gebhart/patrepeval huggingface dataset:
Detection of Relation Assertion Errors in Knowledge Graphs (2017)

Although the link prediction problem, where missing relation assertions are predicted, has been widely researched, error detection did not receive as much attention. In this paper, we investigate the problem of error detection in relation assertions of knowledge graphs, and we propose an error detection method which relies on path and type features used by a classifier for every relation in the graph exploiting local feature selection. We perform an extensive evaluation on a variety of datasets, backed by a manual evaluation on DBpedia and NELL, and we propose and evaluate heuristics for the selection of relevant graph paths to be used as features in our method.
IGFBP7 plays a potential tumor suppressor role against colorectal carcinogenesis with its expression associated with DNA hypomethylation of exon 1 (2006)

Insulin-like growth factor binding-protein-7 (IGFBP7) was obtained from our previous colonic adenocarcinoma (CRC) and normal mucosa suppression subtraction hybridization (SSH) cDNA libraries. By RT-PCR and immunohistochemistry, we found that IGFBP7 was overexpressed in CRC tissue compared to normal tissue. However, our in vitro experiments performed in 10 CRC cell lines showed that IGFBP7 expressed only in SW480 and Caco2 cell lines, which implied an underlying reversible regulatory mechanism. Using methylation-specific PCR (MSP) and bisulfite sodium PCR (BSP), we found that its expression was associated with DNA hypomethylation of exon1. This was further supported by the in vitro study which showed restored IGFBP7 expression after demethylation agent 5-aza-2'-deoxycytidine treatment. Correlation analysis between IGFBP7 expression and prognosis indicated that overexpression of IGFBP7 in CRC tissue correlated with favourable survival. Investigation of the functional role of IGFBP7 through transfection studies showed that IGFBP7 protein could inhibit growth rate, decrease colony formation activity, and induce apoptosis in RKO and SW620 cells, suggesting it a potential tumor suppressor protein in colorectal carcinogenesis. In conclusion, our study clearly demonstrated that IGFBP7 plays a potential tumor suppressor role against colorectal carcinogenesis and its expression is associated with DNA hypomethylation of exon 1.
Transcript Heterogeneity of the p44 Multigene Family in a Human Granulocytic Ehrlichiosis Agent Transmitted by Ticks (2002)

Human granulocytic ehrlichiosis (HGE) is an emerging tick-borne zoonosis caused by a strain of Anaplasma phagocytophila called the HGE agent, an obligatory intracellular bacterium. The agent expresses immunodominant 44-kDa outer membrane proteins (P44s) encoded by a multigene family. The present study established an experimental process for transmission of the HGE agent from infected mice (a reservoir model) to nymphal Ixodes scapularis ticks (a biological vector) and subsequently to horses (a patient model) by the adult infected ticks. Overall, a total of 20 different p44 transcripts were detected in the mammals, ticks, and cell cultures. Among them, a transcript from a p44-18 gene was major at acute stage in mice and horses but minor in ticks. Both mRNA and protein produced from the p44-18 gene were detected in the HGE agent cultivated in HL-60 cells at 37 degrees C, but their expression levels decreased in the organisms cultivated at 24 degrees C, suggesting that temperature is one of the factors that influence the expression of members of the p44 multigene family. Several additional p44 transcripts that were not detected in the mammals at the acute stage of infection were detected in ticks. Phylogenetic analysis of the 20 different p44 transcripts revealed that the major transcripts found in mammals and ticks were distinct, suggesting a difference in surface properties between populations of the HGE agent in different host environments. The present study provides new information for understanding the role of the p44 multigene family in transmission of the HGE agent between mammals and ticks.
Regulation of KiSS-1 Metastasis Suppressor Gene Expression in Breast Cancer Cells by Direct Interaction of Transcription Factors Activator Protein-2α and Specificity Protein-1 (2005)

