gebhart/patrepeval huggingface dataset:
Augmenting Visualizations with Interactive Data Facts to Facilitate Interpretation and Communication (2018)

Recently, an increasing number of visualization systems have begun to incorporate natural language generation (NLG) capabilities into their interfaces. NLG-based visualization systems typically leverage a suite of statistical functions to automatically extract key facts about the underlying data and surface them as natural language sentences alongside visualizations. With current systems, users are typically required to read the system-generated sentences and mentally map them back to the accompanying visualization. However, depending on the features of the visualization (e.g., visualization type, data density) and the complexity of the data fact, mentally mapping facts to visualizations can be a challenging task. Furthermore, more than one visualization could be used to illustrate a single data fact. Unfortunately, current tools provide little or no support for users to explore such alternatives. In this paper, we explore how system-generated data facts can be treated as interactive widgets to help users interpret visualizations and communicate their findings. We present Voder, a system that lets users interact with automatically-generated data facts to explore both alternative visualizations to convey a data fact as well as a set of embellishments to highlight a fact within a visualization. Leveraging data facts as interactive widgets, Voder also facilitates data fact-based visualization search. To assess Voder's design and features, we conducted a preliminary user study with 12 participants having varying levels of experience with visualization tools. Participant feedback suggested that interactive data facts aided them in interpreting visualizations. Participants also stated that the suggestions surfaced through the facts helped them explore alternative visualizations and embellishments to communicate individual data facts.
XForms 1.0 (2003)

XForms is an XML application that represents the next generation of forms for the Web. By splitting traditional XHTML forms into three parts—XForms model, instance data, and user interface—it separates presentation from content, allows reuse, gives strong typing—reducing the number of round-trips to the server, as well as offering device independence and a reduced need for scripting.

XForms is not a free-standing document type, but is intended to be integrated into other markup languages, such as XHTML or SVG.
Multistep tumor targeting in nude mice using bispecific antibodies and a gallium chelate suitable for immunoscintigraphy with positron emission tomography. (1995)

To improve tumor:tissue ratios in immunoscintigraphy, a three-step targeting method has been developed. The reagents used were (a) a radioactive, low molecular weight chelate prepared from ionic gallium and a phenolic polyaminocarboxylic acid, which can be labeled either with the single-photon emitter 67Ga or with the short-lived positron emitter 68Ga (t1/2 = 68 min); (b) a bispecific monoclonal antibody (bs-mAb) synthesized from the F(ab)2 fragment of the 1.1ASML antibody specific for the glycoprotein CD44v associated with a rat pancreas carcinoma cell line and the F(ab') fragment of an antibody specific for the gallium chelate; and (c) the nonradioactive gallium chelate covalently coupled to transferrin, which served as a high molecular weight blocker to prevent binding of the radioactive gallium chelate to bs-mAbs in the circulation. Targeting experiments in tumor-bearing nude mice with different doses of bs-mAbs, blocker, and 67Ga chelate were adjusted to maximize tumor to tissue contrasts and tumor uptake. Compared with the biodistribution of the 131I-labeled, native 1.1ASML antibody 24 h postinjection, a schedule using 100 pmol bs-mab 24 h later 100 pmol blocker, 15 min later 16 pmol 67Ga chelate, 1 h later examination, increased tumor:blood and tumor: liver ratios by a factor of 5 while keeping the localization of radioactivity in the tumor constant (10.1% injected dose/g). High-contrast images using either 67Ga or 68Ga were obtained within 1 h. The targeting method described enables the use of the short-lived positron emitter 68Ga and thus allows the combination of an improved immunoscintigraphy and positron emission tomography.
Computer Modeling of Protein Folding: Conformational and Energetic Analysis of Reduced and Detailed Protein Models (1995)

