gebhart/patrepeval huggingface dataset:
Learning sequence kernels (2008)

Kernel methods are used to tackle a variety of learning tasks including classification, regression, ranking, clustering, and dimensionality reduction. The appropriate choice of a kernel is often left to the user. But, poor selections may lead to a sub-optimal performance. Instead, sample points can be used to learn a kernel function appropriate for the task by selecting one out of a family of kernels determined by the user. This paper considers the problem of learning sequence kernel functions, an important problem for applications in computational biology, natural language processing, document classification and other text processing areas. For most kernel-based learning techniques, the kernels selected must be positive definite symmetric, which, for sequence data, are found to be rational kernels. We give a general formulation of the problem of learning rational kernels and prove that a large family of rational kernels can be learned efficiently using a simple quadratic program both in the context of support vector machines and kernel ridge regression. This improves upon previous work that generally results in a more costly semi-definite or quadratically constrained quadratic program. Furthermore, in the specific case of kernel ridge regression, we give an alternative solution based on a closed-form solution for the optimal kernel matrix. We also report results of experiments with our kernel learning techniques in classification and regression tasks.
Effect of O6-methylguanine on DNA interstrand cross-link formation by chloroethylnitrosoureas and 2-chloroethyl(methylsulfonyl)methanesulfonate. (1988)

Exposure of HT29 cells in culture to O6-methylguanine is known to result in a reduction in O6-alkylguanine-DNA alkyltransferase (AGT) activity and an enhancement of sensitivity to the cytotoxic effects of chloroethylating agents. Since cytotoxicity of these agents may be mediated by the formation of interstrand cross-links, alkaline elution analysis was performed on HT29 cells treated with 1-(2-chloroethyl)-1-nitrosourea, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea, and Clomesone [2-chloroethyl(methylsulfonyl)methanesulfonate] in the presence or absence of O6-methylguanine pretreatment to determine if the enhanced toxicity was due to an increase in the number of cross-links formed. Interstrand cross-linking by 1-(2-chloroethyl)-1-nitrosourea or 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea was increased by pretreatment with 0.4 mM O6-methylguanine for 24 h. Cross-linking by Clomesone was observed only in cells exposed to 0.4 mM O6-methylguanine for 24 h prior to administration of the drug and for 12 h after administration, suggesting that the resynthesis of the AGT may prevent the cross-linking by Clomesone. Complete recovery of AGT activity after reduction to 20 to 30% of the basal level upon treatment with 0.4 mM O6-methylguanine required between 8 h and 15 h in both HT29 cells and in Raji cells which were also sensitized to 1-(2-chloro-ethyl)-3-cyclohexyl-1-nitrosourea by exposure to O6-methylguanine. These data suggest that the enhancement of chloroethylnitrosourea toxicity after treatment with O6-methylguanine may be related to an increase in the number of DNA cross-links and that the relatively rapid rate of AGT recovery plays a role in prevention of cross-links resulting from Clomesone.
The virtual reality technology in art design (2012)

Virtual reality technology is a new technology. It has great application prospects in the field of art design. At first, this paper analyzed the concept of virtual reality technology. At second, this paper analyzed the concept of art design. At third, this paper introduced the applications of VR technology in display design, including: panoramic image technology, three-dimensional display technology, stereo sound display technology, and interactive display technology. At fourth, this paper introduced the applications of virtual reality technology in product design. At fifth, this paper introduced the applications of virtual reality technology in environment art design. Finally, this paper discussed the importance and the future of art design based the VR technology.
Immune checkpoint blockade and its combination therapy with small-molecule inhibitors for cancer treatment (2018)

Initially understood for its physiological maintenance of self-tolerance, the immune checkpoint molecule has recently been recognized as a promising anti-cancer target. There has been considerable interest in the biology and the action mechanism of the immune checkpoint therapy, and their incorporation with other therapeutic regimens. Recently the small-molecule inhibitor (SMI) has been identified as an attractive combination partner for immune checkpoint inhibitors (ICIs) and is becoming a novel direction for the field of combination drug design. In this review, we provide a systematic discussion of the biology and function of major immune checkpoint molecules, and their interactions with corresponding targeting agents. With both preclinical studies and clinical trials, we especially highlight the ICI + SMI combination, with its recent advances as well as its application challenges.
Balance of life and death in alveolar epithelial type II cells: proliferation, apoptosis, and the effects of cyclic stretch on wound healing (2011)

