gebhart/patrepeval huggingface dataset:
Fuzzy Cognitive Maps in Business Analysis and Performance-Driven Change (2004)

Business process reengineering (BPR) has made a significant impact on managers and academics. Despite the rhetoric surrounding BPR, articulated mechanisms, which support reasoning on the effect of the redesign activities to the performance of the business model, are still emerging. This paper describes an attempt to build and operate such a reasoning mechanism as a novel supplement to performance-driven change (PDC) exercises. This new approach proposes the utilization of the fuzzy causal characteristics of fuzzy cognitive maps (FCMs) as the underlying methodology in order to generate a hierarchical and dynamic network of interconnected performance indicators. By using FCMs, the proposed mechanism aims at simulating the operational efficiency of complex process models with imprecise relationships to quantify the impact of performance-driven reengineering activities. This research also establishes generic maps that supplement the strategic planning and business analysis phases of typical redesign projects in order to implement the integration of hierarchical FCMs into PDC activities. Finally, this paper discusses experiments with the proposed mechanism and comments on its usability.
Enzymatic Oxidative Phenolic Coupling (1997)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTEnzymatic Oxidative Phenolic CouplingZhi-wei Guo, Grzegorz M. Salamonczyk, Kang Han, Koji Machiya, and Charles J. SihView Author Information School of Pharmacy, University of Wisconsin, 425 N. Charter St., Madison, Wisconsin 53706-1515Cite this: J. Org. Chem. 1997, 62, 20, 6700–6701Publication Date (Web):October 3, 1997Publication History Received6 June 1997Published online3 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/jo970995chttps://doi.org/10.1021/jo970995crapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views834Altmetric-Citations23LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Mixtures,Monomers,Oxidative coupling,Peptides and proteins,Reaction products Get e-Alerts
On Safari in the File Format Jungle—Why Can't You Visualize My Data? (2009)

Lots of glossy images and striking movies on the one side, lots of numbers and full hard disks on the other—seems like a natural pair. So why can't visualization people "just visualize" some data?
Controlling False Discoveries During Interactive Data Exploration (2016)

Recent tools for interactive data exploration significantly increase the chance that users make false discoveries. The crux is that these tools implicitly allow the user to test a large body of different hypotheses with just a few clicks thus incurring in the issue commonly known in statistics as the multiple hypothesis testing error. In this paper, we propose solutions to integrate multiple hypothesis testing control into interactive data exploration tools. A key insight is that existing methods for controlling the false discovery rate (such as FDR) are not directly applicable for interactive data exploration. We therefore discuss a set of new control procedures that are better suited and integrated them in our system called Aware. By means of extensive experiments using both real-world and synthetic data sets we demonstrate how Aware can help experts and novice users alike to efficiently control false discoveries.
HIV-1 Vaccine-Induced C1 and V2 Env-Specific Antibodies Synergize for Increased Antiviral Activities (2014)

The RV144 ALVAC/AIDSVax HIV-1 vaccine clinical trial showed an estimated vaccine efficacy of 31.2%. Viral genetic analysis identified a vaccine-induced site of immune pressure in the HIV-1 envelope (Env) variable region 2 (V2) focused on residue 169, which is included in the epitope recognized by vaccinee-derived V2 monoclonal antibodies. The ALVAC/AIDSVax vaccine induced antibody-dependent cellular cytotoxicity (ADCC) against the Env V2 and constant 1 (C1) regions. In the presence of low IgA Env antibody levels, plasma levels of ADCC activity correlated with lower risk of infection. In this study, we demonstrate that C1 and V2 monoclonal antibodies isolated from RV144 vaccinees synergized for neutralization, infectious virus capture, and ADCC. Importantly, synergy increased the HIV-1 ADCC activity of V2 monoclonal antibody CH58 at concentrations similar to that observed in plasma of RV144 vaccinees. These findings raise the hypothesis that synergy among vaccine-induced antibodies with different epitope specificities contributes to HIV-1 antiviral antibody responses and is important to induce for reduction in the risk of HIV-1 transmission. Importance: The Thai RV144 ALVAC/AIDSVax prime-boost vaccine efficacy trial represents the only example of HIV-1 vaccine efficacy in humans to date. Studies aimed at identifying immune correlates involved in the modest vaccine-mediated protection identified HIV-1 envelope (Env) variable region 2-binding antibodies as inversely correlated with infection risk, and genetic analysis identified a site of immune pressure within the region recognized by these antibodies. Despite this evidence, the antiviral mechanisms by which variable region 2-specific antibodies may have contributed to lower rates of infection remain unclear. In this study, we demonstrate that vaccine-induced HIV-1 envelope variable region 2 and constant region 1 antibodies synergize for recognition of virus-infected cells, infectious virion capture, virus neutralization, and antibody-dependent cellular cytotoxicity. This is a major step in understanding how these types of antibodies may have cooperatively contributed to reducing infection risk and should be considered in the context of prospective vaccine design.
Transcriptional activity of domain A of the rat glucagon G3 element conferred by an islet-specific nuclear protein that also binds to similar pancreatic islet cell-specific enhancer sequences (PISCES). (1995)

