gebhart/patrepeval huggingface dataset:
Synthesis, Structure, and Carbon Dioxide Capture Properties of Zeolitic Imidazolate Frameworks (2009)

Zeolites are one of humanity's most important synthetic products. These aluminosilicate-based materials represent a large segment of the global economy. Indeed, the value of zeolites used in petroleum refining as catalysts and in detergents as water softeners is estimated at $350 billion per year. A major current goal in zeolite chemistry is to create a structure in which metal ions and functionalizable organic units make up an integral part of the framework. Such a structure, by virtue of the flexibility with which metal ions and organic moieties can be varied, is viewed as a key to further improving zeolite properties and accessing new applications. Recently, it was recognized that the Si-O-Si preferred angle in zeolites (145 degrees ) is coincident with that of the bridging angle in the M-Im-M fragment (where M is Zn or Co and Im is imidazolate), and therefore it should be possible to make new zeolitic imidazolate frameworks (ZIFs) with topologies based on those of tetrahedral zeolites. This idea was successful and proved to be quite fruitful; within the last 5 years over 90 new ZIF structures have been reported. The recent application of high-throughput synthesis and characterization of ZIFs has expanded this structure space significantly: it is now possible to make ZIFs with topologies previously unknown in zeolites, in addition to mimicking known structures. In this Account, we describe the general preparation of crystalline ZIFs, discussing the methods that have been developed to create and analyze the variety of materials afforded. We include a comprehensive list of all known ZIFs, including structure, topology, and pore metrics. We also examine how complexity might be introduced into new structures, highlighting how link-link interactions might be exploited to effect particular cage sizes, create polarity variations between pores, or adjust framework robustness, for example. The chemical and thermal stability of ZIFs permit many applications, such as the capture of CO(2) and its selective separation from industrially relevant gas mixtures. Currently, ZIFs are the best porous materials for the selective capture of CO(2); furthermore, they show exceptionally high capacity for CO(2) among adsorbents operating by physisorption. The stability of ZIFs has also enabled organic transformations to be carried out on the crystals, yielding covalently functionalized isoreticular structures wherein the topology, crystallinity, and porosity of the ZIF structure are maintained throughout the reaction process. These reactions, being carried out on macroscopic crystals that behave as single molecules, have enabled the realization of the chemist's dream of using "crystals as molecules", opening the way for the application of the extensive library of organic reactions to the functionalization of useful extended porous structures.
Prognostic markers and their clinical applicability in chronic lymphocytic leukemia: where do we stand? (2013)

Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease where the majority of patients have an indolent disease course, while others may experience a far more aggressive disease, treatment failure and poor overall survival. During the last two decades, there has been an intense search to find novel biomarkers that can predict prognosis as well as guide treatment decisions. Two of the most reliable molecular prognostic markers, both of which are offered in routine diagnostics, are the immunoglobulin heavy chain variable (IGHV) gene mutational status and fluorescence in situ hybridization (FISH) detection of prognostically relevant genomic aberrations (e.g. 11q-, 13q-, +12 and 17p-). In addition to these markers, a myriad of additional biomarkers have been postulated as potential prognosticators in CLL, on the protein (e.g. CD38, ZAP70, TCL1), the RNA (e.g. LPL, CLLU1, micro-RNAs) and the genomic (e.g. TP53, NOTCH1, SF3B1 and BIRC3 mutations) level. Efforts are now being made to test these novel markers in larger patient cohorts as well as in prospective trials, with the ultimate goal to combine the "best" markers in a "CLL prognostic index" applicable for the individual patient. Although it is clear that these studies have significantly improved our knowledge regarding both prognostication and the biology of the disease, there is still an immediate need for recognizing biomarkers that can predict therapy response, and efforts should now focus on addressing this pertinent issue. In the present article, we review the extensive literature in the field of prognostic markers in CLL, focus on the most clinically relevant markers and discuss future directions regarding biomarkers in CLL.
Cytotoxic aromatic alkaloids from the ascidian Amphicarpa meridiana and Leptoclinides sp.: meridine and 11-hydroxyascididemin (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCytotoxic aromatic alkaloids from the ascidian Amphicarpa meridiana and Leptoclinides sp.: meridine and 11-hydroxyascidideminFrancis J. Schmitz, Forecita S. DeGuzman, M. Bilayet Hossain, and Dick Van der HelmCite this: J. Org. Chem. 1991, 56, 2, 804–808Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://doi.org/10.1021/jo00002a055RIGHTS & PERMISSIONSArticle Views277Altmetric-Citations95LEARN 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 InReddit PDF (612 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Motion-compensating prediction with fractional-pel accuracy (1993)

