gebhart/patrepeval huggingface dataset:
Development and characterization of anti‐glycopeptide monoclonal antibodies against human podoplanin, using glycan‐deficient cell lines generated by <scp>CRISPR</scp>/Cas9 and <scp>TALEN</scp> (2017)

Human podoplanin (hPDPN), which binds to C-type lectin-like receptor-2 (CLEC-2), is involved in platelet aggregation and cancer metastasis. The expression of hPDPN in cancer cells or cancer-associated fibroblasts indicates poor prognosis. Human lymphatic endothelial cells, lung-type I alveolar cells, and renal glomerular epithelial cells express hPDPN. Although numerous monoclonal antibodies (mAbs) against hPDPN are available, they recognize peptide epitopes of hPDPN. Here, we generated a novel anti-hPDPN mAb, LpMab-21. To characterize the hPDPN epitope recognized by the LpMab-21, we established glycan-deficient CHO-S and HEK-293T cell lines, using the CRISPR/Cas9 or TALEN. Flow cytometric analysis revealed that the minimum hPDPN epitope, in which sialic acid is linked to Thr76, recognized by LpMab-21 is Thr76-Arg79. LpMab-21 detected hPDPN expression in glioblastoma, oral squamous carcinoma, and seminoma cells as well as in normal lymphatic endothelial cells. However, LpMab-21 did not react with renal glomerular epithelial cells or lung type I alveolar cells, indicating that sialylation of hPDPN Thr76 is cell-type-specific. LpMab-21 combined with other anti-hPDPN antibodies that recognize different epitopes may therefore be useful for determining the physiological function of sialylated hPDPN.
Potential of Host Markers Produced by Infection Phase-Dependent Antigen-Stimulated Cells for the Diagnosis of Tuberculosis in a Highly Endemic Area (2012)

Multiple cytokines other than IFN-γ in whole blood culture supernatants after stimulation with M.tb infection phase-dependent antigens show promise as diagnostic markers for active TB. These preliminary findings should be verified in well-designed diagnostic studies employing short-term culture assays.
Multi-Cell Channel Estimation using Virtual Pilots (2008)

Multicellular radio systems are often limited due to the presence of cochannel interference. Proposed physical layer concepts, e.g. coordinated joint transmission and interference rejection combining, try to strengthen the signal while combating the interference. However, the performance may be limited by the available channel knowledge. We provide a concept for multi-cell channel estimation in the downlink applicable for for both physical layer concepts. This concept uses virtual pilots based on block-orthogonal sequences, e.g. Hadamard.
Passive Altimeter Study Using GPS Flight Data (Preprint) (2003)

Software GPS receiver results are presented for an over-land, passive altimeter application utilizing GPS signals. The flight data were collected using a DC-3 aircraft operated by Ohio University. The flight took place over southeast Ohio, where the terrain is hilly and forested. The GPS receiver on board the aircraft contains two channels. One channel has a right-hand-circular-polarized antenna facing upward, and the second has a left-hand-circular-polarized antenna facing downward. The upward antenna primarily receives the GPS direct signals, while the downward antenna primarily receives the ground-reflected GPS signals. Software radio GPS algorithms are used to process the data received from the upward channel. The information obtained after processing includes receiver position data, visible satellites, C/A code delay, Doppler frequency and navigation data bits as functions of time. This information is used to generate a reference signal to correlate the data received from the downward channel. Since the Doppler shift can be different between the reference and the reflected signals, the length of the coherent integration time is limited. Furthermore, the Doppler shift of the reflected signal can change rapidly as a function of the terrain. Therefore, a combination of coherent and noncoherent integration is used to enhance the signal-to-noise ratio of the reflected signals. The correlation result shows a C/A code delay corresponding to the path length difference between the direct and reflected signals. From the known locations of the receiver and the satellites, the height above ground of the receiver can be calculated. The flight data cover heights ranging from 0 to 3000 meters above the terrain.
Fabrication method for phase mask with spatially variable diffraction efficiency (1997)

