gebhart/patrepeval huggingface dataset:
Analysis of induction responses from metal objects using the method of auxiliary sources (2002)

The method of auxiliary sources (MAS) is developed for analyzing the low frequency response of conducting and permeable objects. The method uses elementary auxiliary magnetic dipoles/charges to produce the unknown fields. Sources are located on virtual surfaces that usually conform to, but do not coincide with the real surface of the object, where application of the boundary conditions determines the unknown source coefficients. The source fields automatically satisfy Maxwell's equations and, using point collocation on the real surface, one avoids all singularities and all integrations. The accuracy in satisfying the boundary conditions can be evaluated explicitly using non-collocation points. Highly efficient results here show the low frequency response of spheroids and cylinders depending on object size and shape. The method is of use for the detection of unexploded ordinance.
Computer-Aided Diagnosis of Melanoma Using Border- and Wavelet-Based Texture Analysis (2012)

This paper presents a novel computer-aided diagnosis system for melanoma. The novelty lies in the optimised selection and integration of features derived from textural, borderbased and geometrical properties of the melanoma lesion. The texture features are derived from using wavelet-decomposition, the border features are derived from constructing a boundaryseries model of the lesion border and analysing it in spatial and frequency domains, and the geometry features are derived from shape indexes. The optimised selection of features is achieved by using the Gain-Ratio method, which is shown to be computationally efficient for melanoma diagnosis application. Classification is done through the use of four classifiers; namely, Support Vector Machine, Random Forest, Logistic Model Tree and Hidden Naive Bayes. The proposed diagnostic system is applied on a set of 289 dermoscopy images (114 malignant, 175 benign) partitioned into train, validation and test image sets. The system achieves and accuracy of 91.26% and AUC value of 0.937, when 23 features are used. Other important findings include (i) the clear advantage gained in complementing texture with border and geometry features, compared to using texture information only, and (ii) higher contribution of texture features than border-based features in the optimised feature set.
Delayed VERSUS Immediate Pushing in Second Stage of Labor (2010)

Delaying pushing for up to 90 minutes after complete cervical dilation resulted in a significant decrease in the time mothers spent pushing without a significant increase in total time in second stage of labor.In clinical practice, healthcare providers sometimes resist delaying the onset of pushing after second stage of labor has begun because of a belief it will increase labor time. This study's finding of a 51% reduction in pushing time when mothers delay pushing for up to 90 minutes, with no significant increase in overall time for second stage of labor, disputes that concern.
Closing the Loop for Memory Prosthesis: Detecting the Role of Hippocampal Neural Ensembles Using Nonlinear Models (2012)

A major factor involved in providing closed loop feedback for control of neural function is to understand how neural ensembles encode online information critical to the final behavioral endpoint. This issue was directly assessed in rats performing a short-term delay memory task in which successful encoding of task information is dependent upon specific spatio-temporal firing patterns recorded from ensembles of CA3 and CA1 hippocampal neurons. Such patterns, extracted by a specially designed nonlinear multi-input multi-output (MIMO) nonlinear mathematical model, were used to predict successful performance online via a closed loop paradigm which regulated trial difficulty (time of retention) as a function of the "strength" of stimulus encoding. The significance of the MIMO model as a neural prosthesis has been demonstrated by substituting trains of electrical stimulation pulses to mimic these same ensemble firing patterns. This feature was used repeatedly to vary "normal" encoding as a means of understanding how neural ensembles can be "tuned" to mimic the inherent process of selecting codes of different strength and functional specificity. The capacity to enhance and tune hippocampal encoding via MIMO model detection and insertion of critical ensemble firing patterns shown here provides the basis for possible extension to other disrupted brain circuitry.
Squalenoyl Gemcitabine Monophosphate: Synthesis, Characterisation of Nanoassemblies and Biological Evaluation (Eur. J. Org. Chem. 14/2011) (2011)

