gebhart/patrepeval huggingface dataset:
Molecular analyses of HIV-1 group O and HIV-2 variants from Africa. (1997)

Genetic variation among HIV isolates creates challenges for their detection by serologic and genetic techniques. To characterize the sequence variation and its correlation to serologic diversity of HIV-1 Group O and HIV-2 isolates, samples were identified by differential reactivity in selected commercial and research assays. Analysis of sera from Equatorial Guinea (EG) led to identification of 4 HIV-1 Group O variants. Viral RNA, extracted from these samples was used to PCR amplify overlapping sequences of the entire envelope gene using multiple primer pairs. Sequence analysis indicated that the V3 loop nucleotide and protein sequences aligned more closely with HIVANT70 compared to other Group O sequences. The amino acid sequences at the octameric tip of the V3 loop were RIGPLAWY, RIGPMAWY, or GLGPLAVY. The tetrameric tip GPLA is represented only once in the published 1994 HIV database (Los Alamos) but was present in 2 of 4 of EG samples. The immuno-dominant region (IDR) sequences derived from EG sera were unique in that none of the sequences were completely homologous to other HIV-1 group O variants. Further, the HIV-1 group O sequence variation could be correlated with differential serologic reactivity using IDR peptides. Compared to HIV-1, the sequence information on HIV-2 isolates is relatively limited, though the HIV-2 isolates also show genetic variation similar to HIV-1. To further establish a correlation between the genetic diversity and serologic detection of HIV-2, plasma samples from Western Africa were evaluated. Eight samples were selected based on weak serologic reactivity to env proteins. PCR amplification and sequence analysis of the gag, env V3 loop, and env IDR regions indicated that the samples could be classified as subtypes A (4 samples), B (3 samples) and D (1 sample). Across the subtypes, there was conservation in the IDR region of the sequence WGCAFRQVCHT. This region is absolutely conserved among the majority of currently known HIV-2 and related SIV viruses (1994 HIV database). One subtype B sample had a unique sequence immediately adjacent to the IDR, however, this did not change the serologic detection using a HIV-2 IDR specific monoclonal antibody.
Cellulose nanofibrils decorated by inorganic nanoparticles and used in magnetic nanocomposite membranes of high toughness (2012)

Cellulose nanofibrils decorated by inorganic nanoparticles and used in magnetic nanocomposite membranes of high toughness
Human CD8 T cells generated in vitro from hematopoietic stem cells are functionally mature (2011)

Taken together, the ability to direct human hematopoietic stem cell or T-progenitor cells towards a mature functional phenotype raises the possibility of establishing cell-based treatments for T-immunodeficiencies by rapidly restoring CD8 effector function, thereby mitigating the risks associated with opportunistic infections.
Evolution of an Inhibin a ELISA Method: Implications for Down's Syndrome Screening (1998)

The development of a sensitive and specific enzyme-linked immunoassay (ELISA) for inhibin A stimulated the observation that inhibin A was a useful prenatal marker of Down's syndrome. Modifications of that ELISA, in terms of preassay sample treatment, detection methods and standard preparation, were subsequently introduced to improve assay performance and reduce costs. These modified formats have been validated and reported. We describe the modifications in detail, explaining the rationale for each, and report the results of a study directly comparing the various ELISA formats in terms of assay performance when applied to clinical samples and ability to differentiate between normal and Down's syndrome pregnancies. A format involving sample pretreatment with sodium dodecylsulphate at 100 degrees C was found to give better assay performance and a modest improvement in discrimination between Down's syndrome samples and controls, and we recommend this format for use by other investigators.
Proteome-wide drug screening using mass spectrometric imaging of bead-arrays (2016)

A fundamental challenge in the drug discovery process is to develop compounds with high efficacy and minimal side-effects. We describe a new approach to proteome-wide drug screening for detection of on- and off-target binding which combines the advantages of mass spectrometry with microarray technology. The method involves matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) of agarose micro-beads randomly arrayed at high-density in custom micro-well plates. Each bead carries a unique protein target and a corresponding photocleavable mass-tag for coding (PC-Mass-Tag). Compounds bound to specific protein beads and a photo-released coding PC-Mass-Tag are detected simultaneously using MALDI-MSI. As an initial demonstration of this approach, two kinase-targeted drugs, Dasatinib and Brigatinib (AP26113), were simultaneously screened against a model 50-member kinase-bead library. A MALDI-MSI scan performed at the equivalent density of 495,000 beads in the footprint of a microscope slide yielded 100% sensitivity for detecting known strong interactions with no false positives.
Fundamental Studies of New Ionization Technologies and Insights from IMS-MS (2019)