KiSS-1 has been shown to function as a tumor metastasis suppressor gene and reduce the number of metastases in different cancers. The expression of KiSS-1 or KiSS1, like other tumor suppressor, is commonly reduced or completely ablated in a variety of cancers via an unknown mechanism. Here we show that the loss of KiSS-1 expression in highly metastatic breast cancer cell lines correlates directly with the expression levels of two transcription factors, activator protein-2alpha (AP-2alpha) and specificity protein 1 (Sp1), which synergistically activate the transcriptional regulation of KiSS-1 in breast cancer cells. Although the KiSS-1 promoter contains multiple AP-2alpha binding elements, AP-2alpha-mediated regulation occurs indirectly through Sp1 sites, as determined by deletion and mutation analysis. Overexpression of AP-2alpha into highly metastatic breast cell lines did not alter KiSS-1 promoter-driven luciferase gene activity. However, co-transfection of AP-2alpha wild-type or the dominant negative form of AP-2 lacking its C-terminal DNA-binding domain, AP-2B, together with Sp1, increased KiSS-1 promoter activity dramatically, suggesting that AP-2alpha regulation of KiSS-1 transcription does not require direct binding to the KiSS-1 promoter. Furthermore, we demonstrated that AP-2alpha directly interacted with Sp1 to form transcription complexes at two tandem Sp1-binding sites of the promoter to activate KiSS-1 transcription. Together, our results indicate that AP-2alpha and Sp1 are strong transcriptional regulators of KiSS-1 and that loss or decreased expression of AP-2alpha in breast cancer may account for the loss of tumor metastasis suppressor KiSS-1 expression and thus increased cancer metastasis.
Evaluation of Docking Functions for Protein−Ligand Docking (2001)

Docking functions are believed to be the essential component of docking algorithms. Both physically and statistically based functions have been proposed, but there is no consensus about their relative performances. Here, we propose an evaluation approach based on exhaustive enumeration of all possible docking solutions obtained with a discretized description of a rigid docking process. We apply the approach to study both molecular mechanics and statistical potentials. It is found that the statistical potential evaluated is less effective than the AMBER molecular mechanics function to provide an accurate description of the docking process when the exact experimental coordinates are used. However, when coordinates of crystal structures obtained with analogous ligands are used, similar performances are obtained in both cases. Possible reasons for the successes and failures of both docking schemes have been uncovered using linear discriminant analysis, on the basis of a set of physicochemical descriptors capturing the main physical effects at play during protein-ligand docking. In both types of potentials steric effects appear critical to obtain a successful docking. Our results also indicate that neglecting desolvation effects and the explicit treatment of hydrogen bonds are the main source of the failures observed with the molecular mechanics potential. On the other hand, detailed consideration of steric interactions, with a careful treatment of dispersive forces, seems to be needed when using statistical potentials derived from a structural database. The possibility of filtering combinatorial libraries in order to maximize the probability of correct docking is discussed.
Spontaneous flux in ad-wave superconductor with time-reversal-symmetry-broken pairing state at{110}-oriented boundaries (1999)

The induction of an s-wave component in a d-wave superconductor is considered. Near the ${110}$-oriented edges of such a sample, the induced s-wave order parameter together with the d-wave component forms a complex combination ${d+e}^{i\ensuremath{\varphi}}s,$ which breaks the time-reversal symmetry (BTRS) of the pairing state. As a result, the spontaneous current is created. We numerically study the current distribution and the formation of the spontaneous flux induced by the current. We show that the spontaneous flux formed from a number of defect lines with ${110}$ orientation has a measurable strength. This result may provide an unambiguous way to check the existence of the BTRS pairing state at ${110}$-oriented boundaries.
DNA sequencing by capillary electrophoresis (1997)

