gebhart/patrepeval huggingface dataset:
Plant responses to plant growth-promoting rhizobacteria (2007)

Non-pathogenic soilborne microorganisms can promote plant growth, as well as suppress diseases. Plant growth promotion is taken to result from improved nutrient acquisition or hormonal stimulation. Disease suppression can occur through microbial antagonism or induction of resistance in the plant. Several rhizobacterial strains have been shown to act as plant growth-promoting bacteria through both stimulation of growth and induced systemic resistance (ISR), but it is not clear in how far both mechanisms are connected. Induced resistance is manifested as a reduction of the number of diseased plants or in disease severity upon subsequent infection by a pathogen. Such reduced disease susceptibility can be local or systemic, result from developmental or environmental factors and depend on multiple mechanisms. The spectrum of diseases to which PGPR-elicited ISR confers enhanced resistance overlaps partly with that of pathogen-induced systemic acquired resistance (SAR). Both ISR and SAR represent a state of enhanced basal resistance of the plant that depends on the signalling compounds jasmonic acid and salicylic acid, respectively, and pathogens are differentially sensitive to the resistances activated by each of these signalling pathways. Root-colonizing Pseudomonas bacteria have been shown to alter plant gene expression in roots and leaves to different extents, indicative of recognition of one or more bacterial determinants by specific plant receptors. Conversely, plants can alter root exudation and secrete compounds that interfere with quorum sensing (QS) regulation in the bacteria. Such two-way signalling resembles the interaction of root-nodulating Rhizobia with legumes and between mycorrhizal fungi and roots of the majority of plant species. Although ISR-eliciting rhizobacteria can induce typical early defence-related responses in cell suspensions, in plants they do not necessarily activate defence-related gene expression. Instead, they appear to act through priming of effective resistance mechanisms, as reflected by earlier and stronger defence reactions once infection occurs.
An Application of Markov Random Fields to Range Sensing (2005)

This paper describes a highly successful application of MRFs to the problem of generating high-resolution range images. A new generation of range sensors combines the capture of low-resolution range images with the acquisition of registered high-resolution camera images. The MRF in this paper exploits the fact that discontinuities in range and coloring tend to co-align. This enables it to generate high-resolution, low-noise range images by integrating regular camera images into the range data. We show that by using such an MRF, we can substantially improve over existing range imaging technology. 1
Protease-Mediated Fragmentation of p-Amidobenzyl Ethers:  A New Strategy for the Activation of Anticancer Prodrugs (2002)

A new anticancer prodrug activation strategy based on the 1,6-elimination reaction of p-aminobenzyl ethers is described. Model studies were undertaken with the N-protected peptide benzyloxycarbonyl-valine-citrulline (Z-val-cit), which was attached to the amino groups of p-aminobenzyl ether derivatives of 1-naphthol and N-acetylnorephedrine. The amide bond that formed was designed for hydrolysis by cathepsin B, a protease associated with rapidly growing and metastatic carcinomas. Upon treatment with the enzyme, the Z-val-cit-p-amidobenzyl ether of 1-naphthol (2) underwent peptide bond hydrolysis with the rapid release of 1-naphthol. The aliphatic Z-val-cit-p-amidobenzyl ether of N-acetylnorephedrine (5) also underwent amide bond hydrolysis, but without the ensuing elimination of N-acetylnorephedrine. On the basis of these results, the phenolic anticancer drugs etoposide (6) and combretastatin A-4 (7) were attached to the Z-val-cit-p-amidobenzyl alcohol through ether linkages, forming the peptide-drug derivatives 8 and 9, respectively. Both compounds were stable in aqueous buffers and serum and underwent ether fragmentation upon treatment with cathepsin B, resulting in the release of the parent drugs in chemically unmodified forms. The released drugs were 13-50 times more potent than were the prodrug precursors on a panel of cancer cell lines. In contrast, the corresponding carbonate derivative of combretastatin A-4 (13) was unstable in aqueous environments and was as cytotoxic as combretastatin A-4. This result extends the use of the self-immolative p-aminobenzyl group for the fragmentation of aromatic ethers and provides a new strategy for anticancer prodrug development.
Human Cytomegalovirus-Associated Immunosuppression Is Mediated Through Interferon-α (1997)

