gebhart/patrepeval huggingface dataset:
Purification and cDNA Cloning of Porcine Brain GDP-L-Fuc:N-Acetyl-β-D-Glucosaminide α1→6Fucosyltransferase (1996)

GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1-->6fucosyltransferase (alpha1-6FucT; EC 2.4.1.68), which catalyzes the transfer of fucose from GDP-Fuc to N-linked type complex glycopeptides, was purified from a Triton X-100 extract of porcine brain microsomes. The purification procedures included sequential affinity chromatographies on GlcNAcbeta1-2Manalpha1-6(GlcNAcbeta1-2Manalpha1- 2)Manbeta1-4GlcNAcbet a1-4GlcNAc-Asn-Sepharose 4B and synthetic GDP-hexanolamine-Sepharose 4B columns. The enzyme was recovered in a 12% final yield with a 440, 000-fold increase in specific activity. SDS-polyacrylamide gel electrophoresis of the purified enzyme gave a major band corresponding to an apparent molecular mass of 58 kDa. The alpha1-6FucT has 575 amino acids and no putative N-glycosylation sites. The cDNA was cloned in to pSVK3 and was then transiently transfected into COS-1 cells. alpha1-6FucT activity was found to be high in the transfected cells, as compared with non- or mock-transfected cells. Northern blotting analyses of rat adult tissues showed that alpha1-6FucT was highly expressed in brain. No sequence homology was found with other previously cloned fucosyltransferases, but the enzyme appears to be a type II transmembrane protein like the other glycosyltransferases.
2D THICKNESS AND TEMPERATURE MAPPING OF FLUIDS BY MEANS OF A TWO-DYE LASER INDUCED FLUORESCENCE RATIOMETRIC SCHEME (2002)

This paper presents the principles behind the use of a two-dye Laser Induced Fluorescence (LIF) technique for two-dimensional film thickness and temperature mapping of fluids. The need for two fluorescent emissions arises as a consequence of the fluorescence dependence on excitation light intensity. A ratiometric scheme that normalizes the fluorescent emission of one dye against the fluorescent emission of a second dye is used in order to eliminate undesirable effects due to illumination intensity fluctuations, in both space and time, and optical distortions. The same ratiometric scheme is applied for both film thickness and temperature measurements, but the required spectral characteristics of the dyes used and the optical conditions differ significantly between the two measurements. The concepts of emission reabsorption and optical thickness are discussed in light of the requirements for each particular measurement. Experimental validation of the technique in measuring the thickness and temperature of a film of lubricating oil is also presented.
Characterization of the TPR-MET oncogene p65 and the MET protooncogene p140 protein-tyrosine kinases. (1988)

The proteins encoded by the human TPR-MET oncogene (p 65tpr-met) and the human MET protooncogene (p140met) have been identified. The p65tpr-met and p140met, as well as a truncated TPR-MET product expressed in Escherichia coli, p50met, are autophosphorylated in vitro on tyrosine residues. Using the immunocomplex kinase assay, p140met activity was detected in various human tumor epithelial cell lines. In vivo, p65tpr-met is phosphorylated on both serine and tyrosine residues, while p140met is phosphorylated on serine and threonine. p140met is labeled by cell-surface iodination procedures, suggesting that it is a receptor-like transmembrane protein-tyrosine kinase.
Coordinated plant defense responses in Arabidopsis revealed by microarray analysis (2000)

Disease resistance is associated with a plant defense response that involves an integrated set of signal transduction pathways. Changes in the expression patterns of 2,375 selected genes were examined simultaneously by cDNA microarray analysis in Arabidopsis thaliana after inoculation with an incompatible fungal pathogen Alternaria brassicicola or treatment with the defense-related signaling molecules salicylic acid (SA), methyl jasmonate (MJ), or ethylene. Substantial changes (up- and down-regulation) in the steady-state abundance of 705 mRNAs were observed in response to one or more of the treatments, including known and putative defense-related genes and 106 genes with no previously described function or homology. In leaf tissue inoculated with A. brassicicola, the abundance of 168 mRNAs was increased more than 2.5-fold, whereas that of 39 mRNAs was reduced. Similarly, the abundance of 192, 221, and 55 mRNAs was highly (>2.5-fold) increased after treatment with SA, MJ, and ethylene, respectively. Data analysis revealed a surprising level of coordinated defense responses, including 169 mRNAs regulated by multiple treatments/defense pathways. The largest number of genes coinduced (one of four induced genes) and corepressed was found after treatments with SA and MJ. In addition, 50% of the genes induced by ethylene treatment were also induced by MJ treatment. These results indicated the existence of a substantial network of regulatory interactions and coordination occurring during plant defense among the different defense signaling pathways, notably between the salicylate and jasmonate pathways that were previously thought to act in an antagonistic fashion.
The Role of Surface Chemistry in Bonding of Standard Silicon Wafers (1997)

