gebhart/patrepeval huggingface dataset:
Oligonucleotides targeting coagulation factor mRNAs: use in thrombosis and hemophilia research and therapy (2017)

Small interfering (si) RNAs and antisense oligonucleotides (ASOs; here for simplicity reasons, both referred to as oligonucleotides) are small synthetic RNA or DNA molecules with a sequence complementary to a (pre)mRNA. Although the basic mechanisms of action between siRNAs and ASO are distinct, a sequence-specific interaction of the both oligonucleotides with the target (pre)mRNA alters the target's fate, which includes highly effective sequence-specific blockade of translation and consequently depletion of the corresponding protein. For a number of years, these oligonucleotides have been used as a tool in biological research to study gene function in vitro. More recently, safe and specific delivery of these oligonucleotides to the liver of mammals has been achieved and optimized. This not only allowed their use for in vivo gene studies in physiology and disease, but also opened the opportunity for the development of a new generation of RNA-specific drugs for therapeutic purposes. In 2013, the first oligonucleotide product targeting RNA from the hepatic cholesterol pathway was approved. For blood coagulation, a large portion of key proteins are produced in the liver, and thereby siRNAs and ASOs can also be used as appropriate tools to target these proteins in vivo. In this review, we describe the first use of oligonucleotides for this purpose from zebrafish to primates. As the use of oligonucleotides allows avoidance of early lethality associated with full deficiency of several coagulation factors, it has proved to be of value for studying these proteins in physiology and disease. Currently, oligonucleotides are tested as therapeutics, with the ultimate goal to beneficially modulate the hemostatic balance in thrombosis and hemophilia patients. We discuss both the preclinical and clinical studies of a number of siRNAs and ASOs with the potential to be introduced as drugs for prophylactic and/or treatment of thrombosis or hemophilia. We conclude that for the coagulation field, oligonucleotides are of value for research purposes, and now the moment has come to fulfill their promise as therapeutics.
An optical residue arithmetic unit (1978)

The residue number system is used to partition addition, subtraction, multiplication, or integer polynomial transforms into several simpler calculations, each of which can be processed in parallel with complete independence. These segments are computationally simple such that all the arithmetic interactions can be enumerated as mathematical mappings. By routing signals through various mappings a number may be encoded into residue form, processed in various ways, and eventually decoded back to a normal number system. The signals may be routed in a manner to reflect calculations involving a plurality of operands and operations. By routing several signals in close sequence calculations may be pipelined. By routing different types of signals independently several calculations may be multiplexed. Detection of abnormalities in a segment's signal may be used to exclude the segment from the decoding process, thus preserving the correctness of the calculations. By reducing and conveniently deferring the signal detections necessary, a greater variety of phenomena may be considered for digital computation. Optical implementations are of particular interest.
Tumor Necrosis Factor-α Induces Functionally Active Hyaluronan-adhesive CD44 by Activating Sialidase through p38 Mitogen-activated Protein Kinase in Lipopolysaccharide-stimulated Human Monocytic Cells (2003)

