gebhart/patrepeval huggingface dataset:
Analysis of alterations of WFDC1, a new putative tumour suppressor gene, in hepatocellular carcinoma (2002)

WFDC1 is a recently isolated human gene identified as a tumour suppressor gene candidate. It is not known whether alterations in this gene are associated with human cancers. The WFDC1 gene maps in human chromosome 16q24, an area of frequent loss of heterozygosity (LOH) in several tumour types, in particular in hepatocellular carcinoma (HCC). We investigated its role in 46 European HCC by means of the detection of LOH at the WFDC1 locus. We describe here an assay for the detection of loss of heterozygosity at this locus using two dinucleotide repeat polymorphisms identified in WFDC1 introns, with a combined informativity of 86%. LOH was observed in 4/40 informative HCC samples. We further investigated the role of WFDC1 as a tumour suppressor gene candidate in five hepatocellular cell lines and in tumours exhibiting LOH by means of mutation, promoter methylation and gene expression analysis. In HCC samples showing LOH, no mutation of the remaining allele was observed. No significant up or down gene expression was observed in tumour samples comparatively to normal liver and gene expression did not seem related to promoter methylation. These results suggest a minor role, if any, of WFDC1 in hepatocarcinogenesis. However, this approach might be useful for investigating the role of this candidate tumour suppressor gene in other tumour types.
Communication-Efficient Tracking of Distributed Cumulative Triggers (2007)

In recent work, we proposed D-Trigger, a framework for tracking a global condition over a large network that allows us to detect anomalies while only collecting a very limited amount of data from distributed monitors. In this paper, we expand our previous work by designing a new class of queries (conditions) that can be tracked for anomaly violations. We show how security violations can be detected over a time window of any size. This is important because security operators do not know in advance the window of time in which measurements should be made to detect anomalies. We also present an algorithm that determines how each machine should filter its time series measurements before back-hauling them to a central operations center. Our filters are computed analytically such that upper bounds on false positive and missed detection rates are guaranteed. In our evaluation, we show that botnet detection can be carried out successfully over a distributed set of machines, while simultaneously filtering out 80 to 90% of the measurement data.
Éxitos del programa de cría en cautividad del águila perdicera: el CERI de Castilla-La-Mancha, centro pionero (2004)

ULI es el nombre de la primera aguila perdicera que nace en cautividad en Espana. El logro, obtenido en abril de 2003 mediante inseminacion intrauterina en el CERI, el centro especializado que la Junta de Castilla-La Mancha tiene en
Sevilleja de la Jara (Toledo), sera de gran ayuda para garantizar la supervivencia de una de las rapaces mas amenazadas de Europa. Es tambien una llamada de atencion sobre los problemas
reproductivos que padece la especie en su medio natural.
Dynamic control of liquid-core/liquid-cladding optical waveguides (2004)

This report describes the manipulation of light in waveguides that comprise a liquid core and a liquid cladding (liq/liq waveguide). These waveguides are dynamic: Their structure and function depend on a continuous, laminar flow of the core and cladding liquids. Because they are dynamic, they can be reconfigured and adapted continuously in ways that are not possible with solid-state waveguides. The liquids are introduced into the channels of a microfluidic network designed to sandwich the flowing core liquid between flowing slabs of the cladding fluid. At low and moderate Reynolds numbers, flow is laminar, and the liq/liq interfaces are optically smooth. Small irregularities in the solid walls of the channels do not propagate into these interfaces, and liq/liq waveguides therefore exhibit low optical loss because of scattering. Manipulating the rate of flow and the composition of the liquids tunes the characteristics of these optical systems.
The Preparation of 3,4-Dimethoxy-2,5-dicarbethoxythiophene. 3,4-Dimethoxythiophene (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Preparation of 3,4-Dimethoxy-2,5-dicarbethoxythiophene. 3,4-DimethoxythiopheneC. G. Overberger and Joginder LalCite this: J. Am. Chem. Soc. 1951, 73, 6, 2956–2957Publication Date (Print):June 1, 1951Publication History Published online1 May 2002Published inissue 1 June 1951https://pubs.acs.org/doi/10.1021/ja01150a525https://doi.org/10.1021/ja01150a525research-articleACS PublicationsRequest reuse permissionsArticle Views412Altmetric-Citations35LEARN 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
Monodisperse and Corrosion‐Resistant Metallic Nanoparticles Embedded into Sepiolite Particles for Optical and Magnetic Applications (2006)