Abstract The cover picture shows the overall process leading to the elaboration of a squalenoyl nanomedicine, going from the chemical modification of natural squalene to the biological evaluation of the drug in mice. On a background of nanoparticles observed by electron microscopy, the synthesis of squalenoylgemcitabine monophosphate is depicted in a reaction scheme. This amphiphilic molecule self‐assembles to nanoparticles of about 100 nm in aqueous solution, as shown in the two vials. In the central circle, unilamellar liposomes with a membrane thickness of about 70 Å are seen from a microscope lens. Details are discussed in the article by D. Desmaële et al. on p. 2615 ff.
What is the Dimension of Your Binary Data? (2006)

Many 0/1 datasets have a very large number of variables; however, they are sparse and the dependency structure of the variables is simpler than the number of variables would suggest. Defining the effective dimensionality of such a dataset is a nontrivial problem. We consider the problem of defining a robust measure of dimension for 0/1 datasets, and show that the basic idea of fractal dimension can be adapted for binary data. However, as such the fractal dimension is difficult to interpret. Hence we introduce the concept of normalized fractal dimension. For a dataset D, its normalized fractal dimension counts the number of independent columns needed to achieve the unnormalized fractal dimension of D. The normalized fractal dimension measures the degree of dependency structure of the data. We study the properties of the normalized fractal dimension and discuss its computation. We give empirical results on the normalized fractal dimension, comparing it against PCA.
Correlation of 125I‐LSD autoradiographic labeling with serotonin voltage clamp responses in Aplysia neurons (1991)

Autoradiographic receptor binding studies using 125I-LSD (2-[125I]lysergic acid diethyamide) revealed intense labelling on the soma of a symmetrically located pair of cells in the abdominal ganglion of Aplysia californica. This binding was blocked by micromolar concentrations of serotonin and lower concentrations of the serotonergic antagonists, cyproheptadine and mianserin (Kadan and Hartig, 1988). Electrophysiological investigation of responses to serotonin of neurons in the left upper quadrant, where one of the labeled neurons is located, revealed a range of serotonin responses. Cells L3 and L6 have a K+ conductance increase in response to serotonin that is not blocked by cyproheptadine or mianserin. Cells L2 and L4 have a biphasic response to serotonin: a Na+ conductance increase, which can be blocked by cyproheptadine and mianserin, followed by a voltage dependent Ca2+ conductance which is blocked by Co2+ but not the serotonergic antagonists. Cell L1, and its symmetrical pair, R1, have in addition to the Na+ and Ca2+ responses observed in L2 and L4, a Cl- conductance increase blocked by LSD, cyproheptadine and mianserin. LSD had little effect on the other responses. We conclude that the symmetrically located cells L1 and R1 have a Cl- channel linked to a cyproheptadine- and mianserin-sensitive serotonin receptor that is selectively labelled by 125I-LSD. This receptor has many properties in common with the mammalian serotonin 1C receptor.
Improved branched endovascular aortic stent used to treat DeBaKey β aortic dissection (2011)

Objective To observe the efficacy and safety of improved branched endovascular aortic stent used to treat DeBaKey β aortic dissection with proximal crevasse &lt;10 mm from left subclavian artery. Methods Thirty patients of DeBaKey β aortic dissection with proximal crevasse &lt;10 mm from left subclavian artery ((27 males and three females), range age 48–76 (average age 50.2±24.6) years old) selected from October 2006 to December 2010 in our hospital. All patients were treated by thin steel binding improved branched endovascular aortic stents, an innovative method of delivery and release of stent. Stent implantation after successful repeat aortic angiography, understanding stent location, shape, sandwich break closed, internal leakage and patency of aortic branches. Results Thirty one improved branched endovascular aortic stents were used in 30 patients. Six patients with endoleak after stent implantation were given angioplasty, and endoleak disappeared after 20 min by repeated angiography. One patient was found a new distal crevasse after 3 months and then given a straight-type stent successfully. All patients were followed up for 18 months after stenting, aortic CT examination showed reduction or disappearance of the false lumen, true lumen enlargement, and have no complications. For example, left common carotid artery and left subclavian artery involvement, internal leakage, tumour rupture and stent migration. Conclusion The improved branched aortic stent, innovative method of delivery and release of stent treatment of endovascular repair of DeBaKey β aortic dissection with proximal crevasse &lt;10 mm from left subclavian artery is safe, reliable and high success rate.
Supplementary Figure S7 from A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors (2023)

