gebhart/patrepeval huggingface dataset:
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences (2004)

A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.
Movement disorders in multiple sclerosis (1995)

Movement disorders (MD), other than tremor, associated with multiple sclerosis (MS) occur infrequently. We report 14 new cases of whom nine had dystonia, three parkinsonism, and two had myoclonus. We also reviewed 135 such cases from the literature. From an analysis of the individual MDs and the site of the lesions described, we conclude that paroxysmal dystonias (tonic spasms), ballism/chorea, and palatal myoclonus can be caused by demyelinating lesions. Parkinsonism, dystonia, and other types of myoclonus, however, often appear to be coincidental.
Perpendicular Orientation of Domains in Cylinder-Forming Block Copolymer Thick Films by Controlled Interfacial Interactions (2009)

We report the induction of perpendicularly oriented cylindrical domains in PS-b-PMMA block copolymer (BCP) films thicker than 100 nm by thermally annealing on a substrate modified with a random copolymer. The effects of annealing temperature, composition of the substrate-modifying random copolymer, and BCP film thickness on the morphology of PMMA cylinder forming PS-b-PMMA were studied. For BCP films thicker than 100 nm, the fabrication of perpendicular PMMA cylinders is highly dependent on both the substrate-modifying random copolymer and the annealing temperature as these two parameters control the interactions of the BCP with the substrate and the free surface, respectively. We found the best perpendicular structures to be created by using a random copolymer brush with a styrene fraction (FSt) near 0.70 and an annealing temperature near 230 °C. Perpendicular cylinder structures were achieved in ∼300 nm thick films using these conditions. When the BCP film was thicker than 300 nm, nucleation and growth of the microdomains proceeded independently from each interface. We present scanning electron microscope (SEM) and cross-sectional transmission electron microscope (TEM) images of these perpendicular structures and explain the results on the basis of previous simulation reports.
Potential role of interleukin 28B-gene polymorphism and natural immune enhancer treatment response in chronic HCV patients (2015)

HCV infection is a major health problem in Egypt. Studies using safe natural products BlueÂ greenÂ® tablet showed its antiviral effect. Polymorphisms in the interleukin-28B (IL28B) geneÂ are associated with outcomes from infection with HCV. The rationale of the present study is toÂ evaluate the potential role of interleukin 28B gene polymorphism (IL28B) and natural immuneenhancer treatment response in chronic HCV patients. This study included 100 chronic HCVÂ patients. Patients were classified into two groups: Group I, fifty patients with cirrhosis andÂ advanced liver disease. Patients were unfit INF/ Ribavirin: Group II, fifty patients who refusedÂ INF/Ribavirin. Patients were treated with combination of natural products of Blue greenÂ® tabletÂ (4 tablets daily which equivalent to 100 mg AFA/30 kg BW), vitamin D, tea spoon field paste ofÂ black seeds, olive oil and honey. Alanine Aminotransferase (AST), Aspartate AminotransferaseÂ (ALT), complete blood count (CBC) were measured in the two groups. Detection of HCV-RNAÂ level by quantitative PCR was done before &amp; after 3, 6, 12 and 18 months of treatment. GenomicÂ DNA extracted from all the 100 patientâ€™s blood samples was analyzed for the rs12979860 SNPof IL28B using a real-time polymerase chain technique incorporating SYBR Green. The resultsÂ showed that, the activities of hepatic marker enzymes (AST and ALT), complete blood picturesÂ (Hb, WBCs and Platelets), HCV RNA PCR, IL 28-B gene polymorphism were non-significantlyÂ (p&gt;0.05) differences when compared untreated patients (Group I) and treated patients (Group )were CC genotype before treatment was 8 (34%) &amp; was 13 (26%) after treatment, CT genotypeÂ before treatment was 26 (52%) &amp; was 28 (56%) after treatment, TT genotype before treatmentÂ was 7 (14%) &amp; was 9 (18%) after treatment. Also, there were non-significant (p&gt;0.05)Â differences between responder &amp; non-responder in treated patients. In conclusion, the treatmentwith natural immune enhancer in chronic HCV patients showed no significance correlation withÂ IL 28 gene polymorphism
The challenge of multiple sclerosis: How do we cure a chronic heterogeneous disease? (2009)

