gebhart/patrepeval huggingface dataset:
Microfluidic, Label-Free Enrichment of Prostate Cancer Cells in Blood Based on Acoustophoresis (2012)

Circulating tumor cells (CTC) are shed in peripheral blood at advanced metastatic stages of solid cancers. Surface-marker-based detection of CTC predicts recurrence and survival in colorectal, breast, and prostate cancer. However, scarcity and variation in size, morphology, expression profile, and antigen exposure impairs reliable detection and characterization of CTC. We have developed a noncontact, label-free microfluidic acoustophoresis method to separate prostate cancer cells from white blood cells (WBC) through forces generated by ultrasonic resonances in microfluidic channels. Implementation of cell prealignment in a temperature-stabilized (±0.5 °C) acoustophoresis microchannel dramatically enhanced the discriminatory capacity and enabled the separation of 5 μm microspheres from 7 μm microspheres with 99% purity. Next, we determined the feasibility of employing label-free microfluidic acoustophoresis to discriminate and divert tumor cells from WBCs using erythrocyte-lysed blood from healthy volunteers spiked with tumor cells from three prostate cancer cell-lines (DU145, PC3, LNCaP). For cells fixed with paraformaldehyde, cancer cell recovery ranged from 93.6% to 97.9% with purity ranging from 97.4% to 98.4%. There was no detectable loss of cell viability or cell proliferation subsequent to the exposure of viable tumor cells to acoustophoresis. For nonfixed, viable cells, tumor cell recovery ranged from 72.5% to 93.9% with purity ranging from 79.6% to 99.7%. These data contribute proof-in-principle that label-free microfluidic acoustophoresis can be used to enrich both viable and fixed cancer cells from WBCs with very high recovery and purity.
Query, and: Holy Saturday (1978)

16 THE MISSOURI REVIEW QUERY / Joyce Carol Oates For instance, why does the blood coagulate: why does the tiny mouth of a wound turn prim when touched by air: why don't we drain away like fluid in cracked vases? And why is it an axiom that the posthumous move among us airy of spirit: why do they claim more, claim us: why are their grins earth-full and wicked? Why are there certain weathers that contract giants to shadows: that reduce the splendor of our cries to echoes: the blossom of our souls to mere seeds? Joyce Carol Oates 17 HOLY SATURDAY / Joyce Carol Oates For Milton White The imperial city was heaped with broken concrete we tried all night to piece together again blinded by the glare of headlights from cars and vans our timid fingers minutely stung In play men of the city carried their smaller companions high in play they threw them down onto the rubble we unloosed fire-bright sirens, we consulted our maps the web of stars overhead had begun to fray Intoxicated with pride the great Schopenhauer was flown about in a Detroit police helicopter "Here—and here—and here also! And here" he shouted above the heaving streets The night was snarled and immense and pocked with tiny lights and I do not think we have come to the end for our heads reel like cracked crockery and the stench of oil is on our clothes and at midnight one of the children shot his younger brother dead with a .22 rifle of his father's and again we unloosed sirens, we flattened our wrinkled maps Once day came we could of course rejoice in tulips delicate as the streaked shells of painted Easter eggs— and the Bell Tower on the green stroke by stroke defining its noble art against an eager country silence ...
Validation of a wireless dry electrode system for electroencephalography (2015)

This report demonstrates preliminary but compelling evidence that EEG data recorded from the wireless dry electrode system is comparable to data recorded from a conventional system. Small correlation values in delta activity were discussed in relation to minor differences in hardware filter settings, variation in electrode placement, and participant artifacts observer during the simultaneous EEG recordings. Study limitations and impact of this research on neurorehabilitation were discussed.
Phytic acid interactions in food systems (1980)

