gebhart/patrepeval huggingface dataset:
Modeling knowledge, archival and bibliographic standards in comparison. 1st JLIS.it Seminar - May 19th 2022 (2022)

The editorial gives an account of the insights that emerged during the Jlis.it seminar Modelling Knowledge, held in Florence on 19 May 2022. First, the political potential of the initiative in terms of integration and collaboration between documentary disciplines is emphasised. It then dwells on the descriptive habits of the different domains in search of more effective knowledge management models in a broad sense. Finally, the text opens up to the readiness of the journal to become a meeting place for different reflections on knowledge modelling.
The 3Rs as a framework to support a 21st century approach for nanosafety assessment (2016)

Due to the plethora of nanomaterials being manufactured, it is crucial that their effects on human health are understood. It is not feasible to assess the safety of all nanomaterials using animal-based toxicity tests. There are also scientific, business, legislative and ethical drivers to reconsider the use of such toxicity tests. Utilising non-traditional methods has the potential to improve the human relevance of nanosafety assessment, reduce the numbers of animals that are used, and shift the paradigm to a ‘21st century’ approach that exploits recent scientific and technological advances. This article considers how application of the 3Rs principles can be used as a framework to support and guide this paradigm shift in the short, medium and long-term. Bringing the community together to facilitate the transition is necessary to ensure that tangible impacts are made on the efficiency and robustness of the nanosafety assessment process.
The Estimation and Correction of Rigid Motion in Helical Computed Tomography (2015)

X-ray CT is a tomographic imaging tool used in medicine and industry. Although technological developments have significantly improved the performance of CT systems, the accuracy of images produced by state-of-the-art scanners is still often limited by artefacts due to object motion. To tackle this problem, a number of motion estimation and compensation methods have been proposed. However, no methods with the demonstrated ability to correct for rigid motion in helical CT scans appear to exist. The primary aims of this thesis were to develop and evaluate effective methods for the estimation and correction of arbitrary six degree-of-freedom rigid motion in helical CT. As a first step, a method was developed to accurately estimate object motion during CT scanning with an optical tracking system, which provided sub-millimetre positional accuracy. Subsequently a motion correction method, which is analogous to a method previously developed for SPECT, was adapted to CT. The principle is to restore projection consistency by modifying the source-detector orbit in response to the measured object motion and reconstruct from the modified orbit with an iterative reconstruction algorithm. The feasibility of this method was demonstrated with a rapidly moving brain phantom, and the efficacy of correcting for a range of human head motions acquired from healthy volunteers was evaluated in simulations. The methods developed were found to provide accurate and artefact-free motion corrected images with most types of head motion likely to be encountered in clinical CT imaging, provided that the motion was accurately known. The method was also applied to CT data acquired on a hybrid PET/CT scanner demonstrating its versatility. Its clinical value may be significant by reducing the need for repeat scans (and repeat radiation doses), anesthesia and sedation in patient groups prone to motion, including young children.
A Computer Model Simulating the Intestinal Absorption of Bile Acids (1984)

Mathematical models were developed for assessment of the absorption kinetics of compounds passing down the length of a perfused intestinal segment. The models considered the intestinal segment as a cylinder composed of a large number of very small (infinitesimal) cylinders and described the concentration decline of the compound in situations with active, passive and combined active and passive transport. The maximal velocity of active transport, Vmax, the Michaëlis-Menten constant, Km, and the permeability coefficient, P, were calculated. A computer program was developed to operate the mathematical expressions. The models were validated by jejunal and ileal perfusions of various bile acids in six healthy volunteers. The fit between the mathematical models and the actually measured data showed an average standard deviation of 0.14 mmol/l (substrate infusion concentration ranging from 0.25 mmol/l to 3.0 mmol/l). It was concluded that the computer models were feasible for practical purposes. Moreover, the models reduced the number of perfusions necessary to determine the absorption kinetics of a given bile acid.
Machine Learning for Vehicular Networks: Recent Advances and Application Examples (2018)

The emerging vehicular networks are expected to make everyday vehicular operation safer, greener, and more efficient and pave the path to autonomous driving in the advent of the fifth-generation (5G) cellular system. Machine learning, as a major branch of artificial intelligence, has been recently applied to wireless networks to provide a data-driven approach to solve traditionally challenging problems. In this article, we review recent advances in applying machine learning in vehicular networks and attempt to bring more attention to this upcoming area.
A Multimedia Cross-Layer Protocol for Underwater Acoustic Sensor Networks (2010)

