gebhart/patrepeval huggingface dataset:
Methylated CpG Island Amplification for Methylation Analysis and Cloning Differentially Methylated Sequences (2003)

CpG islands are clusters of CpG dinucleotides that can be found in the 5′ region of about half of human genes (1). Methylation of cytosine within the 5′ CpG islands is associated with transcriptional inactivation of the involved gene. Aberrant methylation of CpG islands is an important mechanism of gene inactivation in cancer (2,3) and other states such as aging and age-related diseases (4). Such methylation often involves numerous CpG islands, and emerging data suggests that methylation profiles may be of some utility in disease detection, prognosis, and risk assessment. However, the measurement of DNA methylation abnormalities at multiple gene loci is currently cumbersome, time-consuming, and not easily amenable to automation. Furthermore, the identification of novel gene sequences hypermethylated in cancer is relatively difficult and inefficient using current technology (5,6). Methylated CpG island Amplification (MCA) was developed to overcome these problems (7).
Post-hydrogenated chemical vapor deposited amorphous silicon Schottky diodes (1982)

Amorphous Si Schottky diodes are prepared by chemical vapor deposition and a post- hydrogenation treatment. Capacitance and photocurrent measurements on these diodes as a function of doping are discussed in terms of space-charge characteristics and carrier collection mechanisms. For doped samples a full analysis of the C(ω) and C(V) dependences enables us to obtain the space-charge width and the doping efficiency. A correlation between space-charge width and collection length of photogenerated carriers is obtained in these samples. For undoped diodes the photocurrent versus wavelength dependences are used to analyze the collection efficiency. A power efficiency of 2.5% is obtained for a fully depleted cell without antireflection coating under AMl solar simulator conditions.
Leveraging Web Query Logs to Learn User Intent Via Bayesian Discrete Latent Variable Model (2011)

A key task in Spoken Language Understanding (SLU) is interpreting user intentions from speech utterances. This task is considered to be a classication problem with the goal of categorizing a given speech utterance into one of many semantic intent classes. Due to substantial utterance var, signicant quantity of labeled utterances is needed to build robust intent detection systems. In this paper, we approach intent detection as a two-stage semi-supervised learning problem, which utilizes a large number of unlabeled queries collected from internet seach engine click logs. We rst capture the underlying structure of the user queries using bayesian latent feature model. We then propagate this structure onto the unlabeled queries to obtain quality training data via a graph summarization algorithm. Our approach improves intent detection compared to comparison to our baseline, which uses a standard classication model with actual features.
Eosinophil-associated TGF-β1 mRNA Expression and Airways Fibrosis in Bronchial Asthma (1997)

The histopathology of bronchial asthma is associated with structural changes within the airways, including subepithelial fibrosis, as well as chronic eosinophilic inflammation. The mechanisms responsible for this tissue remodeling, and in particular the role of inflammatory cells, remain to be established. Transforming growth factor-beta (TGF-beta) is a potent profibrotic cytokine which may contribute to the thickening of the reticular lamina by the deposition of collagen fibers. To investigate the molecular mechanisms underlying these structural changes, we have investigated the expression of TGF-beta1 mRNA and immunoreactivity within the bronchial mucosa of mild to severe asthmatic individuals and normal control subjects using the techniques of in situ hybridization and immunocytochemistry. As eosinophils are prominent within the asthmatic airway and are known to synthesize pro-inflammatory cytokines, the presence of TGF-beta1 mRNA and immunoreactive protein in eosinophils was also examined. Asthmatic individuals exhibited a greater expression of TGF-beta1 mRNA and immunoreactivity in the airways submucosa than normal control subjects (P < 0.05), and these increases were directly related to the severity of the disorder. The extent of airways fibrosis, as detected histochemically, was also increased in asthmatics compared with normal control subjects (P < 0.005). In asthmatic subjects, the presence of subepithelial fibrosis was associated with the severity of the disease and correlated with the decline in forced expiratory volume in 1 s (r2 = 0.78; P < 0.05). Within the asthmatic airways, EG2-positive eosinophils represented the major source of TGF-beta1 mRNA and immunoreactivity. These results provide evidence that TGF-beta1 may play a role in the fibrotic changes occurring within asthmatic airways and that activated eosinophils are a major source of this cytokine.
Rabbit antibodies to the cell wall polysaccharide of Streptococcus pneumoniae fail to protect mice from lethal challenge with encapsulated pneumococci (1986)