&lt;p&gt;- PDF file 965K, Analysis of microarray data for the different GPCR subunits in SCLC cells and growth inhibition of several other types of neuroendocrine tumors by the TCAs&lt;/p&gt;
Naphtha Reforming and Upgrading of Diesel Fractions (2010)

This chapter contains sections titled: Introduction Catalytic Reforming Upgrading Diesel Fractions: Catalytic Dewaxing Summary and Outlook References
Vapor-Assisted Remodeling of Thin Gold Films (2005)

In this paper we present the results of a systematic study of the remodeling of ultrathin (<20 nm) gold films by exposure to condensable vapors of volatile solvents. The starting gold films, deposited on glass, consist of closely packed gold nanoparticles with controlled nominal thickness. Heating to relatively low temperature (60−120 °C) and exposure to condensable vapor carried by flowing N2 gas lead to remodeling of the films' morphology. Electron and atomic force microscopy images show that the gold nanoparticles coalesce and form islands, interconnected networks, or holey continuous films, depending on the exposure time and the initial film thickness. Associated changes in the UV−vis spectra are similar to those seem in previous studies of thin gold films. Remodeling does not occur for films heated in a vacuum, immersed in solvent, or exposed to gases carrying saturated condensable vapor. Remodeling also occurs for other condensable vapors including water. Intermittent exposure of the films to ambient humidity followed by heating in house N2 gas also leads to remodeling. These observations are rationalized by a theoretical model of capillary condensation and partial flooding of the films' nanoscale pore spaces, leading to attractive capillary forces that draw the gold nanoparticles into intimate contact and accelerate the coalescence process.
CO2 Capture Using PIM-1 Hollow Fiber Sorbents with Enhanced Performance by PEI Infusion (2021)

This paper describes hollow fiber sorbents made of the parent polymer of intrinsic microporosity, PIM-1, using a spinning method designed to control the formation of dense barrier layers followed by a simple post treatment with polyethylenimine (PEI) for further improvement of CO2 uptake. The overall process involved solvent-moderated sheath-core spinning with a variation of core/bore flow rates and quench bath temperatures. Dope compositions to promote micropore interconnectivity were optimized by controlling the dope nonsolvent concentration. Under optimized conditions, undesirable skin layers were not formed, avoiding associated mass transfer resistance. The resulting PIM-1 hollow fiber sorbents achieved good CO2 uptake, with maximum equilibrium capacities of 2.8 mmol-CO2/g-fiber. CO2 sorption kinetics were dependent on PEI loading, allowing the designer to balance between capacity and uptake rate, a control feature unavailable with the pure PIM fiber sorbent.
Spindle pole body-associated Atg11, an autophagy-related protein, regulates microtubule dynamics essential for high-fidelity chromosome segregation (2021)

Abstract Emerging studies hint at the roles of autophagy-related proteins in various cellular processes in a eukaryotic cell. To understand if autophagy-related proteins influence genome stability, we examined a cohort of 35 autophagy mutants in Saccharomyces cerevisiae. We observed cells lacking Atg11 show poor mitotic stability of minichromosomes. Atg11 molecules dynamically localize to the spindle pole bodies (SPBs). Loss of Atg11 leads to a delayed cell cycle progression. Such cells accumulate at metaphase at an elevated temperature that is relieved when the spindle assembly checkpoint is inactivated. Indeed, atg11 Δ cells have stabilized securin levels, that prevent anaphase onset, confirming chromosome biorientation defects associated with the mutant. Atg11 functions in the Kar9-dependent spindle positioning pathway and maintains Kar9 asymmetry by facilitating proper dynamic instability of astral microtubules (aMTs). Taken together, this study uncovers a non-canonical role of Atg11 in facilitating MT dynamics crucial for chromosome segregation.
Development of Specialized Laser Doppler Velocimeters for High Resolution Flow Profile and Turbulence Spectral Measurements (2014)