Exceptional ion mobility spectrometry mass spectrometry (IMS-MS) developments by von Helden, Jarrold, and Clemmer provided technology that gives a view of chemical/biological compositions previously not achievable. The ionization method of choice used with IMS-MS has been electrospray ionization (ESI). In this special issue contribution, we focus on fundamentals of heretofore unprecedented means for transferring volatile and nonvolatile compounds into gas-phase ions singly and multiply charged. These newer ionization processes frequently lead to different selectivity relative to ESI and, together with IMS-MS, may provide a more comprehensive view of chemical compositions directly from their original environment such as surfaces, e.g., tissue. Similarities of results using solvent- and matrix-assisted ionization are highlighted, as are differences between ESI and the inlet ionization methods, especially with mixtures such as bacterial extracts. Selectivity using different matrices is discussed, as are results which add to our fundamental knowledge of inlet ionization as well as pose additional avenues for inquiry. IMS-MS provides an opportunity for comparison studies relative to ESI and will prove valuable using the new ionization technologies for direct analyses. Our hypothesis is that some ESI-IMS-MS applications will be replaced by the new ionization processes and by understanding mechanistic aspects to aid enhanced source and method developments this will be hastened.
Reduction of traps and improvement of carrier lifetime in 4H-SiC epilayers by ion implantation (2007)

The authors report a significant reduction in deep level defects and improvement of carrier lifetime in 4H-SiC material after carrying out carbon or silicon ion implantation into the shallow surface layer of 250nm and subsequent annealing at 1600°C or higher temperature. Reduction of Z1∕2 and EH6∕7 traps from 3×1013cm−3 to below the detection limit (5×1011cm−3) was observed by deep level transient spectroscopy in the material 4μm underneath the implanted layer. Minority carrier lifetime almost doubled in the implanted samples compared to the unimplanted samples. The authors propose that the implanted layer acts as a source of carbon interstitials which indiffuse during annealing and accelerate annealing out of grown-in defects in the layer underneath the implanted region.
Soluble Carbon Nanotubes (2003)

Carbon nanotubes have attracted great interdisciplinary interest because of their unique structure and properties. However, carbon-nanotube research is challenged by several problems, such as: i) mass production of material, ii) control of length, diameter, and chirality, and iii) manipulation for use in diverse technological fields. Issues regarding the synthesis and purification as well as the functionalization and solubilization of carbon nanotubes are relevant topics in this rapidly growing field. In this paper, covalent and noncovalent approaches to functionalized and solubilized nanotubes are examined in detail, with particular emphasis on the change of properties that accompany the chemical modification.
<title>Compression-molded three-dimensional tapered polymeric waveguides for low-loss optoelectronic packaging</title> (1997)

We report for the first time, 3D tapered polymeric waveguides fabricated by the compression-molding technique. Compression-molded polymeric waveguides presented herein provide a feasible solution to bridge discrete optoelectronic devices having the apertures of a few microns to hundreds of microns in both horizontal and vertical directions. One-cm long tapered channel waveguides with the cross-sections of 5 micrometers X 5 micrometers at one end and 100 micrometers X 100 micrometers at the other end were fabricated. These polymeric channel waveguides have a propagation loss of 0.5 dB/cm when the 632.8 nm He-Ne laser light is coupled from the small end to the large end and of 1.1 dB/cm when coupled from the large end to the small end. By confining the energy to the fundamental mode, when coupling from large end to the small end, a low-loss packaging can be achieved bidirectionally.
Data hiding in halftone images by stochastic error diffusion (2002)

We propose a novel method called DHSED (data hiding stochastic error diffusion) to hide binary visual patterns in two error diffused halftone images. While one halftone image is only a regular error diffused image, stochastic error diffusion is applied to the other image to generate special stochastic characteristics with respect to the first image such that the visual pattern would appear when the two halftone images are overlaid Simulation results show that the two halftone images have good visual quality, and the hidden pattern appears with "normal" and "lower-than-normal" intensity when the two halftone images are overlaid.
Purification and Specificity of β1,2-Xylosyltransferase, an Enzyme That Contributes to the Allergenicity of Some Plant Proteins (1997)

