gebhart/patrepeval huggingface dataset:
Design and implementation of a movement history analysis framework for the Taxi telematics system (2008)

This paper addresses a history data analysis framework for the Taxi telematics system, which keeps accumulating a great deal of movement data or location records from tens or hundreds of taxis in Jeju city. Each record consists of GPS-generated field, telematics-generated field, and framework-generated field. Aiming at boosting up diverse analysis on these data, the designed and implemented framework organizes the record into the database, defines a finite state machine to trace the status of each taxi, and provides a graphic interface, particularly for temporal movement change and trajectory visualization. We show that the framework enables us to efficiently extract such information as dispatch time, dispatch distance, traffic pattern, and so on. A new challenging service can be designed and tested using on our system.
Efficient and versatile synthesis of star polymers in water and their use as emulsifiers (2011)

Core cross-linked star polymers of low polydispersity were efficiently prepared in high yield by RAFT-mediated emulsion and dispersion polymerizations in water at high solid content. These star polymers were demonstrated to be effective emulsifiers, and the emulsion was successfully used as template to fabricate polymer particles.
Mechanisms of adoptive immunotherapy: improved methods for in vivo tracking of tumor-infiltrating lymphocytes and lymphokine-activated killer cells. (1993)

Adoptive immunotherapy with tumor-infiltrating lymphocytes (TIL) and lymphokine-activated killer cells has been demonstrated to mediate regression of tumors in murine models and in selected patients with advanced cancer. Improved methods for monitoring immune cell traffic, particularly to sites of tumor, are needed to elucidate mechanisms of antitumor activity and optimize treatment protocols. Traditional cell tracking methods such as fluorescent protein labeling and radiolabeling using 111In, 125I, or 51Cr are limited by isotope half-life, leakage or transfer of label from immune cells, and toxicity or altered cell function caused by the labeling process. Labeling with genetic markers allows long-term cell tracking but is laborious to perform and difficult to quantitate. We have used two recently described lipophilic cell tracking compounds (PKH26 and 125I-PKH95) which stably partition into lipid regions of the cell membrane to track immune cells in vivo. Concentrations of each tracking compound which had no adverse effects were determined for a variety of murine TIL and lymphokine-activated killer cell functions. Viability was unimpaired at labeling concentrations of up to 5 microM for PKH95 and 20 microM for PKH26. TIL proliferation was unaltered by labeling with up to 5 microM PKH95, 20 microM PKH26, or a combination of 15 microM PKH26 and 5 microM PKH95. In vivo cytotoxic effector function and in vivo therapeutic efficacy of lymphokine-activated killer cells and TIL were also unimpaired by labeling with 20 microM PKH26 or 1 microM 125I-PKH95. Subsequent studies in an adoptive transfer immunotherapy model used 125I-PKH95 to track the biodistribution of TIL in tumor and in non-tumor-bearing animals and PKH26 fluorescence to monitor microdistribution within tissues and distinguish TIL from host T-cells. The results suggest that differential accumulation, selective retention, or proliferation at the tumor site cannot account for the observed pattern of therapeutic efficacy. We hypothesize that a minimum number of TIL must reach the tumor site in order to achieve a demonstrable therapeutic effect.
A Feature-Based Solution to the Persistent Naming Problem (2005)

Computer-Aided Design and Applications is an international journal on the applications of CAD and CAM. It publishes papers in the general domain of CAD plus in emerging fields like bio-CAD, nano-CAD, soft-CAD, garment-CAD, PLM, PDM, CAD data mining, CAD and the internet, CAD education, genetic algorithms and CAD engines. The journal is aimed at all developers and users of CAD technology to ptovide CAD solutions for various stages of design and manufacturing. The journal publishes all about Computer-Aided Design and Computer-Aided technologies.
Characterization of Mammalian Selenoproteomes (2003)

In the genetic code, UGA serves as a stop signal and a selenocysteine codon, but no computational methods for identifying its coding function are available. Consequently, most selenoprotein genes are misannotated. We identified selenoprotein genes in sequenced mammalian genomes by methods that rely on identification of selenocysteine insertion RNA structures, the coding potential of UGA codons, and the presence of cysteine-containing homologs. The human selenoproteome consists of 25 selenoproteins.
Attention and mismatch negativity (1993)