After acute lung injury, repair of the alveolar epithelium occurs on a substrate undergoing cyclic mechanical deformation. While previous studies showed that mechanical stretch increased alveolar epithelial cell necrosis and apoptosis, the impact of cell death during repair was not determined. We examined epithelial repair during cyclic stretch (CS) in a scratch-wound model of primary rat alveolar type II (ATII) cells and found that CS altered the balance between proliferation and cell death. We measured cell migration, size, and density; intercellular gap formation; cell number, proliferation, and apoptosis; cytoskeletal organization; and focal adhesions in response to scratch wounding followed by CS for up to 24 h. Under static conditions, wounds were closed by 24 h, but repair was inhibited by CS. Wounding stimulated cell motility and proliferation, actin and vinculin redistribution, and focal adhesion formation at the wound edge, while CS impeded cell spreading, initiated apoptosis, stimulated cytoskeletal reorganization, and attenuated focal adhesion formation. CS also caused significant intercellular gap formation compared with static cells. Our results suggest that CS alters several mechanisms of epithelial repair and that an imbalance occurs between cell death and proliferation that must be overcome to restore the epithelial barrier.
Saving the Murray: troubled waters (2017)

Edwyna Harris examines, in the light of historical experience, John Howards policy to put control of the Murray River into Federal hands. Copyright 2007 Edwyna Harris. No part of this article may be reproduced by any means without the written consent of the publisher.
A Power-Efficient CMOS Adaptive Biasing Operational Transconductance Amplifier (2013)

This paper presents a two-stage power-efficient class-AB operational transconductance amplifier (OTA) based on an adaptive biasing circuit suited to low-power dissipation and low-voltage operation. The OTA shows significant improvements in driving capability and power dissipation owing to the novel adaptive biasing circuit. The OTA dissipates only 0.4 μW from a supply voltage of ±0.6 V and exhibits excellent high driving, which results in a slew rate improvement of more than 250 times that of the conventional class-AB amplifier. The design is fabricated using 0.18-μm CMOS technology.
The pro region is not required for the expression or intracellular routeing of carboxypeptidase E (1997)

Carboxypeptidase E (CPE) is initially synthesized as a larger precursor containing an additional 14-residue propeptide that is highly conserved between human and rat. Previous studies have established that the proenzyme is enzymically active and that deletion of the pro region does not affect the expression of the active enzyme. In the present study the function of the pro region was examined both by deleting this region from CPE and by attaching this region to the N-terminus of albumin. CPE lacking the pro region is sorted into the regulated secretory pathway in AtT-20 cells, based on confocal microscopy and examination of the stimulated secretion of the protein. Stimulation of AtT-20 cells with either forskolin or phorbol 12-myristate 13-acetate induces the secretion of wild-type CPE and of CPE lacking the pro region to similar extents, indicating a similar efficiency of sorting of the mutant. When the pro region of proalbumin is replaced with the pro region of CPE followed by expression in AtT-20 cells, the protein is not sorted into the regulated pathway, based on the lack of stimulated secretion. Confocal microscopy suggests that the proCPE/albumin protein is retained in the endoplasmic reticulum to a greater extent than is proalbumin. Pulse-chase analysis indicates that the pro region of CPE is not efficiently removed from the N-terminus of albumin, and the small amount of propeptide cleavage that does occur takes place soon before secretion of the protein. In contrast, confocal microscopy indicates that the majority of the propeptide is removed from CPE, and that this cleavage occurs in the trans-Golgi network or soon after sorting into the secretory vesicles. Taken together, these results suggest that the pro region of CPE is not required for the expression or intracellular routeing of this protein.
Induction by ethanol of alcohol dehydrogenase activity in Acetobacter pasteurianus (1993)

The membrane-bound alcohol dehydrogenase (ADH) activity of Acetobacter pasteurianus NCI1380 was enhanced more than 10-fold by the addition of ethanol to the medium. In order to elucidate the mechanism of the ethanol induction, a gene cluster encoding the dehydrogenase and cytochrome c subunits of ADH was cloned from this strain, and its nucleotide sequence was determined. Comparison of the deduced amino acid sequences and the NH2-terminal sequences determined with purified proteins showed that the dehydrogenase and cytochrome c subunits contained typical signal peptides of 35 and 26 amino acids, respectively. Transcriptional analysis of the cloned genes by primer extension revealed that the gene cluster was transcribed from two different promoters upstream from the dehydrogenase gene. One (59 bp upstream of the ATG start codon) of the two promoters was used in the presence of ethanol, whereas the other (232 bp upstream of the ATG start codon) was used in the absence of ethanol. Immunoblot analyses showed that almost the same amounts of the cytochrome c and the 15-kDa subunits were produced in both the presence and absence of ethanol and that the amount of the dehydrogenase subunit localized in the membrane was decreased in the absence of ethanol. This incorrect localization of the dehydrogenase subunit might be one of the factors responsible for the low ADH activity in the absence of ethanol.
Theory of flow in unconfined aquifers considering delayed response of the water table (1972)

