gebhart/patrepeval huggingface dataset:
Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus) (2019)

Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted <i>in vitro</i> prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (<i>Ursus maritimus</i>). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within <i>U. maritimus</i> not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
Glycogen Synthase Phosphatase Interacts with Heat Shock Factor To Activate CUP1 Gene Transcription in Saccharomyces cerevisiae (1999)

Upon heat shock, transcription of many stress-inducible genes is rapidly and dramatically stimulated by heat shock factor (HSF). A central region of the yeast HSF (designated HSFrr for "repression region") was previously identified and proposed to be involved in repressing the activation domain under non-heat-shock conditions. Here, we used the phage display system to isolate proteins that interact with HSFrr. This should identify factors that modulate HSF activity or directly participate in HSF-mediated transcriptional activation. We constructed a randomly sheared yeast genomic library to express yeast proteins on the surface of lambda phage. HSFrr binding phages were selected by cycles of affinity chromatography. DNA sequencing identified an HSFrr-interacting phage that contains the GAC1 gene. The GAC1 gene encodes the regulatory subunit for a type 1 serine/threonine phosphoprotein phosphatase, Glc7. Both gac1 and glc7 mutations had little effect on HSF activation of gene transcription of two heat shock genes, SSA4 and HSP82. In contrast, heat shock induction of CUP1 gene expression was completely abolished in a glc7 mutant and reduced in a gac1 mutant. The results demonstrate that the Glc7 phosphatase and its Gac1 regulatory subunit play positive roles in HSF activation of CUP1 transcription.
Modeling of the thermal n-octane oxidation in the liquid phase (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModeling of the thermal n-octane oxidation in the liquid phaseFelix Garcia-Ochoa, Arturo Romero, and Jose QuerolCite this: Ind. Eng. Chem. Res. 1989, 28, 1, 43–48Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/ie00085a009https://doi.org/10.1021/ie00085a009research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations34LEARN 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
Effect of supplemental chromium on antibody responses of newly arrived feeder calves to vaccines and ovalbumin. (1996)

Two trials were conducted to investigate the effects of supplemental chromium (Cr) from organic sources (Cr chelate and high Cr yeast) on antibody responses of newly arrived feeder calves following vaccination with infectious bovine rhinotracheitis (IBR), para-influenza-3 (PI3), bovine respiratory syncytial virus (BRSV), bovine viral diarrhea (BVD) and Pasteurella haemolytica and ovalbumin (OVA). Using cross bred steer calves purchased at sales in Ontario, vaccines and OVA were given on d 0 and 21 after arrival in the feedlot. Immune responses of calves were measured as serum specific antibody titres against all antigens on d 0 and 28 or d 35. The anti-OVA antibody responses (trial 2) were further investigated by measuring antibody concentrations of calves weekly until d 55 after arrival in the feedlot. Supplemental Cr (0.14 ppm) from an amino acid-chelated source had no effect on antibody responses to IBR, P13 and BRSV, but enhanced (P < 0.05) antibody titres of calves in response to the BVD vaccine on d 28 or d 35. Supplemental Cr from Cr yeast had no effect on antibody titres of calves to any vaccines. Chromium from both sources (trial 1 and 2) had no effect on antibody responses of calves following vaccination with P. haemolytica. However, supplemental Cr (0.75 ppm) from Cr yeast enhanced (P < 0.05) serum antibody responses of calves to OVA during the primary response (d 14) and secondary response (d 35) following immunization. These data confirmed our previous finding that supplemental Cr can enhance humoral immune response of market-transit stressed calves, but its enhancement on vaccine efficacy was antigen-dependent and variable.
Fault recovery port-based fast spanning tree algorithm (FRP-FAST) for the fault-tolerant Ethernet on the arbitrary switched network topology (2002)

We present a novel approach, named Fault Recovery Port-Based Fast Spanning Tree Algorithm (FRP-FAST), of the Fault-Tolerant Ethernet (FTE) extension method to the arbitrary switched network topology with providing a significant improvement of failure detection and the spanning tree rebuilding time on the switched Ethernet. We provide a mechanism that expedites failure detection time using peer-based hello message algorithm and eliminates the chance of any transient loop creation during the spanning tree reconstruction using a pre-configured recovery port. As a result, unlike IEEE 802.1D, the scheme does not block data transmission on unaffected data path during the spanning tree discovery phase. The FRP-FAST algorithm has been implemented in the kernel mode of Windows NT-based PC using 3 NICs (3 port switch). The measured failure detection and recovery time meets control industry's 2 seconds requirement.
Tailored graphitized soot as reference material for EC/OC measurement validation (2011)