Interaction of CD44, an adhesion molecule, with its ligand, hyaluronan (HA), in monocytic cells plays a critical role in cell migration, inflammation, and immune responses. Most cell types express CD44 but do not bind HA. The biological functions of CD44 have been attributed to the generation of the functionally active, HA-adhesive form of this molecule. Although lipopolysaccharide (LPS) and cytokines induce HA-adhesive CD44, the molecular mechanism underlying this process remains unknown. In this study, we show that LPS-induced CD44-mediated HA (CD44-HA) binding in monocytes is regulated by endogenously produced tumor necrosis factor (TNF)-alpha and IL-10. Furthermore, p38 mitogen-activated protein kinase (MAPK) activation was required for LPS- and TNF-alpha-induced, but not IL-10-induced, CD44-HA-binding in normal monocytes. To dissect the signaling pathways regulating CD44-HA binding independently of cross-regulatory IL-10-mediated effects, IL-10-refractory promonocytic THP-1 cells were employed. LPS-induced CD44-HA binding in THP-1 cells was regulated by endogenously produced TNF-alpha. Our results also suggest that lysosomal sialidase activation may be required for the acquisition of the HA-binding form of CD44 in LPS- and TNF-alpha-stimulated monocytic cells. Studies conducted to understand the role of MAPKs in the induction of sialidase activity revealed that LPS-induced sialidase activity was dependent on p42/44 MAPK-mediated TNF-alpha production. Blocking TNF-alpha production by PD98059, a p42/44 inhibitor, significantly reduced the LPS-induced sialidase activity and CD44-HA binding. Subsequently, TNF-alpha-mediated p38 MAPK activation induced sialidase activity and CD44-HA binding. Taken together, our results suggest that TNF-alpha-induced p38 MAPK activation may regulate the induction of functionally active HA-binding form of CD44 by activating sialidase in LPS-stimulated human monocytic cells.
Vector-Quantized Autoregressive Predictive Coding (2020)

Autoregressive Predictive Coding (APC), as a self-supervised objective, has enjoyed success in learning representations from large amounts of unlabeled data, and the learned representations are rich for many downstream tasks. However, the connection between low self-supervised loss and strong performance in downstream tasks remains unclear. In this work, we propose Vector-Quantized Autoregressive Predictive Coding (VQ-APC), a novel model that produces quantized representations, allowing us to explicitly control the amount of information encoded in the representations. By studying a sequence of increasingly limited models, we reveal the constituents of the learned representations. In particular, we confirm the presence of information with probing tasks, while showing the absence of information with mutual information, uncovering the model's preference in preserving speech information as its capacity becomes constrained. We find that there exists a point where phonetic and speaker information are amplified to maximize a self-supervised objective. As a byproduct, the learned codes for a particular model capacity correspond well to English phones.
Finite-element analysis and simulation of polymers: a bibliography (1976 - 1996) (1997)

This paper gives a bibliographical review of the finite-element methods applied to the analysis and simulation of polymers. The bibliography at the end of the paper contains references to papers, conference proceedings and theses/dissertations on the subject that were published between 1976 - 1996. The following topics are included: polymer flow and mixing simulation; polymer processing; thermal analysis of polymers; fracture mechanics of polymers; modelling polymer behaviours and their mechanical properties; practical polymer applications in engineering; other topics.
Properties Permitting the Renal Cortex to Be the Oxygen Sensor for the Release of Erythropoietin (2006)

The PO2 at this site where erythropoietin release is regulated should vary only when the hemoglobin concentration changes in capillary blood. The kidney cortex is an ideal location for this O2 sensor for four reasons. First, it extracts a small proportion of the oxygen that is delivered in each liter of blood; this makes the PO2 signal easier to recognize. Second, there is a constant ratio of the work performed (consumption of O2) to the renal blood flow rate (delivery of O2). Third, the high renal blood flow rate improves diffusion of O2 from capillaries to this O2 receptor. Fourth, a high renal cortical PCO2 prevents an additional shift of the O2:hemoglobin dissociation curve by other factors from being a confounding variable. This suggests that the GFR and the renal blood flow rate should be examined in patients with unexplained anemia or erythrocytosis.
Digging in the crates (2012)

An ethnographic study uncovers the work of nightclub DJs, which extends far beyond the act of mixing tracks to also encompass collecting music, preparing for performances, and promotion and networking. We reveal how DJs value vinyl and digital formats in different ways, acquire music through 'crate digging', prepare physical and digital crates of music before gigs, and how these underpin improvised selections during their performances. We document how DJs interact with promoters, venues, dancers and other DJs, revealing an etiquette that governs how they select and share music, and manage an ongoing tension between revealing and hiding metadata so as to maintain a competitive edge. We raise implications for technologies to support DJs, while also shedding light on previous studies of music consumption and sharing in other settings.
On the Physical Chemistry of Kraft Lignin : Fundamentals and Applications (2001)

