gebhart/patrepeval huggingface dataset:
Bioassay of Endotoxin: Correlation Between Pyrogenicity for Rabbits and Lethality for Chick Embryos (1966)

Journal Article Bioassay of Endotoxin: Correlation Between Pyrogenicity for Rabbits and Lethality for Chick Embryos Get access Kelsey C. Milner, Kelsey C. Milner Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard A. Finkelstein Richard A. Finkelstein Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 116, Issue 5, December 1966, Pages 529–536, https://doi.org/10.1093/infdis/116.5.529 Published: 01 December 1966 Article history Received: 21 May 1966 Published: 01 December 1966
Low-cost visual postural feedback with Wii balance board and Microsoft Kinect - a feasibility study (2013)

A posture training paradigm with visual biofeedback is presented for physical rehabilitation following posture disorders (e.g. Pusher Syndrome). The objectives of the current study were: to calculate centre of pressure (CoP) using Wii balance board, to calculate centre of mass (CoM) using Microsoft Kinect sensor, and conceptual design of visual postural-feedback paradigm so that the user can improve functional reach tasks. The algorithm for calculating the posture based on the line connecting CoP-CoM (i.e. the lean-line), which was validated offline with a convenient sampling of 10 elderly (>50 years) subjects, where the maximum angle of the lean-line (with horizontal, i.e. the lean-angle) was compared with the Berg Balance Score - a widely used measure to predict risk of falls in elderly - during maximum forward, sideways, and backward lean. Since both the CoP and CoM moved during the task, the line joining CoP-CoM was indicative of the posture. A high correlation was found between the maximum lean-angle and the Berg Balance Score, and therefore it was proposed as a viable biofeedback for posture training.
Reliable Change Estimates for Assessing Recovery From Concussion Using the ANAM4 TBI-MIL (2015)

Information from this effort, specifically the reliable change parameters and the base rates of reliable decline, can be used to assist with the identification of postdeployment cognitive issues.
Fast and robust mesh arrangements using floating-point arithmetic (2020)

We introduce a novel algorithm to transform any generic set of triangles in 3D space into a well-formed simplicial complex. Intersecting elements in the input are correctly identified, subdivided, and connected to arrange a valid configuration, leading to a topologically sound partition of the space into piece-wise linear cells. Our approach does not require the exact coordinates of intersection points to calculate the resulting complex. We represent any intersection point as an unevaluated combination of input vertices. We then extend the recently introduced concept of indirect predicates [Attene 2020] to define all the necessary geometric tests that, by construction, are both exact and efficient since they fully exploit the floating-point hardware. This design makes our method robust and guaranteed correct, while being virtually as fast as non-robust floating-point based implementations. Compared with existing robust methods, our algorithm offers a number of advantages: it is much faster, has a better memory layout, scales well on extremely challenging models, and allows fully exploiting modern multi-core hardware with a parallel implementation. We thoroughly tested our method on thousands of meshes, concluding that it consistently outperforms prior art. We also demonstrate its usefulness in various applications, such as computing efficient mesh booleans, Minkowski sums, and volume meshes.
Screening and cDNA Cloning of Kv1 Potassium Channel Toxins in Sea Anemones (2010)

When 21 species of sea anemones were screened for Kv1 potassium channel toxins by competitive inhibition of the binding of (125)I-α-dendrotoxin to rat synaptosomal membranes, 11 species (two species of Actiniidae, one species of Hormathiidae, five species of Stichodactylidae and three species of Thalassianthidae) were found to be positive. Furthermore, full-length cDNAs encoding type 1 potassium channel toxins from three species of Stichodactylidae and three species of Thalassianthidae were cloned by a combination of RT-PCR, 3'RACE and 5'RACE. The precursors of these six toxins are commonly composed of signal peptide, propart and mature peptide portions. As for the mature peptide (35 amino acid residues), the six toxins share more than 90% sequence identities with one another and with κ(1.3)-SHTX-She1a (Shk) from Stichodactyla helianthus but only 34-63% identities with the other type 1 potassium channel toxins.
Targeting Cyclin-Dependent Kinases in Human Cancers: From Small Molecules to Peptide Inhibitors (2015)