A phase mask is a phase diffraction grating usually recorded in photoresist and then etched in a bulk substrate as a one-dimensional uniform and periodic surface relief pattern[1,2]. When illuminated at normal incidence with coherent or partially coherent light, the phase mask produces in its near-field self-interference between the first order diffracted beams. This interference fringe pattern will have a spatial frequency that is twice the spatial frequency of the phase mask, and will be photoimprinted in the photosensitive medium placed in close proximity of die phase mask grating. This will generate a uniform periodic modulation of the refractive index acting as a Bragg filter. The Bragg spectral response will then have a narrow-band reflectivity peak at a design wavelength, accompanied by a series of sidelobes at adjacent wavelengths. In today’s global communication, based on wavelength division multiplexing, there is a requirement for Bragg grating with a spectral response having reduced noise and sidelobes to avoid cross talk. Bragg gratings with reduced sidelobes in their spectral response can be generated by recording an index modulation with a spatially varying modulation amplitude[3]. The condition for an efficient sidelobe suppression is that the modulation level decreases continuously to zero at both limits of the Bragg grating. It can be achieved using appropriate apodization profiles[4]. Different approaches have been investigated to realize Bragg gratings that generate a spectral response without sidelobes, with or without the use of a phase mask [5,6,7,8,9]. We propose a new fabrication process leading to improved results in the spectral response of the recorded apodized Bragg grating, suitable for mass production: simplicity, reliability, low cost and short fabrication time.
Database Application Developer Tools Using Static Analysis and Dynamic Profiling. (2014)

Database application developers use data access APIs such as ODBC, JDBC and ADO.NET to execute SQL queries. Although modern program analysis and code profilers are extensively used during application development, there is a significant gap in these technologies for database applications because these tools have little or no understanding of data access APIs or the database system. In our project at Microsoft Research, we have developed tools that: (a) Enhance traditional static analysis of programs by leveraging understanding of database APIs to help developers identify security, correctness and performance problems early in the application development lifecycle. (b) Extend the existing DBMS and application profiling infrastructure to enable correlation of application events with DBMS events. This allows profiling across application, data access and DBMS layers thereby enabling a rich class of analysis, tuning and profiling tasks that are otherwise not easily possible.
Development of Botryococcus Seed Culture System for Future Mass Culture (2012)

The BOT-22 strain of Botryococcus braunii was cultured under laboratory and outdoor conditions. Medium K was developed, which decreased the cost of medium preparation to 1/30th. A polycarbonate bottle (10 L) was replaced with a polyethylene bag for cost effectiveness. Addition of nitrogen substantially increased biomass of the strain; however, the hydrocarbon content remained unchanged. Growth rates of >10 L scale cultures were much lower than those of <200 mL scale flask cultures. BOT-22 grew well in outdoor cultures despite extensive fluctuations in temperature and light conditions during the day from autumn to early winter and at spring. Maximum growth rates obtained using a tube bioreactor were two times higher than those obtained using 10L/30L scale cultures and a dome bioreactor. Thus, the tube bioreactor was more efficient for utilizing the light required for photosynthesis by this strain.
Thiophene systems. 3. Synthesis of thieno[3,4-b][1,5]benzoxazepin-10-one and thieno[3,4-b][1,5]benzothiazepin-10-one (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThiophene systems. 3. Synthesis of thieno[3,4-b][1,5]benzoxazepin-10-one and thieno[3,4-b][1,5]benzothiazepin-10-oneJeffery B. Press, Nancy H. Eudy, and Sidney R. SafirCite this: J. Org. Chem. 1980, 45, 3, 497–501Publication Date (Print):February 1, 1980Publication History Published online1 May 2002Published inissue 1 February 1980https://pubs.acs.org/doi/10.1021/jo01291a025https://doi.org/10.1021/jo01291a025research-articleACS PublicationsRequest reuse permissionsArticle Views288Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Globin gene transfer: a paradigm for transgene regulation and vector safety (2003)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
Analyzing the encoding range of amplitude-phase coupled spatial light modulators (1999)