Multiple sclerosis is (MS) a T-cell autoimmune disease characterized by a relapsing-remitting followed by a progressive phase. Relapses are driven by the adaptive immune system and involve waves of T helper cell 1 (Th1), Th17, and CD8 cells that infiltrate the nervous system and provoke a attack. These cells are modulated by regulatory T and B cells. Infiltration of T cells into the nervous system initiates a complex immunological cascade consisting of epitope spreading, which triggers new attacks, and activation of the innate immune system (microglia, dendritic cells, astrocytes, B cells), which leads to chronic inflammation. The secondary progressive phase is due to neurodegeneration triggered by inflammation and is driven by the innate immune system. Why a shift to the progressive stage occurs and how to prevent it is a central question in MS. Effective treatment of MS must affect multiple disease pathways: suppression of proinflammatory T cells, induction of regulatory T cells, altering traffic of cells into the nervous system, protecting axons and myelin, and controlling innate immune responses. Without biomarkers, the clinical and pathological heterogeneity of MS makes treatment difficult. Treatment is further hampered by untoward adverse effects caused by immune suppression. Nonetheless, major progress has been made in the understanding and treatment of MS. There are three definitions of cure as it applies to MS: (1) halt progression of disease, (2) reverse neurological deficits, and (3) prevent MS. Although the pathways to each of these cures are linked, each requires a unique strategy.
QoS routing mechanisms and OSPF extensions (2002)

This paper presents and discusses path selection algorithms to support QoS routes in IP networks. The work is carried out in the context of extensions to the OSPF protocol, and the initial focus is on unicast flows, although some of the proposed extensions are also applicable to multicast flows. We first review the metrics required to support QoS, and then present and compare several path selection algorithms, which represent different trade-offs between accuracy and computational complexity. We also describe and discuss the associated link advertisement mechanisms, and investigate some options in balancing the requirements for accurate and timely information with the associated control overhead. The overall goal of this study is to identify a framework and possible approaches to allow deployment of QoS routing capabilities with the minimum possible impact to the existing routing infrastructure.
Learning Generative Models of 3D Structures (2020)

Abstract 3D models of objects and scenes are critical to many academic disciplines and industrial applications. Of particular interest is the emerging opportunity for 3D graphics to serve artificial intelligence: computer vision systems can benefit from synthetically‐generated training data rendered from virtual 3D scenes, and robots can be trained to navigate in and interact with real‐world environments by first acquiring skills in simulated ones. One of the most promising ways to achieve this is by learning and applying generative models of 3D content: computer programs that can synthesize new 3D shapes and scenes. To allow users to edit and manipulate the synthesized 3D content to achieve their goals, the generative model should also be structure‐aware : it should express 3D shapes and scenes using abstractions that allow manipulation of their high‐level structure. This state‐of‐the‐art report surveys historical work and recent progress on learning structure‐aware generative models of 3D shapes and scenes. We present fundamental representations of 3D shape and scene geometry and structures, describe prominent methodologies including probabilistic models, deep generative models, program synthesis, and neural networks for structured data, and cover many recent methods for structure‐aware synthesis of 3D shapes and indoor scenes.
Current and Potential Uses of Immunocytokines as Cancer Immunotherapy (2012)

Immunocytokines (ICs) are a class of molecules created by linking tumor-reactive monoclonal antibodies to cytokines that are able to activate immune cells. Tumor selective localization is provided by the ability of the mAb component to bind to molecules found on the tumor cell surface or molecules found selectively in the tumor microenvronment. In this way the cytokine component of the immunocytokine is selectively localized to sites of tumor and can activate immune cells with appropriate receptors for the cytokine. Immunocytokines have been made and tested by us, and others, using a variety of tumor-reactive mAbs linked to distinct cytokines. To date, the majority of clinical progress has been made with ICs that have linked human interleukin-2 (IL2) to a select number of tumor reactive mAbs that had already been in prior clinical testing as non-modified mAbs (Figure 1). Here we briefly review the background for the creation of ICs, summarize current clinical progress, emphasize mechanisms of action for ICs that are distinct from those of their constituent components, and present some directions for future development and testing.
Dehydrogenation of steroidal and triterpenoid ketones using benzeneseleninic anhydride (1980)