The mismatch negativity (MMN) component of the auditory event-related potential (ERP) is elicited by infrequent, physically deviant stimuli in a sequence of frequent homogeneous stimuli (standards). It has been suggested that the MMN is generated by an automatic (attention-independent) neural mismatch process with a memory trace that encodes the physical features of the standard stimulus. The proposed MMN independence of attention was addressed in the present study. Standard stimuli and two types of deviant stimuli, differing from standards either in frequency or intensity, were dichotically presented in random order and at a rapid rate. The subject attended either to left- or right-ear stimuli, counting the number of a designated type of deviants in that ear. In the present conditions of very strongly focused attention, the MMN was elicited even by frequency change in the ignored input stream, and its amplitude was very similar to that of the MMN elicited by equivalent deviant stimuli (targets) in the attended input stream. In contrast, the MMN to intensity deviation was clearly attenuated in the absence of attention. This effect is, however, probably due to the attention effect on the MMN generator itself rather than the antecedent sensory-analysis and -storing functions.
Cytoplasmic Domains of the Leukemia Inhibitory Factor Receptor Required for STAT3 Activation, Differentiation, and Growth Arrest of Myeloid Leukemic Cells (1999)

Leukemia inhibitory factor (LIF) induces growth arrest and macrophage differentiation of mouse myeloid leukemic cells through the functional LIF receptor (LIFR), which comprises a heterodimeric complex of the LIFR subunit and gp130. To identify the regions within the cytoplasmic domain of LIFR that generate the signals for growth arrest, macrophage differentiation, and STAT3 activation independently of gp130, we constructed chimeric receptors by linking the transmembrane and intracellular regions of mouse LIFR to the extracellular domains of the human granulocyte macrophage colony-stimulating factor receptor (hGM-CSFR) alpha and betac chains. Using the full-length cytoplasmic domain and mutants with progressive C-terminal truncations or point mutations, we show that the two membrane-distal tyrosines with the YXXQ motif of LIFR are critical not only for STAT3 activation, but also for growth arrest and differentiation of WEHI-3B D+ cells. A truncated STAT3, which acts in a dominant negative manner was introduced into WEHI-3B D+ cells expressing GM-CSFRalpha-LIFR and GM-CSFRbetac-LIFR. These cells were not induced to differentiate by hGM-CSF. The results indicate that STAT3 plays essential roles in the signals for growth arrest and differentiation mediated through LIFR.
High‐throughput measurement, correlation analysis, and machine‐learning predictions for pH and thermal stabilities of Pfizer‐generated antibodies (2011)

Generating stable antibodies is an important goal in the development of antibody-based drugs. Often, thermal stability is assumed predictive of overall stability. To test this, we used different internally created antibodies and first studied changes in antibody structure as a function of pH, using the dye ANS. Comparison of the pH(50) values, the midpoint of the transition from the high-pH to the low-pH conformation, allowed us for the first time to rank antibodies based on their pH stability. Next, thermal stability was probed by heating the protein in the presence of the dye Sypro Orange. A new data analysis method allowed extraction of all three antibody unfolding transitions and showed close correspondence to values obtained by differential scanning calorimetry. T(1%) , the temperature at which 1% of the protein is unfolded, was also determined. Importantly, no correlations could be found between thermal stability and pH(50) , suggesting that to accurately quantify antibody stability, different measures of protein stability are necessary. The experimental data were further analyzed using a machine-learning approach with a trained model that allowed the prediction of biophysical stability using primary sequence alone. The pH stability predictions proved most successful and were accurate to within pH ±0.2.
Lactate Transport through the Blood-Retinal and the Blood-Brain Barrier in Rats (1985)

The retinal and brain uptake index method was utilized in a study on rats to evaluate the existence of transport systems for lactate in the blood-retinal and the blood-brain barrier, respectively. For both retina and brain a saturable, pH-dependent uptake of L-lactate was observed. The uptake could also be inhibited by pyruvate and 3-hydroxybutyrate. It is concluded that lactate is transported through the blood-retinal and the blood-brain barriers by similar carrier-mediated transport systems with affinity also to other monocarboxylic acids, such as pyruvate, and to the ketone body 3-hydroxybutyrate. The pH-dependence of the lactate transport suggests that co-transport of H+ ions or counter-transport of OH- ions takes place.
Photophysics of preassociated pyrenes in aqueous polymer solutions and in other organized media (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotophysics of preassociated pyrenes in aqueous polymer solutions and in other organized mediaFrancoise M. WinnikCite this: Chem. Rev. 1993, 93, 2, 587–614Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/cr00018a001https://doi.org/10.1021/cr00018a001research-articleACS PublicationsRequest reuse permissionsArticle Views7416Altmetric-Citations1619LEARN 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
Prognostic Markers in Diarrhoea-Associated Haemolytic-Uraemic Syndrome: Initial Neutrophil Count, Human Neutrophil Elastase and Von Willebrand Factor Antigen (1991)