The preparation of large quantities of heterogeneous materials containing non‐agglomerated and monodispersed nanoparticles is becoming one of the bottlenecks that hinders the development of commercial devices. Here we describe a method to prepare monodispersed metallic (Cu, Ag, Au, Ni, Co, and Fe) nanoparticles in a silicate matrix (sepiolite) by means of a reduction process of metallic cations associated with a dehydration process of the matrix. This process is characterized by the huge amount of monodispersed metallic nanoparticles that it produces. Additionally, these nanoparticles have been revealed to be remarkably stable against oxidation because the transformed sepiolite matrix becomes a diffusion barrier for oxygen. Furthermore, the nanoparticles present suitable properties to be used for optical and magnetic applications.
Affinity maturation of human CD4 by yeast surface display and crystal structure of a CD4–HLA-DR1 complex (2011)

Helper T-cell activation generally requires the coreceptor CD4, which binds MHC class II molecules. A remarkable feature of the CD4-MHC class II interaction is its exceptionally low affinity, which ranges from K(D) = ∼200 μM to >2 mM. Investigating the biological role of the much lower affinity of this interaction than those of other cell-cell recognition molecules will require CD4 mutants with enhanced binding to MHC class II for testing in models of T-cell development. To this end, we used in vitro-directed evolution to increase the affinity of human CD4 for HLA-DR1. A mutant CD4 library was displayed on the surface of yeast and selected using HLA-DR1 tetramers or monomers, resulting in isolation of a CD4 clone containing 11 mutations. Reversion mutagenesis showed that most of the affinity increase derived from just two substitutions, Gln40Tyr and Thr45Trp. A CD4 variant bearing these mutations bound HLA-DR1 with K(D) = 8.8 μM, compared with >400 μM for wild-type CD4. To understand the basis for improved affinity, we determined the structure of this CD4 variant in complex with HLA-DR1 to 2.4 Å resolution. The structure provides an atomic-level description of the CD4-binding site on MHC class II and reveals how CD4 recognizes highly polymorphic HLA-DR, -DP, and -DQ molecules by targeting invariant residues in their α2 and β2 domains. In addition, the CD4 mutants reported here constitute unique tools for probing the influence of CD4 affinity on T-cell activation and development.
Key agreement in ad hoc networks (2006)

A new key agreement protocol based on a shared conference password is proposed in this paper. With this protocol, it provides an efficient algorithm and takes less computation cost to construct a secret communication channel. Besides, the honest participant can use passwords to authenticate the other participants. The proposed scheme is suitable for application in ad hoc networks. It also provides an efficient protocol to reconstruct a new session key when some members join or leave the conference.
Binding of an ankyrin-1 isoform to obscurin suggests a molecular link between the sarcoplasmic reticulum and myofibrils in striated muscles (2003)

Assembly of specialized membrane domains, both of the plasma membrane and of the ER, is necessary for the physiological activity of striated muscle cells. The mechanisms that mediate the structural organization of the sarcoplasmic reticulum with respect to the myofibrils are, however, not known. We report here that ank1.5, a small splice variant of the ank1 gene localized on the sarcoplasmic reticulum membrane, is capable of interacting with a sequence of 25 aa located at the COOH terminus of obscurin. Obscurin is a giant sarcomeric protein of approximately 800 kD that binds to titin and has been proposed to mediate interactions between myofibrils and other cellular structures. The binding sites and the critical aa required in the interaction between ank1.5 and obscurin were characterized using the yeast two-hybrid system, in in vitro pull-down assays and in experiments in heterologous cells. In differentiated skeletal muscle cells, a transfected myc-tagged ank1.5 was found to be selectively restricted near the M line region where it colocalized with endogenous obscurin. The M line localization of ank1.5 required a functional obscurin-binding site, because mutations of this domain resulted in a diffused distribution of the mutant ank1.5 protein in skeletal muscle cells. The interaction between ank1.5 and obscurin represents the first direct evidence of two proteins that may provide a direct link between the sarcoplasmic reticulum and myofibrils. In keeping with the proposed role of obscurin in mediating an interaction with ankyrins and sarcoplasmic reticulum, we have also found that a sequence with homology to the obscurin-binding site of ank1.5 is present in the ank2.2 isoform, which in striated muscles has been also shown to associate with the sarcoplasmic reticulum. Accordingly, a peptide containing the COOH terminus of ank2.2 fused with GST was found to bind to obscurin. Based on reported evidence showing that the COOH terminus of ank2.2 is necessary for the localization of ryanodine receptors and InsP3 receptors in the sarcoplasmic reticulum, we propose that obscurin, through multiple interactions with ank1.5 and ank2.2 isoforms, may assemble a large protein complex that, in addition to a structural function, may play a role in the organization of specific subdomains in the sarcoplasmic reticulum.
Combinatorial search strategies for the metabolic engineering of microorganisms (2010)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2010.
SMART POINTERS: THEY''RE SMART, BUT THEY''RE NOT POINTERS (1992)