Hydrophilic silicon surfaces become hydrophobic without microroughening after 200°C low energy hydrogen plasma cleaning. The fully hydrogen‐terminated silicon surfaces do not bond to each other, not even by the application of external pressure. A subsequent 400 to 600°C, 4 min thermal treatment in ultrahigh vacuum converts the wafer surfaces to hydrophilic and bondable which can be attributed to desorption of hydrogen from the surfaces. Hydrophobic silicon surfaces prepared by a dip in HF (without subsequent water rinse) are terminated by H and a small amount of F, or by H and a small amount of OH (after subsequent water rinse). Hydrogen bonding of Si‒F⋯(HF)⋯H‒Si or Si‒OH⋯(HOH)⋯OH‒Si across the two mating surfaces appears to be responsible for room temperature spontaneous hydrophobic or hydrophilic wafer bonding, respectively.
Handbook of Genetic Algorithms (1991)

This book sets out to explain what genetic algorithms are and how they can be used to solve real-world problems. The first objective is tackled by the editor, Lawrence Davis. The remainder of the book is turned over to a series of short review articles by a collection of authors, each explaining how genetic algorithms have been applied to problems in their own specific area of interest. The first part of the book introduces the fundamental genetic algorithm (GA), explains how it has traditionally been designed and implemented and shows how the basic technique may be applied to a very simple numerical optimisation problem. The basic technique is then altered and refined in a number of ways, with the effects of each change being measured by comparison against the performance of the original. In this way, the reader is provided with an uncluttered introduction to the technique and learns to appreciate why certain variants of GA have become more popular than others in the scientific community. Davis stresses that the choice of a suitable representation for the problem in hand is a key step in applying the GA, as is the selection of suitable techniques for generating new solutions from old. He is refreshingly open in admitting that much of the business of adapting the GA to specific problems owes more to art than to science. It is nice to see the terminology associated with this subject explained, with the author stressing that much of the field is still an active area of research. Few assumptions are made about the reader's mathematical background. The second part of the book contains thirteen cameo descriptions of how genetic algorithmic techniques have been, or are being, applied to a diverse range of problems. Thus, one group of authors explains how the technique has been used for modelling arms races between neighbouring countries (a non-linear, dynamical system), while another group describes its use in deciding design trade-offs for military aircraft. My own favourite is a rather charming account of how the GA was applied to a series of scheduling problems. Having attempted something of this sort with Simulated Annealing, I found it refreshing to see the authors highlighting some of the problems that they had encountered, rather than sweeping them under the carpet as is so often done in the scientific literature. The editor points out that there are standard GA tools available for either play or serious development work. Two of these (GENESIS and OOGA) are described in a short, third part of the book. As is so often the case nowadays, it is possible to obtain a diskette containing both systems by sending your Visa card details (or $60) to an address in the USA.
Low-cost fabrication technologies for nanostructures: state-of-the-art and potential (2015)

In the last decade, some low-cost nanofabrication technologies used in several disciplines of nanotechnology have demonstrated promising results in terms of versatility and scalability for producing innovative nanostructures. While conventional nanofabrication technologies such as photolithography are and will be an important part of nanofabrication, some low-cost nanofabrication technologies have demonstrated outstanding capabilities for large-scale production, providing high throughputs with acceptable resolution and broad versatility. Some of these nanotechnological approaches are reviewed in this article, providing information about the fundamentals, limitations and potential future developments towards nanofabrication processes capable of producing a broad range of nanostructures. Furthermore, in many cases, these low-cost nanofabrication approaches can be combined with traditional nanofabrication technologies. This combination is considered a promising way of generating innovative nanostructures suitable for a broad range of applications such as in opto-electronics, nano-electronics, photonics, sensing, biotechnology or medicine.
AN AUTOMATED APPROACH TO SOLVE SIMPLE SUBSTITUTION CIPHERS (1993)