A new analytical model is proposed for the delayed response process characterizing flow to a well in an unconfined aquifer. The present approach differs from that of Boulton [1954 b , 1963, 1970] and Boulton and Pontin [1971] in that it is based only on well‐defined physical parameters of the aquifer system. Therefore it provides a possible physical explanation for the mechanism of delayed water table response and eliminates the conceptual difficulties encountered with Boulton's theory of ‘delayed yield from storage above the water table.’ Contrary to prevailing belief the process of delayed response in a homogeneous anisotropic phreatic aquifer can be simulated by using constant values of specific storage and specific yield without recourse to unsaturated flow theory. The results suggest that, in the absence of significant infiltration at the ground surface, compressibility may often be a much more important factor than unsaturated flow above the water table. Current methods of analyzing field data from unconfined aquifers do not usually consider compressibility. The present theory shows that such methods are limited in their application to relatively large values of time.
Improving Efficiency of XPath-Based XML Querying (2004)

XML is becoming the de facto standard for information exchange. XML querying is a key component for structured information processing and plays a central role in the next generation world wide web, information management systems and databases. Applications relying on XML processing notably depend on XPath, the standard language for adressing parts of XML documents. Besides its fundamental functionality, reasons behind XPath success include being widely accepted by programmers and well-suited for formal treatments. With the growing volume of XML content and XML processing applications, our research is oriented toward efficiency of XML querying. Our approach relies on analysis and transformation of XPath expressions for optimization. This note presents current open issues with XPath, and introduces our preliminary results applied to streaming XPath processing. Moreover, it describes our methodology, which includes XPath modelisation using the Coq proof assistant, and future directions envisioned toward high performance XML querying. 1
Development of low power MPEG1/JPEG encode/decode IC (1997)

We have developed a low power MPEG1 (Moving Picture Expert Group)/JPEG (Joint Photographic Expert Group) encode/decode single chip IC (codec). Using compact ME (motion estimation) process and a power management function we realize a low power consumption. Total power consumption of the codec is 500 mW. Using this chip, we have also developed a compact digital camera for the MPEG1 stream.
Design and Implementation of All-opening Experimental Teaching and Laboratory Management System (2011)

Based on the characteristics of all-opening experiment,an all-opening experimental teaching and laboratory management system was designed and implemented for resolving various problems,such as complex management,fussy manipulation,vast workload,low efficiency etc.It makes all-opening experiment achieve network teaching and intellectualized management,so the experimental teaching level and laboratory management level are enhanced.The system consists of two subsystems.One is the network laboratory for electric and electronic experiment,the other is laboratory management subsystem.The system structure and the functional module of subsystems were explained,and the main operational process was introduced.
Selective regulation of cellular cyclooxygenase by dexamethasone and endotoxin in mice. (1990)

We have studied the effect of glucocorticoids administered in vivo on the activity and synthesis of the cyclooxygenase enzyme (COX) in mice treated with or without concurrent intravenous administration of LPS. Mouse peritoneal macrophages from LPS-treated animals showed a two to three fold increase in COX activity determined by the production of PGE2 and PGI2 after stimulation of the cells with exogenous arachidonate. Dexamethasone injected simultaneously with LPS, 12 h before killing of the animal and removal of the macrophages, completely blocked the LPS-induced increase COX activity in peritoneal macrophages. The regulation observed in COX activity by LPS and dexamethasone are due primarily to changes in COX mass as determined by immunoprecipitation of [35S]methionine endogenously labeled enzyme. In contrast, the COX present in the nonadherent cells and in renal medullary microsomes obtained from the same animals, showed no significant changes between treatments. These results indicate that LPS in vivo stimulates COX synthesis in the peritoneal macrophages but not in the kidney. The effect of dexamethasone to inhibit COX synthesis is selective to the LPS-induced enzyme.
An Overview of Genetic Transformation of Soybean (2013)