Recently we developed methods to generate low-resolution protein tertiary structures using a reduced model of the protein where secondary structure is specified and a simple potential based on a statistical analysis of the Protein Data Bank is employed. Here we present the results of an extensive analysis of a large number of detailed, all-atom structures generated from these reduced model structures. Following side-chain addition, minimization and simulated annealing simulations are carried out with a molecular mechanics potential including an approximate continuum solvent treatment. By combining reduced model simulations with molecular modeling calculations we generate energetically competitive, plausible misfolded structures which provide a more significant test of the potential function than current misfolded models based on superimposing the native sequence on the folded structures of completely different proteins. The various contributions to the total energy and their interdependence are analyzed in detail for many conformations of three proteins (myoglobin, the C-terminal fragment of the L7/L12 ribosomal protein, and the N-terminal domain of phage 434 repressor). Our analysis indicates that the all-atom potential performs reasonably well in distinguishing the native structure. It also reveals inadequacies in the reduced model potential, which suggests how this potential can be improved to yield greater accuracy. Preliminary results with an improved potential are presented.
Lineage-specific Requirement for Signal Transducer and Activator of  Transcription (Stat)4 in Interferon γ Production from CD4+ Versus CD8+ T Cells (1999)

CD4(+) and CD8(+) T cells exhibit important differences in their major effector functions. CD8(+) T cells provide protection against pathogens through cytolytic activity, whereas CD4(+) T cells exert important regulatory activity through production of cytokines. However, both lineages can produce interferon (IFN)-gamma, which can contribute to protective immunity. Here we show that CD4(+) and CD8(+) T cells differ in their regulation of IFN-gamma production. Both lineages require signal transducer and activator of transcription (Stat)4 activation for IFN-gamma induced by interleukin (IL)-12/IL-18 signaling, but only CD4(+) T cells require Stat4 for IFN-gamma induction via the TCR pathway. In response to antigen, CD8(+) T cells can produce IFN-gamma independently of IL-12, whereas CD4(+) T cells require IL-12 and Stat4 activation. Thus, there is a lineage-specific requirement for Stat4 activation in antigen-induced IFN-gamma production based on differences in TCR signaling between CD4(+) and CD8(+) T cells.
Designing-in of quality through axiomatic design (1995)

Decisions made during the design stage of product and process development profoundly affect product quality and process productivity. To aid in design decision making, a theoretical framework is advanced; the axiomatic approach to design. Axiomatic design consists of: (1) domains in the design world; (2) mapping between these domains; (3) characterization of a design by a vector in each domain; (4) decomposition of the characteristic vectors into hierarchies through a process of zigzagging between the domains; and (5) the design axioms, viz, independence and information axioms. Statistical process control (SPC) and other methodologies to improve quality are valid only when they are consistent with the independence and information axioms. This paper presents several criteria that govern the design and manufacture of quality products. To be able to control the quality of products, a design must satisfy the independence axiom. Based on this axiom and some theorems, several design criteria are derived and discussed. These criteria provide the bounds for the validity of some of the SPC techniques being used. When there is more than one acceptable design of a product or process, the information axiom must be used to select the best design(s).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lymphocyte-vascular adhesion protein-2 is a novel 70-kDa molecule involved in lymphocyte adhesion to vascular endothelium. (1993)

Abstract Extravasation of leukocytes from the blood is essential for normal lymphocyte recirculation as well as in mounting an adequate inflammatory response in different tissues. Leukocyte migration from the blood is controlled by sophisticated interactions between surface receptors on leukocytes and their corresponding endothelial cell ligands. Here we describe a novel adhesion molecule, lymphocyte-vascular adhesion protein-2 (L-VAP-2), recognized by 4G4 mAb that was produced by immunizing mice with an enriched endothelial cell preparation isolated from inflamed human synovium. mAb 4G4 stains a subpopulation of venules in lymphoid and nonlymphoid tissues as well as a few high endothelial venules in lymphoid tissues. L-VAP-2 is constitutively expressed on human umbilical vein endothelial cells, and its expression cannot be up-regulated by cytokines and mitogens such as TNF-alpha, IL-1, and LPS. The Ag is expressed on approximately 20% of PBL, whereas granulocytes and monocytes are negative. On lymphocytes, L-VAP-2 is preferentially expressed on B cells and CD8+ T cells. The molecular mass of L-VAP-2 is approximately 70 kDa as determined from immunoprecipitated, 125I-labeled endothelial cell lysates. The involvement of L-VAP-2 in lymphocyte binding to endothelium was tested in vitro using human umbilical vein endothelial cells. Both the intact antibody and F(ab')2 fragments of it consistently inhibited lymphocyte binding to human umbilical vein endothelial cells by approximately 25%. On the basis of the molecular mass estimation and the staining of tissue sections, leukocyte populations, and ICAM-1 and ICAM-2 transfectants, L-VAP-2 appears to be a novel Ag involved in the lymphocyte-endothelial cell interaction.
Less is more, regularly: metronomic dosing of cytotoxic drugs can target tumor angiogenesis in mice (2000)