Fluid dynamicists are always in need of innovative instruments for flow velocity measurements. An ideal instrument would be non-intrusive, have a very fine spatial resolution as well as a very fine temporal resolution, be able to measure three-components of velocity, and be compact. Through recent advancements, laser Doppler velocimetry can now meet all of those requirements making it an important part of aerodynamicist's research toolbox. The first paper presented in this manuscript style thesis explains the development of an advanced three-velocity component, spatially-resolving laser-Doppler velocimetry (LDV) system for highly resolved velocity measurements in situations with limited optical access. The new instrument, a next generation version of the previously developed 'comprehensive' LDV technology, enables measurements of three components of velocity and particle position in the axial direction all through a single transceiving lens. Described here is the design process and the final design for the 'compact, comprehensive' LDV (Comp²LDV). The probe was designed to achieve ± 10 micron root-mean-square uncertainties in axial particle position, which combined with the long measurement volume, allow researchers to obtain a three-velocity-component velocity statistics profiles over a span of approximately 1.5mm without the need for traversing. Results from measurements in a flat plate turbulent boundary layer very near the wall have compared favorably to data from previous studies. The second paper focuses on the motion and evolution of coherent structures in supersonic jet flows and how that relates to the intense noise the flows generate. As a preliminary study to experimentally address these relationships, novel non-intrusive measurements using two-component laser Doppler velocimetry (LDV) have been conducted at exceptionally high data rates to lend insight into the statistical behavior of noise-generating flow structures. A new heated supersonic jet facility has been constructed to provide supersonic flow at total temperatures ratios (T₀/Tₐ) up to 3. In the present work, the instrumentation is validated via comparison of LDV measurements along the centerline of a screeching cold jet with microphone and high-speed shadowgraph results. Reynolds stress spectra are presented for an over-expanded case (nozzle pressure ratio of 3.2) of a design Mach number 1.65 nozzle operated cold (T₀/Tₐ = 1). A preliminary study was then conducted in the near-nozzle shear layer, up to x/d = 4.0, at design nozzle pressure ratio (4.58) and total temperature ratio of 2.0. Results are presented for Reynolds stress time-delay correlations and power spectra at Re_d = 1.1M for this case. The stream-wise Reynolds normal stress spectra are compared with published spectral behavior reported by other researchers, indicating a similar spectral shape in the downstream stations as previously measured with LDV and hot wire anemometry for cold jets, but which differ in shape from density-based techniques.
On the Alkylation of Amino Acid Residues at the Active Site of Ribonuclease (1966)

Abstract Ribonuclease A has been subjected to reaction at pH 8.5 with a series of homologous α-bromo acids and with iodoacetamide. At this pH, carboxyalkylation occurs predominantly at the 3 amino acid residues which have been implicated in the catalytic function of the enzyme: histidine-12, histidine-119, and lysine-41. The histidine reactions proceed at rates which vary from 3 to 25% of those observed at pH 5.5. The extent of reaction at the three positions is dependent upon the structure of the alkylating agent. In the reaction with bromoacetate, the derivative alkylated at lysine-41 accounts for the major proportion of the reaction products, while with d-α-bromo-n-butyrate, histidine-12 is the predominant site of alkylation. In general, the reactions at the histidine residues display the same stereospecificity toward a reagent at pH 8.5 as observed at pH 5.5; reagents of the d configuration favor reaction at histidine-12, while their l antipodes alkylate the 119-position preferentially. No selectivity for the optical isomers of a given reagent is observed for the alkylation of lysine-41. Alkylation of the enzyme with iodoacetamide at pH 8.5 yields a complex mixture of products of which, in the initial stages of the reaction, the derivatives mono- and dicarboxamidomethylated at lysine-41 are prominent. The three products substituted at lysine-41 that have been characterized, namely the carboxymethyl, the carboxamidomethyl, and the dicarboxamidomethyl derivatives, all are essentially inactive. The active site histidine residues in the carboxymethyllysine-41 and carboxamidomethyllysine-41 derivatives react with bromoacetate at pH 5.5 at rates, respectively, 0.8 and 0.25 that of native ribonuclease. The effect of the 41-substituent is in each case to depress the alkylation of histidine-12 in relation to that at histidine-119. These findings indicate that although the chemical modification of lysine-41 inactivates ribonuclease, it does not substantially inhibit the alkylation of the histidine residues which have been implicated as part of the active site of the enzyme. From the information currently available, a tentative working model has been proposed for the spatial relationships of the chemically reactive nitrogen atoms of histidine-12, histidine-119, and lysine-41 in ribonuclease.
Error-free DWDM transmission and crosstalk analysis for a silicon photonics transmitter (2015)