Phytic acid is present in many plant systems, constituting about 1 to 5% by weight of many cereals and legumes. Concern about its presence in food arises from evidence that it decreases the bioavailability of many essential minerals by interacting with multivalent cations and/or proteins to form complexes that may be insoluble or otherwise unavailable under physiologic conditions. The precise structure of phytic acid and its salts is still a matter of controversy and lack of a good method of analysis is also a problem. It forms fairly stable chelates with almost all multivalent cations which are insoluble about pH 6 to 7, although pH, type, and concentration of cation have a tremendous influence on their solubility characteristics. In addition, at low pH and low cation concentration, phytate-protein complexes are formed due to direct electrostatic interaction, while at pH > 6 to 7, a ternary phytic acid-mineral-protein complex is formed which dissociates at high Na+ concentrations. These complexes appear to be responsible for the decreased bioavailability of the complexed minerals and are also more resistant to proteolytic digestion at low pH. Development of methods for producing low-phytate food products must take into account the nature and extent of the interactions between phytic acid and other food components. Simple mechanical treatment, such as milling, is useful for those seeds in which phytic acid tends to be localized in specific regions. Enzyme treatment, either directly with phytase or indirectly through the action of microorganisms, such as yeast during breadmaking, is quite effective, provided pH and other environmental conditions are favorable. It is also possible to produce low-phytate products by taking advantage of some specific interactions. For example, adjustment of pH and/or ionic strength so as to dissociate phytate-protein complexes and then using centrifugation or ultrafiltration (UF) has been shown to be useful. Phytic acid can also influence certain functional properties such as pH-solubility profiles of the proteins and the cookability of the seeds.
Functional Differences in Yeast Protein Disulfide Isomerases (2001)

PDI1 is the essential gene encoding protein disulfide isomerase in yeast. The Saccharomyces cerevisiae genome, however, contains four other nonessential genes with homology to PDI1: MPD1, MPD2, EUG1, and EPS1. We have investigated the effects of simultaneous deletions of these genes. In several cases, we found that the ability of the PDI1 homologues to restore viability to a pdi1-deleted strain when overexpressed was dependent on the presence of low endogenous levels of one or more of the other homologues. This shows that the homologues are not functionally interchangeable. In fact, Mpd1p was the only homologue capable of carrying out all the essential functions of Pdi1p. Furthermore, the presence of endogenous homologues with a CXXC motif in the thioredoxin-like domain is required for suppression of a pdi1 deletion by EUG1 (which contains two CXXS active site motifs). This underlines the essentiality of protein disulfide isomerase-catalyzed oxidation. Most mutant combinations show defects in carboxypeptidase Y folding as well as in glycan modification. There are, however, no significant effects on ER-associated protein degradation in the various protein disulfide isomerase-deleted strains.
Circular Dichroism Spectroscopy and the Vacuum Ultraviolet Region (1978)

Circular dichroism (CD) is a special kind of electronic absorption spectroscopy that uses circularly polarized light rather than isotropic light. CD is a particularly useful technique because it is sensitive to the conformation of a molecule, and because it can be applied to randomly oriented molecules in solution and in the gas phase. For a molecule to exhibit a CD spectrum it must be asymmetric, that is, it must contain no plane or center of symmetry. Since most biological molecules are asymmetric, CD spectroscopy has been used extensively to investigate their conformation. It has also been used to investigate the electronic properties of chromophores when simple asymmetric derivatives of known conformation are available. Most readers will be familiar with plane-polarized light. With this type of polarization the direction of the electric field vector is constant to within a sign, while the magnitude of the electric vector is modulated. Circularly polarized light is the antithesis of plane-polarized light. A snapshot of circularly polarized light is depicted in Figure 1 where we see that the magnitude of the electric vector is
No-Damage Drilling: How to Achieve this Challenging Goal? (2002)