A conjugate, composed of the cell wall polysaccharide (C polysaccharide) of Streptococcus pneumoniae and bovine serum albumin (BSA), was prepared with the bifunctional agent N-succinimidyl-3-(2-pyridyldithio)-propionate. Analysis with monoclonal antibodies provided evidence that the phosphocholine (PC) moiety of the C polysaccharide was retained during the conjugation procedure. The C polysaccharide-BSA conjugate elicited antibodies to C polysaccharide in rabbits; no PC-specific antibodies were detected in globulins prepared from these hyperimmune sera obtained early and late after a second immunization. Rabbit hyperimmune sera were taken after multiple intravenous injections of the pneumococcus strain SRC-2, which has a capsulelike structure composed of the C polysaccharide. Globulin prepared from these antisera had both C polysaccharide- and PC-specific antibodies. Antibodies to C polysaccharide elicited by the C polysaccharide-BSA conjugate failed to protect mice against intraperitoneal challenge with a strain of type 3 or type 6A pneumococci. The anti-SRC-2 globulin conferred protection against both of these pneumococcal strains. Absorption of the SRC-2 globulin with C polysaccharide, however, failed to change its protective activity. These data provide evidence that antibodies to the C polysaccharide do not confer immunity against infection of mice with encapsulated pneumococci inoculated by the intraperitoneal route.
Delayed lupus onset in (NZB × NZW)F1 mice expressing a human C‐reactive protein transgene (2003)

In hCRPtg/BW mice, CRP protects against SLE by increasing blood and mesangial clearance of immune complexes and by preventing their accumulation in the renal cortex.
The Receptor for Advanced Glycation End-Products (RAGE) Protects Pancreatic Tumor Cells Against Oxidative Injury (2010)

Reactive oxygen species, including hydrogen peroxide (H(2)O(2)), can cause toxicity and act as signaling molecules in various pathways regulating both cell survival and cell death. However, the sequence of events between the oxidative insult and cell damage remains unclear. In the current study, we investigated the effect of oxidative stress on activation of the Receptor for Advanced Glycation End-products (RAGE) and subsequent protection against H(2)O(2)-induced pancreatic tumor cell damage. We found that exposure of pancreatic tumor cells to H(2)O(2) provoked a nuclear factor kappa B (NF-κB)-dependent increase in RAGE expression. Further, suppression of RAGE expression by RNA interference increased the sensitivity of pancreatic tumor cells to oxidative injury. Furthermore, targeted knockdown of RAGE led to increased cell death by apoptosis and diminished cell survival by autophagy during H(2)O(2)-induced oxidative injury. Moreover, we demonstrate that RAGE is a positive feedback regulator for NF-κB as knockdown of RAGE decreased H(2)O(2)-induced activity of NF-κB. Taken together, these results suggest that RAGE is an important regulator of oxidative injury.
Molecular Transfer Printing Using Block Copolymers (2009)

Soft lithographic techniques augment or enhance the capabilities of traditional patterning processes and expand the diversity of materials that can be patterned. Realization of robust parallel techniques for creating chemical patterns at the nanoscale has been challenging. Here we present a method for creating and replicating chemical patterns that uses functionalized homopolymer inks that are preferentially segregated into the nanodomains of phase-separated diblock copolymer films. The inks are transferred by reaction to substrates that are brought into contact with block copolymer films, creating chemical patterns on the substrate that mirror the domain structure present at the film surface with high fidelity and resolution. In addition to printing from self-assembled domain structures, we can also direct the assembly of the block copolymer films from which transfer occurs using lithographically defined masters so as to replicate and transfer patterns of inks with controlled and well-defined geometries. The transferred patterns may be at higher resolution than the lithographically defined master, and the process can be repeated to create multiple copies of identical replicas. Transfer of one ink from one block of the copolymer is also possible, and filling the interspatial regions of the pattern with a second ink provides a pathway toward creating patterns with diverse chemical functionalities.
Layer-by-Layer Assembly of Charged Particles in Nonpolar Media (2010)

