gebhart/patrepeval huggingface dataset:
Magnetic particle-based sample-prep and valveing in microfluidic devices (2012)

There is a need to design an integrated microfluidic platform as simple and lean as possible in order to meet the requirements for a miniaturized system. Magnetic particles show a great versatility in performing several of the functions necessary in many microfluidic assays. We therefore have developed a compact portable system to perform magneticbead- based sample preparation steps in a chip such as DNA-extraction or particle-enhanced mixing of reagents. A central application in a standard biochemical/biological/medical laboratory is represented by PCR. The execution of a cyclic heating profile during PCR is a considerable stress for chip and liquid inside the chip because evaporation and uncontrolled condensation or unintended motion of the PCR solution. One strategy to overcome this problem consists of the implementation of valves flanking a stationary PCR in appropriate incubation cavities. In addition to the well-known elastomeric membrane valves, wax-valves mechanical turning or rotary valves flanking the PCR chamber, we present in this paper the use of clustered magnetic particles as blocking valves for such reaction chambers. We report on the capability of assembled magnetic particles to act as rather simple configurated valves during a PCR typical temperature regime. These novel valves efficiently withstand 1.5 bar pressure, prevent loss of aqueous liquid inside the reaction chamber via evaporation or bubble formation, and do not express adverse effects on any biological reaction inside the chip-based PCR cavity. The latter properties have been proven by a set of different PCRs performed in chip-based cavities.
Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical <i>N</i>-Glycosylation Sites on Albumin and α-1B-Glycoprotein (2018)

Most serum proteins are N-linked glycosylated, and therefore the glycoproteomic profiling of serum is essential for characterization of serum proteins. In this study, we profiled serum N-glycoproteome by our recently developed N-glycoproteomic method using solid-phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) coupled with LC-MS/MS and site-specific glycosylation analysis using GPQuest software. Our data indicated that half of identified N-glycosites were modified by at least two glycans, with a majority of them being sialylated. Specifically, 3/4 of glycosites were modified by biantennary N-glycans and 1/3 of glycosites were modified by triantennary sialylated N-glycans. In addition, two novel atypical glycosites (with N-X-V motif) were identified and validated from albumin and α-1B-glycoprotein. The widespread presence of these two glycosites among individuals was further confirmed by individual serum analyses.
A Database-Centric Virtual Chemistry System (2006)

We describe an Oracle database application for general use within virtual chemistry. The application functions as a central hub and repository for chemical data with interfaces to external calculators. It deals with the general problems of merging data from disparate sources and with scheduling of computational tasks for parallel or sequential execution in a mixed environment. The central database is used for the storage of input, intermediary, and final data as well as for job control. A calculation job is split into distinct tasks, or units of work, which are put in a queue. Tasks are dequeued and handled by specialized calculators. These calculators are in-house or commercial programs for which adaptor modules for connection to the database must be written. Tasks are handled in a transactional fashion, so that uncompleted or failed tasks are left in the queue. This makes the system stable to many types of disturbances. Sorting, filtering, and merging operations are handled by the database itself. Usage is very general, but some specific examples are (1) as a back end for a chemical property calculator Web page, (2) in an automated quantitative structure-activity relationship system, and (3) in virtual screens.
Smart Robots (1985)

Here is one of the first really thorough presentations on smart robots. Robots, machine vision systems, sensors, manipulators, expert systems, and artificial intelligence concepts combined in state-of
In Vitro Synthesis of an Infectious Mutant RNA with a Normal RNA Replicase (1966)

When purified Qbeta-RNA replicase is presented alternately with two genetically different Qbeta-RNA molecules, the RNA synthesized is identical to the initiating template. The results establish that the RNA is the instructive agent in the replicative process and hence that it satisfies the operational definition of a self-duplicating entity. The data also eliminate alternative explanations which do not involve self-propagation of the input RNA. An opportunity is now provided for studying the genetics and evolution of a self-duplicating nucleic acid molecule under conditions permitting detailed control of environmental parameters and chemical components.
<i>In Vivo</i>Supervised Analysis of Stent Reendothelialization From Optical Coherence Tomography (2010)