Chemotherapeutic drugs, long the mainstay of cancer treatment, cause DNA damage and disrupt DNA replication in proliferating cells. Drug regimens have been designed to kill as many tumor cells as possible by treating with “maximum tolerated doses” (MTDs) of these cytotoxic agents. Side effects such as neurotoxicity and damage to proliferating cells in healthy tissues pose serious constraints on the use of chemotherapy. In an effort to balance toxicity with efficacy, a conventional dosing schedule calls for episodic application of a cytotoxic drug at or near the MTD, followed by periods of rest to allow normal tissues to recover. Many such chemotherapy regimens are initially efficacious, resulting in tumor regression or stabilization and prolonged survival. In rare cases, cures are achieved. In general, however, responses are short-lived, with relapses often marked by aggressive cancers that are resistant to the cytotoxic drug. Furthermore, the standard MTD regimen as a rule seriously impairs quality of life.

The harsh side effects and the ultimate failures of most chemotherapies have fueled broad investigation of alternatives, including drugs that target not the transformed tumor cells themselves, but rather a genetically stable constituent cell type of tumors, the endothelial cells that form blood vessels. Angiogenesis, the process by which new blood vessels are formed, is a hallmark capability of cancer (1); a compelling body of evidence argues that tumor growth depends on the vasculature, and, in particular, on continuing angiogenesis (2, 3). More than two dozen new drugs that are in or soon to enter clinical trials appear to interfere with tumor angiogenesis (3, 4); there is considerable anticipation about their benefits in treating cancer. Now, two studies suggest a potentially complementary strategy of rescheduling the administration of classical cytotoxic drugs in order to target tumor endothelial cells.

It is well established that tumor-associated endothelial cells proliferate during chronic angiogenesis in tumors, albeit at lower frequencies than the tumor cells themselves. Apparently because of their lower rate of cell division, replication of these endothelial cells is only weakly disrupted by the episodic regimens of standard chemotherapeutic protocols. In these two new studies, however, cytotoxic drugs were administered routinely, to target the slowly proliferating tumor endothelial cells and abrogate their apparent capability to repair and recover during the usual rest periods. Both groups worked with mice bearing subcutaneous tumors, and each presents data suggesting that “metronomic” dosing regimens—either continuous infusion or frequent administration without extended rest periods—could have real value in the clinic. Both also demonstrated combinatorial effects of such altered cytotoxic drug regimens with newer, more specific angiogenesis inhibitors.
Multiplex PCR Assays for Simultaneous Detection of Six Major Serotypes and Two Virulence-Associated Phenotypes ofStreptococcus suisin Tonsillar Specimens from Pigs (2002)