Human cytomegalovirus (HCMV) infections are commonly associated with a generalized immunologic hyporesponsiveness. The present study was designed to evaluate the potential mechanisms of HCMV-associated immunosuppression. In our initial experiments, monocytes in peripheral blood mononuclear cells (PBMCs) exposed to cell-free HCMV appeared morphologically less differentiated than monocytes in PBMCs exposed to a mock preparation. These morphologic changes were closely correlated with a decrease in monocyte oxidative activity and occurred under noncytopathic conditions. HCMV-associated suppression of monocyte differentiation did not require virus replication, occurred in PBMCs from either HCMV seropositive or seronegative donors, and required HCMV interaction with the nonadherent cells. An HCMV-induced soluble factor was found to not only reproduce the identical changes in purified monocytes but to inhibit the phagocytic activity of these cells. Additionally, the HCMV-induced factor accounted for a generalized defect in the ability of PBMCs to proliferate in response to mitogens and recall antigens. In subsequent experiments, interferon-alpha (IFN-alpha) was identified as the soluble factor involved in these immunosuppressive effects. Thus, PBMCs, when exposed to HCMV, produce a soluble factor, identified as IFN-alpha, that appears to be an important mediator of immunosuppression associated with HCMV infection.
Complete genomes in WWW Entrez: data representation and analysis. (1999)

Entrez Genomes can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Entrez/Genome/ org.html.
The Feasibility of Using Blood Bank-Stored (4°C) Cord Blood, Unmatched for HLA for Marrow Transplantation (1999)

The main purpose for storing large numbers of umbilical cord blood (CB) units by cryopreservation is to obtain a close HLA match for use in bone marrow transplantation. The use of partially matched or unmatched CB has been suggested, and publications about the success of 3 antigen mismatches have given some credence to this suggestion. Graft vs host disease still is considered a major barrier for successful CB transplantation. The cost per frozen CB unit of approximately $15,000 considerably limits its availability in developing countries. Eleven human umbilical cord specimens were stored in gas-permeable bags at 4 degrees C for up to 3 weeks. Clonal growth, replating efficiency in methylcellulose cultures, differential count, and flow cytometric immunophenotyping results were examined at intervals up to 21 days. Mixed lymphocyte cultures were evaluated on 13 similarly stored specimens at intervals up to 14 days. When plated at 1, 10, and 21 days, the combined percentage of the more primitive colonies increased on days 10 and 21. Replating efficiency of blast cell colonies when stem cell factor was added was 81.2% and 67.8% on days 10 and 21, respectively. When mononuclear cells were immunophenotyped, the mean percentage of CD34+ and CD117+ cells, considered primitive stem cell markers, increased significantly from day 1 to day 21. The ability of stored CB cells to respond to phytohemagglutinin or alloantigens decreased progressively from day 1 to day 14. By day 14, the reactivity of CB responder cells, in mixed lymphocyte cultures, to fresh allogeneic CB stimulator cells declined significantly. These findings suggest that CB can be stored in existing blood bank facilities and retain its hematopoietic potential for transplantation. Furthermore, it may be feasible to combine individual CB samples to provide a sufficient number of viable stem cells for transplantation, substantially expanding the number of potential recipients.
Comparison of immune activity profiles of microsatellite instable colon tumors to microsatellite stable tumors having high ColoType CMS1-score. (2021)