The observed increase in plasma von Willebrand factor antigen (vWF:Ag) in patients with the haemolytic-uraemic syndrome is presumed to be secondary to endothelial damage, which is a central event in these diseases. As the prognostic value of such changes has not been previously evaluated, vWF:Ag has been measured in plasma from children reported to a national survey of haemolytic-uraemic syndrome. Human neutrophil elastase was also measured, as an initial neutrophilia has been shown to have prognostic value in diarrhoea-associated haemolytic-uraemic syndrome. Despite a significant elevation of plasma vWF:Ag concentration in these patients at presentation, the values did not correlate with the period of thrombocytopenia, the need for dialysis, or outcome. However, children with a poor outcome had significantly greater plasma elastase concentrations compared to those who had a good outcome.
Tumor necrosis factor-alpha strongly potentiates interleukin-3 and granulocyte-macrophage colony-stimulating factor-induced proliferation of human CD34+ hematopoietic progenitor cells (1990)

Previous studies have shown that tumor necrosis factors (TNFs) inhibit the proliferative effects of crude or purified colony-stimulating factors (CSFs) on low density human bone marrow cell fractions. In the present study we investigated the effects of TNF alpha on the growth of highly purified CD34+ human hematopoietic progenitor cells (HPC) in response to recombinant CSFs. In short-term liquid cultures (5 to 8 days), TNF alpha strongly potentiates interleukin-3 (IL-3) and granulocyte-macrophage-CSF (GM-CSF)-induced growth of CD34+ HPC, while it has no proliferative effect per se. Within 8 days, the number of viable cells obtained in TNF alpha-supplemented cultures is threefold higher than in cultures carried out with IL-3 or GM-CSF alone. Secondary liquid cultures showed that the potentiating effect of TNF alpha on IL-3-induced proliferation of CD34+ HPC does not result from an IL-3-dependent generation of TNF alpha responsive cells. Limiting dilution analysis indicates that TNF alpha increases both the frequency of IL-3 responding cells and the average size of the IL-3-dependent clones. The potentiating effect of TNF alpha on IL-3- and GM-CSF- dependent growth of CD34+ HPC is also observed in day 7 colony assays. Under these short-term culture conditions, TNF alpha does not appear to accelerate cell maturation as a precursor morphology is retained. Finally, TNF alpha inhibits the relatively weak growth-promoting effect of granulocyte-CSF (G-CSF), which acts on a more committed subpopulation of CD34+ HPC different from that recruited by IL-3 and GM- CSF. TNF beta displays the same modulatory effects as TNF alpha. Thus, TNFs appear to enhance the early stages of myelopoiesis.
Decoration of the Aromatic Ring of Dihydrocodeinone (Hydrocodone) and 14-Hydroxydihydrocodeinone (Oxycodone) (2005)

Improved protocols for the preparation of 1-bromodihydrocodeinone (1-bromohydrocodone) and 1-bromo-14-hydroxydihydrocodeinone (1-bromooxycodone) and synthesis of the corresponding 1-chloro and 1-iodo derivatives have been achieved using the corresponding N-halosuccinimides in acidic milieu. The corresponding 1-carboethoxy derivative of 14-hydroxydihydrocodeinone (1-carboethoxyoxycodone) has been prepared by Pd-catalyzed reaction with carbon monoxide in ethanol. The ester was hydrolyzed to the corresponding zwitterionic amino acid.
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids (2009)

Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity of the conventional bases. While a large number of modified bases have been identified, many of the enzymes generating them still remain to be discovered. Recently, members of the 2-oxoglutarate- and iron(II)-dependent dioxygenase super-family, which modify diverse substrates from small molecules to biopolymers, were predicted and subsequently confirmed to catalyze oxidative modification of bases in nucleic acids. Of these, two distinct families, namely the AlkB and the kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation of bases in nucleic acids. Using sensitive computational analysis of sequences, structures and contextual information from genomic structure and protein domain architectures, we report five distinct families of 2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be involved in nucleic acid modifications. Among the DNA-modifying families, we show that the dioxygenase domains of the kinetoplastid base J-binding proteins belong to a larger family that includes the Tet proteins, prototyped by the human oncogene Tet1, and proteins from basidiomycete fungi, chlorophyte algae, heterolobosean amoeboflagellates and bacteriophages. We present evidence that some of these proteins are likely to be involved in oxidative modification of the 5-methyl group of cytosine leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs from basidiomycete fungi such as Laccaria and Coprinopsis show large lineage-specific expansions and a tight linkage with genes encoding a novel and distinct family of predicted transposases, and a member of the Maelstrom-like HMG family. We propose that these fungal members are part of a mobile transposon. To the best of our knowledge, this is the first report of a eukaryotic transposable element that encodes its own DNA-modification enzyme with a potential regulatory role. Through a wider analysis of other poorly characterized DNA-modifying enzymes we also show that the phage Mu Mom-like proteins, which catalyze the N6-carbamoylmethylation of adenines, are also linked to diverse families of bacterial transposases, suggesting that DNA modification by transposable elements might have a more general presence than previously appreciated. Among the other families of 2-oxoglutarate- and iron(II)-dependent dioxygenases identified in this study, one which is found in algae, is predicted to mainly comprise of RNA-modifying enzymes and shows a striking diversity in protein domain architectures suggesting the presence of RNA modifications with possibly unique adaptive roles. The results presented here are likely to provide the means for future investigation of unexpected epigenetic modifications, such as hydroxymethyl cytosine, that could profoundly impact our understanding of gene regulation and processes such as DNA demethylation.
Emerging drugs for eating disorder treatment (2006)