Abstract No-Damage DrillingSM is the ultimate goal of all well construction activities, by providing a way to explore and produce the hydrocarbon reserves with minimum reduction of the natural permeability of the reservoir rocks. Conventional drilling is conducted with an over-balanced pressure on the reservoir formation, which causes the drilling fluid to invade and damage the rock. The industry has been trying to come up with alternatives and underbalanced drilling UBD has grown in popularity during the last years. However, in many situations UBD is not feasible to be used, due to economical and/or technical reasons. In cases UBD is not used, a drilling fluid with an overbalanced pressure should be used. A new drilling fluid called Non-Invasive FluidSM – NIFSM has been developed and is in the market to fill this gap. The goal of this paper is to present a new concept, called No-Damage Drilling, addressing the most important points during a well construction activity. The paper describes the different techniques available to achieve the goal of drilling a well with no-damage, including UBD and drilling fluids. A new drilling fluid is described, which has the capability of not invading the rock when a certain overbalance is applied, and the unique technology of the fluid allows an extremely easy removal of the seal, guaranteeing an effective restoration of the original permeability of the rock. The paper presents laboratory tests conducted to evaluate the performance of UBD and drilling fluids related to formation damage, as well as several case histories showing that with careful planning and proper technology a successful No-Damage Drilling operation is possible to be achieved. The paper finally addresses the main points to be followed to decide the best technological option to drill with no-damage, based on a series of questions specially developed.
Konark - a service discovery and delivery protocol for ad-hoc networks (2004)

The proliferation of mobile devices and the pervasiveness of wireless technology have provided a major impetus to replicate the network-based service discovery technologies in wireless and mobile networks. However, existing service discovery protocols and delivery mechanisms fall short of accommodating the complexities of the ad-hoc environment. They also place emphasis on device capabilities as services rather than device independent software services, making them unsuitable for m-commerce oriented scenarios. Konark is a service discovery and delivery protocol designed specifically for ad-hoc, peer-to-peer networks, and targeted towards device independent services in particular. It has two major aspects - service discovery and service delivery. For discovery, Konark uses a completely distributed, peer-to-peer mechanism that provides each device the ability to advertise and discover services in the network. The approach towards service description is XML based. It includes a description template that allows services to be described in a human and software understandable forms. A micro-HTTP server present on each device handles service delivery, which is based on SOAP. Konark provides a framework for connecting isolated services offered by proximal pervasive devices over a wireless medium.
Fisher Encoded Convolutional Bag-of-Windows for Efficient Image Retrieval and Social Image Tagging (2015)

In this paper we present an efficient and accurate method to aggregate a set of Deep Convolutional Neural Network (CNN) responses, extracted from a set of image windows. CNN features are usually computed on the whole frame or with a dense multi scale approach. There is evidence that using multiple windows yields a better image representation nonetheless it is still not clear how windows should be sampled and how CNN responses should be aggregated. Instead of sampling the image densely in scale and space we show that selecting a few hundred windows is enough to obtain an effective image signature. We show how to use Fisher Vectors and PCA to obtain a short and highly descriptive signature that can be used effectively for image retrieval. We test our method on two relevant computer vision tasks: image retrieval and image tagging. We report state-of-the art results for both tasks on three standard datasets.
Single-Sensor RGB-NIR Imaging: High-Quality System Design and Prototype Implementation (2018)

In recent years, many applications using a set of red-green-blue (RGB) and near-infrared (NIR) images, also called an RGB-NIR image, have been proposed. However, RGB-NIR imaging, i.e., simultaneous acquisition of RGB and NIR images, is still a laborious task because existing acquisition systems typically require two sensors or shots. In contrast, single-sensor RGB-NIR imaging using an RGB-NIR sensor, which is composed of a mosaic of RGB and NIR pixels, provides a practical and low-cost way of one-shot RGB-NIR image acquisition. In this paper, we investigate high-quality system designs for single-sensor RGB-NIR imaging. We first present a system evaluation framework using a new hyperspectral image data set we constructed. Different from existing work, our framework takes both the RGB-NIR sensor characteristics and the RGB-NIR imaging pipeline into account. Based on the evaluation framework, we then design each imaging factor that affects the RGB-NIR imaging quality and propose the best-performed system design. We finally present the configuration of our developed prototype RGB-NIR camera, which was implemented based on the best system design, and demonstrate several potential applications using the prototype.
The Endothelial Receptor Tyrosine Kinase Tie1 Activates Phosphatidylinositol 3-Kinase and Akt To Inhibit Apoptosis (2002)