26 Background: Microsatellite instable (MSI) metastatic colorectal cancer (CRC) tumors have been found to be responsive to immune checkpoint inhibitors. Most MSI tumors are in consensus molecular subtype CMS1. Here, in a search for microsatellite stable (MSS) samples that may respond to checkpoint inhibitors, we used the ColoType CMS1-score to identify microsatellite stable (MSS) CRC tumors that have immune activity profiles similar to MSI tumors. Methods: This study was performed in Affymetrix cohort (n = 1,888) of primary CRC tumor samples assayed with hgu133plus2 Affymetrix microarrays. Degrees of infiltration of populations of immune cells were assessed with MCPcounter. Gene Set Enrichment Analysis (GSEA) using the Hallmark gene sets was used to compare biological features between subsets of samples. An 18-gene genomic score (PembroSig) of Ayers, et al, was used to predict response to Pembrolizumab. ColoType 40-gene signature identifies the CMS of a CRC tumor using values of continuous scores, one score for each of CMS1-4. CMS1+ denotes the samples with CMS1-score sufficiently high to predict it is in CMS1. A genomic score was used to predict MSI status for all samples in Affymetrix cohort; MSI predictions using said score had 97% agreement with clinically determined MSI status for 749 Affymetrix cohort samples. Results: The MSI score predicted 240 MSI samples in Affymetrix cohort, and 211 MSS samples in CMS1+ (CMS1+/MSS). The union of MSI and CMS1+/MSS compared to other samples exhibited elevated infiltration of cytotoxic lymphocytes (p &lt; 0.0001) and CD8 T-cells (p &lt; 0.0001), activity of interferon-gamma (p = 0.006) and interferon-alpha signaling (p = 0.012), inflammatory response (p = 0.012), and elevated PembroSig score (p &lt; 0.0001). CMS1+/MSS compared to MSI showed no significance difference in any of these measures. None of the immune regulatory genes PD-1, PD-L1, PD-L2, CTLA4, LAG3, and IDO1 were differentially expressed between CMS1+/MSS and MSI. Of note, the only Hallmark gene sets enriched in MSI compared to CMS1+/MSS were DNA repair (p = 0.002) and MYC targets V1 (p = 0.009) and V2 (p = 0.013). We further analyzed the biological differences between MSI samples in CMS1+ (CMS1+/MSI, n = 190) and MSI samples not in CMS1+ (CMS1-/MSI, n = 50). We found that CMS1+/MSI compared to CMS1-/MSI exhibited elevated cytotoxic lymphocyte infiltration (p &lt; 0.0001), interferon-gamma activity (p = 0.027), and PembroSig score (p &lt; 0.0001), highlighting the relationship between immune activity and CMS1-score. Conclusions: ColoType CMS1-score identified MSS samples in Affymetrix cohort (11%) with similar immune activity as MSI samples (13%) and equivalently high values of a genomic score predictive of Pembrolizumab response.
Methylmalonic acidaemia: Examination of genotype and biochemical data in 32 patients belonging to mut, cblA or cblB complementation group (2007)

Methylmalonic acidaemia (MMA) is a genetic disorder caused by defects in methylmalonyl-CoA mutase or in any of the different proteins involved in the synthesis of adenosylcobalamin. The aim of this work was to examine the biochemical and clinical phenotype of 32 MMA patients according to their genotype, and to study the mutant mRNA stability by real-time PCR analysis. Using cellular and biochemical methods, we classified our patient cohort as having the MMA forms mut (n = 19), cblA (n = 9) and cblB (n = 4). All the mut (0) and some of the cblB patients had the most severe clinical and biochemical manifestations, displaying non-inducible propionate incorporation in the presence of hydroxocobalamin (OHCbl) in vitro and high plasma odd-numbered long-chain fatty acid (OLCFA) concentrations under dietary therapy. In contrast, mut (-) and cblA patients exhibited a milder phenotype with propionate incorporation enhanced by OHCbl and normal OLCFA levels under dietary therapy. No missense mutations identified in the MUT gene, including mut (0) and mut (-) changes, affected mRNA stability. A new sequence variation (c.562G>C) in the MMAA gene was identified. Most of the cblA patients carried premature termination codons (PTC) in both alleles. Interestingly, the transcripts containing the PTC mutations were insensitive to nonsense-mediated decay (NMD).
Enabling personalization recommendation with WeightedFP for text information retrieval based on user-focus (2004)