Most spatial light modulators (SLMs) are limited in that they cannot produce arbitrary complex modulations. Because phase and amplitude are usually coupled, it is difficult to computer design appropriate modulation patterns fast enough for the real-time applications for which SLMs are suited. Dramatic computational speedups can be achieved by using encoding algorithms that directly translate desired complex values into values that the modulator can produce. For coherently illuminated SLMs in a Fourier transform arrangement, pseudorandom encoding can be used. Each SLM pixel is programmed in sequence by selecting a single value of pixel modulation from a random distribution having an average that is identical to the desired fully complex modulation. While the method approximates fairly arbitrary complex modulations, there are always some complex values that are outside the encoding range for each SLM coupling characteristic and for each specific pseudorandom algorithm. Using the binary random distribution leads to methods of evaluating and geometrically interpreting the encoding range. Evaluations are presented of achieving fully complex encoding with SLMs that produce less than 2? of phase shift, identifying an infinite set of encoding algorithms that encode the same value, identification of the maximum encoding range, and geometric interpretation of encoding errors.
Remote Distributed Vibration Sensing Through Opaque Media Using Permanent Magnets (2018)

Vibration sensing is critical for a variety of applications from structural fatigue monitoring to understanding the modes of airplane wings. In particular, remote sensing techniques are needed for measuring the vibrations of multiple points simultaneously, assessing vibrations inside opaque metal vessels, and sensing through smoke clouds and other optically challenging environments. In this paper, we propose a method which measures high-frequency displacements remotely using changes in the magnetic field generated by permanent magnets. We leverage the unique nature of vibration tracking and use a calibrated local model technique developed specifically to improve the frequency-domain estimation accuracy. The results show that two-dimensional local models surpass the dipole model in tracking high-frequency motions. A theoretical basis for understanding the effects of electronic noise and error due to correlated variables is generated in order to predict the performance of experiments prior to implementation. Simultaneous measurements of up to three independent vibrating components are shown. The relative accuracy of the magnet-based displacement tracking with respect to the video tracking ranges from 40 to 190 μm when the maximum displacements approach ±5 mm and when sensor-to-magnet distances vary from 25 to 36 mm. Last, vibration sensing inside an opaque metal vessel and mode shape changes due to damage on an aluminum beam are also studied using the wireless permanent-magnet vibration sensing scheme.
A highly thermally stable sub-20 nm magnetic random-access memory based on perpendicular shape anisotropy (2018)

A new approach to increase the downsize scalability of perpendicular STT-MRAM is presented. It consists of significantly increasing the thickness of the storage layer in out-of-plane magnetized tunnel junctions (pMTJ) as compared to conventional pMTJ in order to induce a perpendicular shape anisotropy (PSA) in this layer. This PSA is obtained by depositing a thick ferromagnetic (FM) layer on top of an MgO/FeCoB based magnetic tunnel junction (MTJ) so that the thickness of the storage layer is of the order of or larger than the diameter of the MTJ pillar. In contrast to conventional spin transfer torque magnetic random access memory (STT-MRAM) wherein the demagnetizing energy opposes the interfacial perpendicular magnetic anisotropy (iPMA), in these novel memory cells, both PSA and iPMA contributions favor the out-of-plane orientation of the storage layer magnetization. Using thicker storage layers in these PSA-STT-MRAMs has several advantages. Due to the PSA, very high and easily tunable thermal stability factors can be achieved, even down to sub-10 nm diameters. Moreover, a low damping material can be used for the thick FM material thus leading to a reduction of the write current. The paper describes this new PSA-STT-MRAM concept, practical realization of such memory arrays, magnetic characterization demonstrating thermal stability factor above 200 for MTJs as small as 8 nm in diameter and possibility to maintain the thermal stability factor above 60 down to 4 nm diameter.
ChemInform Abstract: An Efficient Chemoselective Synthesis of Nitriles from Primary Amides. (1988)