Individual channels of a five-channel microring silicon photonics transmitter are used for bit error ratio analysis and demonstrate error-free transmission at 10Gb/s. Two channels of the same transmitter are concurrently modulated using an 80GHz channel spacing comb laser and demonstrate open eye diagrams at 10Gb/s and 12.5Gb/s. Finally, concurrent modulation with tunable lasers is done to quantify optical power penalty for link bit error ratio versus channel spacing from +100GHz to -100GHz. When using a comb laser for concurrent modulation, no direct power penalty is observed for an 80GHz channel separation.
First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans ) (2017)

Here we describe the sequencing and assembly of the pathogenic fungus <i>Lomentospora prolificans</i> using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,627,092 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8896 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.
Carrier concentration profiling on oxidized surfaces of Si device cross sections by resonant electron tunneling scanning probe spectroscopy (2008)

Quantitative carrier concentration profiles of super-junction power metal-oxide-semiconductor field-effect transistor devices were obtained by resonant electron tunneling (RET) scanning probe spectroscopy making use of a discrete energy level of adsorbed C60 molecules. RET voltage profiles measured on oxidized (100) surfaces of fine-polished cross sections revealed the presence of separated p-type islands in the n-type epitaxial layer and agreed well with the profiles obtained by local work function spectroscopy, although fluctuations were observed owing to surface defects and variations in the oxide and C60 film thickness. The derived boron concentration coincides with the implanted boron density obtained by numerical simulations. These results verify that the C60 RET scanning probe spectroscopy on oxidized surfaces has the ability of quantitative carrier concentration profiling of Si device cross sections, if flat surfaces with good quality are prepared.
Herpesvirus co-infection alters immune responses to human influenza virus infection. (2018)

Abstract Herpesviruses (HVs) cause lifelong infections, and the majority of humans are infected with at least one; whether co-infection with HVs is beneficial or detrimental to the host is a current debate. We sought to determine if co-infection with HVs alters the magnitude or quality of the immune response to influenza infection, and, if so, the extent to which each virus affects illness outcome. We used a longitudinal study of naturally acquired influenza virus infection and linear regression modeling to determine differences in influenza viral load and shedding, cytokine levels, and severity scores, while taking into account the effects of confounding variables. Our results show co-infection with HVs does not significantly affect influenza virus kinetics or clearance, but Cytomegalovirus is associated with decreased symptom severity and increased antibody titers. Furthermore, co-infection alters cytokine levels involved in each step of the immune response. Changes in plasma and nasal wash cytokines were predominately associated with Herpes simplex virus 1/2 and Epstein-Barr virus co-infection, respectively. The cytokines most affected by HV serostatus in the plasma and nasal wash are MIP1b (adj. R2 = 0.3073) and RANTES (adj. R2 = 0.3604), respectively. The strongest effects on cytokine levels are associated with HV interactions and are primarily found in the plasma. In the nasal wash, co-infection mostly results in decreased levels of cytokines, including those implicated in immunopathology during influenza infection (e.g. IL1, MIP1, TNF-α, IL6). Understanding host-virus interactions during co-infection and how that relationship impacts disease severity can ultimately be used for better prognosis and/or prophylactic measures.
Supplementary Table S3 from Immunotherapy with a HER2-Targeting <i>Listeria</i> Induces HER2-Specific Immunity and Demonstrates Potential Therapeutic Effects in a Phase I Trial in Canine Osteosarcoma (2023)

&lt;p&gt;ELISpot analysis of IFN-γ responses to the intracellular and extracellular domains of HER2/neu before and after ADXS31-164 administration.&lt;/p&gt;