Cyclin-dependent kinases (CDK/Cyclins) form a family of heterodimeric kinases that play central roles in regulation of cell cycle progression, transcription and other major biological processes including neuronal differentiation and metabolism. Constitutive or deregulated hyperactivity of these kinases due to amplification, overexpression or mutation of cyclins or CDK, contributes to proliferation of cancer cells, and aberrant activity of these kinases has been reported in a wide variety of human cancers. These kinases therefore constitute biomarkers of proliferation and attractive pharmacological targets for development of anticancer therapeutics. The structural features of several of these kinases have been elucidated and their molecular mechanisms of regulation characterized in depth, providing clues for development of drugs and inhibitors to disrupt their function. However, like most other kinases, they constitute a challenging class of therapeutic targets due to their highly conserved structural features and ATP-binding pocket. Notwithstanding, several classes of inhibitors have been discovered from natural sources, and small molecule derivatives have been synthesized through rational, structure-guided approaches or identified in high throughput screens. The larger part of these inhibitors target ATP pockets, but a growing number of peptides targeting protein/protein interfaces are being proposed, and a small number of compounds targeting allosteric sites have been reported.
Microstructured Nanopore-Walled Porous Silicon as an Anode Material for Rechargeable Lithium Batteries (2008)

Porous silicon (PS) with a micro-nano-hybrid structure has been successfully fabricated with an electrochemical etching process. The micropores consist of one-dimensional tunnels, which vary from ca. 1 to in pore diameter and extend up to in depth. The walls of these micropores are covered with a nanoporous structure that consists of small spherical particles, the feature size of which is of the order of tens of nanometers or smaller. The as-prepared PS structures show cathodic/anodic peaks for lithiation/delithiation during cyclic voltammetry with minimal destruction of either the micropore or nanopore of its wall even after 50 cycles. Furthermore, the peak current, the cumulative charge increase, and the electrochemical impedance for electrode reactions consistently decreases with the surface area of the tunnel wall, indicating that processes at the tunnel wall govern the overall lithiation/delithiation reactions. A hybrid porous structure consisting of microtunnels with nanostructured surface layers appears to provide a viable and practical way to utilize silicon for anode materials in rechargeable microbatteries.
Texture segmentation using directional empirical mode decomposition (2005)

In this paper the technique of directional empirical mode decomposition (DEMD) and its application to texture segmentation are presented. Empirical mode decomposition (EMD) decomposes signals by sifting and then analyzes the instantaneous frequency of the obtained components called intrinsic mode functions (IMF). As a new form of extending 1D EMD to the 2D case, DEMD considers the directional frequency and envelope at each point. One type of 2D Hilbert transform is introduced to compute the analytical functions for the frequency and envelope. The technique of selecting directions for DEMD based on texture's Wold theory is also presented. Experimental results indicate the effectiveness of the method for texture segmentation.
Graphene and graphitic derivative filled polymer composites as potential sensors (2014)

Graphite and numerous graphitic-derived micro- and nano-particles have gained importance in current materials science research. These two-dimensional sheets of sp(2)-hybridized carbon atoms remarkably influence the properties of polymers. Graphene mono-layers, graphene oxides, graphite oxides, exfoliated graphite, and other related materials are derived from a parental graphite structure. In this review, we focus primarily on the role of these fillers in regulating the electrical and sensing properties of polymer composites. It has been demonstrated that the addition of an optimized mixture of graphene and or its derivatives to various polymers produces a record-high enhancement of the electrical conductivity and achieved semiconducting characteristics at small filler loading, making it suitable for sensor manufacture. Promising sensing characteristics are observed in graphite-derived composite films compared with those of micro-sized composites and the properties are explained mainly based on the filler volume fraction, nature and rate of dispersion and the filler polymer interactions at the interface. In short, this critical review aims to provide a thorough understanding of the recent advances in the area of graphitic-based polymer composites in advanced electronics. Future perspectives in this rapidly developing field are also discussed.
Physiological Characterization of Root Zn2+ Absorption and Translocation to Shoots in Zn Hyperaccumulator and Nonaccumulator Species of Thlaspi (1996)