Capillary electrophoresis has been under development for DNA sequencing since 1990. This development has traveled down two parallel tracks. The first track studied the details of DNA separation by gel electrophoresis. Early work stressed rapid separations at high electric fields, which reached the extreme of a 3.5 min sequencing run at 1200 V/cm. While fast separations are useful in clinical resequencing applications for mutation detection, long read-length is important in genomic sequencing. Unfortunately, sequence read-length degrades as electric field and sequencing speed increases; this tradeoff between read-length and sequencing speed appears to be a fundamental result of the physics of DNA separations in a polymer. The longest sequence sequencing read-lengths have been obtained at modest electric fields, high temperature, and with low concentration noncrosslinked polymers. In parallel with our understanding of DNA separations, the second track of DNA sequencing development considered the design of large-scale capillary instruments, wherein hundreds of DNA samples can be sequenced in parallel. Real-world application of these very high throughput capillary electrophoresis systems will require significant investment in sample preparation technology.
The MHC molecule I-E is necessary but not sufficient for the clonal deletion of V beta 11-bearing T cells. (1989)

We have generated an mAb, RR3-15, that recognizes murine TCRs containing the V beta 11 domain. Using this antibody to stain peripheral T cells, we have demonstrated that V beta 11-bearing T cells are largely absent from strains of mice that express the class II MHC molecule, I-E. Studies with F1 mice demonstrate that this effect is dominant, consistent with tolerance. The clonal deletion of V beta 11-bearing T cells appears to occur intrathymically, as immature but not mature V beta 11+ T cells are present in the thymus of I-E-bearing mice. Examination of B6 x DBA/2 recombinant inbred strains demonstrates that the expression of I-E molecules is necessary for the clonal deletion of V beta 11-bearing T cells, but that other non-MHC genes control the clonal deletion process, as well. Paradoxically, only a small fraction of V beta 11+ T cell hybridomas are I-E reactive.
Highly stable charge generation layers using caesium phosphate as n-dopants and inserting interlayers (2012)

Highly stable and efficient charge generation layers (CGLs) comprising caesium phosphate (Cs3PO4) doped 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP) as n-type organic semiconductor and molybdenum trioxide (MoO3) doped N,N′-di-(naphthalen-1-yl)-N,N′-diphenyl-benzidine (α-NPD) as p-type organic semiconductor, respectively, are presented. By inserting narrow-gap organic copper-phthalocyanine (CuPc) and wide-gap insulating aluminum oxide (Al2O3) as interlayer (IL), we show that the long-term stability of the CGL can be improved. The variation of the CuPc IL thickness yields an optimum of 8 nm as a trade-off between minimal operating voltage and maximum voltage stability of the CGL. Luminance-current density-voltage characteristics and lifetime measurements of stacked green organic light emitting diodes (OLEDs) confirm the functionality and high voltage stability of the presented CGL. The luminous efficacy of the stacked OLED compared to the non-stacked reference device is nearly unchanged. However, the lifetime of the stacked device is enhanced by a factor of 3.5. Consistent with our experimental findings, we propose a model of the energy-level diagram of a fully doped CGL with IL based on a field-assisted tunneling mechanism.
Representative metalation and reduction reactions of the superactive metal hydrides, LiH, NaH, and KH (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRepresentative metalation and reduction reactions of the superactive metal hydrides, LiH, NaH, and KHRafael Pi, Thomas Friedl, Paul v. R. Schleyer, Peter Klusener, and Lambert BrandsmaCite this: J. Org. Chem. 1987, 52, 19, 4299–4303Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://doi.org/10.1021/jo00228a027RIGHTS & PERMISSIONSArticle Views1444Altmetric-Citations61LEARN 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 (598 KB) Get e-Alerts Get e-Alerts
Accurate surface voxelization for manipulating volumetric surfaces and solids with application in simulating musculoskeletal surgery (2002)

Existing volumetric representations model a non-thickness surface using voxels, and thus cannot accurately manipulate topology changes in the interactions between surfaces and solids. The study describes a volume representation in which face flags and distance-levels on each voxel represent surface topology and geometry, and an object flag identifies solids. Also presented is a set of algorithms that voxelize solids and surfaces, check the closures of the interactions among the volumetric surfaces and solids and manipulate various operations on the solids. A surgical example, in which the procedures involved in the complex interactions between cutting surfaces and anatomic structures and various geometric and topologic manipulations on the structures, are simulated to demonstrate that these novel volume representation techniques and algorithms are feasible in manipulating the interactions between surfaces and solids in a volume.
A Sulfated Glucosylceramide from Rat Kidney (1989)