This thesis describes the physical chemistry of softwood kraft lignin in aqueous alkaline solutions. Both fundamental and applicational aspects are discussed. Kraft lignin originates either from pulp fibres or from black liquor produced by kraft cooking. In wood, the lignin is an anionic macromolecular colloid of relatively high molecular mass that is gradually depolymerised under the kraft cook. From UV-spectrophotometric measurements, the dissociation of phenolic functional groups was shown to decrease by increasingly higher temperatures. By theoretical considerations, applying the Poisson-Boltzmann cell model, it was shown that high molecular weight macromolecules attribute higher apparent pKa values due to an increased electrostatic attraction of hydrogen ions. From 1H PFG NMR self-diffusion measurements, it was further seen that high molecular weight kraft lignin also expresses lower colloidal stability than low molecular weight fragments. Coagulation caused by kraft lignin self-aggregation could be qualitatively described by the DLVO-theory. It was also shown that the solution conditions at the end of conventional kraft cooking are dangerously close to the stability threshold of high molecular weight kraft lignin. In the kraft process this could be detrimental for the rate of delignification. The kinetics of kraft lignin self-aggregation, determined by light scattering, was shown to be universal and followed reaction-limited cluster-colloid aggregation (RLCA) or diffusion-limited cluster-colloid aggregation (DLCA), depending on the solution conditions. The structures of the formed aggregates, found to be cluster like and to attribute fractality, were shown by cryo-TEM analysis. Fractal dimensions in the range of df = 1.9 – 2.5, were determined for the aggregates. Anions belonging to the Hofmeister series were shown to affect the stability of kraft lignin solutions very differently. Anionic surfactant – kraft lignin interactions were also studied. Among the tested surfactants, the group of bile acid salts was found especially efficient in stabilising kraft lignin solutions also at elevated temperatures. Furthermore, even after that self-aggregation had occurred, the aggregates could be re-dissolved by additions of sodium taurodeoxycholate.
3-D instantaneous frequency used as a coherency/continuity parameter to parameter to interpret reservoir compartment boundaries across an area of complex turbidite deposition (1998)

Abstract In previous unpublished work, we found that anomalous values of instantaneous frequency (that is, frequency values that are negative or that have positive magnitudes greater than the Nyquist limit) are valuable indicators of alterations in reflection waveshape that occur commonly at stratigraphic terminations. Inspection of 3-D seismic data across Nash Draw Field on the northwest slope of the Delaware Basin showed that appreciable wavelet alterations occurred at the boundaries of distinct seismic facies within the targeted Brushy Canyon reservoirs that are being produced in this field. Based on this observation, we used instantaneous frequency as the fundamental database to define the edge positions and areal shapes of individual reservoir facies within this complex, slope-basin distribution of siltstones and sand-stones, commonly thought to be a succession of turbidite depositions. We compared the compartmentalization detail derived from this frequency-based approach with compartmentalization models provided by an amplitude-based interpretation and by coherency/continuity cube technology. These comparisons led us to conclude that a properly executed 3-D interpretation of instantaneous frequency behavior can provide a good first guess of the internal compartmented structure of many reservoirs. We offer our work here for peer evaluation by people who support reservoir characterization studies similar to what we describe. We have used instantaneous frequency behavior to successfully detect lateral disruptions in stratigraphic continuity for several years--long before the current concept of a coherency (or continuity) cube was publicized for this same purpose. This study shows that interpreters who do not have ready access to coherency-cube technology, but who do have Hilbert transform algorithms available to them, can create 3-D volumes of instantaneous frequency that provide valuable indications of reflection discontinuity, much in the same way that continuity/coherency cube technology does.
On reducing test application time for scan circuits using limited scan operations and transfer sequences (2005)