The enzyme that transfers D-xylose from UDP-xylose to the beta-linked mannose of plant N-linked oligosaccharides was purified about 51,000-fold to apparent homogeneity from soybean microsomes. On SDS gels, two proteins of 56 and 59 kDa were detected and both were labeled to the same extent by the photoaffinity label, 5-N3-UDP-[32P]xylose. Labeling of both proteins was inhibited by cold UDP-xylose, but not by UDP-glucose. The amount of 5-N3-UDP-[32P]xylose that bound to the two protein bands was greatly increased in the presence of oligosaccharide acceptors. The best acceptor for xylose transfer and for stimulation of UDP-xylose binding was GlcNAc2Man3GlcNAc2-T, but GlcNAc1Man3GlcNAc2, with the GlcNAc on the 3-branch, was also a good acceptor and a good stimulator. A number of other N-linked oligosaccharides were poor acceptors, especially those with galactose units at the nonreducing termini. Many of the properties of this enzyme have been described, and the product of the reaction of UDP-xylose and GlcNAc2Man3(GlcNAc)2 was characterized as GlcNAcbeta1, 2Manalpha1, 6(GlcNAcbeta1,2Manalpha1,3)(Xylbeta1,2)Manbeta1, 4GlcNA c2-T by chemical and NMR methods.
Spiral Parallel Magnetic Resonance Imaginga (2006)

Spiral k-space scanning is a rapid magnetic resonance imaging (MRI) technique that can provide an order of magnitude reduction in scan time compared to conventional spin warp techniques. Parallel imaging is another method for reducing scan time that exploits spatially varying radiofrequency (RF) coil sensitivities to reduce the amount of data required to reconstruct an image. Combining spiral scanning with parallel imaging provide a scan time reduction factor that is the product of the reduction factors for each of the techniques and thus can permit very rapid imaging. Image reconstruction for spiral parallel MRI is more involved than for spin warp parallel MRI and is an area of active research. Two techniques for performing this image reconstruction are PILS, a simple image-domain method that relies on localized coil sensitivities, and BOSCO, a method that is based on successive convolution operations in k-space
Design of Latches and Flip-Flops using Emerging Tunneling Devices (2016)

Tunneling field-effect transistors (TFETs) stand out among novel device technologies for low-power circuits and systems. While some TFETs exhibits behavior similar to MOSFETs, a group of emerging tunneling devices including symmetric tunneling FETs (SymFETs) and interlayer tunnel FETs (IFETs) demonstrate a bell-shaped I-V characteristic dissimilar to that of MOSFETs. They have shown the potential for image processing and nontraditional computing in analog applications and the design of Boolean gates with SymFETs has also been explored. This paper uses a SymFET as a proxy to design sequential circuits comprised of devices with bell-shaped I-V characteristics. Said circuits are essential as practically any application requires the indefinite storage of data and control modules during computation. We show that the negative differential resistance (NDR) behavior of SymFET transistors can be employed to build compact and low power latches and flip-flops. The relationship of SymFET with another well-known tunneling device, namely resonant tunneling diode (RTD), is investigated. We illustrate how previous research on RTD-based circuits - such as monostable-bistable (MOBILE) self-latching circuits and highly compact MOBILE-based D flip-flop circuits - can be adopted to SymFETs. Our paper provides a novel path of circuit designs based on devices that have characteristics similar to SymFETs and shows that SymFETs are a promising option for image processing applications in terms of power and area.
Telomere length predicts for outcome to FCR chemotherapy in CLL (2019)