Underwater multimedia acoustic sensor networks will enable new underwater applications such as multimedia coastal and tactical surveillance, undersea explorations, picture and video acquisition and classification, and disaster prevention. Because of the different application requirements, there is a need to provide differentiated-service support to delay-sensitive and delay-tolerant data traffic as well as to loss-sensitive and loss-tolerant traffic. While research on underwater communication protocol design so far has followed the traditional layered approach originally developed for wired networks, improved performance can be obtained with a cross-layer design. Hence, the objective of this work is twofold: (1) study the interactions of key underwater communication functionalities such as modulation, forward error correction, medium access control, and routing; and (2) develop a distributed cross-layer communication solution that allows multiple devices to efficiently and fairly share the bandwidth-limited high-delay underwater acoustic medium.
Distinct roles in folding, CD81 receptor binding and viral entry for conserved histidine residues of hepatitis C virus glycoprotein E1 and E2 (2012)

The protonation of histidine in acidic environments underpins its role in regulating the function of pH-sensitive proteins. For pH-sensitive viral fusion proteins, histidine protonation in the endosome leads to the activation of their membrane fusion function. The HCV (hepatitis C virus) glycoprotein E1-E2 heterodimer mediates membrane fusion within the endosome, but the roles of conserved histidine residues in the formation of a functional heterodimer and in sensing pH changes is unknown. We examined the functional roles of conserved histidine residues located within E1 and E2. The E1 mutations, H222A/R, H298R and H352A, disrupted E1-E2 heterodimerization and reduced virus entry. A total of five out of six histidine residues located within the E2 RBD (receptor-binding domain) were important for the E2 fold, and their substitution with arginine or alanine caused aberrant heterodimerization and/or CD81 binding. Distinct roles in E1-E2 heterodimerization and in virus entry were identified for His691 and His693 respectively within the membrane-proximal stem region. Viral entry and cell-cell fusion at neutral and low pH values were enhanced with H445R, indicating that the protonation state of His445 is a key regulator of HCV fusion. However, H445R did not overcome the block to virus entry induced by bafilomycin A1, indicating a requirement for an endosomal activation trigger in addition to acidic pH.
Evaluation of the Performance and Response of the Bacharach TLV Sniffer and H-Nu Photoionization Gas Analyzer to Common Hydrocarbon Solvents (1983)

Two direct reading instruments, the H-Nu PI 101 photoionization analyzer and the J.W. Bacharach TLV Sniffer, were evaluated under laboratory conditions to determine their performance characteristics when challenged by vapors of common hydrocarbon solvent mixtures. Each instrument was evaluated against the manufacturer's recommended test solvent for rise time, fall time, noise, span drift, zero drift, position sensitivity, battery life, and recharge time. The precision, accuracy, and operating linear range were also determined for the test solvents and some petroleum solvent mixtures which are common refinery products. For these latter mixtures, correction factors are presented which allow for an improved estimate of ambient concentrations when monitoring with each of these instruments. All tests except operating humidity range were performed by challenging each instrument with a known concentration of hydrocarbon generated by evaporating calculated liquid volumes into a static chamber. Humidity tests were performed using a dynamic dilution apparatus generating a fixed concentration of hydrocarbon while relative humidity was varied. Concentrations in both systems were verified by gas injection into gas chromatograph. Each instrument performed well when challenged by manufacturers' recommended test solvents. Humidity was shown to influence each instrument's readings. Also, the instruments were shown to have application as monitors of airborne concentrations of common hydrocarbon solvent mixtures.
Liquid crystal director fields in micropores of photonic crystals (2007)

Photonic crystals made of macroporous silicon and liquid crystals are optical materials with a tunable dispersion relation in the infrared frequency range. Three-dimensional structures can be realized by manufacturing a two-dimensional array of pores that show a spatially periodic variation of the pore diameter. The director fields of cholesteric liquid crystals confined to such modulated pores show different topologies that depend essentially on the ratio between the helix pitch of the liquid crystal and the pore size.
Apico-basal cell compression regulates Lamin A/C levels in epithelial tissues (2021)

The levels of nuclear protein Lamin A/C are crucial for nuclear mechanotransduction. Lamin A/C levels are known to scale with tissue stiffness and extracellular matrix levels in mesenchymal tissues. But in epithelial tissues, where cells lack a strong interaction with the extracellular matrix, it is unclear how Lamin A/C is regulated. Here, we show in epithelial tissues that Lamin A/C levels scale with apico-basal cell compression, independent of tissue stiffness. Using genetic perturbations in Drosophila epithelial tissues, we show that apico-basal cell compression regulates the levels of Lamin A/C by deforming the nucleus. Further, in mammalian epithelial cells, we show that nuclear deformation regulates Lamin A/C levels by modulating the levels of phosphorylation of Lamin A/C at Serine 22, a target for Lamin A/C degradation. Taken together, our results reveal a mechanism of Lamin A/C regulation which could provide key insights for understanding nuclear mechanotransduction in epithelial tissues.
Immobilization of Alcohol Dehydrogenase in Phospholipid Langmuir−Blodgett Films To Detect Ethanol (2009)