A novel sulfated glycosphingolipid containing a sulfated glucosyl residue was isolated from rat kidney and purified to homogeneity by column chromatographies with DEAE-Sephadex and silica beads. By compositional analyses, permethylation studies, one- and two-dimensional proton magnetic resonance spectroscopy, infrared spectroscopy, negative secondary ion mass spectrometry, solvolysis, and immunostaining on thin layer chromatogram, the structure of this glycolipid was proposed to be HSO3-3Glc beta 1-1Cer (where Cer is ceramide). The ceramide portion consisted of 4-D-hydroxysphinganine as the sole long chain base, and the fatty acid consisted of predominantly tetracosanoic acid, deduced from both composition analysis and negative secondary ion mass spectrometry. The yield of glucosyl sulfatide was about 5 nmol/g of tissue, being about three times as much as that of lactosylceramide sulfate.
Regulation of the heat stress response in Arabidopsis by MPK6-targeted phosphorylation of the heat stress factor HsfA2 (2013)

So far little is known on the functional role of phosphorylation in the heat stress response of plants. Here we present evidence that heat stress activates the Arabidopsis mitogen-activated protein kinase MPK6. In vitro and in vivo evidence is provided that MPK6 specifically targets the major heat stress transcription factor HsfA2. Activation of MPK6 results in complex formation with HsfA2. MPK6 phosphorylates HsfA2 on T249 and changes its intracellular localisation. Protein kinase and phosphatase inhibitor studies indicate that HsfA2 protein stability is regulated in a phosphorylation-dependent manner, but this mechanism is independent of MPK6. Overall, our data show that heat stress-induced targeting of HsfA2 by MPK6 participates in the complex regulatory mechanism how plants respond to heat stress.
Secondary mAb−vcMMAE Conjugates Are Highly Sensitive Reporters of Antibody Internalization via the Lysosome Pathway (2004)

Monoclonal antibodies (mAb) selectively recognizing tumor surface antigens are an important and evolving approach to targeted cancer therapy. One application of therapeutic mAbs is drug targeting via mAb-drug conjugate (ADC) technology. Identification of mAbs capable of internalizing following antigen binding has been accomplished by tracking decline of surface-bound mAb or by internalization of a secondary mAb linked to a toxin. These methods may not be sufficiently sensitive for screening nor wholly predictive of the mAbs' capacity for a specific drug delivery. We have developed a highly selective and sensitive method to detect mAbs for cell internalization and drug delivery. This system uses secondary anti-human or anti-murine mAbs conjugated to the high-potency drug monomethyl auristatin E (MMAE) via a highly stable, enzymatically cleavable linker. Prior studies of this drug linker technology demonstrated internalization of a primary ADC leads to trafficking to lysosomes, drug release by lysosomal cathepsin B, and ensuing cell death. A secondary antibody--drug conjugate (2 degrees ADC) capable of binding primary mAbs bound to the surface of antigen-positive cells has comparable drug delivery capability. The system is sufficiently sensitive to detect internalizing mAbs in nonclonal hybridoma supernatants and is predictive of the activity of subsequently produced primary ADC. Because of their high extracellular stability, the noninternalized 2 degrees ADC are 100--1000-fold less toxic to cells over extended periods of time, permitting an assay in which components can be added without need for separate wash steps. This homogeneous screening system is amenable to medium-throughput screening applications and enables the early identification of mAbs capable of intracellular trafficking for drug delivery and release.
Overexpression of protein kinase C beta 1 is not sufficient to induce factor independence in the interleukin-3-dependent myeloid cell line FDC-P1. (1990)