The test application time of a scan circuit is a significant factor in the overall test cost of the circuit. Therefore, reducing the test application time is an important problem. The test application time of a test set for a scan circuit is determined by the sum of the number of scan shifts required for applying the test set and the number of primary input vectors in the test set. Compaction procedures that view a full-scan circuit as a combinational circuit reduce the number of test vectors, where a test vector consists of a scan vector and a primary input vector. However, this is not sufficient, and effective procedures must reduce the number of scan operations further than the combinational circuit view allows. Procedures to reduce the test application time by dropping scan operations and applying several primary input vectors between scan operations have been proposed earlier. The compaction procedures proposed in this work reduce the test application time further by using limited scan operations. Under a limited scan operation, the number of shifts is smaller than the length of a scan chain. Scan operations that cannot be dropped are replaced by limited scan operations under the proposed procedures.
Influence of Iron Oxide Brown on Smoke‐Suppression Properties and Combustion Behavior of Intumescent Flame‐Retardant Epoxy Composites (2015)

ABSTRACT This article mainly deals with smoke‐suppression properties and synergistic flame‐retardant effects of iron oxide brown ((Fe 2 O 3 + FeO)· n H 2 O) on intumescent flame‐retardant epoxy resins (IFREP) using ammonium polyphosphate and pentaerythritol as intumescent flame retardants. The smoke‐suppression properties and flame retardancy of iron oxide brown on IFREP compositions were investigated by the cone calorimeter test (CCT), scanning electron microscopy (SEM), and thermogravimetric analysis‐infrared spectrometry. Remarkably, CCT data revealed that the incorporation of iron oxide brown into IFREP compositions can significantly reduce heat release rate, total heat release, smoke production rate, and total smoke release, and so on. On the other hand, the SEM results showed that iron oxide brown can greatly improve the structure of char residue. The thermogravimetric data indicated that iron oxide brown had different effects on the process of thermal degradation of the IFREP compositions. The volatilized products formed on thermal degradation of IFREP compositions indicated that the volatilized products were H 2 O, CO 2 , CO, carboxylic acid, and aliphatic hydrocarbons according to the temperature of onset formation. Here, iron oxide brown is considered to be an effective smoke‐suppression agent and a good synergism with IFR in flame‐retardant epoxy resins, which can greatly enhance the char residue.
Multiple Sclerosis Medical Image Analysis and Information Management (2005)

Magnetic resonance imaging (MRI) has become a central tool for patient management, as well as research, in multiple sclerosis (MS). Measurements of disease burden and activity derived from MRI through quantitative image analysis techniques are increasingly being used. There are many complexities and challenges in building computerized processing pipelines to ensure efficiency, reproducibility, and quality control for MRI scans from MS patients. Such paradigms require advanced image processing and analysis technologies, as well as integrated database management systems to ensure the most utility for clinical and research purposes. This article reviews pipelines available for quantitative clinical MRI research in MS, including image segmentation, registration, time-series analysis, performance validation, visualization techniques, and advanced medical imaging software packages. To address the complex demands of the sequential processes, the authors developed a workflow management system that uses a centralized database and distributed computing system for image processing and analysis. The implementation of their system includes a web-form-based Oracle database application for information management and event dispatching, and multiple modules for image processing and analysis. The seamless integration of processing pipelines with the database makes it more efficient for users to navigate complex, multistep analysis protocols, reduces the user's learning curve, reduces the time needed for combining and activating different computing modules, and allows for close monitoring for quality-control purposes. The authors' system can be extended to general applications in clinical trials and to routine processing for image-based clinical research.
Genetic and Antigenic Diversity of<i>Ehrlichia chaffeensis:</i>Comparative Analysis of a Novel Human Strain from Oklahoma and Previously Isolated Strains (1997)