Multiplex PCR assays for the detection and identification of various Streptococcus suis strains in tonsillar specimens from pigs were developed and evaluated. In two separate reactions, five distinct DNA targets were amplified. Three targets, based on the S. suis capsular polysaccharide (cps) genes specific for serotypes 1 (and 14), 7, and 9, were amplified in multiplex PCR I. Two other targets, based on the serotype 2- (and 1/2-) specific cps gene and the epf gene, encoding the EF proteins of virulent serotype 2 and highly virulent serotype 1 strains, were amplified in multiplex PCR II. To identify false-negative results, firefly luciferase (luc) DNA and primers based on the luc gene were included in the assay. The multiplex PCR assays were evaluated with tonsillar specimens from pigs infected with S. suis strains. The results obtained with the PCR assays were compared with the results obtained with a bacteriological examination. Most (94%) of the results obtained with multiplex PCR assays were confirmed by the bacteriological examination. The PCR method seems to be more sensitive compared to the bacteriological method, since the remaining 6% of the samples were positive by PCR and negative by bacteriological examination. These results indicate that the PCR method is highly specific for the detection of S. suis strains most frequently involved in clinical disease in infected pig herds. The serotypes found by PCR in tonsillar specimens from diseased pigs were compared with the serotypes of the strains isolated from the affected tissues of the same pigs. The results showed that there is significant association between carriership and clinical illness for S. suis serotype 9 and EF-positive serotype 2 strains and not for serotype 7 and EF-negative serotype 2 (or 1/2) strains.
Blockchain Based Decentralized Management of Demand Response Programs in Smart Energy Grids (2018)

In this paper, we investigate the use of decentralized blockchain mechanisms for delivering transparent, secure, reliable, and timely energy flexibility, under the form of adaptation of energy demand profiles of Distributed Energy Prosumers, to all the stakeholders involved in the flexibility markets (Distribution System Operators primarily, retailers, aggregators, etc.). In our approach, a blockchain based distributed ledger stores in a tamper proof manner the energy prosumption information collected from Internet of Things smart metering devices, while self-enforcing smart contracts programmatically define the expected energy flexibility at the level of each prosumer, the associated rewards or penalties, and the rules for balancing the energy demand with the energy production at grid level. Consensus based validation will be used for demand response programs validation and to activate the appropriate financial settlement for the flexibility providers. The approach was validated using a prototype implemented in an Ethereum platform using energy consumption and production traces of several buildings from literature data sets. The results show that our blockchain based distributed demand side management can be used for matching energy demand and production at smart grid level, the demand response signal being followed with high accuracy, while the amount of energy flexibility needed for convergence is reduced.
Tracking Musical Beats in Real Time. (1990)

: Identifying the temporal location of downbeats is a fundamental musical skill. Observing that previous attempts to automate this process are constrained to hold a single current notion of beat timing and placement, we find that they will fail to predict beats and not recover beyond the point at which the first mistake is made. We propose a new model that uses beam search to consider multiple interpretations of the performance. At any time, predictions of beat timing and placement are made according to the most credible of many interpretations under consideration. Introduction. Identifying the temporal location of downbeats is a fundamental musical skill. Even musically untrained humans can tap their foot with the beat when they hear a musical performance. Humans generally perform this task with ease and precision even in the face of unusual rhythms, musical expressiveness, and imprecise performances. A fully general, automatic beat tracker would be of great value in many task...
Conditional Activation of Akt in Adult Skeletal Muscle Induces Rapid Hypertrophy (2004)

Skeletal muscle atrophy is a severe morbidity caused by a variety of conditions, including cachexia, cancer, AIDS, prolonged bedrest, and diabetes. One strategy in the treatment of atrophy is to induce the pathways normally leading to skeletal muscle hypertrophy. The pathways that are sufficient to induce hypertrophy in skeletal muscle have been the subject of some controversy. We describe here the use of a novel method to produce a transgenic mouse in which a constitutively active form of Akt can be inducibly expressed in adult skeletal muscle and thereby demonstrate that acute activation of Akt is sufficient to induce rapid and significant skeletal muscle hypertrophy in vivo, accompanied by activation of the downstream Akt/p70S6 kinase protein synthesis pathway. Upon induction of Akt in skeletal muscle, there was also a significant decrease in adipose tissue. These findings suggest that pharmacologic approaches directed toward activating Akt will be useful in inducing skeletal muscle hypertrophy and that an increase in lean muscle mass is sufficient to decrease fat storage.
Distinct spatial and temporal expression patterns of two type I receptors for bone morphogenetic proteins during mouse embryogenesis (1995)