Abstract. The lack of standard reference materials for calibrating, troubleshooting and intercomparing techniques that measure the composition of black carbon, commonly referred to as soot, has been a major obstacle that hinders improved understanding of how climate and health is impacted by this ubiquitous component of the atmosphere. A different approach is offered here as a means of constructing precisely controlled material with fractions of organic carbon (OC) on the surface of elemental carbon (EC) whose structure reflects that of the combustion produced particles found in the atmosphere. The proposed soot reference material (SRM) uses EC as a basis substrate for surface coatings of organic compounds that are representative of the main classes of organics identified in the coverage of soot produced by fossil fuel burning. A number of methods are used to demonstrate the quality and stability of the reference EC and SRM. Comparison of the nominal fraction of OC deposited on the EC substrate with the fraction measured with thermal/optical analysis (TOA) shows excellent agreement. Application of this type of reference material for evaluating the different methods of carbon analysis may help resolve differences that currently exist between comparable measurement techniques when trying to separate OC and EC from ambient samples.
Time-resolved magnetic relaxation of a nanomagnet on subnanosecond time scales (2012)

We present a two-current-pulse temporal correlation experiment to study the intrinsic subnanosecond nonequilibrium magnetic dynamics of a nanomagnet during and following a pulse excitation. This method is applied to a model spin-transfer system, a spin-valve nanopillar with perpendicular magnetic anisotropy. Two pulses separated by a short delay ($&lt;500$ ps) are shown to lead to the same switching probability as a single pulse with a duration that depends on the delay. This demonstrates a remarkable symmetry between magnetic excitation and relaxation and provides a direct measurement of the magnetic relaxation time. The results are consistent with a simple finite-temperature Fokker-Planck macrospin model of the dynamics, suggesting more coherent magnetization dynamics in this short-time nonequilibrium limit than near equilibrium.
Induction of cvtokines and expression of surface receptors in Mono Mac 6 cells after infection with different Legionella species (1998)

The ability of Legionella species to multiply within human mononuclear phagocytes is usually regarded as being associated with their pathogenicity. Activation of host cells results in inhibition of intracellular Legionella multiplication. The most effective substance to induce macrophage activation, both in vivo and in vitro, is interferon-gamma. In addition, some evidence exists that macrophage-derived cytokines may contribute to the host defense against L. pneumophila, but the production of pro- and antiinflammatory cytokines by monocytes after infection with different Legionella species has not been reported with regard to their ability to multiply within the host cells. We therefore examined the production of TNF-alpha, IL-1, IL-6, IL-8, IL-10 and TGF-beta by Mono Mac 6 cells after infection with Legionella species of different human prevalence that differ in their ability to replicate within this macrophage-like cell line. After infection, Mono Mac 6 cells showed a cytokine response with time kinetics characteristic for the cytokine. Maximum cytokine levels produced differed with Legionella species, but were not related to intracellular multiplication rates. Moreover, LPS-tolerant Mono Mac 6 cells, which failed to produce cytokines, showed intracellular increase or decrease of bacterial numbers identical to that of untreated Mono Mac 6 cells. By FACS analysis, an up-regulation of CD14 (LPS receptor) and CD54 (ICAM-1) could be demonstrated. We conclude that, in the Mono Mac 6 cell line, induction of macrophage-derived cytokines after infection with members of the genus Legionella mimics an inflammatory reaction without association with intracellular multiplication rate.
Fast selective antialiasing for direct volume rendering (2019)