Radiotracer techniques were employed to characterize 65Zn2+ influx into the root symplasm and translocation to the shoot in Thlaspi caerulescens, a Zn hyperaccumulator, and Thlaspi arvense, a nonaccumulator. A protocol was developed that allowed us to quantify unidirectional 65Zn2+ influx across the root-cell plasma membrane (20 min of radioactive uptake followed by 15 min of desorption in a 100 [mu]M ZnCl2 + 5 mM CaCl2 solution). Concentration-dependent Zn2+ influx in both Thlaspi species yielded nonsaturating kinetic curves that could be resolved into linear and saturable components. The linear kinetic component was shown to be cell-wall-bound Zn2+ remaining in the root after desorption, and the saturable component was due to Zn2+ influx across the root-cell plasma membrane. This saturable component followed Michaelis-Menten kinetics, with similar apparent Michaelis constant values for T. caerulescens and T. arvense (8 and 6 [mu]M, respectively). However, the maximum initial velocity for Zn2+ influx in T. caerulescens root cells was 4.5-fold higher than for T. arvense, indicating that enhanced absorption into the root is one of the mechanisms involved in Zn hyperaccumulation. After 96 h 10-fold more 65Zn was translocated to the shoot of T. caerulescens compared with T. arvense. This indicates that transport sites other than entry into the root symplasm are also stimulated in T. caerulescens. We suggest that although increased root Zn2+ influx is a significant component, transport across the plasma membrane and tonoplast of leaf cells must also be critical sites for Zn hyperaccumulation in T. caerulescens.
Inhibition of ApoCIII (2014)

The central role of apoCIII in hypertriglyceridemia and cardiovascular disease was further cemented by recent findings and promising intervention data that showed the possibility of using antisense therapy to lower apoCIII and triglyceride levels. Currently, planned phase 3 trials should provide answers in regards to long-term efficacy and safety of this novel therapy.
Modeling of RF energy scavenging for batteryless wireless sensors with low input power (2013)

RF energy scavenging enables batteryless operation of wireless sensors. In particular, a system with a central controller that transfers wireless energy to and exchanges information with RF energy scavenging sensors is very suitable for a wide range of applications. State-of-the-art analysis of RF energy scavenging is mostly based on RF-DC rectifier models operating with relatively high input power to achieve high rectification efficiency. However, to enable larger distance between the central controller and sensors and/or to increase the operating frequencies, which can lead to small and low-cost smart dust like sensors, a good model describing the RF-DC rectification with low input power is needed to aid system design and optimization. In this paper, we develop such a model. Using the model, we derive closed-form solutions for the equilibrium voltage and the input resistance of the rectifier. We further propose a quasi-static model to describe the dynamic charging of the capacitor in the rectifier. A comparison with circuit simulations using Cadence Virtuoso Spectre circuit simulator shows good match between our model and the circuit simulation.
Analysis of Proteus mirabilis Distribution in Multi-Species Biofilms on Urinary Catheters and Determination of Bacteria Resistance to Antimicrobial Agents (2013)