A pancreatic islet cell-specific enhancer element in the rat glucagon gene, Glu-G3, contains two domains, one of which, domain A, has been shown to be necessary for Glu-G3 activity. In the present study, the functions of the isolated domain A of Glu-G3 were investigated by using transient reporter fusion gene expression and DNA binding assays. A single copy of domain A was transcriptionally inactive in glucagon-producing islet cell lines, whereas it did confer activity when combined with domain B, suggesting that Glu-G3 may be a bipartite element. Multiple copies of domain A did function independently as transcriptional enhancer in phenotypically distinct islet cell lines but not in several nonislet cell lines. Sequences (PISCES, pancreatic islet cell-specific enhancer sequences), similar to that of domain A of Glu-G3 and present in cell-specific control elements of the rat insulin I (Ins-E1) and rat somatostatin genes (SMS-UE), are shown to be required for transcriptional activity of these elements. In addition, a protein was detected in islet cell lines that bound to the PISCES motifs within Glu-G3, Ins-E1, and SMS-UE. These results support the view that cell-specific control elements of the glucagon, insulin, and somatostatin genes share a functional regulatory sequence, PISCES, and provide direct evidence for the existence of an islet-specific, PISCES-binding transcription factor or closely related proteins being involved in the coordinate expression of islet hormone genes.
A Comparison of the Proteins of Rat Skeletal Muscle and Liver Ribosomes by Two-Dimensional Polyacrylamide Gel Electrophoresis (1974)

Abstract We have determined the number of proteins in rat skeletal muscle 80 S ribosomes and ribosomal subparticles by two-dimensional polyacrylamide gel electrophoresis. The proteins were compared with those from liver ribosomes. The small subunit of muscle ribosomes contained 31 proteins: it had two proteins (Sm1 and Sm2) which were not found in liver 40 S particles; one protein (S31*) was always found in the small subunit of muscle ribosomes but was present in the 40 S subparticle of liver ribosomes only if they were prepared in buffer containing 500 mm potassium and 3 mm magnesium (it was absent if the cation concentrations during preparation were 830 and 12.5 mm, respectively); muscle small subparticles lacked S10 and S22; finally, S8 was absent if muscle subunits were prepared in buffer containing lower concentrations of potassium and magnesium (500 and 3 mm) whereas it was present if the cation concentration was higher (830 mm potassium and 12.5 mm magnesium). The large subunit of muscle ribosomes had 38 proteins: it lacked two (L1 and L41*) that always were present in liver 60 S subunits; and lacked one (L20) found only in the large subunit of liver ribosomes prepared in buffer containing 830 mm potassium and 12.5 mm magnesium; L20 is also absent from the large subunit of liver ribosomes if they are prepared in 500 mm magnesium and 3 mm potassium. We have detected two acidic proteins (L40* and L41*) in the large subunit of ribosomes that may be homologous with Escherichia coli L7 and L12. Preparations of muscle 80 S monomers contained five proteins (1, 2, 3, L1, M4) not present in either subunit; one of the five proteins (M4) was absent from liver ribosomes. We estimate muscle ribosomes have 67 to 74 different proteins; liver ribosomes have 69 to 74. Most of the apparent variance between the proteins of muscle and liver ribosomes can be accounted for either by differential partition of selected proteins to one or the other of the two subunits, or by differences in the methods required to prepare pure muscle ribosomes in high yield and those used to prepare liver ribosomes. Thus certain proteins that occur with the large subunit of liver ribosomes are found with the small subunit of muscle ribosomes or vice versa. If liver and muscle ribosomes and ribosomal subunits are prepared by the same method there are few if any differences in the proteins.
Simulation of diesel fuel injection system based on different kinds of delivery valves (2010)

In this paper, the simulation of diesel fuel injection system using different kinds of delivery valves is studied. And the performance differences of the fuel injection system under different spraying pressure are compared. The influence of three basic delivery valves, which are damping valve, constant pressure delivery valve and constant volume delivery valve, to pump pressure, nozzle pressure, injection rate and secondary injection under the different spraying pressures are researched according to analyzing the performance parameters of injection pump with them. The simulation results show that the constant pressure delivery valve has obvious advantages in the injection time stability and avoiding secondary injection compared with the other two when the spraying pressure is low. On the other hand, when the pressure is high, the damping valve and constant pressure delivery valve have advantages in above mentioned, they can keep spraying pressure higher during the whole injection process, and the fuel droplet can reach a long distance, form a better spraying cone angle.
Handling Datasets in a Multi-Relational Environment: Cluster Dispersion vs Cluster Purity (2007)