The effect of fractional-pel accuracy on the efficiency of motion-compensating predictors is studied using various spatial prediction/interpolation filters. In model calculations, the power spectral density of the prediction error is related to the probability density function of the displacement error. Prediction can be improved both by higher accuracy of motion-compensation and by spatial Wiener filtering in the predictor. Beyond a critical accuracy, the possibility of further improving prediction by more accurate motion-compensation is small. Experiments with videophone signals and with broadcast TV signals confirm these model calculations. Sinc-interpolation, bilinear interpolation, and Wiener filtering are compared at integer-pel, 1/2-pel, 1/4-pel, and 1/8-pel accuracies. A three-state technique for reliable displacement estimation with fractional-pel accuracy is introduced. It is based on phase correlation. For motion-compensation with block size of 16 pels*16 pels, 1/4-pel accuracy appears to be sufficient for broadcast TV signals, whereas for videophone signals, 1/2-pel accuracy is desirable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ratio of CD44 Epithelial Variant to CD44 Hematopoietic Variant is a Useful Prognostic Indicator in Gastric and Colorectal Carcinoma (1998)

Our results suggest that the E/H ratio is a useful indicator of prognosis in gastric and colorectal carcinoma.
Non-invasive prenatal diagnosis using fetal DNA in maternal plasma: a preliminary study for identification of paternally-inherited alleles using single nucleotide polymorphisms (2015)

This preliminary research demonstrates that paternal allele of SNP can be used as a non-invasive prenatal diagnosis approach for at-risk couples to determine the β-thalassaemia status of the fetus.
Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum (2009)

Mass spectrometry-based strategies for the quantification of low-abundance putative protein biomarkers in human blood currently require extensive sample fractionation steps which hamper their implementation in a routine and robust way across clinical laboratories. We demonstrate that a technique using MS(3) reconstructed chromatograms on a signature of secondary ions issued from a trapped primary product ion, termed multiple reaction monitoring cubed (MRM(3)), enables targeting protein biomarkers in the low nanogram/milliliter range in nondepleted human serum. The simple two-step workflow is based on a trypsin proteolysis of whole serum (100 microL) followed by enrichment of targeted proteotypic peptides on a solid phase extraction column using mixed-cation exchange resin. MRM(3)'s fidelity of peak detection extends the dynamic range and limit of quantitation (LOQ) of protein biomarkers to the low nanogram/milliliter range, corresponding to a concentration that is 10(6)-fold lower than the concentration of the most abundant proteins in serum. The power of the MRM(3) method is illustrated by the assay of prostate specific antigen in nondepleted human sera of patients. The results correlate well with the established method for determining PSA levels in serum, i.e., enzyme-linked immunosorbent assay (ELISA) tests.
Proteomic analysis of differential protein expression in response to epidermal growth factor in neonatal porcine pancreatic cell monolayers (2005)

We have proposed that porcine neonatal pancreatic cell clusters (NPCCs) may be a useful alternative source of cells for islet transplantation, and that monolayer cultures might provide an opportunity to manipulate the cells before transplantation. In addition we previously identified 10 genes up-regulated by epidermal growth factor (EGF) in cultured porcine NPCC monolayers. We have now analyzed the intracellular signaling pathways activated by EGF and searched for proteins differentially expressed following EGF treatment of the monolayers, using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). EGF treatment resulted in phosphorylation of both Erk 1/2 and Akt, as well as increased cell proliferation. Five unknown and 13 previously identified proteins were differentially expressed in response to EGF. EGF treatment increased the expression of several structural proteins of epithelial cells, such as cytokeratin 19 and plakoglobin, whereas vimentin, the intermediate filament protein of mesenchymal cells, and non-muscle myosin alkali chain isoform 1, decreased. Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 factor, which promotes epithelial cell proliferation, and hemoglobin alpha I & II also increased, whereas cyclin A1, immunoglobulin heavy chain, apolipoprotein A1, 5,10-ethylenetetrahydrofolated reductase (5,10-MTHFR), angiotensin-converting enzyme 2 (ACE2), co-lipase II precursor, and NAD+ isocitrate dehydrogenase (NAD+ IDH) alpha chain proteins decreased. Our results show that EGF stimulates proliferation of pancreatic epithelial cells by simultaneously activating the MAPK and PI-3K pathways. HnRNP A2/B1, hemoglobin, cyclin A1, and ACE2 may play roles in the proliferation of epithelial cells in response to EGF.
The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing (1981)

We have determined the complete primary structure (8031 base pairs) of an infectious clone of cauliflower mosaic virus strain CM1841. The sequence was obtained using the strategy of cloning shotgun restriction fragments in the sequencing vector M13mp7. Comparison of the CM1841 sequence with that published for another caMV strain (Strasbourg) reveals 4.4% changes, mostly nucleotide substitutions with a few small insertions and deletions. The six open reading frames in the sequence of the Strasbourg isolate are also present in CM1841.
Long-Term Ambulatory Monitoring for Cerebral Emboli Using Transcranial Doppler Ultrasound (2003)

