gebhart/patrepeval huggingface dataset:
Microarrays for Genotyping Human Group A Rotavirus by Multiplex Capture and Type-Specific Primer Extension (2003)

Human group A rotavirus (HRV) is the major cause of severe gastroenteritis in infants worldwide. HRV shares the feature of a high degree of genetic diversity with many other RNA viruses, and therefore, genotyping of this organism is more complicated than genotyping of more stable DNA viruses. We describe a novel microarray-based method that allows high-throughput genotyping of RNA viruses with a high degree of polymorphism by multiplex capture and type-specific extension on microarrays. Denatured reverse transcription (RT)-PCR products derived from two outer capsid genes of clinical isolates of HRV were hybridized to immobilized capture oligonucleotides representing the most commonly occurring P and G genotypes on a microarray. Specific primer extension of the type-specific capture oligonucleotides was applied to incorporate the fluorescent nucleotide analogue cyanine 5-labeled dUTP as a detectable label. Laser scanning and fluorescence detection of the microarrays was followed by visual or computer-assisted interpretation of the fluorescence patterns generated on the microarrays. Initially, the method detected HRV in all 40 samples and correctly determined both the G and the P genotypes of 35 of the 40 strains analyzed. After modification by inclusion of additional capture oligonucleotides specific for the initially unassigned genotypes, all genotypes could be correctly defined. The results of genotyping with the microarray fully agreed with the results obtained by nucleotide sequence analysis and sequence-specific multiplex RT-PCR. Owing to its robustness, simplicity, and general utility, the microarray-based method may gain wide applicability for the genotyping of microorganisms, including highly variable RNA and DNA viruses.
Configuration compression for FPGA-based embedded systems (2001)

FPGAs are a promising technology for developing high-performance embedded systems. The density and performance of FPGAs have drastically improved over the past few years. Consequently, the size of the configuration bit-streams has also increased considerably. As a result, the cost-effectiveness of FPGA-based embedded systems is significantly affected by the memory required for storing various FPGA configurations. This paper proposes a novel compression technique that reduces the memory required for storing FPGA configurations and results in high decompression efficiency. Decompression efficiency corresponds to the decompression hardware cost as well as the decompression rate. The proposed technique is applicable to any SRAM-based FPGA device since configuration bit-streams are processed as raw data. The required decompression hardware is simple and is independent of the individual semantics of configuration bit-streams or specific features of the on-chip configuration mechanism. Moreover, the time to configure the device is not affected by our compression technique. Using our technique, we demonstrate up to $41 \%$ savings in memory for configuration bit-streams of several real-world applications.
Optimizing datalog programs (1987)

Datalog programs, i.e., Prolog programs without function symbols, are considered It is assumed that a variable appearing in the head of a rule must also appear in the body of the rule. The input of a program is a set of ground atoms (which are given in addition to the program's rules) and, therefore, can be viewed as an assignment of relations to some of the program's predicates. Two programs are equivalent if they produce the same result for all possible assignments of relations to the extensional predicates (i.e., the predicates that do not appear as heads of rules). Two programs are uniformly equivalent if they produce the same result for all possible assignments of initial relations to all the predicates (i.e., both extensional and intentional). The equivalence problem for Datalog programs is known to be undecidable. It is shown that uniform equivalence is decidable, and an algorithm is given for minimizing a Datalog program under uniform equivalence. A technique for removing parts of a program that are redundant under equivalence (but not under uniform equivalence) is developed. A procedure for testing uniform equivalence is also developed for the case in which the database satisfies some constraints.
Characteristics of Metal and Ceramic Total Hip Bearing Surfaces and Their Effect on Long-Term Ultra High Molecular Weight Polyethylene Wear (1993)

