gebhart/patrepeval huggingface dataset:
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics (2015)

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.
The Good CPD GuideThe Good CPD Guide Janet Grant Radcliffe £29.99 190pp 9781846195709 1846195705 (2012)

WHILE THIS book is written specifically for continuing professional development (CPD) in medicine, the wisdom largely holds good for nursing too. In hard times, the role of CPD has to be spelt out and the structuring of work and its material benefits to practitioners and the health service have to be crystal clear if investments of money, time and professional effort are to be made.
Spectra of Stable Non-Noble Gas Single Bubble Sonoluminescence (2006)

A commonly accepted view is that stable Single Bubble Sonoluminescence (SBSL) can only be achieved in the presence of a noble gas or hydrogen. In air-seeded bubbles, the content of diatomic gasses is burned off to leave the small amount of argon needed to sustain stable operation. Here we report that long term stable SBSL can be sustained with only nitrogen, oxygen, or nitrogen/oxygen mixtures being present. Compared to that of a stable argon bubble, the emission is much weaker and the spectrum looks much colder. Oscillating states as well as recycling states are also observed. An intriguing saturation effect seems connected with the presence of water vapor in the bubble.
An estimation of the frequency of precursor cells which generate cytotoxic lymphocytes. (1976)

The cell-mediated immune response has been generated in vitro with a polyacrylamide culture system which allows the segregation of foci (clones?) of cytotoxic lymphocytes. Using the method of limiting dilutions, the frequency of precursor cells in CBA spleen cells able to generate a cytotoxic response against DBA mastocytoma is estimated at 1 per 1,700 cells.
Current status of the therapy of advanced renal carcinoma (1977)

A preclinical murine renal model system is available for evaluation of the effectiveness of therapeutic agents. Clinical review reveals that objective response rates to hormonal agents reported since 1971 have been substantially lower than those reported prior to 1971. Many chemotherapeutic agents have not been adequately evaluated clinically or with the experimental model. Vinblastine to date may be the most active single agent with a 25% objective response rate. At the present time, it is uncertain whether combination chemotherapy or hormonal chemotherapy add to response rates obtained with single agents. There is some evidence that immunotherapy may be of some adjuvant benefit and, thus may provide an additional avenue of investigation.
BIOFEEDBACK SYSTEMS FOR STRESS REDUCTION - Towards a Bright Future for a Revitalized Field (2012)

Stress has recently been baptized as the black death of the 21st century, which illustrates its threat to current health standards. This article proposes biofeedback systems as a means to reduce stress. A concise state-ofthe-art introduction on biofeedback systems is given. The field of mental health informatics is introduced. A compact state-of-the-art introduction on stress (reduction) is provided. A pragmatic solution for the pressing societal problem of illness due to chronic stress is provided in terms of closed loop biofeedback systems. A concise set of such biofeedback systems for stress reduction is presented. We end with the identification of several development phases and ethical concerns.
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection (2005)

Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to model the variation in omega among sites, allowing a subset of sites to have omega > 1 while the rest of the sequence may be under purifying selection with omega < 1. An empirical Bayes (EB) approach is then used to calculate posterior probabilities that a site comes from the site class with omega > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and omega ratios for the site classes. In small data sets lacking information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated data sets. The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites.
6D SLAM—3D mapping outdoor environments (2007)

Abstract 6D SLAM (simultaneous localization and mapping) or 6D concurrent localization and mapping of mobile robots considers six dimensions for the robot pose, namely, the x , y , and z coordinates and the roll, yaw, and pitch angles. Robot motion and localization on natural surfaces, e.g., driving outdoor with a mobile robot, must regard these degrees of freedom. This paper presents a robotic mapping method based on locally consistent 3D laser range scans. Iterative Closest Point scan matching, combined with a heuristic for closed loop detection and a global relaxation method, results in a highly precise mapping system. A new strategy for fast data association, cached k d‐tree search, leads to feasible computing times. With no ground‐truth data available for outdoor environments, point relations in maps are compared to numerical relations in uncalibrated aerial images in order to assess the metric validity of the resulting 3D maps. © 2007 Wiley Periodicals, Inc.
Distinct signals are required for proliferation and lymphokine gene expression in murine T cell clones. (1986)