The objectives of the investigation presented in this paper were: to examine the frequency of P. mirabilis isolation from catheters and assess the complexity of multi-species biofilms which these bacteria form, as well as to determine the vulnerability of planktonic and sessile P. mirabilis populations to popular antibiotics and compare it to the susceptibility of other Gram-negative bacteria isolated as associated flora from multi-species biofilm. 88 urological catheters, collected from long-term catheterized patients were examined. Uropathogens were recovered from the catheter surface by sonication, and identified on standard diagnostic media. The broth-microdilution method and the MBEC High-throughput Screening assay were used to determine the bacterial resistance to antibiotics. 279 microorganisms were isolated from 88 urinary catheter biofilms. The Enterobacteriaceae family were the most frequently detected bacteria (53.2% of isolates), whereas Proteus spp. isolation accounted for 17.9%, which placed these bacilli on the third position in the Enterobacteraceae family. Among all the tested drugs, amikacin and cephalosporins (ceftriaxone, cefotaxime and cefaclor) exhibited the highest activity against P. mirabilis planktonic cells, 86% and 73% of strains were susceptible to these antibiotics, respectively. 100% of P. mirabilis sessile forms were resistant to cefepime, ciprofloxacin, gatifloxacin, and norfloxacin. Amikacin and ceftriaxone affected only 5% of sessile forms. The planktonic cells of the other studied uropathogens were mostly vulnerable to the all tested drugs (exception P. aeruginosa strains), the most effective of which occurred to be amikacin and cefepime. Obtained MBECs values were 2-512-fold higher than MICs assessed for planktonic forms.
A joint localization and synchronization technique using time of arrival at multiple antenna receivers (2013)

In this work, a system scheme is proposed for tracking a radio emitting target moving in two-dimensional space. The localization is based on the use of biased time-of-arrival (TOA) measurements obtained at two asynchronous receivers, each equipped with two closely spaced antennas. By exploiting the multi-antenna configuration and using all the TOA measurements up to current time step, the relative clock bias at each receiver and the target position are jointly estimated by solving a nonlinear least-squares (NLS) problem. To this end, a novel time recursive algorithm is proposed which fully takes advantage of the problem structure to achieve computational efficiency while using orthogonal transformations to ensure numerical reliability. The Cramer-Rao lower bound (CRLB) is also derived as a lower bound on the error in estimating the position and biases. Simulation results show that the mean-squared error (MSE) of the proposed method approaches the CRLB closely.
Removal of Organic Micropollutants from Contaminated Groundwater by Oxidation and Stripping (1987)

Abstract In 1984, Environment Canada carried out a bench scale study on the removal of organic micropollutants from contaminated groundwater. The groundwater samples were obtained from the Special Waste Compound at Gloucester Landfill Site, near Ottawa, Ontario. The objective of the study was to evaluate the effectiveness of chemical oxidation to destroy the organic micropollutants present in this groundwater. Comparison was made between the results of ozonation and the air stripping effects. The oxidants evaluated were ozone (O3), sodium hypochlorite (NaOCl), chlorine dioxide (ClO2) and hydrogen peroxide (H2O2) with hydrated iron sulphate FeSO4 7H2O (Fenton’s reagent). The organics present in the contaminated groundwater included the following, predominantly volatile, compounds: bromodichloro-methane, bromoform, 1,1,1-trichloroethane, chloroform, 1,1-dichloroethane, dichloromethane, 1,2-dichloroethane, 1,1-dichloroethylene, and trichloroethylene. The process variables investigated were pH and oxidant dosage. The significance of low and high values of these variables was examined by using a full 22 factorial design. From the results, it appeared that the best removal efficiency was achieved by using ozone as an oxidant. However, during the experiments, it was observed that the ozonation process was being confounded with the air stripping process. Chlorine dioxide and hydrogen peroxide, in that order, were determined to be less effective oxidants. Sodium hypochlorite was found to be the least effective oxidant in this study. The results of this study demonstrated that air stripping was the most appropriate technology for the removal of the organic compounds from this groundwater.
Interaction of Polar and Nonpolar Polyfluorenes with Layers of Two-Dimensional Titanium Carbide (MXene): Intercalation and Pseudocapacitance (2017)