Soybean (Glycine max (L.) Merrill) is a model legume crop, widely grown in the world for hu‐ man consumption or animal fodder. Moreover, soybeans have gained worldwide research in‐ terest in many public laboratories and industrial sectors. Soybean seeds contain protein, oil, carbohydrates, dietary fibers, vitamins, and minerals. For the last few decades the majority of research laboratories have been investigating genetic traits to improve the yield of protein or oil in soybean seeds through genetic engineering, thereby achieving improved quantity and quality of soybean seeds. Until now, most of the transformation experiments have implement‐ ed a single functional gene not multiple genes. Those agronomically and economically impor‐ tant traits affect the enhancement of grain quantity and quality [1]. However, the majority of agronomic and genetic traits such as complex metabolic, biological, and pharmaceutical path‐ ways are polygenetic traits and are produced in a complex pathway. Therefore, those traits are encoded and regulated by a number of genes. In an attempt to study and manipulate those pathways, the transfer of multigene or large inserts into plants have been developed by multi‐ gene engineering technology and have also been involved in metabolic engineering. Several examples of multigene or large insert transfers have been reported such as the application of carotenogenic genes in rice, canola, and maize [2-4], and of polyunsaturated fatty acid and vi‐ tamin E genes in soybean and Arabidopsis [5-7]. Therefore, reliable systems for transforming large DNA fragments into plants make it feasible to introduce a natural gene cluster or a series of previously unlinked foreign genes into a single locus.
Alkaline hydrolysis of phospholipids in model membranes and the dependence on their state of aggregation (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkaline hydrolysis of phospholipids in model membranes and the dependence on their state of aggregationCharlotte Read Kensil and Edward A. DennisCite this: Biochemistry 1981, 20, 21, 6079–6085Publication Date (Print):October 13, 1981Publication History Published online1 May 2002Published inissue 13 October 1981https://pubs.acs.org/doi/10.1021/bi00524a025https://doi.org/10.1021/bi00524a025research-articleACS PublicationsRequest reuse permissionsArticle Views612Altmetric-Citations63LEARN 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
Analysis and synthesis of neural networks with lower block triangular interconnecting structure (1990)

The authors present a qualitative analysis of Hopfield-type neural network models with lower block triangular interconnecting structure. Such networks are viewed as interconnected systems and the present results are phrased in terms of the qualitative properties of the subsystems of the networks and in terms of the properties of the interconnecting structure of the networks. The results address the stability properties of equilibrium points and estimates of trajectory properties. These results enable one to devise a design method for the class of neural networks considered to establish desired relationships between scalar-valued analog input signals and output signals in binary form.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Paradoxical roles for lysyl oxidases in cancer—A prospect (2007)

Abstract Lysyl oxidase (LOX) is an extracellular matrix (ECM) enzyme that catalyzes the cross‐linking of collagens or elastin in the extracellular compartment, thereby regulating the tensile strength of tissues. However, recent reports have demonstrated novel roles for LOX, including the ability to regulate gene transcription, motility/migration, and cell adhesion. These diverse functions have led researchers to hypothesize that LOX may have multiple roles affecting both extra‐ and intracellular cell function(s). Particularly noteworthy is aberrant LOX expression and activity that have been observed in various cancerous tissues and neoplastic cell lines. Both down and upregulation of LOX in tumor tissues and cancer cell lines have been described, suggesting a dual role for LOX as a tumor suppressor, as well as a metastasis promoter gene—creating a conundrum within the LOX research field. Here, we review the body of evidence on LOX gene expression, regulation, and function(s) in various cancer cell types and tissues, as well as stromal–tumor cell interactions. Lastly, we will examine putative mechanisms in which LOX facilitates breast cancer invasion and metastasis. Taken together, the literature demonstrates the increasingly important role(s) that LOX may play in regulating tumor progression and the necessity to elucidate its myriad mechanisms of action in order to identify potentially novel therapeutics. J. Cell. Biochem. 101: 1338–1354, 2007. © 2007 Wiley‐Liss, Inc.
Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system (2019)

Establishing causal relationship between epigenetic marks and gene transcription requires molecular tools, which can precisely modify specific genomic regions. Here, we present a modular and extensible CRISPR/dCas9-based toolbox for epigenetic editing and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to various effector domains and includes a multi-gRNA system for simultaneous targeting dCas9 orthologs to up to six loci. The C- and N-terminal dCas9 fusions with DNMT3A and TET1 catalytic domains were thoroughly characterized. We demonstrated simultaneous use of the DNMT3A-dSpCas9 and TET1-dSaCas9 fusions within the same cells and showed that imposed cytosine hyper- and hypo-methylation altered level of gene transcription if targeted CpG sites were functionally relevant. Dual epigenetic manipulation of the HNF1A and MGAT3 genes, involved in protein N-glycosylation, resulted in change of the glycan phenotype in BG1 cells. Furthermore, simultaneous targeting of the TET1-dSaCas9 and VPR-dSpCas9 fusions to the HNF1A regulatory region revealed strong and persistent synergistic effect on gene transcription, up to 30 days following cell transfection, suggesting involvement of epigenetic mechanisms in maintenance of the reactivated state. Also, modulation of dCas9 expression effectively reduced off-target effects while maintaining the desired effects on target regions.