Steroid and triterpenoid ketones can be smoothly dehydrogenated in high yield with benzeneseleninic anhydride in chlorobenzene at 95–120 °C. With an excess of benzeneseleninic anhydride and longer reaction times 4,4-dimethyl ketones give ring-A-contracted diketones in moderate yield.
Electric current and voltage recordings on the myocardium during electrosurgical procedures in canines. (1987)

Voltage and current spectra were measured with probes placed directly on the canine myocardium during transurethral resection (TUR). It was determined that three factors may be related to potential cardiac effects during electrosurgical procedures: obvious low frequency components modulated from a center frequency of the electrosurgical generator; high current density due to high power setting during TUR, and duration of application of the cutting waveform.
Chemotactic Responsiveness Toward Ligands for CXCR3 and CXCR4 Is Regulated on Plasma Blasts During the Time Course of a Memory Immune Response (2002)

Plasma blasts formed during memory immune responses emigrate from the spleen to migrate into the bone marrow and into chronically inflamed tissues where they differentiate into long-lived plasma cells. In this study, we analyze the chemokine responsiveness of plasma blasts formed after secondary immunization with OVA. Starting from day 4 and within approximately 48 h, OVA-specific plasma blasts emigrate from spleen and appear in the bone marrow. Although these migratory cells have lost their responsiveness to many B cell attracting chemokines, e.g., CXC chemokine ligand (CXCL)13 (B lymphocyte chemoattractant), they migrate toward CXCL12 (stromal cell-derived factor 1 alpha), and toward the inflammatory chemokines CXCL9 (monokine induced by IFN-gamma), CXCL10 (IFN-gamma-inducible protein 10), and CXCL11 (IFN-inducible T cell alpha chemoattractant). However, the responsiveness of plasma blasts to these chemokines is restricted to a few days after their emigration from the spleen, indicating a role for these molecules and their cognate receptors, i.e., CXCR3 and CXCR4, in the regulation of plasma blast migration into the bone marrow and/or inflamed tissues.
Bayesian Interpolation (1992)

Although Bayesian analysis has been in use since Laplace, the Bayesian method of model-comparison has only recently been developed in depth. In this paper, the Bayesian approach to regularization and model-comparison is demonstrated by studying the inference problem of interpolating noisy data. The concepts and methods described are quite general and can be applied to many other data modeling problems. Regularizing constants are set by examining their posterior probability distribution. Alternative regularizers (priors) and alternative basis sets are objectively compared by evaluating the evidence for them. “Occam's razor” is automatically embodied by this process. The way in which Bayes infers the values of regularizing constants and noise levels has an elegant interpretation in terms of the effective number of parameters determined by the data set. This framework is due to Gull and Skilling.
The Lectin Pathway of Complement Activation Is a Critical Component of the Innate Immune Response to Pneumococcal Infection (2012)

The complement system plays a key role in host defense against pneumococcal infection. Three different pathways, the classical, alternative and lectin pathways, mediate complement activation. While there is limited information available on the roles of the classical and the alternative activation pathways of complement in fighting streptococcal infection, little is known about the role of the lectin pathway, mainly due to the lack of appropriate experimental models of lectin pathway deficiency. We have recently established a mouse strain deficient of the lectin pathway effector enzyme mannan-binding lectin associated serine protease-2 (MASP-2) and shown that this mouse strain is unable to form the lectin pathway specific C3 and C5 convertases. Here we report that MASP-2 deficient mice (which can still activate complement via the classical pathway and the alternative pathway) are highly susceptible to pneumococcal infection and fail to opsonize Streptococcus pneumoniae in the none-immune host. This defect in complement opsonisation severely compromises pathogen clearance in the lectin pathway deficient host. Using sera from mice and humans with defined complement deficiencies, we demonstrate that mouse ficolin A, human L-ficolin, and collectin 11 in both species, but not mannan-binding lectin (MBL), are the pattern recognition molecules that drive lectin pathway activation on the surface of S. pneumoniae. We further show that pneumococcal opsonisation via the lectin pathway can proceed in the absence of C4. This study corroborates the essential function of MASP-2 in the lectin pathway and highlights the importance of MBL-independent lectin pathway activation in the host defense against pneumococci.
Monoclonal antibodies that recognize a common pneumococcal protein with similarities to streptococcal group A surface glyceraldehyde-3-phosphate dehydrogenase (1996)