Bone morphogenetic proteins (BMPs) are multifunctional proteins structurally related to transforming growth factor-beta (TGF beta) and activin that can induce cartilage and bone growth in vivo. Members of the TGF beta superfamily exert their biological effects via heteromeric serine/threonine kinase complexes of type I and type II receptors. We previously obtained six different type I receptors, termed activin receptor-like kinase-1 (ALK-1) to -6. ALK-5 is a TGF beta type I receptor, ALK-2 and ALK-4 are activin type I receptors, and ALK-3 and ALK-6 are type I receptors for osteogenic protein-1 (OP-1)/bone morphogenetic protein-7 (BMP-7) and BMP-4. Here we report the complementary DNA cloning of the mouse homolog of ALK-3, which is highly conserved between mouse and man. ALK-3 messenger RNA (mRNA) is ubiquitously expressed in various adult mouse tissues, whereas ALK-6 mRNA is only found in brain and lung. The distribution of ALK-3 and ALK-6 mRNA in the postimplantation mouse embryo [6.5-15.5 days postcoitum (pc)] was studied by in situ hybridization. ALK-3 was nearly ubiquitously expressed throughout these stages of development, but was notably absent in the liver. In contrast, ALK-6 showed a more restricted expression pattern. ALK-6 mRNA was absent in early postimplantation embryos, was detected first in 9.5 days pc embryos, and persisted until 15.5 days pc. In midgestation embryos, ALK-6 transcripts were detected in mesenchymal precartilage condensations, premuscle masses, blood vessels, central nervous system, parts of the developing ear and eye, and epithelium. The expression in sites of developing cartilage and bone supports the idea that ALK-3 and -6 are receptors for BMPs in vivo. In addition, the expression of these genes in many soft tissues suggests broader functions for BMPs in embryogenesis.
Comparative Topography of the Immunoreactive Alpha-Melanocyte-Stimulating Hormone Neuronal Systems in the Brains of Horses and Rats (1988)

The present study describes and compares the topography of alpha-melanocyte-stimulating hormone (alpha-MSH)-immunoreactive neurons in the forebrain of rats and horses. Two groups of immunoreactive cells were present in both species. These groups were distinguished by their cross-immunoreactivity and topography. The topography of cell bodies with cross-immunoreactivity for peptides derived from pro-opiomelanocortin (POMC) including adrenocorticotropin, 16K, alpha-MSH and beta-endorphin was similar in both species. However, the topography of perikarya which stained only for alpha-MSH, and not for other POMC-derived neuropeptides, was subject to pronounced species differences. In rats, perikarya which stained only for alpha-MSH (alpha 2-system) have a specific distribution in the dorsal and lateral hypothalamic regions from the level of the midoptic chiasm to the premamillary region of the posterior hypothalamus. At anterior levels of the rat brain, the cells are bipolar and oriented horizontally. Posteriorly, all alpha 2-group perikarya are stellate in rats. In the equine species, alpha 2-group cell bodies occupy a shorter anterioposterior field extending from the posterior level of the paraventricular nucleus to the supramamillary nucleus. Stellate cells are mixed with bipolar cells at all levels of the alpha 2-field in the equine hypothalamus. Further, in contrast to the continuous cell group found in rats, the alpha 2-group divides into perifornical and periventricular subpopulations at posterior levels of the equine hypothalamus. The results from this study suggest that the topography of the arcuate opiocortin cell pool, which contains peptides derived from POMC, is similar in phylogenetically diverse mammalian species whereas the topography of the cell pool staining only for alpha-MSH is subject to species differences. In both species, the major terminus of alpha 2-neurons appears to be the cerebral cortex and hippocampus. It has been proposed that alpha-MSH is one of several neuropeptides concerned with memory and behavior. Thus, species differences in the topography of the alpha 2-pool may reflect evolutionary changes in the importance of this peptide to these physiological processes.
Galectins in hematological malignancies (2013)

Current knowledge indicates a key role for galectins in hematological neoplasms by favoring the growth and survival of tumor cells and facilitating tumor immune escape. Intervention using specific galectin inhibitors is emerging as an attractive therapeutic option to alter the course of these malignancies.