Anorexia nervosa (AN), bulimia nervosa (BN) and binge eating disorder (BED) comprise the currently recognised eating disorders. Although distinct diagnostic entities, they share certain forms of comorbid psychopathology, particularly anxiety and mood disorders. BN and BED have been studied most intensively as targets for pharmacotherapy. The list of drugs tested in eating disorders is substantial; however, the number of therapeutic classes of medications tested in these conditions is relatively modest. Antidepressant medications, including tricyclic antidepressants, selective serotonin re-uptake inhibitors, as well as some of the novel antidepressants, have shown evidence of some therapeutic value in both BN and BED. Their efficacy in AN, however, has been disappointing. The pharmacological options for AN are very limited. The number of controlled trials that have been conducted is small, and the research that has been successfully completed has generally failed to demonstrate medication efficacy. Patients with BN typically show reduced binge eating and purging frequency in medication trials, but rarely attain abstinence. In BED, patients often measure the value of their medication therapy by its ability to stimulate weight loss, which is another area on which future pharmacotherapy may improve. Novel pharmacological interventions are needed for each of these conditions. Peptide hormones are increasingly being evaluated for eating disorder treatment, including ghrelin agonists, neuropeptide Y1 and -5 antagonists, orexin receptor antagonists, corticotropin-releasing factor receptor 2 antagonists, histamine 3 antagonists, melanocortin 4 receptor antagonists, beta3-adrenoceptor agonists, 5-hydroxytryptamine-2A antagonists and growth hormone agonists. Although these compounds are in early phases of clinical testing for eating disorder treatments, data from these studies will be instructive in the quest for effective pharmacotherapy for these conditions. An overview of the current pharmacotherapy options for eating disorders is presented with a discussion of the emerging potential treatments.
Type 4 Cyclic Adenosine Monophosphate Phosphodiesterase as a Therapeutic Target in Chronic Lymphocytic Leukemia (1998)

Abstract Theophylline, a drug known to inhibit several classes of adenosine 3′5′ cyclic monophosphate (cAMP) phosphodiesterases (PDEs), induces apoptosis in chronic lymphocytic leukemia (CLL) cells. Because the PDE target for theophylline in CLL remains unknown, we examined the ability of isoform-specific PDE inhibitors to increase cAMP levels and induce apoptosis in primary CLL cells. Reverse transcriptase-polymerase chain reaction of purified CLL cDNA amplified transcripts for PDE1B, 4A and 4B. The type 4 PDE inhibitor rolipram but not the type 1 inhibitor vinpocetine increased CLL cAMP levels. Rolipram-inhibitable (type 4) but not calcium-calmodulin augmented (type 1) PDE enzyme activity was detected in CLL samples. In samples from 13 of 14 CLL patients, rolipram induced apoptosis in a dose-dependent fashion over a 48-hour period. Interleukin-2 (IL-2)–cultured whole mononuclear cells (WMC) and anti-Ig stimulated CD19+ B cells were resistant to the induction of apoptosis by rolipram while unstimulated CD19+ B cells, which had a high basal apoptotic rate, were more sensitive. Rolipram stimulated elevations in cAMP levels in all four of these cell populations, suggesting that they differed in sensitivity to cAMP-induced apoptosis. Consistent with this hypothesis, incubation with the cell permeable cAMP analog dibutyryl-cAMP induced apoptosis in CLL cells and unstimulated B cells but not in IL-2–cultured WMC or anti-Ig stimulated B cells. These data identify PDE4 as a family of enzymes whose inhibition induces apoptosis in CLL cells.
Alternatives to Bpref (2007)

Recently, a number of TREC tracks have adopted a retrieval effectiveness metric called bpref which has been designed for evaluation environments with incomplete relevance data. A graded-relevance version of this metric called rpref has also been proposed. However, we show that the application of Q-measure, normalised Discounted Cumulative Gain (nDCG) or Average Precision (AveP)to condensed lists, obtained by ?ltering out all unjudged documents from the original ranked lists, is actually a better solution to the incompleteness problem than bpref. Furthermore, we show that the use of graded relevance boosts the robustness of IR evaluation to incompleteness and therefore that Q-measure and nDCG based on condensed lists are the best choices. To this end, we use four graded-relevance test collections from NTCIR to compare ten different IR metrics in terms of system ranking stability and pairwise discriminative power.