Abstract The primary amides (I) are dehydrated with the inner salt of (methoxycarbonylsulfamoyl)triethylammonium hydroxide (Burgess reagent) to form the nitriles (II).
Effects of Orally Administered Epidermal Growth Factor on Enteropathogenic <i>Escherichia coli</i> Infection in Rabbits (1998)

The increased intestinal absorption induced by epidermal growth factor (EGF) is associated with diffuse lengthening of brush border microvilli. The aim of this study was to examine the in vivo effects of oral administration of EGF during infection with enteropathogenic Escherichia coli. New Zealand White rabbits (4 weeks old) received orogastric EGF daily starting 3 days prior to infection with enteropathogenic E. coli RDEC-1 and were compared with sham-treated infected animals and uninfected controls. Weight gain, food intake, fecal E. coli, and stool consistency were assessed daily. On day 10, segments of jejunum, ileum, proximal, and distal colon were assessed for gram-negative bacterial colonization, disaccharidase activities, and epithelial ultrastructure. Effects of EGF on E. coli RDEC-1 proliferation were studied in vitro. E. coli RDEC-1 caused diarrhea and reduced weight gain. Seven days postinfection, the small and large intestines were colonized with numerous bacteria, brush border microvilli were disrupted, and maltase and sucrase activities were significantly reduced in the jejunum. Daily treatment with EGF prevented the occurrence of diarrhea and reduction of weight gain. These effects were associated with significant inhibition of E. coli colonization in the small and large intestine, improved jejunal maltase and sucrase activities and reduced microvillous injury. EGF did not affect the proliferation of E. coli in vitro. The findings suggest that EGF protects the gastrointestinal tract against colonization by enteropathogenic E. coli.
Biomarker Discovery: Identification of a Growth Factor Gene Signature (2009)

Gene expression signatures can be developed as comprehensive pathway readouts and used as pharmacodynamic or patient-stratification biomarkers. While a consensus on the best practices for selecting gene expression signatures from microarray data is evolving, we have developed basic guidelines to ensure consistency and quality. Here we illustrate these guidelines through the identification of a growth factor gene expression signature that is responsive to phosphatidylinositol 3-kinase (PI3K) pathway perturbations in vitro and related to phosphatase and tensin homolog (PTEN) deregulation in vivo.
Spin-valve heads with self-stabilized free layer by antiferromagnet (2002)

We demonstrate the feasibility of a spin-valve read head using an adjacent antiferromagnetic (AFM) layer to provide a stabilization Held, eliminating the hard bias permanent magnet layer. The head stack consists of seed/AFM/CoFe/Ru/CoFe/Cu/CoFe (and/or NiFe)/Cu/IrMn/cap where the AFM is PtMn or IrMn. The abutted junction is about 0.1 /spl mu/m wide at the free layer and no permanent magnet materials are used. Micromagnetic modeling indicates that a proper bias field is needed to have a stable head response. The bias field from the AFM layer can be modified by a nonmagnetic spacer layer between AFM and FM. The coupling field decays exponentially with the thickness of the spacer layer, consistent with a pinhole-dominated mechanism. Unshielded sensors show much higher sensitivity as,compared with a standard PM abutted junction head. Microtrack profile based on the spin-stand test shows a regular shape without apparent lumps. The electrical reader width is about 6 /spl mu/" (0.15 /spl mu/m), corresponding to a track density of 112 ktpi. Combined with a linear density of 591 kbpi the heads in this work are capable of areal density around 66 Gb/in/sup 2/.
High-power leaky mode multiple-stripe laser (1980)

A new kind of multiple-stripe injection laser has been developed. By fabricating a stripe array of buried heterostructures configured to operate in leaky modes, strong coupling is produced between the stripes leading to linear operation and stable output characteristics. Efficient utilization of the total emitting area results from leaky mode operation, and peak pulsed output powers to 1.5 W have been observed.
Criticality computation in parameterized statistical timing (2006)