The micromechanics of ultra high molecular weight polyethylene (UHMWPE) wear in total hip replacement are very complex. Polyethylene wear from the metal head and debris formation are two common types of wear. There are additional wear-related processes occurring at the metal-bearing surfaces that are not well-known, however. This study outlines these processes, including (1) surface wettability changes, (2) oxidative wear of metal surfaces, (3) microabrasion of metal surfaces from oxide film damage, and (4) surface abrasion from three-body polymethylmethacrylate and bone debris. These processes can contribute to metal ion release and a gradual increase in the roughness of the metal surfaces. This can lead to increased long-term UHMWPE wear. Of the metal alloys currently used in total hip replacements, Co-Cr-Mo alloy is significantly more resistant to roughening processes. Hard, stable, oxide: ceramic surfaces articulating against UHMWPE are essentially immune to these surface-roughening processes, however. In addition, they provide a more wettable surface, further minimizing polyethylene wear relative to metal surfaces. By analyzing metal release rates from metal-polyethylene wear tests, it is shown here that Co-Cr-Mo is gradually removed at a rate of about 0.1 micron per year (10(6) cycles), whereas 316L stainless steel is removed on the order of 0.2 microns per year and Ti-6Al-4V on the order of 1 micron per year. The wear rate of Co-Cr-Mo articulating against itself is reported to be still greater, at about 2-4 microns per year after an initial wear-in period. Because metal is gradually removed with articulation time, surface-hardening methods such as nitrogen ion implantation can be expected to provide only temporary resistance to these metal removal and surface-roughening processes. Hard, stable ceramic surfaces such as Al2O3 and ZrO2, however, can be expected to maintain their initial surface finish and thus minimize UHMWPE wear in the long term.
The Contribution of Vascular Smooth Muscle to Aortic Stiffness Across Length Scales (2013)

The operation of the cardiovascular system in health and disease is inherently mechanical. Clinically, aortic stiffness has proven to be of critical importance as an early biomarker for subsequent cardiovascular disease; however, the mechanisms involved in aortic stiffening are still unclear. The etiology of aortic stiffening with age has been thought to primarily involve changes in extracellular matrix protein composition and quantity, but recent studies suggest a significant involvement of the differentiated contractile vascular smooth muscle cells in the vessel wall. Here, we provide an overview of vascular physiology and biomechanics at different spatial scales. The processes involved in aortic stiffening are examined with particular attention given to recent discoveries regarding the role of vascular smooth muscle.
Advanced Fuels and Oxidizers (1969)

Guidelines for developing advanced liquid fuels and oxidizers are outlined from theoretical considerations of the reaction principle of rocket propulsion. Advanced oxidizers are based on oxygen and, increasingly, on fluorine. The potential of these elements, their blends, inter compounds, and compounds with nitrogen, chlorine, noble gases, and other carrier elements in advanced chemical propulsion is discussed. Fuel research and development are oriented largely toward incorporating metal additives into liquid fuels to form chemically and mechanically stable heterogeneous gels and emulsions of high heating value and/or density. Factors pertinent to this relatively new area of liquid propellant technology are discussed.
Chronic graft-versus-host disease: disease biology and novel therapeutic strategies. (2013)

Graft-versus-host disease (GVHD) is a major complication after allogeneic hematopoietic stem cell transplantation. Chronic GVHD often presents with clinical manifestations that resemble those observed in autoimmune diseases. Standard treatment is 1-2mg/kg/day of prednisone or an equivalent dose of methylprednisolone, with continued administration of a calcineurin inhibitor for steroid sparing. However, the prognosis of steroid-refractory chronic GVHD remains poor. Classically, chronic GVHD was said to involve predominantly Th2 responses. We are now faced with a more complex picture, involving possible roles for thymic dysfunction, transforming growth factor-β (TGF-β) and platelet-derived growth factor (PDGF), B cells and autoantibodies, and Th1/Th2/Th17 cytokines, as well as regulatory T cells (Tregs), in chronic GVHD. More detailed research on the pathophysiology of chronic GVHD may facilitate the establishment of novel strategies for its prevention and treatment.
Abstract 3410: B-type Natriuretic Peptide, Subclinical Atherosclerosis and Prognosis (2006)