Monoclonal antibodies (MAbs) against clinical isolates of Streptococcus pneumoniae were produced in a search for common pneumococcal proteins. One of the fusions generated two MAbs, 174,B-8 (immunoglobulin G2a) and 177,D-8 (immunoglobulin G1), which by Western blotting (immunoblotting) stained with a main band of 40 kDa found in all isolates of S. pneumoniae examined. Cross-reactivity studies with streptococci other than pneumococci revealed very weak or moderate reactions with the MAbs. The 40-kDa protein was isolated by immunoaffinity chromatography and subsequent preparative Western blotting. N-terminal amino acid sequencing showed 90% amino acid sequence homology with a surface-located glyceraldehyde-3-phosphate dehydrogenase from Streptococcus pyogenes. This protein has also been reported to exhibit binding to mammalian proteins such as fibronectin, which may serve as host receptors. The epitopes for MAbs 174,B-8 and 177,D-8 reacting with the pneumococcal analog were not accessible to antibody binding in live bacteria but were exposed after heat killing. The MAbs showed negligible cross-reactions with S. pyogenes.
cDNA Library Construction from Single Cells (2002)

Analysis of gene expression or comparing gene expression patterns between cells and/or tissues facilitates the identification of molecules activated by a cellular program or by a particular physiological or pharmacological treatment. This unit presents a protocol for studying these molecules at the level of a single cell.
Device physics, performance simulations and measured results of SOI MOS and DTMOS transistors and integrated circuits (2002)

A dynamic threshold MOSFET (DTMOS) was invented by Assaderaghi et al.(1994), connecting the gate to the contact terminal. There are four ways to connect the contact terminal: (1) keep the contact terminal floating; (2) connect the contact terminal to the source; (3) connect the contact terminal to the gate; and (4) take the contact terminal as a new input. We have designed fabricated and simulated all four ways of connecting the contact terminal.
Copper homeostasis inEnterococcus hirae (2003)

Copper is an essential component of life because of its convenient redox potential of 200-800 mV when bound to protein. Extensive insight into copper homeostasis has only emerged in the last decade and Enterococcus hirae has served as a paradigm for many aspects of the process. The cop operon of E. hirae regulates copper uptake, availability, and export. It consists of four genes that encode a repressor, CopY, a copper chaperone, CopZ, and two CPx-type copper ATPases, CopA and CopB. Most of these components have been conserved across the three evolutionary kingdoms. The four Cop proteins have been studied in vivo as well as in vitro and their function is understood in some detail.
Digital Enhancement of the Peripheral Admittance Plethysmogram (1987)

Limb segment pulse volume (PV) is the maximum change in the volume (V) of a limb segment during the cardiac cycle. Peak net inflow (PNI) is the maximum value of dV/dt during the cardiac cycle. These parameters are difficult to measure because they are so small (PV is approximately 0.0003 ×V). As a result, conventional analog plethysmographic measurements of PV and PNI are inherently inaccurate and difficult to reproduce. A digital enhancement (DE) technique using selective signal averaging to improve PV and PNI reproducibility is described.
Using Soluble Calcium to Stimulate Plant Growth (1998)