One of the most popular method of 3d datasets visualization is direct volume rendering. The paper describes an algorithm which accelerates an antialiasing process in it. The new method works in two passes: the first one is executed at pixel level, the second one is done at subpixel level. In the first pass the rays are going not through the pixel centers of resulting image but with half-pixel offset. The values of volume integral for the rays including values of the volume integral over a predefined set of intervals are stored in so-called G-buffer. In the second pass if the resulting colors for adjacent rays are close, then the color of the pixel between those rays is interpolated bilinearly; otherwise several subpixels are processed for the pixel to get more accurate color value. The color values over intervals from G-buffer are used to accelerate calculation of volume integral over subpixels’ rays. The more subpixels are used the higher efficiency the approach shows. The speed also increases with growing of dataset coherence. For example, for typical medical volume data selective antialiasing with four subpixels accelerates the rendering about three times in comparison with the full-screen antialiased direct volume rendering.
Table S2 from Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4<sup>+</sup> T-cell Responses in Glioblastoma (2023)

&lt;p&gt;Over-/highly expressed genes in the primary glioblastoma when compared with glioblastoma cohort in TCGA Database.&lt;/p&gt;
BEIRUT: Repository Mining for Defect Prediction (2021)

Software Defect Prediction is an important activity used in the Testing Phase of the software development life cycle. Within the research of new defect prediction approaches and the selection of training sets for the classification task, different benchmarks have been analyzed in the literature. They provide several features and defective information over specific software archives. Therefore, they are commonly used in research to evaluate new approaches. However, the current benchmarks contain several limitations, such as lack of project variability, outdated benchmarks, single-version projects, a small number of projects and metrics, unavailable resources, poor usability, and non-extensible tools. Therefore, we introduce a novel tool Bgu rEpository mlning foR bUg predicIion (BEIRUT) for benchmark generation for defect prediction, composed of three main features: Given an open-source repository from GitHub, BEIRUT mines the software repository by (1) selecting the best <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$k$</tex> versions, based on the defective rate of each version, (2) generating training sets and a testing set for defect prediction, composed of a large number of metrics and defective information extracted from each of the selected versions and (3) creating defect prediction models from those extracted metrics. In the end, BEIRUT extracts a diversified catalog of 644 metrics and the defective information from each component of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$k$</tex> versions, automatically selected based on the rate of defects in each version. They were collected from 512 different projects, starting from 2009. The tool is also supplemented with an easy-to-use web interface that provides a configurable selection of projects and metrics and an interface to manage the defect prediction tasks. Moreover, this tool is adapted to be extended with new projects and new extractors, introducing new metrics to the benchmark. The web service tool can be found at rps.ise.bgu.ac.il/beirut.
Intelligent design synthesis: an object-oriented approach (1991)

Conceptual design is a process of converting design requirements into an acceptable design solution. An object-oriented system for conceptual design is presented. The process of component synthesis is guided by production rules. An object-oriented programming paradigm is chosen since it simulates the designer's way of thinking during conceptual design. The system is implemented in Smalltalk-80 programming language and environment. Besides providing all the characteristics of an object-oriented language, Smalltalk-80 allows for development of highly user-friendly interfaces. The design synthesis process is presented using a graphical and textual description.
A stripline-like coil element structure for high field phased array coils and its application for a 8-channel 9.4T small animal transceive array (2010)

Introduction Ultra-high magnetic field strength, as widely utilised in small animal MRI systems, has advantages of being able to enhance signal-to-noise ratio (SNR) and gain high spectral resolution [1]. However, the homogeneity of B1 field worsens along with the move to higher RF-frequencies. Methods such as RF shimming and transmit SENSE, which require transceive volume-arrays had been proposed to circumvent the high-field inhomogeneity problem [2]. Currently, the trend in designing transceive volume arrays is to fit the highest feasible number of coil-elements within a given geometry. Consequently, the aperture of each coil element will be small and RF field penetration depth is sacrificed. In addition, with increased number of coil elements, mutual decoupling is harder to control and good channel isolation is difficult to achieve. Therefore, it is very important to consider these two issues when designing a transceive volume-array system. In this work, the development of an optimized, shielded 8-element transceive volume-array for small animal MRI applications at 9.4T is discussed. To take into consideration the mentioned designing issues, a novel radiating structure for the coil element has been proposed. A prototype was constructed and tested in a Bruker 9.4T Biospec MRI system. Simulated and experimental results presented herein demonstrate the potential of the design.
Stoichiometric molecular imprinting using polymerisable urea and squaramide receptors for the solid phase extraction of organo-arsenic compound roxarsone (2020)