A new Ehrlichia strain, designated as Ehrlichia chaffeensis, Sapulpa strain, was isolated from a patient from Oklahoma with severe ehrlichiosis. Isolation of the ehrlichial pathogen was achieved by inoculating patient blood onto HEL cells and DH82 cells. Antigenic properties of the new isolate were characterized with monoclonal antibodies, homologous patient serum, and polyclonal rabbit serum by Western immunoblotting. The results showed antigenic differences and protein size variation of Sapulpa strain compared with the other 2 strains of E. chaffeensis. Sequencing of the 16S rRNA gene showed 100% identity to that of E. chaffeensis, strain 91HE17. Polymerase chain reaction and sequencing of DNA homologous to the 120-kDa protein gene of E. chaffeensis, Arkansas strain, showed that this gene of Sapulpa strain was smaller than that of Arkansas strain and contained a repeat region with three tandem repeat units.
Stereochemistry of free-radical eliminations on .beta.-phenylsulfonyl radicals (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of free-radical eliminations on .beta.-phenylsulfonyl radicalsThomas E. Boothe, Joseph L. Greene Jr., and Philip B. ShevlinCite this: J. Org. Chem. 1980, 45, 5, 794–797Publication Date (Print):February 1, 1980Publication History Published online1 May 2002Published inissue 1 February 1980https://pubs.acs.org/doi/10.1021/jo01293a006https://doi.org/10.1021/jo01293a006research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-Citations18LEARN 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
Autologous stem cell transplantation for paediatric‐onset polyarteritis nodosa: changes in autoimmune phenotype in the context of reduced diversity of the T‐ and B‐cell repertoires, and evidence for reversion from the CD45RO+ to RA+ phenotype (2001)

We have studied immune reconstitution in a patient with paediatric-onset polyarteritis nodosa treated with high-dose immunosuppressive agents followed by stem cell rescue. The patient developed several new autoimmune phenomena over the 18 months after immunosuppression and stem cell rescue. Flow cytometry, reverse transcription-polymerase chain reaction (RT-PCR) heteroduplex and isotype-specific RT-PCR analysis of immunoglobulin expression showed that the T- and B-cell repertoires were highly restricted in the first few months after treatment. The dominant T-cell clones seen after reconstitution were persistently expanded, were different from those which could be demonstrated before autologous stem cell transplantation, and were in the CD8(+) population. Our data also show that 12 months after treatment these expanded T-cell clones were within the CD45RA(+) population, suggesting that reversion from the CD45RO(+) to the CD45RA(+) phenotype had occurred in vivo.
Chromosomal location of structural genes encoding murine immunoglobulin lambda light chains. Genetics of murine lambda light chains. (1981)

To determine the chromosomal localization of murine lambda light (L) chain structural genes, DNA from a panel of 11 mouse x hamster somatic cell hybrids was scored for the presence of sequences homologous to cloned lambda DNA probe molecules. Six of the hybrids had detectable lambda I and lambda II gene sequences. In all six, the full complement of murine sequences was present, and in its germline configuration. The remaining hybrids lacked any detectable murine lambda L chain gene sequences. The only mouse chromosome present in all of the positive hybrids and absent from the negative ones was number 16, allowing the assignment of lambda L chain structural genes to this chromosome. Together with the previous assignments of the kappa L chain genes to chromosome 6 and heavy chain genes to chromosome 12, this finding completes the mapping of Ig structural genes in the mouse at the chromosomal level.
Regulatory T Cell Differentiation and Regulators (2012)

Regulatory T cell is a recently discovered immuno-inhibitory CD4+ T cell subset.The differentiation of regulatory T cells can take place in the thymus as well as in peripheral lymphoid organs with the induction of cytokines like transforming growth factor-β.Here,the authors review the essential signal pathways and regulators in regulators T cell differentiation,which influences the regulatory T cell abundance in vivo and might be a therapeutic target of auto-immune diseases,immuno-surveillance,rejection and allergy.