Clustering multiple-instances in a multi-relational environment requires data transformations (e.g. data aggregation) from datasets stored in multiple tables into a single table. Unfortunately, most relational databases are limited to a few basic methods of aggregation (e.g. max, min, sum, count, ave) to aggregate continuous and categorical values. Therefore, data transformation is limited only to aggregation of continuous and categorical values. In this paper, to get the best number of clusters, we propose a genetic semi-supervised clustering technique as a means of aggregating data stored in multiple tables. This algorithm is suitable for classification of datasets with a high degree of one-to-many associations, in which a single record has multiple instances that are associated with it. The clustering algorithm can be used in two ways. One is the unsupervised clustering, where the user may control the result of clustering by optimizing the value of cluster dispersion. The other is a semi-supervised clustering, where the user uses an unsupervised clustering method optimized with a genetic algorithm incorporating a measure of classification accuracy used in decision tree algorithm, the GINI index. In this paper, we examine both methods to dynamically cluster multiple instances, as a means of aggregating them, and illustrate the effectiveness of the semi-supervised genetic algorithm-based clustering technique.
X-ray diffraction studies of protein crystal disorder (1999)

Protein crystals contain many kinds of disorder, but only a small fraction of these are likely to be important in limiting the diffraction properties of interest to crystallographers. X-ray topography, high-angular-resolution reciprocal space measurements, and standard crystallographic data collection have been used to probe three factors that may produce diffraction-limiting disorder: (1) solution variations during crystal growth, (2) macromolecular impurities, and (3) post-growth crystal treatments. Variations in solution conditions that occur in widely used growth methods may lead to variations in equilibrium protein conformation and crystal packing as a crystal grows, and these may introduce appreciable disorder for sensitive proteins. Tetragonal lysozyme crystals subjected to abrupt changes in temperature, pH, or salt concentration during growth show increased disorder, consistent with this mechanism. Macromolecular impurities can have profound effects on protein crystal quality. A combination of diffraction measurements provides insight into the mechanisms by which particular impurities create disorder, and this insight leads to a simple approach for reducing this disorder. Substantial degradation of diffraction properties due to conformation and lattice constant changes can occur during post-growth crystal treatments such as heavy-atom compound and drug binding. Measurements of the time evolution of crystal disorder during controlled crystal dehydration – a simple model for such treatments – suggest that structural metastability conferred by the constraints of the crystal lattice plays an important role in determining the extent to which the diffraction properties degrade.
Safeguards in laparoscopy: education equipment care and electron control. (1978)

Laparoscopy 1 of the most frequently performed procedures in gynecology must be performed only by skilled and qualified surgeons. 3 areas especially require attention: 1) physician education 2) equipment maintenance and 3) understanding of the basics of electricity. An education program on laparoscopic procedures has been established by the American Association of Gynecologic Laparoscopists. The recommendations of manufacturers in the use of electrogenerators should be closely followed and only low voltage high frequency generators used. Bipolar laparoscopic instruments should reduce inherent dangers. However the safety and long-term efficiency of these instruments have not yet been definitely ascertained.
Isolation of the Hybrid Between Ribosomal RNA and DNA of Bacillus subtilis (1968)

The highly specific recognition of complementary sequences that is the basis of RNA-DNA hybridization would offer a way to purify a given gene, if the messenger RNA corresponding to that gene were available in purified form.
Using latent semantic analysis to identify similarities in source code to support program understanding (2002)

The paper describes the results of applying Latent Semantic Analysis (LSA), an advanced information retrieval method, to program source code and associated documentation. Latent semantic analysis is a corpus based statistical method for inducing and representing aspects of the meanings of words and passages (of natural language) reflective in their usage. This methodology is assessed for application to the domain of software components (i.e., source code and its accompanying documentation). Here LSA is used as the basis to cluster software components. This clustering is used to assist in the understanding of a nontrivial software system, namely a version of Mosaic. Applying latent semantic analysis to the domain of source code and internal documentation for the support of program understanding is a new application of this method and a departure from the normal application domain of natural language.
Is N-acetyl-d-glucosamine a rigid 4C1 chair? (2011)

Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-D-glucosamine (GlcNAc), deviates from a rigid 4 C 1 chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 s to reach a conformational equilibrium, which comprised a metastable 4 C 1 chair that underwent 4 C 1 1 C 4 transitions at a predicted forward rate of 0.8 s -1 with an average 1 C 4 -chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid 4 C 1 chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 s -1 ) and a more stable 4 C 1 conformer (0.2 kcal mol -1 ), suggesting that pivotal 3D intermediates ( particularly 2 S O , 1 S 5 and B 2,5 ) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.
Short RNA Duplexes Elicit RIG-I–Mediated Apoptosis in a Cell Type– and Length-Dependent Manner (2011)

Short double-stranded RNAs (dsRNAs) induce type I interferon (IFN)-mediated innate immune responses. In functional studies with short interfering RNAs or synthetic mimics of microRNA precursors in vitro, we found that short dsRNAs readily induced apoptosis in cells derived from human granulosa cell tumors, but not in other cell types. Apoptosis was independent of the sequence of the dsRNA, but depended on its length, and was induced by 23- and 24-nucleotide (nt) dsRNAs, but not by shorter dsRNAs (< 22 nt) or by the long dsRNA polyinosinic-polycytidylic acid. Microarray analysis revealed that apoptosis was accompanied by the increased expression of IFN-stimulated genes; however, several lines of evidence showed that IFNs did not directly induce apoptosis. Subsequent analyses revealed that the short dsRNAs increased the expression of retinoic acid-inducible gene I (RIG-I) through dsRNA-activated protein kinase (PKR). Although these dsRNAs bore 3' overhangs and nontriphosphate 5' termini, which are not thought to be RIG-I-activating structures, the dsRNAs bound to RIG-I and triggered proapoptotic signaling mostly by activating RIG-I, which was followed by activation of the mitogen-activated protein kinase p38. Thus, we suggest that ligand recognition and subsequent signaling by RNA sensors are more complicated than previously believed. In addition, short dsRNAs may serve as pharmacological agents to target specific tumors, such as granulosa cell tumors.
Fusion of the transcription factor <i>TFE3</i> gene to a novel gene, <i>PRCC</i> , in t(X;1)(p11;q21)-positive papillary renal cell carcinomas (1996)

The (X;1)(p11;q21) translocation is a recurrent chromosomal abnormality in a subset of human papillary renal cell carcinomas, and is sometimes the sole cytogenetic abnormality present. Via positional cloning, we were able to identify the genes involved. The translocation results in a fusion of the transcription factor TFE3 gene on the X chromosome to a novel gene, designated PRCC, on chromosome 1. Through this fusion, reciprocal translocation products are formed, which are both expressed in papillary renal cell carcinomas. PRCC is ubiquitously expressed in normal adult and fetal tissues and encodes a putative protein of 491 aa with a relatively high content of prolines. No relevant homologies with known sequences at either the DNA or the protein level were found.
A Novel Mechanism of Aberrant Pre-mRNA Splicing in Humans (1997)

Eukaryotic pre-mRNA splicing is regulated by consensus sequences at the intron boundaries and branch site. Recently, Sirand-Pugnet et al. reported the importance of an additional intronic sequence, an (A/U)GGG repeat in chicken beta-tropomyosin that is a binding site for a protein required for spliceosome assembly. Interestingly, we have detected mutations in IVS3 of the human growth hormone (GH) gene that affect a putative, homologous consensus sequence and which also perturb splicing. In a series of dominant-negative GH mutations that cause exon skipping, we found two mutations that do not occur within the 5' and 3' splice sites, or branch consensus sites. The first mutation is a G-->A transition of the 28th base (+28G-->A) of and the second deletes 18 bp (del+28-45) of IVS3 of the human GH gene. These mutations segregated with autosomal dominant GH deficiency in both kindreds and no other allelic GH gene changes were detected. RT-PCR amplification of transcripts from expression vectors containing the +28G-->A or del+28-45 alleles yielded products showing a >10-fold preferred use of alternative splicing, similar to findings previously reported for IVS3 donor site mutations. Both mutations are located 28 bp downstream from the 5' splice site and examination of the sequences perturbed revealed an intronic XGGG repeat similar to the repeat found to regulate mRNA splicing in chicken beta-tropomyosin. Interestingly, the XGGG repeats involved in our mutations exhibit homologous spacing to those in a so-called 'winner' RNA sequence. Binding of A1 heterogeneous nuclear ribonucleoprotein (hnRNP) by 'winner' sequences in pre-mRNA transcripts is thought to play an important role in pre-mRNA packaging and transport as well as 5' splice site selection in pre-mRNAs that contain multiple 5' splice sites. Our findings suggest that (i) XGGG repeats may regulate alternative splicing in the human GH gene and (ii) mutations of these repeats cause GH deficiency by perturbing alternative splicing. Mutations of homologous intron sequences may underlie other human diseases.