Layer-by-layer (LbL) assembly of charged species such as nanoparticles and polymers has been widely used to generate functional thin films with unique wetting, optical, catalytic, and biological properties. Although LbL assembly is a versatile tool for creating functional thin films on a variety of substrates, it is generally restricted to aqueous media, in which electrolytes ionize readily due to the large dielectric constant of water. LbL assembly of non-water-soluble materials would expand the range of film properties and functionalities that are attainable. In this study, we have successfully performed LbL deposition of charged particles in a nonpolar solvent, toluene. In toluene, carbon black (CB) and alumina acquired negative and positive surface charge, respectively, in the presence of a charge-inducing agent, Aerosol OT (AOT). The dependence of particle surface charge on the concentration of AOT in toluene was probed by electrophoretic mobility analysis. The two oppositely charged particles were sequentially deposited onto glass slides to form CB/Al(2)O(3) nanocomposite thin films. UV-vis spectroscopy, optical profilometry, and thermogravimetric analysis (TGA) were used to investigate the effect of assembly conditions (i.e., the concentration of AOT in each suspension) on the composition and growth behavior of CB/Al(2)O(3) nanocomposite films. Our results demonstrate that LbL assembly can indeed be performed using charged particles in nonpolar media. Such possibility will widen the library of materials that can be incorporated into thin films based on the LbL technique, which can ultimately lead to the generation of multifunctional nanocomposite thin films.
Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA (2003)

To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection. Further, when the divergence between human and chimpanzee is compared with the extent of nucleotide polymorphisms among humans in the same sequences, there is significantly higher divergence in the 5' untranslated regions (UTRs) but not in other parts of the transcript. This indicates that positive selection may have had a considerable influence on 5'UTRs. The dinucleotide CG (CpG) also exhibits a different substitution pattern within 5'UTRs as compared with other parts of the genome.
Pulmonary Fibrogenesis After Three Consecutive Inhalation Exposures to Chrysotile Asbestos (1996)

Previously, this laboratory developed a model of asbestos-induced pulmonary fibrogenesis in rats and mice after a brief (1 to 3-h) inhalation exposure. However, typical human environmental exposures would be repeated, although at lower concentrations than those used in our animal model. Here we have extended this model to encompass repeated exposures and consequent long-term effects. Groups of rats were exposed to chrysotile aerosol (10 mg/m3) for 3- to 5-h periods over 3 consecutive days. Lung fiber burden and pathologic features were studied for as long as 6 mo after exposure. We found that many of the longest (> or = 8 microm) fibers were retained in the lung for at least 6 mo, whereas shorter fibers were cleared more rapidly. The three exposures to chrysotile caused a large increase in DNA synthesis in the epithelium of terminal bronchioles and more proximal airways. When compared with a single exposure, the triple exposure caused an enhanced inflammatory response as well as a prolonged period of increased DNA synthesis in the proximal alveolar region. Hyperplastic, fibrotic lesions subsequently developed in the same region and persisted for at least 6 mo after exposure. These findings will be valuable in directing future studies of the mechanisms of pulmonary fibrosis in this model.
Fractionation of Immune RNA Isolated from the Spleens of Mice Infected with Trypanosoma cruz (1981)

Immune RNA was extracted from the spleens of mice infected with Trypanosoma cruzi. The immunologic activity of crude immune RNA and the fractions that were obtained by sucrose density gradient centrifugation was assessed by the in vitro macrophage migration-inhibition assay. Crude immune RNA can convert nonsensitized mouse peritoneal cells to a state of specific immunologic reactivity to T. cruzi antigens. The transfer activity of crude immune RNA was abolished by treatment with pancreatic ribonuclease. The 4S–5S RNA was the only fraction active in transferring delayed hypersensitivity in experimental Chagas' disease; however, the 4S transfer RNA also isolated from the spleens of mice with Chagas' disease has no immunologic activity. Immune RNA in experimental Chagas' disease may be an informational RNA.
The tetrapeptide analogue of the cell attachment site of fibronectin inhibits platelet aggregation and fibrinogen binding to activated platelets. (1985)

Fibrinogen binding to receptors on activated platelets is a prerequisite for platelet aggregation. However, the regions of fibrinogen interacting with these receptors have not been completely characterized. Fibronectin also binds to platelet fibrinogen receptors. Moreover, the amino acid sequence Arg-Gly-Asp-Ser, corresponding to the cell attachment site of fibronectin, is located near the carboxyl-terminal region of the alpha-chain of fibrinogen. We have examined the ability of this tetrapeptide to inhibit platelet aggregation and fibrinogen binding to activated platelets. Arg-Gly-Asp-Ser, but not the peptide Arg-Gly-Tyr-Ser-Leu-Gly, inhibited platelet aggregation stimulated by ADP, collagen, and gamma-thrombin without inhibiting platelet shape change or secretion. At a concentration of 60-80 microM, Arg-Gly-Asp-Ser inhibited the aggregation of ADP-stimulated gel-filtered platelets approximately equal to 50%. Arg-Gly-Asp-Ser, but not Arg-Gly-Tyr-Ser-Leu-Gly, also inhibited fibrinogen binding to ADP-stimulated platelets. This inhibition was competitive with a Ki of approximately equal to 25 microM but was incomplete even at higher tetrapeptide concentrations, indicating that Arg-Gly-Asp-Ser is a partial competitive inhibitor of fibrinogen binding. These data suggest that a region near the carboxyl-terminus of the alpha-chain of fibrinogen interacts with the fibrinogen receptor on activated platelets. The data also support the concept that the sequence Arg-Gly-Asp-Ser has been conserved for use in a variety of cellular adhesive processes.
Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair (2013)