Tie1 is an orphan receptor tyrosine kinase that is expressed almost exclusively in endothelial cells and that is required for normal embryonic vascular development. Genetic studies suggest that Tie1 promotes endothelial cell survival, but other studies have suggested that the Tie1 kinase has little to no activity, and Tie1-mediated signaling pathways are unknown. To begin to study Tie1 signaling, a recombinant glutathione S-transferase (GST)-Tie1 kinase fusion protein was produced in insect cells and found to be autophosphorylated in vitro. GST-Tie1 but not a kinase-inactive mutant associated with a recombinant p85 SH2 domain protein in vitro, suggesting that Tie1 might signal through phosphatidylinositol (PI) 3-kinase. To study Tie1 signaling in a cellular context, a c-fms-Tie1 chimeric receptor (fTie1) was expressed in NIH 3T3 cells. Ligand stimulation of fTie1 resulted in Tie1 autophosphorylation and downstream activation of PI 3-kinase and Akt. Stimulation of fTie1-expressing cells potently inhibited UV irradiation-induced apoptosis in a PI 3-kinase-dependent manner. Moreover, both Akt phosphorylation and inhibition of apoptosis were abrogated by mutation of tyrosine 1113 to phenylalanine, suggesting that this residue is an important PI 3-kinase binding site. These findings are the first biochemical demonstration of a signal transduction pathway and corresponding cellular function for Tie1, and the antiapoptotic effect of Tie1 is consistent with the results of previous genetic studies.
How Nucleic Acids Cope with High Temperature (2014)

This chapter discusses the question of coping up of the nucleic acids with high temperature at the polynucleotide level—RNA, DNA, and their ribonucleoprotein derivatives (RNP/DNP). When nucleic acids are heated in aqueous solution, two types of phenomena take place: denaturation of their architecture and chemical degradation of their building blocks. In vivo, the half-lives of both RNA and DNA of thermophilic organisms are usually longer than that estimated in vitro, attesting to cellular strategies protecting the nucleic acids against the deleterious effects of heat. Despite the susceptibility of certain modified bases and of the ribonucleotide chain to thermal degradation, most naturally occurring tRNAs (especially those from hyperthermophilic organisms) appear fairly resistant to heat denaturation. Despite the intrinsic potentiality of nucleic acids to degrade at elevated temperatures, many hyperthermophiles can survive at very high temperatures approaching or even surpassing the boiling point of water. The majority of stable cellular RNAs, such as tRNA and rRNA molecules, contain a variety of modified nucleosides. Stabilizing strategies of RNAs and DNAs may be classified into three major categories: (i) those which are intrinsic to the chemical structures of the nucleic acids; (ii) those which are dependent on extrinsic interactions with other biomolecules; and (iii) those which are dependent on a battery of enzymes for detecting and repairing the DNA damage or to constantly renew functional RNA molecules. Genetic approach using mutant strains mutated in one or more biomolecules supposedly involved directly or indirectly in stabilization of nucleic acids should be more systematically used.
Improved Oblique-Incidence Interferometer (1975)

An oblique-incidence interferometer for testing the flatness of fine-ground surfaces is described. This uses reflecting diffraction gratings to divide and recombine the beams, resulting in a very compact optical system. In addition, the relative amplitudes of the interfering beams can be adjusted, by a suitable choice of the grating orders used, to give fringes of excellent visibility with surfaces having a wide range of refleetances.
Kinetics of Monodisperse Iron Oxide Nanocrystal Formation by “Heating-Up” Process (2007)