There are numerous times when a C++ user could benefit from a pointer variant that has more functionality than is provided by the basic, language-defined pointer. For example, type-accurate garbage collection, reference counting, or transparent references to distributed or persistent objects, might be implemented with classes that provide pointer functionality. The C++ language directly supports one kind of pointer substitute, the smart pointer, in the form of overloadable indirection operators: -< and *. In this paper we evaluate how *seamlessly* smart pointers can replace raw pointers. The ideal is for client code not to care whether it is using raw pointers or smart pointers. For example, if a typedef selects whether raw or smart pointers are used throughout the program, changing the value of the typedef should not introduce syntax errors. Unfortunately, C++ does not support pointer substitutes well enough to permit seamless integration. This paper presents the desired behavior of smart pointers in terms of the semantics of raw pointers that the smart pointers try to emulate. Then, we describe several ways of implementing smart pointers. For each, we show cases in which the smart-pointers fail to behave like raw pointers. From among the choices, we explain which is the best for emulating the standard pointer conversions. *Accessors* are similar to smart pointers, but have certain advantages. This paper discusses the differences between accessors and smart pointers, and shows why our conclusions about type conversion behavior also apply to accessors. Whether a programmer prefers smart pointers or accessors, this paper shows the limitations and recommends an implementation.
C‐terminal titin deletions cause a novel early‐onset myopathy with fatal cardiomyopathy (2007)

M-line titin homozygous truncations cause the first congenital and purely recessive titinopathy, and the first to involve both cardiac and skeletal muscle. These results expand the spectrum of early-onset myopathies and suggest that titin segments downstream of the kinase domain are dispensable for skeletal and cardiac muscle development, but are crucial for maintaining sarcomere integrity.
The use of oral ranolazine to convert new or paroxysmal atrial fibrillation: a review of experience with implications for possible "pill in the pocket" approach to atrial fibrillation. (2009)

High dose oral ranolazine shows utility as a possible safe agent to convert new or paroxysmal AF. Lack of blinded controls and small numbers limits the power of this observation.
Which Reference View is Effective for Gait Identification Using a View Transformation Model? (2006)

Gait identification is a promising method of individual identification at a distance from a camera and identification of those who observed from various views or those who going to various directions is required in particular for actual use. In this paper, we discuss a selection of reference views for the various-view gait identification using a view transformation model (VTM). In the gait identification process, we first extract frequency-domain gait features from gait silhouette sequences, and then obtain the various-view gait features by transforming a few reference features with the VTM. We made experiments using 736 sequences from 20 subjects of 24 view directions. We evaluate the performance for each single reference and for each combination of two references. In addition, we inspect the relation between the performance and the number of references.
IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions (1992)

The IncN plasmid pKM101 (a derivative of R46), like the IncI1 plasmid ColIb-P9, carries a gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function. ardA was located about 4 kb from the origin of transfer, in the region transferred early during bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that these proteins have about 60% identity. Like ColIb Ard, pKM101 ArdA specifically inhibits both the restriction and modification activities of five type I systems of E. coli tested and does not influence type III (EcoP1) restriction or the 5-methylcytosine-specific restriction systems McrA and McrB. However, in contrast to ColIb Ard, pKM101 ArdA is effective against the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR and ardK, which seem to control ardA activity and ardA-mediated lethality, respectively. Our findings suggest that ardR may serve as a genetic switch that determines whether the ardA-encoded antirestriction function is induced during mating.
Continuous and Embedded Learning for Multi-Agent Systems (2006)