Intro: B-type Natiuretic Peptide (BNP) has prognostic implications in pts with heart failure. Its prognostic role in asymptomatic pts with subclinical disease remains unclear. Methods: We studied 2...
Design and implementation of DVB-T receiver system for digital TV (2004)

This paper presents a DVB-T receiver system based on the OFDM modulation method, which exhibited a good mobile reception performance in the presence of obstacles. An improved OFDM receiver is developed for a DVB-T system that considers the function expansion for further development. Experiments confirmed the performance of the proposed DVB-T receiver. The GUI and EPG are also developed for the DTV user.
Chebyshev optimization for the design of broadband beamformers in the near field (1998)

The use of microphone arrays for video conferences, hands-free mobile telephony and computer applications has created the demand for near-field broadband beamformer design methods. Here, a general broadband beamformer design problem is formulated as a weighted Chebyshev optimization problem, and a method to solve the resulting functionally-constrained problem is presented. The formulation can also be applied to the design of multidimensional digital finite-impulse response (FIR) filters with an arbitrarily specified amplitude and phase. Numerical results that demonstrate the minimax near-field behavior of the designed beamformers are given.
Trematodiasis in Turkey: comparative efficacy of triclabendazole and niclofolan against natural infections of Fasciola hepatica and F. gigantica in sheep (1984)

A new fasciolicide, triclabendazole, tested at single oral dose rates of 5 and 10 mg/kg body-weight, proved to be highly effective (greater than 99%) against chronic field infections of Fasciola hepatica and F. gigantica in sheep. The performance of the new drug compared favourably with niclofolan at the recommended dose. Neither product was effective against Dicrocoelium dendriticum and Paramphistomum spp.
Use of UV irradiation to identify the genetic information of vesicular stomatitis virus responsible for shutting off cellular RNA synthesis (1979)

UV irradiation of infectious vesicular stomatitis virus was employed to study the relationship between the expression of certain viral gene functions and viral inhibition of RNA synthesis in mouse myeloma (MPC-11) cells. Viral infectivity, protein synthesis, and viral mRNA synthesis were all highly susceptible to inactivation by UV radiation; however, low levels of viral transcriptase activity were detected in vitro in virus preparations subjected to large doses of UV radiation. In sharp contrast, the capacity of vesicular stomatitis virus to shut off cellular transcription was quite resistant to UV radiation. The data presented here indicate that viral transcription is essential to inhibit host RNA metabolism, even though synthesis of viral polypeptides in the inhibited cells could not be detected. At those levels of UV radiation that inactivated all viral gene functions, except viral inhibition of cellular RNA synthesis, the only viral product detected was non-adenylated, low-molecular-weight RNA species.
Synthesis of Peptides by Solution Methods (2001)

Peptides are essentially small version of proteins and the structure of peptides is best described as a chain of amino acids linked to each other through amide bonds. In the chemical synthesis of peptides, two procedures are primarily used, although they are both based on fundamentally same principles one is a solution method and the other being a solid-phase method carried out on a resin. The chemistry of peptide synthesis was developed based on the following basic chemical principles 1) selection of protecting groups for amino acids and deprotection and 2) peptide bond formation. Therefore, studies on peptide synthesis in solution can be directly applied to solid phase methodology. This review deals with the fundamental chemistry of peptide synthesis in solution and considers the following points (1) principle of peptide synthesis, (2) protection procedures, (3) chain elongation procedures by either stepwise or segment condensation reactions and (4) final deprotection of protected peptides. Keywords: Synthesis of Peptide, Solution Methods, Solid phase methodology, peptide bond formation, Chain elongation procedure, Urethane protected, C terminus, Benzyloxycarbonyl group, Triphenylmethyl group, Fmoc amino acids, Tetrabutyl, Methyl Ester, tert Butyl Ester, Phenacyl Esters, Guanidino Group, Aliphatic Hydroxy Function, Indole Nitrogen, Segment Condensatio, Azide procedure, Catalytic Hydrogenation, Final Deprotection, Hard soft Acid
Modulation of Innate Immune Signalling by Lipid-Mediated MAVS Transmembrane Domain Oligomerization (2015)