Personalization recommendation is a valid method for lightening the user's burden on information retrieval. In order to implement personalization recommendation for text information retrieval (TR), user-focus is defined and algorithms for the construction of user-focus are given in this paper. The construction of user-focus for a user depends on his entire query requests at a period of time. Each query request of the user is treated as a transaction between TR system and him. Items in a transaction are non-noise words in the query request corresponding with the transaction. Each item is weighted with a value to measure the importance of the item for the user. Weighted frequent itemset is used for the user-focus's construction. In order to mine weighted frequented itemset fast, an algorithm named as WeightedFP is presented. The experimental result shows that the implementation of personalization recommendation based on user-focus can lighten the user's burden caused by the work of filtering valid information from vast information in some degree while time requirement of TR is satisfied well.
Polymerization of monomers containing functional silyl groups. 5. Synthesis of new porous membranes with functional groups (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerization of monomers containing functional silyl groups. 5. Synthesis of new porous membranes with functional groupsJae Suk Lee, Akira Hirao, and Seiichi NakahamaCite this: Macromolecules 1988, 21, 1, 274–276Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://doi.org/10.1021/ma00179a057RIGHTS & PERMISSIONSArticle Views921Altmetric-Citations145LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
Efficient Synthesis of the Aonidiella aurantii (Mask.) Sex Pheromone Component: (3S,6RS)-3-Methyl-6-(1-Methylethenyl)-9-decenyl Acetate (1995)

The title compound, active component of the sex pheromone of Aonidiella aurantii (California Red Scale), was synthesized in three steps starting from S-citronellyl acetate with a 30% overall yield. The key feature of the synthesis is a copper salt assisted, highly regioselective attack of the 4-butenyl bromide Grignard reagent on the γ-site of the chloroallylic system of (S)-8-chloro-3,7-dimethyl-6-octenyl acetate (8a).
Singlet oxygen generation in porphyrin-doped polymeric surface coating enables antimicrobial effects on Staphylococcus aureus (2014)

Surfaces can be coated with photosensitizer molecules, which generate singlet oxygen ((1)O2) when the surface is exposed to light. (1)O2 may diffuse from the coating and has the potential to kill microorganisms present on the surface. In the present study a derivative of the meso-tetraphenylporphyrin (TPP) was immobilized onto polyurethane (PU) after being sprayed and polymerized as a thin layer onto poly-methylmethacrylate (PMMA). PU is gas permeable and thus a sufficient amount of oxygen reaches the photosensitizer in this coating. The surface generation of (1)O2 and its diffusion were investigated by detecting its luminescence at 1270 nm and a tri-iodide assay. Antimicrobial photodynamic surface effects were tested on Staphylococcus aureus. The spectrally resolved detection of (1)O2 luminescence yielded a clear peak at 1275 nm. The time-resolved luminescence showed multi-exponential decay, revealing rise and decay times in the range of 5-2 × 10(2)μs. The photodynamic inactivation of S. aureus was monitored at different photosensitizer concentrations and radiant exposures of light. A photodynamic killing of >99.9% (>3log10-steps) was achieved within an irradiation time of 30 min. The photodynamic killing on the bioactive surface confirmed the antimicrobial effect of (1)O2 that was generated in the PU-coating and reached the bacteria by diffusion.
Interpolation based transmit beamforming for MIMO-OFDM with limited feedback (2004)

Transmit beamforming with receive combining is a simple method for exploiting the significant diversity provided by multiple-input multiple-output (MIMO) systems, and the use of orthogonal frequency division multiplexing (OFDM) enables low complexity implementation of this scheme over frequency selective MIMO channels. This paper proposes a beamforming technique that reduces feedback requirements for optimal beamforming. In the proposed architecture, the receiver sends back quantized versions of select beamforming vectors and the transmitter reconstructs the missing beamforming vectors through interpolation. Since a beamforming vector is phase invariant and has unit norm, a new spherical linear interpolator is proposed that exploits additional parameters for phase rotation. These parameters are determined at the receiver in the sense of maximizing the minimum channel gain or capacity, and sent back to the transmitter along with the quantized beamforming vectors. Simulation results show that the proposed beamforming method requires much less feedback information than optimal beamforming with only slight diversity loss.
N-Terminal Domain-Deleted Mu Transposase Exhibits Increased Transposition Activity with Low Target Site Preference in Modified Buffers (2008)