We have previously shown that dividing patients with CLL into those with telomeres inside the fusogenic range (TL-IFR) and outside the fusogenic range (TL-OFR) is powerful prognostic tool. Here, we used a high-throughput version of the assay (HT-STELA) to establish whether telomere length could predict for outcome to fludarabine, cyclophosphamide, rituximab (FCR)-based treatment using samples collected from two concurrent phase II studies, ARCTIC and ADMIRE (n = 260). In univariate analysis, patients with TL-IFR had reduced progression-free survival (PFS) (P < 0.0001; HR = 2.17) and shorter overall survival (OS) (P = 0.0002; HR = 2.44). Bifurcation of the IGHV-mutated and unmutated subsets according to telomere length revealed that patients with TL-IFR in each subset had shorter PFS (HR = 4.35 and HR = 1.48, respectively) and shorter OS (HR = 3.81 and HR = 2.18, respectively). In addition, the OS of the TL-OFR and TL-IFR subsets were not significantly altered by IGHV mutation status (P = 0.61; HR = 1.24 and P = 0.41; HR = 1.47, respectively). In multivariate modeling, telomere length was the dominant co-variable for PFS (P = 0.0002; HR = 1.85) and OS (P = 0.05; HR = 1.61). Taken together, our data suggest that HT-STELA is a powerful predictor of outcome to FCR-based treatment and could be used to inform the design of future risk-adapted clinical trials.
Variable-period undulators as synchrotron radiation sources (2003)

A concept for variable-period undulators for the production of synchrotron radiation from both medium- and high-energy storage rings is described. This concept is based on a staggered array of permeable poles placed in a magnetic solenoid that produces a longitudinal field. The concept permits variations in the short magnetic period of the undulator of as much as 100%. The unique capabilities of such undulators will allow them to be tuned by the variation of the period length and of the solenoid field. The device can be operated at either constant flux or constant power, independent of X-ray energy. It is expected that the new concept will have a major impact on the production and applications of X-rays because of the inherent simplicity and flexibility of the design and the absence of radiation damage. Analyses of the magnetic and mechanical design concepts are presented.
Dietary bovine osteopontin increases vaccine response, T‐cell phenotype and cytokine secretion in piglets (623.7) (2014)

Osteopontin (OPN) is a multifunctional milk protein with immunoregulatory activities. Herein, the impact of the addition of bovine OPN to formula on influenza vaccination response, T‐cell phenotype and ex vivo cytokine secretion was assessed. Newborn piglets were fed formula alone (FF), formula+140 mg/L OPN (OPN) or were sow‐reared (SR) for 21d. Half the piglets in each diet group were vaccinated (FZ) against human influenza (Fluzone, Sanofi Pasteur) on d7 and 14. Blood samples were collected on d21 and peripheral blood mononuclear cells (PBMC) were isolated for flow cytometry and ex vivo stimulation assays. Serum FZ‐specific IgG in OPN piglets was significantly greater than FF and was comparable to SR. Dietary OPN increased the percentage of CD4+ (T‐helper cells), while vaccination alone led to a higher percentage of natural killer (NK) cells in PBMCs. Dietary OPN alone, or in combination with vaccination, increased PHA‐induced secretion of IL‐12 and IL‐10 by PBMC ex vivo. Secretion of IL‐6, IL‐10 and IL‐12 were highest in PBMCs from the OPN group upon LPS stimulation. These findings indicate that OPN modulates both cell‐mediated and humoral immune response to the influenza vaccine. Furthermore, the addition of OPN to formula may support immune responses more similar to those observed in breast‐fed infants. Grant Funding Source : Arla Foods Ingredients Group P/S
<title>X-ray mask fabrication techniques for micromachining</title> (1995)

In this paper we present specifics of x-ray mask fabrication suitable for high-aspect ratio microlithography in micromachining. Results of fabrication and exposures using x-ray masks with approximately 4 micrometer thick gold absorber (one level resist) are illustrated. For conventional x-ray masks commercially available substrates were used: B-doped Si membrane (2-3 micrometers thick) on a 4' Si wafer bonded to a Pyrex glass ring. A new approach -- the transfer mask technique -- is demonstrated. This technique is based on forming an absorber pattern directly onto the resist surface of the sample. The transfer mask method is suitable for any radiation (visible, UV, and x-rays) and is based on the use of a master mask (optical or x- ray) to achieve patterns with desired aspect ratio. When used in conjunction with multiple x- ray exposures and sequential developments the transfer mask method produces patterns with extremely high aspect ratio.
Characteristics of early murine B-lymphocyte precursors and their direct sensitivity to negative regulators (2001)