The aim of this study is to interactively assess reendothelialization of stents at an accuracy of down to a few micrometer by analyzing endovascular optical coherence tomography (OCT) sequences. Vessel wall and stent struts are automatically detected by using morphological, gradient, and symmetry operators coupled with active contour models; alerts are issued to ask for user supervision over some extreme irregular geometries caused by thrombotic lesions or dissections. A complete distance map is then computed from sparse distances measured between wall and struts. Missing values are interpolated by thin-plate spline (TPS) functions. Accuracy and robustness are increased by taking into account the inhomogeneity of data points and integrating in the same framework orthogonalized forward selection of support points, optimal selection of regularization parameters by generalized cross-validation, and rejection of detection outliers. Validation is performed on simulated data, phantom acquisitions and 11 typical in vivo OCT sequences. The comparison against manual expert measurements demonstrates a bias of the order of OCT resolution (less than 10 microm) and a standard deviation of the order of the strut width (less than 150 microm).
Association between inaccurate estimation of body size and obesity in schoolchildren (2015)

The results of this study suggest there is a high prevalence of inaccurate body size estimation and that inaccurate estimation is associated with obesity. Accurate estimation of own body size is important among obese schoolchildren because it may be the first step towards adopting healthy lifestyle behaviors.
3-Hydroxy-5-Methoxystilbene-2-Carboxylic acid, a phytotoxic compound isolated from methanolic extracts of pigeonpea (<i>Cajanus cajan</i>Millsp.) leaves (1993)

Abstract A phytotoxic compound was identified in methanolic extracts of pigeonpea leaves. Results of fractionation of methanolic extracts to acidic, basic, and neutral compounds revealed that the acidic fraction exerted a strong inhibitory activity on lettuce radicle elongation. Further purification of the acidic fraction by preparative silica gel TLC showed that the one fraction inhibited lettuce germination completely. Analysis of the biological active fraction by HPLC enabled to detect a single peak with maximum UV absorption at 258 nm. The phytotoxic compound was crystallized from methanolic extracts of fresh leaves (5 kg) with subsequent purification by silica gel column chromatography after extraction of the acidic compounds. The structure of the isolated phytotoxic compound analyzed by MS and NMR was found to correspond to 3-hydroxy-5-methoxystilbene-2-carboxylic acid that inhibited the lettuce radicle elongation by about 80% at the concentration of 500 μmol L-1. The possible role of the phytotoxic compound identified in pigeonpea leaves was discussed in relation to allelopathy. Key Words: allelopathy3-hydroxy-5-methoxystilbene-2-carboxylic acidinhibitionlettuce (Lactuca sativa L.)pigeonpea (Cajanus cajan Millsp.)
Network-adaptive rate control with TCP-friendly protocol for multiple video objects (2002)

Delivering visual content over the Internet with acceptable quality is an important and challenging task. In order to maintain good quality of service (QoS) in the current best-effort Internet, bandwidth adaptation to the varying network conditions is desired for streaming video over the Internet. In this paper, we propose a new rate control scheme for streaming MPEG4 video containing multiple video objects in conjunction with a TCP-friendly transport protocol that dynamically estimates available network bandwidth on the fly. Furthermore, network packet loss rate is taken into account in rate adaptation so that the end-to-end distortion is minimized. Simulation results demonstrate the effectiveness of our proposed scheme.
Biologics in organ transplantation (2012)