Chips manufactured in 90 nm technology have shown large parametric variations, and a worsening trend is predicted. These parametric variations make circuit optimization difficult since different paths are frequency-limiting in different parts of the multi-dimensional process space. Therefore, it is desirable to have a new diagnostic metric for robust circuit optimization. This paper presents a novel algorithm to compute the criticality probability of every edge in the timing graph of a design with linear complexity in the circuit size. Using industrial benchmarks, we verify the correctness of our criticality computation via Monte Carlo simulation. We also show that for large industrial designs with 442,000 gates, our algorithm computes all edge criticalities in less than 160 seconds.
Observation of Ionic Liquid by Scanning Electron Microscope (2006)

Abstract It has been discovered that ionic liquid can be observed by a scanning electron microscope without accumulation of electron charges, allowing SEM observation of insulating specimens wetted with ionic liquid.
Evaluation of CSF flow in shunts using a non-invasive thermal technique (2009)

Background Cerebrospinal fluid (CSF) shunts have dramatically improved effective treatment for patients with hydrocephalus, but fundamental aspects of their function, including typical rates of fluid flow through the system, remain unknown. Despite advances in the quality of shunts, shunt failure rates remain significantly high and evaluation of CSF flow in shunts with invasive techniques continues to present diagnostic and clinical difficulties involving patients' comfort and hospital resources.
Nanosecond, pulsed, frequency-modulated optical parametric oscillator (1995)

For certain applications, a spectrum comprised of several longitudinal modes from a laser or optical parametric oscillator (OPO) is desirable. For example, a broad spectrum can reduce speckle in remote sensing. One way to achieve this is to allow an OPO to operate on several modes that evolve from quantum noise. Unfortunately, in this case, the spectrum fluctuates from pulse to pulse and can be a noise source. An alternative is to seed the OPO on several longitudinal modes simultaneously so the spectrum is broad but does not fluctuate. This can be done by frequency modulating a cw seed laser so the sidebands and carrier all match longitudinal modes of the signal wave in the OPO. Such an FM OPO would also have applications in FM-modulation absorption measurements, including remote sensing.
Characterization of a novel inhibitory human monoclonal antibody directed against Plasmodium falciparum Apical Membrane Antigen 1 (2016)

Malaria remains a major challenge to global health causing extensive morbidity and mortality. Yet, there is no efficient vaccine and the immune response remains incompletely understood. Apical Membrane Antigen 1 (AMA1), a leading vaccine candidate, plays a key role during merozoite invasion into erythrocytes by interacting with Rhoptry Neck Protein 2 (RON2). We generated a human anti-AMA1-antibody (humAbAMA1) by EBV-transformation of sorted B-lymphocytes from a Ghanaian donor and subsequent rescue of antibody variable regions. The antibody was expressed in Nicotiana benthamiana and in HEK239-6E, characterized for binding specificity and epitope, and analyzed for its inhibitory effect on Plasmodium falciparum. The generated humAbAMA1 shows an affinity of 106-135 pM. It inhibits the parasite strain 3D7A growth in vitro with an expression system-independent IC<sub>50</sub>-value of 35 μg/ml (95% confidence interval: 33 μg/ml-37 μg/ml), which is three to eight times lower than the IC<sub>50</sub>-values of inhibitory antibodies 4G2 and 1F9. The epitope was mapped to the close proximity of the RON2-peptide binding groove. Competition for binding between the RON2-peptide and humAbAMA1 was confirmed by surface plasmon resonance spectroscopy measurements. The particularly advantageous inhibitory activity of this fully human antibody might provide a basis for future therapeutic applications.
Abstract 3224: Optical Coherence Tomography Imaging of Radiofrequency Ablation Lesions (2007)

Background: Cardiac arrhythmias are abnormalities of the electrical conduction of the heart and occur in patients of all ages with and without heart disease, compromising heart function. Catheter a...