Recently, a collection of surface markers was exploited to isolate viable Lin(-) TdT(+) cells from murine bone marrow. These early pro-B cells were enriched for B-lineage lymphocyte precursor activity measured by short-term culture and had little responsiveness to myeloid growth factors. Early precursors can be propagated with remarkably high cloning frequencies in stromal cell-free, serum-free cultures, permitting this analysis of direct regulatory factors. Expression of the interleukin-7 receptor (IL-7Ralpha) chain marks functional precursors and IL-7 is necessary for progression beyond the CD45RA(+) CD19(-) stage. Efficient survival and differentiation were only observed when stem cell factor and Flt-3 ligand were also present. IL-7-responsive CD19(+) precursors are estrogen resistant. However, B-lineage differentiation was selectively abrogated when highly purified Lin(-) precursors were treated with hormone in the absence of stromal cells. In addition, early stages of B lymphopoiesis were arrested by limitin, a new interferon (IFN)-like cytokine as well as IFN-alpha, IFN-gamma, or transforming growth factor beta (TGF-beta), but not by epidermal growth factor (EGF). Lin(-) TdT(+) early pro-B cells are shown here to be CD27(+) AA4.1(+/-)Ki-67(+) Ly-6C(-) Ly-6A/Sca-1(Lo/-)Thy-1(-)CD43(+) CD4(+/-)CD16/32(Lo/-)CD44(Hi) and similar in some respects to the "common lymphoid progenitors" (CLP) identified by others. Although early pro-B cells have lost myeloid differentiation potential, transplantation experiments described here reveal that at least some can generate T lymphocytes. Of particular importance is the demonstration that a pivotal early stage of lymphopoiesis is directly sensitive to negative regulation by hormones and cytokines.
Nanowires for Biosensing: Lightguiding of Fluorescence as a Function of Diameter and Wavelength (2018)

Semiconductor nanowires can act as nanoscaled optical fibers, enabling them to guide and concentrate light emitted by surface-bound fluorophores, potentially enhancing the sensitivity of optical biosensing. While parameters such as the nanowire geometry and the fluorophore wavelength can be expected to strongly influence this lightguiding effect, no detailed description of their effect on in-coupling of fluorescent emission is available to date. Here, we use confocal imaging to quantify the lightguiding effect in GaP nanowires as a function of nanowire geometry and light wavelength. Using a combination of finite-difference time-domain simulations and analytical approaches, we identify the role of multiple waveguide modes for the observed lightguiding. The normalized frequency parameter, based on the step-index approximation, predicts the lightguiding ability of the nanowires as a function of diameter and fluorophore wavelength, providing a useful guide for the design of optical biosensors based on nanowires.
Detection and identification of cardiac arrhythmias using an adaptive, linear-predictive filter (2002)

In order to detect an abrupt change in morphology of intracardiac electrograms, the authors have developed a supplemental algorithm to rate criteria which utilizes the mean-squared error of an adaptive, linear-predictive filter (ALPF). Further analysis of the filter error is invoked when such a change is detected to identify the rhythm. ALPF successfully identified 10/11 (91%) cases of ventricular tachycardia (VT), 6/8 (75%) cases of ventricular fibrillation (VF), and 4/4 (100%) cases of sinus tachycardia (ST). As a basis of comparative analysis, correlation waveform analysis (CWA) was used to identify the same test set of arrhythmias. CWA correctly identified 11/11 (100%) cases of VT, 4/8 (50%) cases of VF, and 4/4 (100%) cases of ST. When compared to CWA, ALPF has similar accuracy in differentiating VT and ST. ALPF appears to be superior to CWA in identifying VF.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Nonlinear Echo Cancellation of Data Signals (1982)

This paper describes a new technique for implementing an echo canceller for full-duplex data transmission (such as in digital subscriber loops and volceband data sets). The canceller can operate in spite of time-invariant nonlinearities in the echo channel or in the implementation of the echo canceller itself (such as in the D/A converters). The basic structure of the linear echo canceller is not changed, but taps are simply added to account for the nonlinearity. The number of taps which must be added depends on the degree of nonlinearity which must be compensated. Numerical results based on computer simulation are given which show that typical nonlinearities encountered in MOS D/A converters can be compensated by a relatively small number of taps added to the linear echo canceller, and substantial improvement in the cancellation results.