We studied the kinetics of the formation of iron oxide nanocrystals obtained from the solution-phase thermal decomposition of iron-oleate complex via the "heating-up" process. To obtain detailed information on the thermal decomposition process and the formation of iron oxide nanocrystals in the solution, we performed a thermogravimetric-mass spectrometric analysis (TG-MS) and in-situ magnetic measurements using SQUID. The TG-MS results showed that iron-oleate complex was decomposed at around 320 degrees C. The in-situ SQUID data revealed that the thermal decomposition of iron-oleate complex generates intermediate species, which seem to act as monomers for the iron oxide nanocrystals. Extensive studies on the nucleation and growth process using size exclusion chromatography, the crystallization yield data, and TEM showed that the sudden increase in the number concentration of the nanocrystals (burst of nucleation) is followed by the rapid narrowing of the size distribution (size focusing). We constructed a theoretical model to describe the "heating-up" process and performed a numerical simulation. The simulation results matched well with the experimental data, and furthermore they are well fitted to the well-known LaMer model that is characterized by the burst of nucleation and the separation of nucleation and growth under continuous monomer supply condition. Through this theoretical work, we showed that the "heating-up" and "hot injection" processes could be understood within the same theoretical framework in which they share the characteristics of nucleation and growth stages.
Real-Time Reservoir Surveillance Utilizing Permanent Downhole Pressures—An Operator's Experience (2006)

Abstract Permanent downhole pressure gauges supply important information for reservoir surveillance and management. Technology has evolved over the more than 40 years since the first installation. Service companies have made significant improvements to the components of a permanent downhole gauge installation for a well. The components include gauges, housing, cable, connections, and acquisition systems. Installation and use of these gauges has become routine in many situations because of the improved reliability and the value of information that the gauges provide. Pressures from permanent downhole gauges can be examined almost as soon as they are acquired, depending on communication speed. The data is used for many applications including pressure monitoring, interference testing, water and gas injection monitoring, transient well testing, evaluation of well performance, reducing the flowback time of new wells, monitoring hydraulic fracturing operations, and monitoring pump inlet and outlet pressures for pumping wells. On the practical side, there are issues associated with the data that these gauges collect. Vast amounts of data are being gathered continuously at intervals down to one second over numbers of years. This data must be communicated from the well to the office. Since the data is an asset, it must be stored and archived. Individuals require access to the data at different times, for different reasons, and at differing resolutions. Interpretation of the data poses new challenges as there is more hidden in the long term pressure record than just a collection of drawdowns and buildups. The data contains information about parameters changing during short and long time intervals both near the well and in the reservoir. As more and more permanent downhole gauges are deployed, maximizing the corporate benefits becomes an asset management issue. Companies are faced with stewardship of the investment, communicating learnings across the organization, developing or acquiring software tools for data management and analysis, proposing and supporting industry- wide standards for consistent data capture and communication, and integrating data into work processes and into applications such as smart wells and smart fields.
Sample handling for proteome analysis (1998)

The main factor limiting the sensitivity range for the identification of proteins isolated by two-dimensional (2-D) electrophoresis is sample handling: protein detection limits on the gel, losses during extraction and digestion, as well as interference of gel contaminants and detergents with the mass spectrometry (MS) detection increasing background noise. At the one hundred picomole level, losses are fairly negligible but when the amounts drop below 1 picomole (and subfemtomole peptide detection limits have been reported recently by MS), the losses become a critical point. In order to extend proteome analysis to include very low copy number proteins, methods must be developed to minimize losses and handling steps, maximize digestion and extraction yields, as well as to lower chemical noise. We present several methods that we have developed in our laboratory to: (i) increase the amount of material available in a sodium dodecyl sulfate (SDS)-free form which does not require staining, (ii) increase protein extraction and digestion yields and lower the contamination by autoproteolytic products, and (iii) allow direct modification of the peptide mixture to generate sequence tags.