Enzyme immobilization in nanostructured films may be useful for a number of biomimetic systems, particularly if suitable matrixes are identified. Here we show that alcohol dehydrogenase (ADH) has high affinity toward a negatively charged phospholipid, dimyristoylphosphatidic acid (DMPA), which forms a Langmuir monolayer at an air-water interface. Incorporation of ADH into the DMPA monolayer was monitored with surface pressure measurements and polarization-modulation infrared reflection absorption spectroscopy, with the alpha-helices from ADH being mainly oriented parallel to the water surface. ADH remained at the interface even at high surface pressures, thus allowing deposition of Langmuir-Blodgett (LB) films from the DMPA-ADH film. Indeed, interaction with DMPA enhances the transfer of ADH, where the mass transferred onto a solid support increased from 134 ng for ADH on a Gibbs monolayer to 178 ng for an LB film with DMPA. With fluorescence spectroscopy it was possible to confirm that the ADH structure was preserved even after one month of the LB deposition. ADH-containing films deposited onto gold-interdigitated electrodes were employed in a sensor array capable of detecting ethanol at concentrations down to 10 ppb (in volume), using impedance spectroscopy as the method of detection.
Synergistic Effect of Polymer Additives and Chloride Ions on Copper Electrorefining (2007)

The synergistic effect of polymer additives such as gelatin, polyethylene glycol (PEG) and Cl- on Cu electrodeposition behavior have been investigated by measuring the polarization curves for Cu deposition, by rotating ring-disk electrode technique and by AC impedance measurement. In the polymer additive-free solution containing Cl-, the cathode potential shifted to less noble direction with increased concentration of Cl- in solution, resulting in a decrease in grain size of deposited Cu. The rotating ring-disk electrode technique revealed that Cu deposition in the solution containing slight amount of Cl- proceeded with preceding formation of adsorbed intermediate CuClad. The reduction of intermediate CuClad to Cu seems to polarize the cathode potential for Cu deposition. In the solutions containing both polymer additives and Cl-, the cathode potential for Cu deposition was more greatly polarized and deposited Cu was consisted of smaller grains, showing evident synergistic effect of polymer additives and Cl- on Cu deposition. The Nyquist plots obtained by AC impedance techniques suggest that the reduction of CuClad to Cu is suppressed by polymer additives.
Exploring the Effects of Spousal Race on the Self-rated Health of Intermarried Adults (2016)

Marital health advantages and the increase of interracial marriage (intermarriage) are well documented, but few studies investigate the health of intermarried people. We address this issue using aggregated data from the 2000–2013 Current Population Survey (CPS) and find that people with racial/ethnic minority spouses report lower self-rated health than those married to whites. Spousal race significantly moderated the association between respondent’s race and self-rated health such that minorities in same-race marriages had lower odds of reporting better health than those intermarried to whites. However, we found no differences in self-rated health among minorities intermarried to other minorities. There was also limited evidence that gender and socioeconomic status (SES) moderated the interaction between respondent’s race and spousal race. Our findings highlight the effects of marriage on the self-rated health of respondents and their spouse as well as the importance of examining differences in couple’s racial composition when investigating racial disparities in spousal health.
Innate Immunity in a Pyralid Moth (2004)

Invertebrates, like vertebrates, utilize pattern recognition proteins for detection of microbes and subsequent activation of innate immune responses. We report structural and functional properties of two domains from a beta-1,3-glucan recognition protein present in the hemolymph of a pyralid moth, Plodia interpunctella. A recombinant protein corresponding to the first 181 amino-terminal residues bound to beta-1,3-glucan, lipopolysaccharide, and lipoteichoic acid, polysaccharides found on cell surfaces of microorganisms, and also activated the prophenoloxidase-activating system, an immune response pathway in insects. The amino-terminal domain consists primarily of an alpha-helical secondary structure with a minor beta-structure. This domain was thermally stable and resisted proteolytic degradation. The 290 residue carboxyl-terminal domain, which is similar in sequence to glucanases, had less affinity for the polysaccharides, did not activate the prophenoloxidase cascade, had a more complicated CD spectrum, and was heat-labile and susceptible to proteinase digestion. The carboxyl-terminal domain bound to laminarin, a beta-1,3-glucan with beta-1,6 branches, but not to curdlan, a beta-1,3-glucan that lacks branching. These results indicate that the two domains of Plodia beta-1,3-glucan recognition protein, separated by a putative linker region, bind microbial polysaccharides with differing specificities and that the amino-terminal domain, which is unique to this class of pattern recognition receptors from invertebrates, is responsible for stimulating prophenoloxidase activation.
Extraintestinal focal infections in adults with Salmonella enterica serotype Choleraesuis bacteremia. (2007)