The use of the N-terminally deleted MuA with the newly established condition enhanced the relative transposition activity about 280-fold compared to that of wild-type MuA with the conventional buffer. In addition, the optimized buffer decreased the target site preference of N-terminally deleted MuA resulting in a more even distribution of integration events throughout the target gene.
VEGFc and VEGFR3 expression in human thyroid pathologies (2000)

In vertebrates, vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are major determinants of angiogenesis. In adults, the interaction between VEGFc and VEGFR3 (previously FLT4) is more specifically involved in the biology of lymphatics. Using PCR amplification of reverse-transcribed mRNA, we studied the expression of the VEGFR3 (including its short and long forms) and VEGFc genes in 38 samples of various human thyroid pathologies. VEGFR3 mRNA was detected in all samples of adenomas, nodular goiters and focal goitrogenic alterations; in all samples of thyroid tissue from patients with auto-immune diseases; and in some samples of adenocarcinomas. VEGFc mRNA was detected in most samples. We studied expression of the VEGFR3 and VEGFc proteins in thyroid tumors using appropriate antibodies. Co-expression of VEGFR3 and VEGFc was observed in most samples.
Optical emission characteristics of semipolar (1\,1\,\bar{2}\,2) GaN light-emitting diodes grown on m-sapphire and stripe-etchedr-sapphire (2012)

We demonstrate the growth and optical characterization of semipolar GaN light-emitting diodes (LEDs) on sapphire utilizing two distinct heteroepitaxial growth methodologies. The properties of semipolar LEDs are analyzed by the simultaneous growth of LED structures on templates prepared by both two-step growth on m-sapphire and selective growth on etched r-plane sapphire. Typically, growth on m-sapphire yields a high density of microstructural defects and surface morphological features which complicate the understanding of emission properties in devices. In this study, we find improved spectral properties of devices grown on etched r-sapphire due to improved surface roughness and microstructural quality (x-ray diffraction rocking curves of 280–550 arcsec for on-axis and off-axis (1 0 1 n), n = 0–5 diffractions), and reveal that the commonly observed broad emission and sub-bandgap peak in semipolar LEDs on sapphire are caused by a tunneling-assisted radiative recombination mechanism.
Mitochondrial metabolism and ROS generation are essential for Kras-mediated tumorigenicity (2010)

Otto Warburg's theory on the origins of cancer postulates that tumor cells have defects in mitochondrial oxidative phosphorylation and therefore rely on high levels of aerobic glycolysis as the major source of ATP to fuel cellular proliferation (the Warburg effect). This is in contrast to normal cells, which primarily utilize oxidative phosphorylation for growth and survival. Here we report that the major function of glucose metabolism for Kras-induced anchorage-independent growth, a hallmark of transformed cells, is to support the pentose phosphate pathway. The major function of glycolytic ATP is to support growth under hypoxic conditions. Glutamine conversion into the tricarboxylic acid cycle intermediate alpha-ketoglutarate through glutaminase and alanine aminotransferase is essential for Kras-induced anchorage-independent growth. Mitochondrial metabolism allows for the generation of reactive oxygen species (ROS) which are required for Kras-induced anchorage-independent growth through regulation of the ERK MAPK signaling pathway. We show that the major source of ROS generation required for anchorage-independent growth is the Q(o) site of mitochondrial complex III. Furthermore, disruption of mitochondrial function by loss of the mitochondrial transcription factor A (TFAM) gene reduced tumorigenesis in an oncogenic Kras-driven mouse model of lung cancer. These results demonstrate that mitochondrial metabolism and mitochondrial ROS generation are essential for Kras-induced cell proliferation and tumorigenesis.