This paper reports a method to automatically solve simple substitution ciphers where the message length is about 160 characters and the space character is suppressed during encryption. Patterns available in the crypt are used as opening points. With the help of a dictionary system, words are fitted at these points after suitable filtering. Subsequently, a tuple generator-cum-selector is used to select a meaningful tuple of words for decoding the crypt. During test runs, 70 out of 100 randomly chosen messages were solved to as sufficient a degree as to facilitate manual completion. Manual completion was found to be fairly simple when the algorithm had correctly identified 70 percent or more of the character positions. The time required for the algorithm to reach this stage was, on an average, about twenty minutes on a standard personal computer.
Temporal abstraction in reinforcement learning (2000)

Decision making usually involves choosing among different courses of action over a broad range of time scales. For instance, a person planning a trip to a distant location makes high-level decisions regarding what means of transportation to use, but also chooses low-level actions, such as the movements for getting into a car. The problem of picking an appropriate time scale for reasoning and learning has been explored in artificial intelligence, control theory and robotics. In this dissertation we develop a framework that allows novel solutions to this problem, in the context of Markov Decision Processes (MDPs) and reinforcement learning. In this dissertation, we present a general framework for prediction, control and learning at multiple temporal scales. In this framework, temporally extended actions are represented by a way of behaving (a policy) together with a termination condition. An action represented in this way is called an option. Options can be easily incorporated in MDPs, allowing an agent to use existing controllers, heuristics for picking actions, or learned courses of action. The effects of behaving according to an option can be predicted using multi-time models, learned by interacting with the environment. In this dissertation we develop multi-time models, and we illustrate the way in which they can be used to produce plans of behavior very quickly, using classical dynamic programming or reinforcement learning techniques. The most interesting feature of our framework is that it allows an agent to work simultaneously with high-level and low-level temporal representations. The interplay of these levels can be exploited in order to learn and plan more efficiently and more accurately. We develop new algorithms that take advantage of this structure to improve the quality of plans, and to learn in parallel about the effects of many different options.
Comparison of Gene Expression Patterns Induced by Treatment of Human Umbilical Vein Endothelial Cells with IFN- α 2b vs. IFN- β 1a: Understanding the Functional Relationship Between Distinct Type I Interferons That Act Through a Common Receptor (2002)

We analyzed whether interferon-alpha 2b (IFN-alpha 2b) and IFN-beta 1a engage their common receptor to generate activated receptor complexes possessing distinct signaling properties. Human vascular endothelial cells (HUVEC) are 100-1000-fold more sensitive to IFN-beta 1a than to IFN-alpha 2b in in vitro assays. An nonarray-based expression profiling (GeneCalling) technology was employed to compare the patterns and levels of gene expression induced by these IFN as the broadest means by which signaling events could be measured. To distinguish subtype-related differences from dose-related effects, RNA was prepared from HUVEC treated with 50-5000 pg/ml of each IFN. The results showed that at 50 pg/ml IFN, only a subset of the genes induced by IFN-beta 1a were also induced by IFN-alpha 2b and that individual genes were induced to higher levels by IFN-beta 1a. In contrast, at 5000 pg/ml, both subtypes induced essentially identical sets of genes to similar levels of expression. No genes were seen to be induced uniquely by IFN-alpha 2b but not by IFN-beta 1a. The results show that the two IFN are intrinsically capable of inducing similar gene induction responses and do not provide evidence that they generate activated receptor complexes possessing distinct signaling properties. In contrast, the two IFN generate gene induction patterns that are both qualitatively and quantitatively distinct at subsaturating and potentially physiologically more relevant concentrations.
특별주제 / N 세대의 새로운 행동 패러다임 : 청소년의 사회성 , 도덕성을 중심으로 ; 신세대 ( N 세대 ) 의 자기 표현과 사이버 공간에서의 상호작용 - 사고와 행동 양식의 변화를 중심으로 (2000)

