral Leishmaniasis (2013)

The infection model described here shows some degree of similarity when compared with naturally infected dogs opening new perspectives for the study of CVL using an experimental model that employs the combination of parasites and sand fly saliva both present during natural transmission.
Blimp1 and the Emergence of the Germ Line during Development in the Mouse (2005)

To elucidate the mechanism for the specification of primordial germ cells (PGCs) in mice, we have developed and exploited the methods of single cell analysis. Based on these studies, we proposed a molecular program associated with this process, a key event of which is the repression of homeobox genes that are, without exception, upregulated in somatic neighbors. We have now identified Blimp1, a potent transcriptional repressor of a histone methyltransferase subfamily, as a key regulator of PGC specification. Indeed, the unexpected early onset of Blimp1 expression in a few cells at the most proximal-posterior epiblast cells marks the origin of the germ cell lineage. Disruption of Blimp1 function resulted in aberrant PGC-like cells with a deregulated intrinsic gene expression program at a very early stage, which demonstrates that Blimp1 is a critical determinant of the germ line in mice.
Performance Evaluation of Spatial Multiplexing Systems over Finite Scattering Channel (2006)

This paper evaluates the BER performance of a spatial multiplexing system over finite scattering channel. We employ a 'DBLAST-like' space-time convolutional code, which directly maps a convolutional code frame to a space-time code word. The finite scatterers channel model is used to account for the limited multipath scattering which occurs in practical channels. In the receiver, iterative joint MMSE detection, decoding and interference cancellation is applied to improve the system performance. Numerical results are presented to illustrate the performance of this spatial multiplexing system over this channel. We analyse the impact of this channel model on the system performance and examine the performance improvement obtained by the use of the iterative receiver.
THE DEVELOPMENT OF FIBROBLAST COLONIES IN MONOLAYER CULTURES OF GUINEA‐PIG BONE MARROW AND SPLEEN CELLS (1970)

ABSTRACT In monolayer cultures of guinea‐pig bone marrow and spleen the development of discrete fibroblast colonies takes place on days 9–12. The linear increase in the number of colonies with increasing numbers of explanted cells and the distribution of male and female cells in mixed cultures support the view that fibroblast colonies are clones. The concentration of colony‐forming cells in bone marrow and spleen is approximately 10 ‐5 . Bone marrow culture (but not spleen culture) fibroblasts are capable of spontaneous bone formation in diffusion chambers. Fibroblasts from both bone marrow and spleen cultures are inducible to osteogenesis in diffusion chambers in the presence of transitional epithelium.
A Nitric Oxide-Releasing Heparin Conjugate for Delivery of a Combined Antiplatelet/Anticoagulant Agent (2014)

Heparin is a widely used anticoagulant due to its ability to inhibit key components in the coagulation cascade such as Factor Xa and thrombin (Factor IIa). Its potential to preferentially bind to antithrombin (ATIII) results in a conformational change and activation that leads to the prevention of fibrin formation from fibrinogen and ultimately obstructs a hemostatic plug from forming. Nitric oxide (NO) exhibits potent antiplatelet activity attributed to its capacity to increase the amount of cyclic guanosine monophosphate (cGMP) within platelets, which decreases the Ca(2+) concentration required for platelet activation. Currently there is no single agent that combines the functions of both antiplatelet and anticoagulant (anti-Xa and anti-IIa) activities to effectively block both the extrinsic and the intrinsic coagulation pathways. The research reported herein demonstrates the ability to combine the physiological capabilities of both heparin and NO into one functional compound via use of a spermine derivative of heparin, thus enabling formation of a novel diazeniumdiolate (NONOate). The heparin-spermine NONOate has a half-life of 85 min at 25 °C (pH 7.4). The heparin backbone of the conjugate maintains its anticoagulant activity as demonstrated via an anti-Xa assay, providing an anticoagulant conversion of 3.6 μg/mL of the heparin-spermine-NONO conjugate being equivalent to 2.5 μg/mL (0.50 IU/mL) of underivatized heparin in terms of anti-Xa activity. Using standard platelet aggregometry, it is shown that the functionality of the NO release portion of the heparin conjugate prevents (nearly 100%) platelet aggregation in the presence of adenosine diphosphate (ADP, platelet agonist).
Application of Optical Biosensors in Small-Molecule Screening Activities (2012)

The last two decades have seen remarkable progress and improvements in optical biosensor systems such that those are currently seen as an important and value-adding component of modern drug screening activities. In particular the introduction of microplate-based biosensor systems holds the promise to match the required throughput without compromising on data quality thus representing a sought-after complement to traditional fluidic systems. This article aims to highlight the application of the two most prominent optical biosensor technologies, namely surface plasmon resonance (SPR) and optical waveguide grating (OWG), in small-molecule screening and will present, review and discuss the advantages and disadvantages of different assay formats on these platforms. A particular focus will be on the specific advantages of the inhibition in solution assay (ISA) format in contrast to traditional direct binding assays (DBA). Furthermore we will discuss different application areas for both fluidic as well as plate-based biosensor systems by considering the individual strength of the platforms.