The design, preparation and evaluation of molecularly imprinted polymers for roxarsone (4-hydroxy-3-nitrophenylarsonic acid), an organo-arsenic swine and poultry feed additive, using bi-substituted ureas and squaramide receptors as the functional monomers, are demonstrated. Pre-polymerisation studies of the template-monomer complexation performed by <sup>1</sup>H NMR experiments show that squaramide-based monomers provide association equilibrium constant values higher than urea-based monomers. Equilibrium rebinding experiments in methanol show that two squaramide-based materials have good molecular recognition properties towards roxarsone, with high affinity (K<sub>eq</sub> = 16.85 × 10<sup>3</sup> L mol<sup>-1</sup> and 14.65 × 10<sup>3</sup> L mol<sup>-1</sup>, respectively), high imprinting factors (4.73 and 3.64 respectively) and good selectivity towards two roxarsone-related compounds, acetarsone (3-acetamido-4-hydroxyphenylarsonic acid) and nitarsone (4-nitrophenylarsonic acid). Polymer MIP-SQ2 was successfully used to setup an experimental protocol for the direct solid phase extraction of roxarsone from surface water samples. The method gives clean HPLC traces, with recoveries between 91% and 95% at concentration levels of 5.0, 10, and 25 mg L<sup>-1</sup>. Sample preconcentration with good recoveries between 87% and 97%, are shown, confirming that it is possible to employ the developed materials to measure roxarsone down to 1 μg L<sup>-1</sup> in water samples.
Error Probability Minimizing Pilots for OFDM With M-PSK Modulation Over Rayleigh-Fading Channels (2004)

Orthogonal frequency division multiplexing (OFDM) with pilot symbol assisted channel estimation is a promising technique for high rate transmissions over wireless frequency-selective fading channels. In this paper, we analyze the symbol error rate (SER) performance of OFDM with M-ary phase-shift keying (M-PSK) modulation over Rayleigh-fading channels, in the presence of channel estimation errors. Both least-squares error (LSE) and minimum mean-square error (MMSE) channel estimators are considered. For prescribed power, our analysis not only yields exact SER formulas, but also quantifies the performance loss due to channel estimation errors. We also optimize the number of pilot symbols, the placement of pilot symbols, and the power allocation between pilot and information symbols, to minimize this loss, and thereby minimize SER. Simulations corroborate our SER performance analysis, and numerical results are presented to illustrate our optimal claims.
Modeling of Frequency-Dependent Damping for Fast Vibration Prediction in Permanent Magnet Synchronous Machines (2022)

Vibration prediction enhancement in permanent magnet synchronous machines (PMSMs) through frequency-dependent damping is proposed in this work. Rayleigh damping coefficients are used to implement frequency-dependent damping. Mass- and stiffness-dependent Rayleigh damping coefficients are determined by utilizing frequency response functions (FRFs) from the impact hammer test for two prototype 12-slot 10-pole (12s10p) PMSM designs and are used during vibration prediction rather than the assumption of constant damping. Predicted vibration spectra are experimentally validated through run-up tests of two prototypes. A damping coefficient prediction strategy is proposed to enable fast vibration prediction of future builds and to reduce the dependency of accurate vibration prediction on the availability of a prototype. The damping prediction method uses the change in mass, natural frequency, and stiffness from one design to another to predict the Rayleigh damping coefficients of a future build. The proposed damping prediction method is experimentally validated using a third prototype.
Lung preservation. (1992)

Pulmonary transplantation is now a clinical reality that offers hope to large numbers of patients with end-stage lung disease. Current methods of preserving pulmonary function allow for transplantation, but operation must be expeditious, and transportation time and operating time become critical factors in determining outcome. The ability to preserve lungs for longer time intervals could potentially allow for more widespread distribution of donor organs of unusual size or blood type, and could set the stage for more appropriate HLA matching between donor and recipient. Furthermore, a more thorough understanding of the pathophysiology of preservation injury will likely lead to a better understanding of the pathophysiology of other types of lung injury. In turn, this could increase the size of the pulmonary donor pool by allowing transplantation of lungs with suboptimal gas exchange function at the time of donor brain death. Finally, a more thorough understanding of lung metabolism and determinants of cellular viability in the lung would be useful for the potential application of the use of lungs from circulation-arrested cadavers for transplantation.