사이버 공간을 또 다른 생활공간으로 경험하는 청소년 세대의 등장은 정체성 형성이라는 전통적인 발달과업을 다른 관점으로 보게 하였다. 현실 공간에서 고정적이고 안정적인 모습으로 자신을 나타내는 정체성 발달과업이 사이버 공간에서는 다양한 모습의 자기를 타인과 공유하는 가변적이면서도 공동체적 방식으로 변화한다. 인터넷 문화에 기초한 새로운 방식의 의사소통, 인간관계 그리고 놀이 문화는 청소년의 삶의 방식을 변화시킬 뿐 아니라 이들의 사고 방식 및 행동 양식도 변화시켰다. 남과 다른 생활 방식의 추구 속에 동일한 양식의 행동에 대한 집단적 추종 행동이 있으며, 이와 동시에 뭔가 다르게 표현하고 싶은 자기 변신의 욕구도 있다. 현실세계의 인간발달을 이해하는 틀이 논리적이고 합리적인 사고에 기초한 세계관이었다면, 사이버 공간의 인간발달은 다양성과 불규칙성을 내포하는 카오스적인 특성을 보인다. 변화하는 사회 속에서의 발달심리학의 과제는 현실과 사이버의 각기 다른 인간발달의 과정 속에 담겨있는 질서를 파악하고, 사이버 공간 속에서 이루어지는 새로운 인간 심리의 변화 특성을 이해해야 하는 것이다.
Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1 (1991)

Methanol dehydrogenase from the thermotolerant Bacillus sp. C1 was studied by electron microscopy and image processing. Two main projections can be distinguished: one exhibits 5-fold symmetry and has a diameter of 15 nm, the other is rectangular with sides of 15 and 9 nm. Subsequent image processing showed that the 5-fold view possesses mirror symmetry. The rectangular views can be divided into two separate classes, one of which has 2-fold rotational symmetry. It is concluded that methanol dehydrogenase is a decameric molecule, and a tentative model is presented. The estimated molecular weight is 430,000, based on a subunit molecular weight of 43,000. The enzyme contains one zinc and one to two magnesium ions per subunit. N-terminal amino acid sequence analysis revealed substantial similarity with alcohol dehydrogenases from Saccharomyces cerevisiae, Zymomonas mobilis, Clostridium acetobutylicum, and Escherichia coli, which contain iron or zinc but no magnesium. In view of the aberrant structural and kinetic properties, it is proposed to distinguish the enzyme from common alcohol dehydrogenases (EC 1.1.1.1) by using the name NAD-dependent methanol dehydrogenase.
Objective Responses to Ketoconazole Therapy in Patients with Relapsed Progressive Prostatic Cancer (1986)

The contribution of adrenal androgens to the maintenance and progression of so-called hormone-unresponsive prostatic carcinoma was studied in 20 patients with advanced relapsed disease. The role played by testicular androgens had been negated by prior orchiectomy or concurrent LHRH analogue therapy. Ketoconazole, an antifungal agent which inhibits adrenal and testicular androgenesis, administered in a dose of 400 mg 8-hourly, resulted in optimal suppression of adrenal androgens. The mean serum androstenedione concentration fell from 8.01 +/- 0.84 nMol/l to 1.55 +/- 0.25 nMol/l, P less than 0.001, and serum testosterone from 1.25 +/- 0.14 nMol/l to 0.36 +/- 0.06 nMol/l, P less than 0.01, after 6 months treatment. There was, however, no significant difference between patients receiving 400 and those receiving 200 mg. Androgen suppression resulted in six objective and ten subjective clinical responses. Ablation of both testicular and adrenal androgens can now be achieved using ketoconazole in combination with orchiectomy or LHRH analogues, but the high incidence of side effects may preclude its use in all patients with prostatic cancer. The results of this study support the concept of "total androgen ablation" as primary therapy in advanced prostatic cancer as a possible means of improving survival in this common malignancy.
Zinc-finger recombinase activities in vitro (2011)

Zinc-finger recombinases (ZFRs) are chimaeric proteins comprising a serine recombinase catalytic domain linked to a zinc-finger DNA binding domain. ZFRs can be tailored to promote site-specific recombination at diverse 'Z-sites', which each comprise a central core sequence flanked by zinc-finger domain-binding motifs. Here, we show that purified ZFRs catalyse efficient high-specificity reciprocal recombination between pairs of Z-sites in vitro. No off-site activity was detected. Under different reaction conditions, ZFRs can catalyse Z-site-specific double-strand DNA cleavage. ZFR recombination activity in Escherichia coli and in vitro is highly dependent on the length of the Z-site core sequence. We show that this length effect is manifested at reaction steps prior to formation of recombinants (binding, synapsis and DNA cleavage). The design of the ZFR protein itself is also a crucial variable affecting activity. A ZFR with a very short (2 amino acids) peptide linkage between the catalytic and zinc-finger domains has high activity in vitro, whereas a ZFR with a very long linker was less recombination-proficient and less sensitive to variations in Z-site length. We discuss the causes of these phenomena, and their implications for practical applications of ZFRs.
Tandem constructs to mitigate transgene persistence: tobacco as a model (2004)