To examine whether overexpression of protein kinase C (PKC) is sufficient to allow for factor-independent growth in hematopoietic cells, we used a recombinant retroviral expression vector system to introduce a cDNA encoding the beta 1 isoform of the PKC gene into IL-3-dependent cells FDC-P1. Cell lines were generated which contained up to 24-fold increases in PKC activity. Analysis of these cell lines demonstrated that PKC activation does not play a significant role in IL-3-mediated growth control, as evidenced by the following: (1) IL-3 addition to either overexpressor cell lines did not induce morphologic changes whereas activators of PKC stimulated cellular clumping; (2) early passage FDC-P1 cells, either carrying normal or elevated levels of PKC, were not stimulated to grow by activators of PKC; and (3) addition of phorbol esters or bryostatin 1 to these cells markedly decreased the levels of PKC without affecting the ability of these cells to grow in IL-3. Therefore, we suggest that IL-3 mediated growth occurs through pathways other than involving PKC.
Chronic motor cortex stimulation in patients with thalamic pain (1993)

Analysis of the authors' experience over the last 10 years has indicated that excellent pain control has rarely been obtained by thalamic relay nucleus stimulation in patients with thalamic pain. In the present study, 11 patients with thalamic pain were treated by chronic stimulation of the precentral gyrus. In eight patients (73%), the stimulation system was internalized since excellent pain control was achieved during a 1-week test period of precentral gyrus stimulation. In contrast, no clear effect was noted or the original pain was even exacerbated by postcentral gyrus stimulation. The effect of precentral stimulation was unchanged in five patients (45%) for follow-up periods of more than 2 years. In the remaining three patients, the effect decreased gradually over several months. This outcome was significantly better than that obtained in an earlier series tested by the authors with thalamic relay nucleus stimulation (p < 0.05). The pain inhibition usually occurred at intensities below the threshold for production of muscle contraction (pulse duration 0.1 to 0.5 msec, intensity 3 to 8 V). When good pain inhibition was achieved, the patients reported a slight tingling or mild vibration sensation during stimulation projected in the same area of distribution as their pain. The authors discuss the possibility that, in deafferentation pain, sensory neurons below the level of deafferentation cannot exert their normal inhibitory influences toward deafferented nociceptive neurons because of the development of aberrant connections. Thus, while stimulation of the first- to third-order sensory neurons at the level of the thalamic relay nucleus or below cannot bring about good pain inhibition in patients with thalamic pain, activation of hypothetical fourth-order sensory neurons through precentral stimulation may be able to inhibit deafferented nociceptive neurons within the cortex. None of the patients developed either observable or electroencephalographic seizure activity.
Phase-controlled stair-step decay of autoionizing radial wave packets (2002)

The time-dependent survival probabilities of autoionizing $4pNd$ wave packets in calcium have been measured. Femtosecond laser pulses induce sequential isolated-core excitations of singly excited $4sNd$ radial wave packets to create and probe the nonstationary doubly excited states. Stair step rather than exponential decay of the wave packets is observed. Moreover, we show that the autoionization lifetime can be varied by a factor of five by adjusting the relative phases of the constituent eigenstates in the packet. The stair-step decay structure and its dependence on the wave packet phase is interpreted using an intuitive time-domain picture. The experimental results are in excellent agreement with a K-matrix based, 28-channel quantum-defect theory calculation as well as with an approximate two-channel formulation.
Pax6 is required for establishing naso-temporal and dorsal characteristics of the optic vesicle (2002)

The establishment of polarity is an important step during organ development. We assign a function for the paired and homeodomain transcription factor Pax6 in axis formation in the retina. Pax6 is a key factor of the highly conserved genetic network implicated in directing the initial phases of eye development. We recently demonstrated that Pax6 is also essential for later aspects of eye development, such as lens formation and retinogenesis. In this study, we present evidence that a highly conserved intronic enhancer, alpha, in the Pax6 gene is essential for the establishment of a distal(high)-proximal(low) gradient of Pax6 activity in the retina. In the mature retina, the activity mediated by the alpha-enhancer defines a population of retinal ganglion cells that project to two sickle-shaped domains in the superior colliculus and lateral geniculate nucleus. Deletion of the alpha-enhancer in vivo revealed that retinal Pax6 expression is regulated in two complementary topographic domains. We found that Pax6 activity is required for the establishment, as well as the maintenance of dorsal and nasotemporal characteristics in the optic vesicle and, later, the optic cup.