This paper describes multi-agent strategies for applying continuous and embedded learning (CEL). In the CEL architecture, an agent maintains a simulator based on its current knowledge of the world and applies a learning algorithm that obtains its performance measure using this simulator. The simulator is updated to reflect changes in the environment or robot state that can be detected by a monitor, such as sensor failures. In this paper, we adapt this architecture to a multi-agent setting in which the monitor is communicated among the team members effectively creating a distributed monitor. The parameters of the current control algorithm (in our case rulebases learned by genetic algorithms) used by all of the agents are added to the monitor as well, allowing for cooperative learning. We show that communication of agent status (e.g. failures) among the team members allows the agents to dynamically adapt to team properties, in this case team size. Furthermore, we show that an agent is able to switch between specializing within a section of the domain when there are many team members and generalizing to other parts of the domain when the rest of the team members are disabled. Finally, we also discuss future potential of this method, most notably in the creation of a distributed case based reasoning system in which the cases are actual genetic algorithm population members that can be swapped among team members
Accessibility and Lateral Order Distribution of the Cellulose in the Developing Cotton Fiber1 (1965)

Cotton fibers from bolls harvested at 5-day intervals beginning at 20 days after flowering and ending at 50 days ( when the bolls had opened on the plant) 'were preserved in three ways for study in the never-dned state. Preservation was accom plished in 70% aqueous ethanol, 50% aqueous dioxane, and by freezing. Measurements of iodine sorption, red-green ("differential") dye uptake, and liquid-phase deuteration rehydrogenation gave different kinds of estimates of accessibility. These data were interpreted as indicating a relatively open structure during the 20- to 30-day period of growth, and a consolidation of the cellulosic component of the cell wall during the subsequent period of wall-thickening (35 to 45 days after flowering). There was only a small change in magnitude of these data upon boll opening. The leveling-off D.P. was nearly constant from the 30th to the 45th day, but showed a slight decrease after boll opening. Lateral order distribution was assessed by treatment with sodium hydroxide solu tions of increasing concentrations, followed by moisture sorption measurements and x-ray evaluation of extent of lattice transformation. The data indicated perhaps a slight increase in lateral order from 20 to 30 days after flowering, then a leveling-off from 30 to 45 days and a small increase upon boll opening at 50 days. These data are interpreted as indicating that the high crystallinity of the mature cotton fiber does not suddenly appear when the fiber first dries as the boll opens, but begins to develop concurrently with the deposition of cellulose during the period of wall thickening, and reaches the final high value by crystallization of an additional small fraction of cellulose upon initial drying.
Asymmetric Cell Divisions of Human Hematopoietic Stem and Progenitor Cells Meet Endosomes (2007)

Hematopoietic stem cells (HSC) are undifferentiated cells, which self-renew over a long period of time and give rise to committed hematopoietic progenitor cells (HPC) containing the capability to replenish the whole blood system. Since both uncontrolled expansion as well as loss of HSC would be fatal, the decision of self-renewal versus differentiation needs to be tightly controlled. There is good evidence that both HSC niches as well as asymmetric cell divisions are involved in controlling whether HSC self-renew or become committed to differentiate. In this context, we recently identified four proteins which frequently segregate asymmetrically in dividing HSC/HPC. Remarkably, three of these proteins, the tetraspanins CD53 and CD63, and the transferrin receptor are endosome-associated proteins. Here, we highlight these observations in conjunction with recent findings in model organisms which show that components of the endosomal machinery are involved in cell-fate specification processes.
Malware behavior image for malware variant identification (2014)

Several methods have been devised by researchers to facilitate malware analysis and one of them is through malware visualization. Malware visualization is a field that focuses on representing malware features in a form of visual cues that could be used to convey more information about a particular malware. There has been works in malware visualization but unfortunately, there seems to be a lack of focus in visualizing malware behavior. In this paper, we highlight our findings in visualizing malware behavior and its potential benefit for malware classification. Our research shows that malware behavior visualization can be used as a way to identify malware variants with high accuracy.
Reciprocity principles for magnetoresistive heads (1993)

A generalized reciprocity principle for magnetoresistive (MR) heads is derived. The results apply primarily to the linear (small signal) reproduce performance of any MR head type (shielded or unshielded, single or multiple active MR elements) of arbitrary three-dimensional geometry. Reciprocity principles provide a powerful technique for calculating the intrinsic sensitivity function that is characteristic of a given MR reproduce head, and which in principle contains all information regarding the linearized reproduce response of the MR head with respect to any record medium of arbitrary recorded magnetization. The computational work required to evaluate the sensitivity function via reciprocity is a small fraction of that which would be required by direct means.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>