Sequence-specific nucleases like TALENs and the CRISPR/Cas9 system have greatly expanded the genome editing possibilities in model organisms such as zebrafish. Both systems have recently been used to create knock-out alleles with great efficiency, and TALENs have also been successfully employed in knock-in of DNA cassettes at defined loci via homologous recombination (HR). Here we report CRISPR/Cas9-mediated knock-in of DNA cassettes into the zebrafish genome at a very high rate by homology-independent double-strand break (DSB) repair pathways. After co-injection of a donor plasmid with a short guide RNA (sgRNA) and Cas9 nuclease mRNA, concurrent cleavage of donor plasmid DNA and the selected chromosomal integration site resulted in efficient targeted integration of donor DNA. We successfully employed this approach to convert eGFP into Gal4 transgenic lines, and the same plasmids and sgRNAs can be applied in any species where eGFP lines were generated as part of enhancer and gene trap screens. In addition, we show the possibility of easily targeting DNA integration at endogenous loci, thus greatly facilitating the creation of reporter and loss-of-function alleles. Due to its simplicity, flexibility, and very high efficiency, our method greatly expands the repertoire for genome editing in zebrafish and can be readily adapted to many other organisms.
Three-space representation of phase-mismatch switching in coupled two-state optical systems (1986)

A three-space graphical representation for the operation of optical switch/modulators based on two-state systems is reviewed. This visual framework provides insight into the behavior of devices such as the waveguide directional coupler and Mach-Zehnder interferometric switches and combiners and the concept of delta-beta reversal. I is based on the covering map of the group <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SU(2)</tex> onto <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SO(3)</tex> and is analogous to the Poincaré formulation for polarization. Because of its pictorial nature, this representation can serve as an aid in the conception of innovative device structures. A class of switches identified using this approach is described and demonstrated by experiment.
Light-activated DNA binding in a designed allosteric protein (2008)

An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an alpha-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical "allosteric lever arm" is a general scheme for coupling the function of two proteins.
The Runx1 Transcription Factor Inhibits the Differentiation of Naive CD4 + T Cells into the Th2 Lineage by Repressing GATA3 Expression (2003)

Differentiation of naive CD4+ T cells into helper T (Th) cells is controlled by a combination of several transcriptional factors. In this study, we examined the functional role of the Runx1 transcription factor in Th cell differentiation. Naive T cells from transgenic mice expressing a dominant interfering form of Runx1 exhibited enhanced interleukin 4 production and efficient Th2 differentiation. In contrast, transduction of Runx1 into wild-type T cells caused a complete attenuation of Th2 differentiation and was accompanied by the cessation of GATA3 expression. Furthermore, endogenous expression of Runx1 in naive T cells declined after T cell receptor stimulation, at the same time that expression of GATA3 increased. We conclude that Runx1 plays a novel role as a negative regulator of GATA3 expression, thereby inhibiting the Th2 cell differentiation.
Factors Affecting Online Purchase Behavior: Implications to Improve the Existing Credit Rating System (2009)

Dishonest sellers, low-quality merchandise, invalid credit evaluation system, low efficient dispute-resolution mechanism are the key factors that make credit become primary concern for consumers making online consumption decision, and hamper the development of C-C market. This article firstly analyzes consumers' demand and behavioral characteristics and the occurred problems of credit system, then focuses on how consumer perceive the credit status and make decision based on Theory of Reasoned Action; further, it sets up a Model of Four Aspects to explain how the factors from four aspects affect consumer's building confidence. Credit assessment index and consumer behavior intention index are put forward as the main factors which affect online consumer confidence and generate consumption behavior. Finally, this paper makes substantive recommendations to improve the existing credit system.