We have developed the first ambulatory TCD system. Good-quality recordings of > or =5 hours can be obtained. In view of the demonstrated temporal variability in embolization, this technique is likely to improve the predictive value of recording for asymptomatic embolic signals and may be particularly useful in patients in whom embolic signals are relatively infrequent, such as those with asymptomatic carotid stenosis and atrial fibrillation.
Nonbenzamidine Isoxazoline Derivatives as Factor Xa Inhibitors. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Convenient Method for Synthesis of Cyclic Peptide Libraries (2005)

Cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. Owing to the robustness of amide bond chemistry, the ability to explore extensive chemical diversity by incorporation of unnatural and natural amino acids, and the ability to explore conformational diversity, through the incorporation of various constraints, arrays of cyclic peptides can be tailored to broadly sample chemical diversity. We describe the combination of a safety catch linker with a directed-sorted procedure for the synthesis of large arrays of diverse cyclic peptides for high-throughput screening.
The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. (1997)

The splicing variant, 5T allele, in intron 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene was shown to be associated with partial penetrance of the clinical expression. This splicing variant leads to two possible transcripts: one normal and the other aberrantly spliced that lacks exon 9. The aim of this study was to analyze the molecular basis of the partial penetrance in individuals carrying the 5T allele. We analyzed the level of the correctly spliced RNA transcribed from the 5T allele in nasal and epididymal epithelium and correlated it with disease expression. Semiquantitative nondifferential reverse-transcriptase-PCR showed a considerable variability (6%-37%) in the total level of correctly spliced RNA transcribed from the 5T allele in nasal epithelium from 11 patients. A significant nonlinear correlation (r = .82, P = .002) between the level of the normal CFTR transcripts and the severity of lung disease was shown. No individuals with normal lung function and minimal or no lung disease (FEV1 >80% predicted) had <25% of normal transcripts, and individuals with <15% of normal transcripts did not have FEV1 >80%. The level of normal transcripts in epididymal epithelial cells from four infertile males with congenital bilateral absence of the vas deferens was low (6%-24%). In infertile males with normal lung function the level of correctly spliced transcripts in the nasal epithelium was higher than the level in the epididymal epithelium. These results indicate that there is variability in the efficiency of the splicing mechanism, among different individuals and between different organs of the same individual. This variability provides the molecular basis of the partial penetrance of cystic fibrosis disease in patients carrying the 5T allele.
Impact of Diabetes on Mortality After the First Myocardial Infarction (1998)

The high mortality rate of diabetic patients after their first myocardial infarction and the high proportion of out-of-hospital deaths in this group imply that vigorous primary and secondary preventive measures should become an integral part of their medical care.
A novel pathway down-modulating T cell activation involves HPK-1–dependent recruitment of 14-3-3 proteins on SLP-76 (2007)

The SH2 domain-containing leukocyte protein of 76 kD (SLP-76) is a pivotal element of the signaling machinery controlling T cell receptor (TCR)-mediated activation. Here, we identify 14-3-3epsilon and zeta proteins as SLP-76 binding partners. This interaction was induced by TCR ligation and required phosphorylation of SLP-76 at serine 376. Ribonucleic acid interference and in vitro phosphorylation experiments showed that serine 376 is the target of the hematopoietic progenitor kinase 1 (HPK-1). Interestingly, either S376A mutation or HPK-1 knockdown resulted in increased TCR-induced tyrosine phosphorylation of SLP-76 and phospholipase C-gamma1. Moreover, an SLP-76-S376A mutant induced higher interleukin 2 gene transcription than wild-type SLP-76. These data reveal a novel negative feedback loop involving HPK-1-dependent serine phosphorylation of SLP-76 and 14-3-3 protein recruitment, which tunes T cell activation.
Suramin Interacts with the Calmodulin Binding Site on the Ryanodine Receptor, RYR1 (2002)

Apocalmodulin and Ca(2+) calmodulin bind to overlapping sites on the ryanodine receptor skeletal form, RYR1, but have opposite functional effects on channel activity. Suramin, a polysulfonated napthylurea, displaces both forms of calmodulin, leading to an inhibition of activity at low Ca(2+) and an enhancement of activity at high Ca(2+). Calmodulin binding motifs on RYR1 are also able to directly interact with the carboxy-terminal tail of the transverse tubule dihydropyridine receptor (DHPR) (Sencer, S., Papineni, R. V., Halling, D. B., Pate, P., Krol, J., Zhang, J. Z., and Hamilton, S. L. (2001) J. Biol. Chem. 276, 38237-38241). Suramin binds directly to a peptide that corresponds to the calmodulin binding site of RYR1 (amino acids 3609-3643) and blocks the interaction of this peptide with both calmodulin and the carboxyl-terminal tail of the DHPR alpha(1)-subunit. Suramin, added to the internal solution of voltage-clamped skeletal myotubes, produces a concentration-dependent increase in the maximal magnitude of voltage-gated Ca(2+) transients without significantly altering L-channel Ca(2+) channel conducting activity. Together, these results suggest that an interaction between the carboxyl-terminal tail of the DHPR alpha(1)-subunit with the calmodulin binding region of RYR1 serves to limit sarcoplasmic reticulum Ca(2+) release during excitation-contraction coupling and that suramin-induced potentiation of voltage-gated Ca(2+) release involves a relief of this inhibitory interaction.
Messenger RNA expression of the cytokine gene cluster, interleukin 3 (IL-3), IL-4, IL-5, and granulocyte/macrophage colony-stimulating factor, in allergen-induced late-phase cutaneous reactions in atopic subjects. (1991)