Some transgenic crops can introgress genes into other varieties of the crop, to related weeds or themselves remain as 'volunteer' weeds, potentially enhancing the invasiveness or weediness of the resulting offspring. The presently suggested mechanisms for transgene containment allow low frequency of gene release (leakage), requiring the mitigation of continued spread. Transgenic mitigation (TM), where a desired primary gene is tandemly coupled with mitigating genes that are positive or neutral to the crop but deleterious to hybrids and their progeny, was tested as a mechanism to mitigate transgene introgression. Dwarfism, which typically increases crop yield while decreasing the ability to compete, was used as a mitigator. A construct of a dominant ahasR (acetohydroxy acid synthase) gene conferring herbicide resistance in tandem with the semidominant mitigator dwarfing Delta gai (gibberellic acid-insensitive) gene was transformed into tobacco (Nicotiana tabacum). The integration and the phenotypic stability of the tandemly linked ahasR and Delta gai genomic inserts in later generations were confirmed by polymerase chain reaction. The hemizygous semidwarf imazapyr-resistant TM T1 (= BC1) transgenic plants were weak competitors when cocultivated with wild type segregants under greenhouse conditions and without using the herbicide. The competition was most intense at close spacings typical of weed offspring. Most dwarf plants interspersed with wild type died at 1-cm, > 70% at 2.5-cm and 45% at 5-cm spacing, and the dwarf survivors formed no flowers. At 10-cm spacing, where few TM plants died, only those TM plants growing at the periphery of the large cultivation containers formed flowers, after the wild type plants terminated growth. The highest reproductive TM fitness relative to the wild type was 17%. The results demonstrate the suppression of crop-weed hybrids when competing with wild type weeds, or such crops as volunteer weeds, in seasons when the selector (herbicide) is not used. The linked unfitness would be continuously manifested in future generations, keeping the transgene at a low frequency.
Confidentiality and Electronic Medical Records (1998)

Letters15 March 1998Confidentiality and Electronic Medical RecordsJohn Roberts, MT, Sheila R. Decter, MA, and Denise Nagel, MDJohn Roberts, MTAmerican Civil Liberties Union of Massachusetts; Boston, MA 02111American Jewish Congress, New England Region; Boston, MA 02210National Coalition for Patient Rights; Lexington, MA 02173Search for more papers by this author, Sheila R. Decter, MAAmerican Civil Liberties Union of Massachusetts; Boston, MA 02111American Jewish Congress, New England Region; Boston, MA 02210National Coalition for Patient Rights; Lexington, MA 02173Search for more papers by this author, and Denise Nagel, MDAmerican Civil Liberties Union of Massachusetts; Boston, MA 02111American Jewish Congress, New England Region; Boston, MA 02210National Coalition for Patient Rights; Lexington, MA 02173Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-128-6-199803150-00032 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail TO THE EDITOR:We write in response to Rind and colleagues' article on maintaining the confidentiality of electronic medical records shared over the Internet [1]. Although the proposed policy has some excellent features, we believe it also contains the following flaws.First, no explicit procedure is provided for informing all patients that they may object to the electronic transmission of their records between institutions. Second, it is not clear how clinicians will obtain information about the existence of a patient's records at other institutions and whether this will be done in a way that does not violate patient confidentiality. Third, ...References1. Rind DM, Kohane IS, Szolovits P, Safran C, Chueh HC, Barnett GO. Maintaining the confidentiality of medical records shared over the Internet and the World Wide Web. Ann Intern Med. 1997; 127:138-41. Google Scholar Author, Article, and Disclosure InformationAuthors: John Roberts, MT; Sheila R. Decter, MA; Denise Nagel, MDAffiliations: American Civil Liberties Union of Massachusetts; Boston, MA 02111American Jewish Congress, New England Region; Boston, MA 02210National Coalition for Patient Rights; Lexington, MA 02173 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited byRe-presenting Reality, Recovering the Social: The Poetics and Politics of Social Realism and Visual Art 15 March 1998Volume 128, Issue 6Page: 510KeywordsElectrode recordingElectronic medical recordsHealth careInternet ePublished: 15 August 2000 Issue Published: 15 March 1998 Copyright & PermissionsCopyright © 1998 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...