S. Choleraesuis bacteremia was usually complicated with extraintestinal focal infections in the elderly. With a high level of resistance among S. Choleraesuis, fluoroquinolones should be avoided for critically ill patients with suspected Salmonella bacteremia.
Generation of mice with a conditional and reporter allele for <i>Tmem100</i> (2010)

Activin receptor-like kinase 1 (ACVRL1; ALK1) is predominantly expressed in arterial endothelial cells and plays an important role in angiogenesis. ACVRL1 mutations cause hereditary hemorrhagic telangiectasia (HHT), a genetic vascular disorder for which the underlying mechanism is poorly understood. We have found that expression of transmembrane protein 100 (Tmem100) is downregulated in the lung of Acvrl1-deficient mice; however, its function is unknown. To elucidate the role of Tmem100 in vivo, we generated a conditional knockout allele for Tmem100 in which exon3, containing the entire coding sequence, was flanked by loxP sequences. The targeted allele also possessed a lacZ reporter cassette in intron2 for visualization of Tmem100 expression. We found that Tmem100 was predominantly expressed in arterial endothelial cells of developing embryos. The conditional and reporter allele will be a useful resource to investigate the in vivo role of Tmem100, especially in angiogenesis.
Neural Rough Differential Equations for Long Time Series (2020)

Neural controlled differential equations (CDEs) are the continuous-time analogue of recurrent neural networks, as Neural ODEs are to residual networks, and offer a memory-efficient continuous-time way to model functions of potentially irregular time series. Existing methods for computing the forward pass of a Neural CDE involve embedding the incoming time series into path space, often via interpolation, and using evaluations of this path to drive the hidden state. Here, we use rough path theory to extend this formulation. Instead of directly embedding into path space, we instead represent the input signal over small time intervals through its \textit{log-signature}, which are statistics describing how the signal drives a CDE. This is the approach for solving \textit{rough differential equations} (RDEs), and correspondingly we describe our main contribution as the introduction of Neural RDEs. This extension has a purpose: by generalising the Neural CDE approach to a broader class of driving signals, we demonstrate particular advantages for tackling long time series. In this regime, we demonstrate efficacy on problems of length up to 17k observations and observe significant training speed-ups, improvements in model performance, and reduced memory requirements compared to existing approaches.
Computer aided lung cancer diagnosis with deep learning algorithms (2016)

Deep learning is considered as a popular and powerful method in pattern recognition and classification. However, there are not many deep structured applications used in medical imaging diagnosis area, because large dataset is not always available for medical images. In this study we tested the feasibility of using deep learning algorithms for lung cancer diagnosis with the cases from Lung Image Database Consortium (LIDC) database. The nodules on each computed tomography (CT) slice were segmented according to marks provided by the radiologists. After down sampling and rotating we acquired 174412 samples with 52 by 52 pixel each and the corresponding truth files. Three deep learning algorithms were designed and implemented, including Convolutional Neural Network (CNN), Deep Belief Networks (DBNs), Stacked Denoising Autoencoder (SDAE). To compare the performance of deep learning algorithms with traditional computer aided diagnosis (CADx) system, we designed a scheme with 28 image features and support vector machine. The accuracies of CNN, DBNs, and SDAE are 0.7976, 0.8119, and 0.7929, respectively; the accuracy of our designed traditional CADx is 0.7940, which is slightly lower than CNN and DBNs. We also noticed that the mislabeled nodules using DBNs are 4% larger than using traditional CADx, this might be resulting from down sampling process lost some size information of the nodules.
Acid-Fast Positive and Acid-Fast Negative<i>Mycobacterium tuberculosis</i>: The Koch Paradox (2017)

Acid-fast (AF) staining, also known as Ziehl-Neelsen stain microscopic detection, developed over a century ago, is even today the most widely used diagnostic method for tuberculosis. Herein we present a short historical review of the evolution of AF staining methods and discuss Koch's paradox, in which non-AF tubercle bacilli can be detected in tuberculosis patients or in experimentally infected animals. The conversion of Mycobacterium tuberculosis from an actively growing, AF-positive form to a nonreplicating, AF-negative form during the course of infection is now well documented. The mechanisms of loss of acid-fastness are not fully understood but involve important metabolic processes, such as the accumulation of triacylglycerol-containing intracellular inclusions and changes in the composition and spatial architecture of the cell wall. Although the precise component(s) responsible for the AF staining method remains largely unknown, analysis of a series of genetically defined M. tuberculosis mutants, which are attenuated in mice, pointed to the primary role of mycolic acids and other cell wall-associated (glyco)lipids as molecular markers responsible for the AF property of mycobacteria. Further studies are now required to better describe the cell wall reorganization that occurs during dormancy and to develop new staining procedures that are not affected by such cell wall alterations and that are capable of detecting AF-negative cells.