The last two decades have witnessed a pandemic in antibody development, with over 600 entering clinical studies and a total of 28 approved by the FDA and European Union. The incorporation of biologics in transplantation has made a significant impact on allograft survival. Herein, we review the armamentarium of clinical and preclinical biologics used for organ transplantation--with the exception of belatacept--from depleting and IL-2R targeting induction agents to costimulation blockade, B-cell therapeutics, BAFF and complement inhibition, anti-adhesion, and anti-cytokine approaches. While individual agents may be insufficient for tolerance induction, they provide possibilities for reduction of steroid or calcineurin inhibitor use, alternatives to rejection episodes refractory to conventional therapies, and specialized immunosuppression for highly sensitized patients.
Effect of Ultraviolet Radiation on Organic Photovoltaic Materials and Devices (2019)

Organic photovoltaics are a sustainable and cost-effective power-generation technology that may aid the move to zero-emission buildings, carbon neutral cities, and electric vehicles. While state-of-the-art organic photovoltaic devices can be encapsulated to withstand air and moisture, they are currently still susceptible to light-induced degradation, leading to a decline in the long-term efficiency of the devices. In this study, the role of ultraviolet (UV) radiation on a multilayer organic photovoltaic device is systematically uncovered using spectral filtering. By applying long-pass filters to remove different parts of the UV portion of the AM1.5G spectrum, two main photodegradation processes are shown to occur in the organic photovoltaic devices. A UV-activated process is found to cause a significant decrease in the photocurrent across the whole spectrum and is most likely linked to the deterioration of the charge extraction layers. In addition, a photodegradation process caused by UV-filtered sunlight is found to change the micromorphology of the bulk heterojunction material, leading to a reduction in photocurrent at high photon energies. These findings strongly suggest that the fabrication of inherently photostable organic photovoltaic devices will require the replacement of fullerene-based electron transporter materials with alternative organic semiconductors.
Stability of monodisperse polystyrene latex dispersions of various sizes (1966)

A series of monodisperse polystyrene latex dispersions has been prepared covering a range of particle sizes from 600 to 4230 Å. The kinetics of flocculation of the latex dispersions by barium nitrate solutions were examined and the results used to construct curves of the logarithm of the stability ratio against the logarithm of electrolyte concentration. The slopes of the curves were calculated theoretically and compared with those obtained experimentally. The theory predicted an increase of slope with particle size which was not observed experimentally. Experimental estimates of the Hamaker constant give values ranging from 1.03 × 10–14 to 1.10 × 10–13 erg.
Role of PGE<sub>2</sub>in α<sub>2</sub>-induced inhibition of AVP- and cAMP-stimulated H<sub>2</sub>O, Na<sup>+</sup>, and urea transport in rat IMCD (2000)

PGE(2) inhibits osmotic water permeability (P(f)) in the rat inner medullary collecting duct (IMCD) via cellular events occurring after the stimulation of cAMP, i.e., post-cAMP-dependent events. The alpha(2)-agonists also inhibit P(f) in the rat IMCD via post-cAMP-dependent events. The purpose of this study was to determine whether PGE(2) plays a role in alpha(2)-mediated inhibition of P(f), Na(+), and urea transport in the rat IMCD. Isolated terminal IMCDs from Wistar rats were perfused to measure, in separate experiments, P(f), lumen-to-bath (22)Na(+) transport (J(lb)), and urea permeability (P(u)). Transport was stimulated with 220 pM arginine vasopressin (AVP) or 0.1 mM 8-(4-chlorophenylthio)-cAMP (CPT-cAMP). Indomethacin was used to inhibit endogenous prostaglandin synthesis, and the alpha(2)-agonists clonidine, oxymetazoline, and dexmedetomidine were used to test the role of PGE(2) in the alpha(2)-mediated mechanism that inhibits transport. All agents were added to the bath. Indomethacin at 5 microM significantly elevated CPT-cAMP-stimulated P(f), J(lb), and P(u), and subsequent addition of 100 nM PGE(2) reduced these transport parameters. Indomethacin reversed alpha(2) inhibition of CPT-cAMP-stimulated P(f), J(lb), and P(u), and subsequent addition of PGE(2) reduced transport in each case. Indomethacin partially reversed alpha(2) inhibition of AVP-stimulated P(f), J(lb), and P(u), and PGE(2) reduced transport back to the alpha(2)-inhibited level. These results indicate that PGE(2) is a second messenger involved in the mechanism of transport inhibition mediated by alpha(2)-adrenoceptors via post-cAMP-dependent events in the rat IMCD.
Importin β Can Mediate the Nuclear Import of an Arginine-Rich Nuclear Localization Signal in the Absence of Importin α (1999)