Research has shown that applying soluble calcium with urea, an ammonium form of nitrogen, can improve crop production.Calcium increases ammonium, potassium and phosphorus absorption, stimulates photosynthesis, and increases the size of sellable plant parts.It also makes the use of nitrogen more efficient, which improves the economics of production and reduces nitrogen contamination of the environment. How the Research Was ConductedVarious plant species grown in greenhouses were fertilized several times during the growing season with nutrient solutions containing various calcium-to-ammonium ratios, so that the value of increasing the amount of soluble calcium could be tested.Check plants were given nitrate fertilizer with no increased amounts of soluble calcium.Most field plots were planted in 40-inch rows and most greenhouse tests were accompanied by field experiments.Greenhouse plants were grown to certain stages and then harvested.The harvested plants were weighed and divided into seeds, bulbs, leaves, stems and roots so the parts could be tested for nutrient concentrations.In the field experiments, the commercial products were harvested and the yields recorded.
SCD1 Expression Is Dispensable for Hepatocarcinogenesis Induced by AKT and Ras Oncogenes in Mice (2013)

Increased de novo lipogenesis is one of the major metabolic events in cancer. In human hepatocellular carcinoma (HCC), de novo lipogenesis has been found to be increased and associated with the activation of AKT/mTOR signaling. In mice, overexpression of an activated form of AKT results in increased lipogenesis and hepatic steatosis, ultimately leading to liver tumor development. Hepatocarcinogenesis is dramatically accelerated when AKT is co-expressed with an oncogenic form of N-Ras. SCD1, the major isoform of stearoyl-CoA desaturases, catalyzing the conversion of saturated fatty acids (SFA) into monounsaturated fatty acids (MUFA), is a key enzyme involved in de novo lipogenesis. While many studies demonstrated the requirement of SCD1 for tumor cell growth in vitro, whether SCD1 is necessary for tumor development in vivo has not been previously investigated. Here, we show that genetic ablation of SCD1 neither inhibits lipogenesis and hepatic steatosis in AKT-overexpressing mice nor affects liver tumor development in mice co-expressing AKT and Ras oncogenes. Molecular analysis showed that SCD2 was strongly upregulated in liver tumors from AKT/Ras injected SCD1(-/-) mice. Noticeably, concomitant silencing of SCD1 and SCD2 genes was highly detrimental for the growth of AKT/Ras cells in vitro. Altogether, our study provides the evidence, for the first time, that SCD1 expression is dispensable for AKT/mTOR-dependent hepatic steatosis and AKT/Ras-induced hepatocarcinogenesis in mice. Complete inhibition of stearoyl-CoA desaturase activity may be required to efficiently suppress liver tumor development.
Breakthrough Mobile Water Treatment Converts 75% of Fracturing Flowback Fluid to Fresh Water and Lowers CO2 Emissions (2009)

Abstract Treating and recycling flowback from a hydraulically fractured gas shale reservoir is vital to the development of several shale plays. The use and disposal of water in emerging shale plays is expensive and a significant public and political concern. A breakthrough in water treatment combines an advanced oxidation process (AOP) using ozone and ultrasonic transducers to oxidize heavy metals, soluble and insoluble organics. When combined with reverse osmosis (RO) in a mobile unit, this process allows for significant volumes of flowback to be returned to the environment as fresh, clean water, thereby significantly reducing truck traffic. The hydraulic fracturing process in the Woodford Shale requires 50,000 to 110,000 barrels of water per well. By treating flowback on location with the AOP/RO process, 75% of the volume treated will become clean water with total dissolved solid levels less than 500 ppm. 25% will be clean, concentrated brine water which can be used in subsequent hydraulic fracturing operations. Newfield Exploration executed a pilot 4Q08 during which flowback was processed on location with an AOP/RO unit. Sample analysis from this pilot will be provided to state and federal agencies as a validation of the technology. The mobile unit processed 100 barrels per hour using 220 kW power generation to provide a fresh water stream and brine stream from flowback. The proper application of the AOP/RO process could reduce the fluid disposal carbon footprint by 50 tons of CO2 per well and transform a large portion of industry water use from consumptive to non-consumptive—as much as 25,000 bbl per well. The AOP/RO process could untangle complex operating environments, reduce operating expense and help the environment.