RIG-I-like receptors detect viral RNA in infected cells and promote oligomerization of the outer mitochondrial membrane protein MAVS to induce innate immunity to viral infection through type I interferon production. Mitochondrial reactive oxygen species (mROS) have been shown to enhance anti-viral MAVS signalling, but the mechanisms have remained obscure. Using a biochemical oligomerization-reporter fused to the transmembrane domain of MAVS, we found that mROS inducers promoted lipid-dependent MAVS transmembrane domain oligomerization in the plane of the outer mitochondrial membrane. These events were mirrored by Sendai virus infection, which similarly induced lipid peroxidation and promoted lipid-dependent MAVS transmembrane domain oligomerization. Our observations point to a role for mROS-induced changes in lipid bilayer properties in modulating antiviral innate signalling by favouring the oligomerization of MAVS transmembrane domain in the outer-mitochondrial membrane.
Federal funds for instruments scarce (1992)

RETURN TO ISSUEPREVNewsNEXTFederal funds for instruments scarcePAMELA ZURERCite this: Chem. Eng. News 1992, 70, 47, 15–16Publication Date (Print):November 23, 1992Publication History Published online10 November 2010Published inissue 23 November 1992https://pubs.acs.org/doi/10.1021/cen-v070n047.p015https://doi.org/10.1021/cen-v070n047.p015newsACS PublicationsCopyright © 1992 AMERICAN CHEMICAL SOCIETYArticle Views7Altmetric-Citations-LEARN 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 options SUBJECTS:Energy,Physiology,Students Get e-Alerts
Features induction for product named entity recognition with CRFs (2012)

A framework for product named entity recognition in Chinese was presented using Conditional Random Fields with multiple features in this paper. It differentiates from most of the previous approaches mainly as follows. Firstly, introducing the domain ontology features to the CRFs model can use its semantic information. Secondly, combining internal and external features to compound features can use more rich overlapping features. so that it can improve the performance of product named entity Recognition. Experimental results show that this approach can achieve an overall F-measure around 87.16%, which seems to achieve the current state-of-the-art performance. However, due to the imperfect of Domain Ontology and the complication of reviews texts, the recognition for product named entity may not be better than the research of the traditional named entity recognition.
Response of Starch-EncapsulatedBacillus thuringiensisContaining Ultraviolet Screens to Sunlight (1989)

Formulations of Bacillus thuringiensis Berliner spores and crystals, encapsulated together within a starch matrix containing no ultraviolet screens, lost all spore viability and insecticidal activity against the European corn borer, Ostrinia nubilalis (Hübner), within 4 d. Encapsulated crystals and spores with Congo red or folic acid as screens exhibited moderate spore viability and retained at least 50% of their original toxicity after 12 d. Congo red was the most effective protectant, followed by folic acid and para amino benzoic acid. Because Bacillus thuringiensis is likely sensitive to the entire ultraviolet-component in sunlight, ability to provide broad-band ultraviolet protection is required to prolong insecticidal activity effectively.
Bmi‐1 expression predicts prognosis for patients with gastric carcinoma (2007)

Bmi-1 may serve as a valuable marker for diagnosis and prognosis of GC.
Middle infrared beam-steering using liquid crystals for spatial light modulation (2018)