Experiments were performed to assess the capacity of lectin (Con A), ionomycin, phorbol ester (PMA), and recombinant IL 2 to mediate proliferation as well as the expression of cell surface IL 2 receptors, two lymphokine genes, IL 2 and IFN-gamma, and the c-myc proto-oncogene in cloned T cell populations. Stimulation of T cell clones with recombinant IL 2 resulted in proliferation and sustained expression of the c-myc cellular proto-oncogene, but did not induce the expression of mRNA for the lymphokines IFN-gamma and IL 2. In contrast, stimulation of cloned T cells with lectin alone induced significant IFN-gamma and IL 2 mRNA expression, up-regulation of the number of cell surface IL 2 receptors, and transient c-myc expression. Ionomycin alone was not a sufficient signal for lymphokine mRNA induction. The phorbol ester PMA alone induced neither proliferation nor lymphokine gene expression but potentiated lectin and ionomycin-mediated signals. We also performed experiments to examine whether the T cell response to extracellular stimuli was a function of the activation state of the cell. Reexposure of 48-hr antigen-activated cloned cells to identical stimuli revealed several differences. Low but significant levels of IFN-gamma mRNA were now also reinduced in activated clones cells in response to IL 2 or PMA alone. Activated cells were refractory to reinduction of IL 2 mRNA by any stimulus, which may reflect a physiologic mechanism to limit clonal expansion after antigenic stimulation. This could be partially reversed by restimulation with lectin in the presence of cycloheximide, suggesting a role for a labile protein repressor in the down-regulation of IL 2 mRNA expression. PMA alone induced an IL 2-independent proliferative response. We demonstrate that distinct signals are required for lymphokine gene expression vs cellular proliferation in cloned T lymphocyte populations, and that the capacity of extracellular stimuli to reinduce expression of lymphokine genes or to mediate cell proliferation is altered by prior activation.
An efficient VLSI architecture for fingerprint recognition using O2D-DWT architecture and modified CORDIC-FFT (2015)

The real time biometric systems are used to authenticate persons for various applications. In this paper, we propose an efficient VLSI architecture for fingerprint recognition using O2D-DWT architecture and modified CORDIC-FFT. The O2D-DWT architecture is designed using only adders and shifters for high speed operation and is applied on fingerprint image to generate four sub-bands. The optimized Fast Fourier Transform (OFFT) architecture is designed by computing different twiddle factor angles using modified CORDIC processor and is applied on LL sub-band coefficients to generate final fingerprint features. The test fingerprint features are compared with features of fingerprint images in database using Euclidean Distance. It is observed that the performance of proposed architecture is better compared to existing architectures.
T-Cell Therapy Using Interleukin-21–Primed Cytotoxic T-Cell Lymphocytes Combined With Cytotoxic T-Cell Lymphocyte Antigen-4 Blockade Results in Long-Term Cell Persistence and Durable Tumor Regression (2016)

Purpose Peripheral blood-derived antigen-specific cytotoxic T cells (CTLs) provide a readily available source of effector cells that can be administered with minimal toxicity in an outpatient setting. In metastatic melanoma, this approach results in measurable albeit modest clinical responses in patients resistant to conventional therapy. We reasoned that concurrent cytotoxic T-cell lymphocyte antigen-4 (CTLA-4) checkpoint blockade might enhance the antitumor activity of adoptively transferred CTLs. Patients and Methods Autologous MART1-specific CTLs were generated by priming with peptide-pulsed dendritic cells in the presence of interleukin-21 and enriched by peptide-major histocompatibility complex multimer-guided cell sorting. This expeditiously yielded polyclonal CTL lines uniformly expressing markers associated with an enhanced survival potential. In this first-in-human strategy, 10 patients with stage IV melanoma received the MART1-specific CTLs followed by a standard course of anti-CTLA-4 (ipilimumab). Results The toxicity profile of the combined treatment was comparable to that of ipilimumab monotherapy. Evaluation of best responses at 12 weeks yielded two continuous complete remissions, one partial response (PR) using RECIST criteria (two PRs using immune-related response criteria), and three instances of stable disease. Infused CTLs persisted with frequencies up to 2.9% of CD8<sup>+</sup> T cells for as long as the patients were monitored (up to 40 weeks). In patients who experienced complete remissions, PRs, or stable disease, the persisting CTLs acquired phenotypic and functional characteristics of long-lived memory cells. Moreover, these patients also developed responses to nontargeted tumor antigens (epitope spreading). Conclusion We demonstrate that combining antigen-specific CTLs with CTLA-4 blockade is safe and produces durable clinical responses, likely reflecting both enhanced activity of transferred cells and improved recruitment of new responses, highlighting the promise of this strategy.
Transmit antenna beamforming for the Advanced Mobile Phone System (2002)