The import of proteins into the nucleus is dependent on cis-acting targeting sequences, nuclear localization signals (NLSs), and members of the nuclear transport receptor (importin-beta-like) superfamily. The most extensively characterized import pathway, often termed the classical pathway, is utilized by many basic-type (lysine-rich) NLSs and requires an additional component, importin alpha, to serve as a bridge between the NLS and the import receptor importin beta. More recently, it has become clear that a variety of proteins enter the nucleus via alternative import receptors and that their NLSs bind directly to those receptors. By using the digitonin-permeabilized cell system for protein import in vitro, we have defined the import pathway for the Rex protein of human T-cell leukemia virus type 1. Interestingly, the arginine-rich NLS of Rex uses importin beta for import but does so by a mechanism that is importin alpha independent. Based on the ability of the Rex NLS to inhibit the import of the lysine-rich NLS of T antigen and of both NLSs to be inhibited by the domain of importin alpha that binds importin beta (the IBB domain), we infer that the Rex NLS interacts with importin beta directly. In addition, and in keeping with other receptor-mediated nuclear import pathways, Rex import is dependent on the integrity of the Ran GTPase cycle. Based on these results, we suggest that importin beta can mediate the nuclear import of arginine-rich NLSs directly, or lysine-rich NLSs through the action of importin alpha.
Architecture of neural synaptic array, design and simulation (2007)

In this paper, we present the design of artificial neural network architecture to implement the look-up table of reconfigurable circuits. The various cells of schematic used only the carbon nanotubes semiconductors (CNTFET), and the non volatile multi-level resistance. The compatibility between CNTFET and non volatile multi-level resistance in the state of the art has been studied. Then the electrical circuit simulation results demonstrate successful learning of the linearly separable logical functions.
The phosphorylation of protein kinase C as a potential measure of activation (1989)

As a means of determining the role of protein kinase C in the signal transduction from novel growth factors and hormones, we investigated the effects of well-characterized agents on the phosphorylation state of protein kinase C itself. These studies show that agents that stimulate protein kinase C either directly (phorbol esters) or indirectly through phosphatidylinositol breakdown (platelet-derived growth factor) induce an increase in the phosphorylation state of the kinase. By contrast, epidermal growth factor, which does not stimulate protein kinase C in fibroblasts, does not increase the phosphorylation state of protein kinase C, but leads to a decrease. The data suggest that the phosphorylation state of protein kinase C is dynamically controlled and can be used to provide evidence of protein kinase C activation.
Production of ion beams in high-power laser–plasma interactions and their applications (2004)

Energetic ion beams are produced during the interaction of ultrahigh-intensity, short laser pulses with plasmas. These laser-produced ion beams have important applications ranging from the fast ignition of thermonuclear targets to proton imaging, deep proton lithography, medical physics, and injectors for conventional accelerators. Although the basic physical mechanisms of ion beam generation in the plasma produced by the laser pulse interaction with the target are common to all these applications, each application requires a specific optimization of the ion beam properties, that is, an appropriate choice of the target design and of the laser pulse intensity, shape, and duration.
Analysis of the mechanical behavior of a titanium scaffold with a repeating unit‐cell substructure (2009)