Middle infrared beam-steering is attractive for a number of applications, particularly in the defence sector, where infrared countermeasures are a cornerstone in protecting lives and assets from infrared seeking weapons. Liquid crystal based alternatives to the current opto-mechanical state of the art are investigated, in particular electrically addressed optical phased arrays. Material and design challenges are addressed. CVD graphene is found to be an appropriate transparent conductor, with a sheet resistance $ < 1 $k$ \Omega / \square $ and an optical transmission $ > 97 \% $ in the frequency band of interest. Liquid crystal BL-037 was found to have a birefringence of 0.23 in the middle infrared, where absorption bands exist between 3.3$ \mu $m and 3.6$ \mu $m, and at 4.5$ \mu $m. When incorporated into a single-pixel anti-parallel aligned cell subject to an electric field, the response time for the liquid crystal layer was found to be slower than expected for typical thicknesses required for middle infrared operation (7.5$ \mu $m - 30$ \mu $m). This was due to high angle reorientation which is typically absent in visible operation. The effects of various considerations, such as aperture size and shape, illumination, pixelation, dead-space and fringing effects, on the performance of a spatial light modulator were investigated. Liquid crystal on silicon implementation was simulated. For $ \lambda= 2.3 \mu$m an efficiency $ > 10 \% $ was attained for angles up to $ 7^{\circ} $. For longer wavelengths this was attained for angles up to $ 11^{\circ} $. Multi-interaction and non-diffractive devices were investigated as alternatives for increasing the viewing range while preserving resolution.
An Electric Field Approach to Independent Component Analysis (2000)

We propose a novel algorithm for Independent Component Analysis (ICA) that is based on an electric eld metaphor. As with all ICA techniques, the algorithm searches for a demixing model that produces components whose joint distribution matches the factorial distribution (i.e., the product of the marginal distributions) . The joint and factorial distributions are represented as positively and negatively charged particles, respectively, and the dynamics of the search are based on the interactions among particles. The algorithm can deal with arbitrary distributions for the sources, nonlinear mixing functions, noisy observations, and an unequal number of source and mixture components. The limitation of the algorithm is that it does not scale with the number of sources. Nonetheless, we demonstrate that the algorithm can solve challenging ICA problems that are beyond the capabilities of other ICA methods.
Facile Synthesis of 9-Substituted 9-Deazapurines as Potential Purine Nucleoside Phosphorylase Inhibitors. (2002)

A facile synthesis of 9-substituted 9-deazapurines as potential inhibitors of purine nucleoside phosphorylase has been achieved by the direct Friedel-Crafts aroylation or arylmethylation of 9-deazapurines using trifluoromethanesulfonic acid as catalyst. The aroylated 9-deazapurines could be transformed into the corresponding 9-aryimethyl derivatives by the Wolff-Kishner reaction. A novel synthesis of 9-deazahypoxanthine was also developed by treatment of 4-hydroxy-5-phenylazo-6-methylpyrimidin-2-thione with triethyl orthoformate in trifluoroacetic acid (TFA) to yield 8-oxo-7H-2-phenylpyrimido[5,4-c]pyridazin-6-thione followed by Raney nickel reduction.
BERTology Meets Biology: Interpreting Attention in Protein Language Models (2020)

Abstract Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. Through the lens of attention, we analyze the inner workings of the Transformer and explore how the model discerns structural and functional properties of proteins. We show that attention (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We also present a three-dimensional visualization of the interaction between attention and protein structure. Our findings align with known biological processes and provide a tool to aid discovery in protein engineering and synthetic biology. The code for visualization and analysis is available at https://github.com/salesforce/provis .
Cancer of the colon (1980)

Incidence of colorectal cancer in Israel was studied in 1035 patients who were divided by ethno-geography into a Euro-American group and an Afro-Asian group. The majority of patients were in the age groups over 50 years, with a markedly higher incidence rate of disease in the Euro-American group. In the younger age group the incidence rate of the disease was significantly higher in the Afro-Asian group. These findings, if verified by others, must lead to revision of our present concepts of epidemiology of colorectal cancer.