Adaptive antenna arrays at the base station in cellular radio can be used in both a receive and transmit mode to improve system performance. While the receive problem is well-studied, methods for transmit beamforming have only recently become available. We propose a "closed loop" transmit beamforming method for the Advanced Mobile Phone System (AMPS) which uses feedback from the base to the mobile to aid the base in adapting its beampatterns. This method does not require modification or exchange of the handsets. Preliminary results show the's method is able to track spatial channel variations if either the angle spread or Doppler spread is low.
Generalized Techniques of Harmonic Elimination and Voltage Control in Thyristor Inverters: Part I--Harmonic Elimination (1973)

This paper considers the theoretical problem of eliminating harmonics in inverter-output waveforms. Generalized methods are developed for eliminating a fixed number of harmonics in the half-bridge and full-bridge inverter-output waveforms, and solutions are presented for eliminating up to five harmonics. Numerical techniques are applied to solve the nonlinear equations of the problem on the computer. The uneliminated higher order harmonics can be easily attenuated by using filter circuits in the output stage of the inverter. The results show the feasibility of obtaining practically sinusoidal output waveforms, which are highly desirable in most inverter applications.
Color Error from RGB-Stripe Pixel Structure (2002)

Most direct-view type color displays have a sub pixel structure such as the RGB-stripe structure. The video data for R and B are produced on condition that they are reproduced at the same position as G but they are displayed on the screen with 1/3 of a pixel separation from the corresponding G pixel. This pixel structure thus entails a convergence error of 1/3 of a pixel. The modified s-CIELAB method was applied to investigate color errors produced by the RGB-stripe pixel structure. The results show that the pixel structure can degrade the image quality even in a viewing distance where the pixel structure is not visible, because the color difference caused by the structure has a low frequency component and the human vision can detect it. The same method was applied to the convergence error and showed that the necessary convergence accuracy is around 1/4 of a pixel.
Clinical outcomes in ALK-rearranged lung adenocarcinomas according to ALK fusion variants (2016)

Among ALK fusion variants, v1 is the most common subtype. It showed superior progression-free survival on pemetrexed than did non-EML4 variants. No survival difference was demonstrated between variants treated with crizotinib or ceritinib.
Methods for the extraction and RNA profiling of exosomes (2013)

We have successfully developed a set of reagents and a workflow allowing fast and efficient extraction of exosomes, followed by isolation of RNA and its analysis by qRT-PCR and other techniques.
<i>Cucumber mosaic virus</i> : viral genes as virulence determinants (2011)

In tobacco sap, the thermal inactivation point of the viral infectivity is approximately 70 °C (10 min), the dilution end-point is approximately 10(-4) and viral infectivity is lost after a few days of exposure to 20 °C. Viral infectivity can be retained in freeze-dried tissues and in the form of virions purified using 5 mm sodium borate, 0.5 mm ethylenediaminetetraacetic acid and 50% glycerol (pH 9.0) at -20 °C. CMV particles are isometric, approximately 28-30 nm in diameter and are composed of 180 capsid subunits arranged in pentamer-hexamer clusters with T= 3 symmetry. The sedimentation coefficient (s(20) ,(w) ) is c. 98 S and the particle weight is (5.8-6.7) × 10(6) Da. The virions contain 18% RNA. The RNA-protein interactions that stabilize the CMV virions are readily disrupted by sodium dodecylsulphate or neutral chloride salts. GENOMIC PROPERTIES: The genomic RNAs are single-stranded messenger sense RNAs with 5' cap and 3' tRNA-like structures containing at least five open reading frames. The viral RNA consists of three genomic RNAs, RNA 1 (c. 3.3 kb), RNA 2 (c. 3.0 kb) and RNA 3 (c. 2.2 kb), and two subgenomic RNAs, RNA 4 (c. 1.0 kb) and RNA 4A (c. 0.7 kb). The 3' untranslated regions are conserved across all viral RNAs. CMV is often accompanied by satellite, noncoding, small, linear RNA that is nonhomologous to the helper CMV.
Adaptive blind source separation with HRTFs beamforming preprocessing (2012)

We propose an adaptive blind source separation algorithm in the context of robot audition using a microphone array. Our algorithm presents two steps: a fixed beamforming step to reduce the reverberation and the background noise and a source separation step. In the fixed beamforming preprocessing, we build the beamforming filters using the Head Related Transfer Functions (HRTFs) which allows us to take into consideration the effect of the robot's head on the near acoustic field. In the source separation step, we use a separation algorithm based on the l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm minimization. We evaluate the performance of the proposed algorithm in a total adaptive way with real data and varying number of sources and show good separation and source number estimation results.
25. The photo-oxides of 9 : 10-dixenylanthracene and 9 : 10-diphenyl-2-methylanthracene (1939)

D. Duveen and A. Willemart, J. Chem. Soc., 1939, 116 DOI: 10.1039/JR9390000116
Murine encephalitozoonosis: the effect of age and mode of transmission on occurrence of infection. (1988)