Titanium scaffolds with controlled microarchitecture have been developed for load bearing orthopedic applications. The controlled microarchitecture refers to a repeating array of unit-cells, composed of sintered titanium powder, which make up the scaffold structure. The objective of this current research was to characterize the mechanical performance of three scaffolds with increasing porosity, using finite element analysis (FEA) and to compare the results with experimental data. Scaffolds were scanned using microcomputed tomography and FEA models were generated from the resulting computer models. Macroscale and unit-cell models of the scaffolds were created. The material properties of the sintered titanium powders were first evaluated in mechanical tests and the data used in the FEA. The macroscale and unit-cell FEA models proved to be a good predictor of Young's modulus and yield strength. Although macroscale models showed similar failure patterns and an expected trend in UCS, strain at UCS did not compare well with experimental data. Since a rapid prototyping method was used to create the scaffolds, the original CAD geometries of the scaffold were also evaluated using FEA but they did not reflect the mechanical properties of the physical scaffolds. This indicates that at present, determining the actual geometry of the scaffold through computed tomography imaging is important. Finally, a fatigue analysis was performed on the scaffold to simulate the loading conditions it would experience as a spinal interbody fusion device.
Renal and vascular benefits of C-peptide: Molecular mechanisms of C-peptide action (2008)

C-peptide has long been thought to be an inert byproduct of insulin production, but it has become apparent, and accepted, that C-peptide has important biological properties. C-peptide displays beneficial effects in many tissues affected by diabetic complications, such as increased peripheral blood flow and protection from renal damage. However, the mechanisms mediating these effects remain unclear. C-peptide interacts with cellular membranes at unidentified sites distinctive of the insulin family of receptors, and signals to multiple targets known to play a role in diabetes and diabetic complications, such as Na(+)/K(+)-ATPase and NOS. In general, the physiological and molecular effects of C-peptide resemble insulin, but C-peptide also possesses traits separate from those of insulin. These basic studies have been confirmed in human studies, suggesting that C-peptide may lend itself to clinical applications. However, the molecular and physiological properties of C-peptide are not completely elucidated, and large clinical studies have not begun. In order to further these goals, we critically summarize the current state of knowledge regarding C-peptide's renal and vascular effects and the molecular signaling of C-peptide.
Weighted selection of image features for resolved rate visual feedback control (1991)

The authors develop methodologies for the automatic selection of image features to be used to visually control the relative position and orientation (pose) between the end-effector of an eye-in-hand robot and a workpiece. A resolved motion rate control scheme is used to update the robot's pose based on the position of three features in the camera's image. The selection of these three features depends on a blend of image recognition and control criteria. The image recognition criteria include feature robustness, completeness, cost of feature extraction, and feature uniqueness. The control criteria include system observability, controllability, and sensitivity. A weighted criteria function is used to select the combination of image features that provides the best control of the end-effector of a general six-degrees-of-freedom manipulator. Both computer simulations and laboratory experiments on a PUMA robot arm were conducted to verify the performance of the feature-selection criteria.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A fault tolerant technique for scheduling periodic tasks in real-time systems (2004)

We present a heuristic for producing a fault-tolerant schedule of given periodic tasks in distributed real-time systems. Tasks are divided into two classes according to their task utilization. In order to recover from faults, a hybrid scheme based on space redundancy and time redundancy is used. We use a very simple and fast heuristic to provide fault tolerance and reduce time overhead in case of transient faults in distributed real-time systems. We show that our approach can improve processor utilization.
Group cognition in computer‐assisted collaborative learning (2005)

Abstract Recent research on instructional technology has focused increasingly on the potential of computer support to promote collaborative learning. Socio‐cultural theories have been imported from cognate fields to suggest that cognition and learning take place at the level of groups and communities as well as individuals. Various positions on this issue have been proposed and a number of theoretical perspectives have been recommended. In particular, the concept of common ground has been developed to explain how meanings and understandings can be shared by multiple individuals. This paper takes a critical look at the concept of shared meaning as it is generally used and proposes an empirical study of how group cognition is constituted in practice.