This article provides insight into the interaction of synthetic conjugated polymers [polyfluorene derivatives (PFDs)] with layers of two-dimensional titanium carbide (Ti3C2Tx). Three derivatives with nonpolar, polar, and charged nitrogen-containing functionalities were synthesized via the Suzuki polycondensation reaction. The organic–inorganic PFD/Ti3C2Tx hybrids were prepared and characterized using X-ray diffraction and a range of microscopic and spectroscopic techniques to elucidate the host–guest interaction mechanism. We show that polar polymers with charged nitrogen-containing ends have the strongest interaction with the Ti3C2Tx layers, yielding an increase in interlayer spacing and large shifts in spectroscopic peaks. Furthermore, the effect of polymer backbone juxtaposition between Ti3C2Tx layers on pseudocapacitance is discussed in detail. Our results suggest that new organic materials capable of intercalation between the layers of Ti3C2Tx and other MXenes may be used in the design of hybrid structures for high-performance energy storage applications and beyond.
Diffeomorphic demons using normalized mutual information, evaluation on multimodal brain MR images (2010)

The demons algorithm is a fast non-parametric non-rigid registration method. In recent years great efforts have been made to improve the approach; the state of the art version yields symmetric inverse-consistent largedeformation diffeomorphisms. However, only limited work has explored inter-modal similarity metrics, with no practical evaluation on multi-modality data. We present a diffeomorphic demons implementation using the analytical gradient of Normalised Mutual Information (NMI) in a conjugate gradient optimiser. We report the first qualitative and quantitative assessment of the demons for inter-modal registration. Experiments to spatially normalise real MR images, and to recover simulated deformation fields, demonstrate (i) similar accuracy from NMI-demons and classical demons when the latter may be used, and (ii) similar accuracy for NMI-demons on T1w-T1w and T1w-T2w registration, demonstrating its potential in multi-modal scenarios.
Dynamical Characterization of the Heme NO Oxygen Binding (HNOX) Domain. Insight into Soluble Guanylate Cyclase Allosteric Transition (2008)

Since the discovery of soluble guanylate cyclase (sGC) as the mammalian receptor for nitric oxide (NO), numerous studies have been performed in order to understand how sGC transduces the NO signal. However, the structural basis of sGC activation is still not completely elucidated. Spectroscopic and kinetic studies showed that the key step in the activation mechanism was the NO-induced breaking of the iron proximal histidine bond in the so-called 6c-NO to 5c-NO transition. The main breakthrough in the understanding of sGC activation mechanism came, however, from the elucidation of crystal structures for two different prokaryotic heme NO oxygen (HNOX) domains, which are homologues to the sGC heme domain. In this work we present computer simulation results of Thermoanaerobacter tencogensis HNOX that complement these structural studies, yielding molecular explanations to several poorly understood properties of these proteins. Specifically, our results explain the differential ligand binding patterns of the HNOX domains according to the nature of proximal and distal residues. We also show that the natural dynamics of these proteins is intimately related with the proposed conformational dependent activation process, which involves mainly the alphaFbeta1 loop and the alphaA-alphaC distal subdomain. The results from the sGC models also support this view and suggest a key role for the alphaFbeta1 loop in the iron proximal histidine bond breaking process and, therefore, in the sGC activation mechanism.
Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology (2000)

The frequency and distribution of putatively nitrite-oxidizing, Nitrospira- like bacteria in nitrifying biofilms from two reactors receiving wastewater with different ammonia and salt concentrations were observed by fluorescent in situ hybridization. For this purpose, new 16S rRNA-directed oligonucleotide probes targeting the bacterial phylum Nitrospira and the three main lineages within this phylum were developed and evaluated. The diversity of Nitrospira-like bacteria in the reactors was additionally investigated by retrieval and comparative analysis of full 16S rRNA sequences from the biofilms. We found that, despite of the differences in the influent composition, Nitrospira-like bacteria form dominant populations in both reactors. In addition, first insights into the physiology of these still unculturable bacteria were obtained by the incubation of active biofilm samples with radioactively labeled substrates followed by the combined application of fluorescent in situ hybridization and microautoradiography. The results are discussed in consideration of the frequently observed dominance of Nitrospira-like bacteria in nitrifying bioreactors. Consequently, high priority should be assigned to future studies on the ecology and physiology of these organisms in order to increase our fundamental understanding of nitrogen cycling and to enable knowledge-driven future improvements of nitrifying wastewater treatment plants.