Cryostat sections from skin biopsies from 24-h allergen-induced late-phase cutaneous reactions (LPR) in 14 human atopic subjects were hybridized with 35S-labeled RNA probes for a number of cytokines. mRNA was detected for interleukin 3 (IL-3) (8/14), IL-4 (10/14), IL-5 (11/14), and granulocyte/macrophage colony-stimulating factor (GM-CSF) (13/14). Only 5 of 14 gave hybridization signals for IL-2, and 0 of 14 for interferon gamma. Biopsies from diluent controls gave only occasional weak signals. These results suggest that cells infiltrating the site of the 24-h LPR transcribe mRNA for the IL-3, IL-4, IL-5, and GM-CSF gene cluster and support the hypothesis that atopy is associated with preferential activation of cells having a similar cytokine profile to the murine T helper type 2 subset.
Learning to Generate Questions by LearningWhat not to Generate (2019)

Automatic question generation is an important technique that can improve the training of question answering, help chatbots to start or continue a conversation with humans, and provide assessment materials for educational purposes. Existing neural question generation models are not sufficient mainly due to their inability to properly model the process of how each word in the question is selected, i.e., whether repeating the given passage or being generated from a vocabulary. In this paper, we propose our Clue Guided Copy Network for Question Generation (CGC-QG), which is a sequence-to-sequence generative model with copying mechanism, yet employing a variety of novel components and techniques to boost the performance of question generation. In CGC-QG, we design a multi-task labeling strategy to identify whether a question word should be copied from the input passage or be generated instead, guiding the model to learn the accurate boundaries between copying and generation. Furthermore, our input passage encoder takes as input, among a diverse range of other features, the prediction made by a clue word predictor, which helps identify whether each word in the input passage is a potential clue to be copied into the target question. The clue word predictor is designed based on a novel application of Graph Convolutional Networks onto a syntactic dependency tree representation of each passage, thus being able to predict clue words only based on their context in the passage and their relative positions to the answer in the tree. We jointly train the clue prediction as well as question generation with multi-task learning and a number of practical strategies to reduce the complexity. Extensive evaluations show that our model significantly improves the performance of question generation and out-performs all previous state-of-the-art neural question generation models by a substantial margin.
Quadratic electro-optic characterization of Pb(Mg 1/3 Nb 2/3 )O 3 -PbTiO 3 transparent ceramics (2011)

The basic quadratic electro-optic (EO) characterization of Pb(Mg 1/3 Nb 2/3 )O 3 -PbTiO 3 (PMN-PT) transparent ceramics is measured. The EO response is relatively flat, which is a merit for optical communication. Piezoelectric resonance was found in this quadratic EO ceramic materials and it give rise to a deflection of half-wave voltage versus frequency of operation.
Data warehousing within intranet: prototype of a web-based executive information system (2002)

A Data Warehouse (DWH) contains a large amount of aggregated data, collected from the various operational, enterprise-wide data sources. The DWH will be logical modeled as a virtual n-dimensional data-cube. Analyses against this n-dim data-cube allow the decision makers (e.g. executives, middle management, controllers, etc.) to view their enterprise in various different ways. This paper describes our ongoing "WWW-EIS-DWH" research project of the development of a simple to use Executive Information System (EIS), which is complete embedded in the Web, res. an enterprise-wide network (Intranet), and based on a multidimensional modeled Data Warehouse. To accomplish our goals we implemented a generic R-OLAP (relational Online Analytical Processing) engine to extract the raw data from the given multidimensional DWH and create the virtual multidimensional OLAP data cubes. The "Information Server" (IS) is responsible for the visualization of the retrieved OLAP data cubes in an easy understandable manner. Our user interface uses commonly used Web technology like Java, JavaScript, HTML 3.2.
Compact design waveguide grating routers (1996)

A novel generic design for waveguide grating routers is demonstrated in the InP/InGaAsP material system that reduces the chip size by 50% while still maintaining relaxed processing tolerances. Experimental results confirm no degradation in device performance for the compact design when compared to conventional devices.