Experiments were conducted to determine whether neonatal mice are more susceptible to E. cuniculi than adult mice, and whether vertical and/or horizontal transmission occur in murine encephalitozoonosis. E. cuniculi infection in neonates did not cause mortality or clinical signs, but did result in chronic infection. Despite initial age-related immunodeficiency, mice infected as neonates eventually developed humoral and cell-mediated immune responses against the parasite comparable to those seen in adult mice. The results suggested that neonatal mice are not more susceptible to E. cuniculi than adult mice. Pups from either infected or normal parents did not differ in humoral and cell-mediated immune responses after challenge, suggesting that pups from infected parents were not infected with E. cuniculi during gestation. In contrast, mice became infected by caging with infected mice demonstrating that horizontal infection does occur.
Diffusivity of native defects in GaN (2004)

The diffusion of relevant native point defects in wurtzite GaN crystals is investigated using first-principles density-functional pseudopotential calculations. Our reexamination of the ground state of the defects, using a higher level of convergence than was previously used, yields results in good agreement with earlier published results [J. Neugebauer and C. G. Van de Walle, Phys. Rev. B $50,$ 8067 (1994)]. Gallium interstitials are stable at the octahedral interstitial site and can occur in 1+, 2+ (metastable), or 3+ charge states. They migrate via an interstitialcy mechanism with an unexpectedly low barrier of 0.9 eV, consistent with the annealing of the $L5$ signal in electron-paramagnetic-resonance experiments [K. H. Chow et al., Phys. Rev. Lett. $85,$ 2761 (2000)]. For the nitrogen interstitial the ground-state configuration is a split interstitial, occurring in charge states ranging from $1\ensuremath{-}$ to 3+. Migration also proceeds via an interstitialcy mechanism, with barriers of 2.4 eV or lower, depending on the charge state. The nitrogen vacancy has two stable charge states 1+ and 3+. The migration barrier for ${V}_{\mathrm{N}}^{+}$ is high (4.3 eV), while the migration barrier for ${V}_{\mathrm{N}}^{3+}$ is significantly lower, at 2.6 eV, consistent with recent positron-annihilation experiments [S. Hautakangas et al., Phys. Rev. Lett. $90,$ 137402 (2003)]. The gallium vacancy, finally, can occur in charge states 0, $1\ensuremath{-},$ $2\ensuremath{-},$ and $3\ensuremath{-},$ and migrates with a barrier of 1.9 eV. For all these defects the lowest-energy migration path results in motion both parallel and perpendicular to the c axis; no anisotropy in the diffusion will therefore be observed. Applications to point-defect-assisted impurity diffusion will also be discussed.
Aggressive breast cancer in western Kenya has early onset, high proliferation, and immune cell infiltration (2016)

We identified clinical biomarkers that may assist in identifying therapy strategies for breast cancer patients in western Kenya. Estrogen receptor status in particular should lead initial treatment strategies in these breast cancer patients. Increased CD25 expression suggests a need for additional treatment strategies designed to overcome immune suppression by CD25+ cells in order to promote the antitumor activity of CD8+ cytotoxic T cells.
Shape-based interpolation (1992)

Extensions to a shape-based interpolation method in which pixels that share a boundary edge (one inside and the other outside the object) are considered to be at a distance between adjacent pixel centers are proposed. Using such an initialization for distance calculations, a generalization of the chamfer distance calculation is developed. The generalization allows the simultaneous calculation of distances within the object and its background by two consecutive chamfering processes. The performances of a number of variants of the methods are evaluated. It is shown that the shape-based interpolation using a near-optimal 3*3 distance and modified cubic spline between-slice interpolation has superior properties to previously proposed methods for estimating object locations in missing slices in tomographic radiology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Spin gapless semiconductor like Ti<sub>2</sub>MnAl film as a new candidate for spintronics application (2015)

A novel Heusler ferrimagnet Ti 2 MnAl film has been grown on Si(001) substrate using magnetron sputtering. Characteristics of its magnetic and transport properties reveal the spin‐gapless‐semiconductor (SGS) nature of the stoichiometric Ti 2 MnAl, in agreement with theoretical prediction. The as‐grown SGS‐like Ti 2 MnAl film demonstrated high Curie temperature, nearly compensated ferrimagnetic properties with small coercivity and low magnetization. It also showed semiconductor‐like behavior at room temperature allowing good compatibility with commercial Si‐based semiconductor. In this regards, Ti 2 MnAl film is a potential candidate material for spintronics application, especially for the minimization of energy consumption of device. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)