gebhart/patrepeval huggingface dataset:
Parent-of-origin effects on seed development inArabidopsis thalianarequire DNA methylation (2000)

Some genes in mammals and flowering plants are subject to parental imprinting, a process by which differential epigenetic marks are imposed on male and female gametes so that one set of alleles is silenced on chromosomes contributed by the mother while another is silenced on paternal chromosomes. Therefore, each genome contributes a different set of active alleles to the offspring, which develop abnormally if the parental genome balance is disturbed. In Arabidopsis, seeds inheriting extra maternal genomes show distinctive phenotypes such as low weight and inhibition of mitosis in the endosperm, while extra paternal genomes result in reciprocal phenotypes such as high weight and endosperm overproliferation. DNA methylation is known to be an essential component of the parental imprinting mechanism in mammals, but there is less evidence for this in plants. For the present study, seed development was examined in crosses using a transgenic Arabidopsis line with reduced DNA methylation. Crosses between hypomethylated and wild-type diploid plants produced similar seed phenotypes to crosses between plants with normal methylation but different ploidies. This is consistent with a model in which hypomethylation of one parental genome prevents silencing of alleles that would normally be active only when inherited from the other parent - thus phenocopying the effects of extra genomes. These results suggest an important role for methylation in parent-of-origin effects, and by inference parental imprinting, in plants. The phenotype of biparentally hypomethylated seeds is less extreme than the reciprocal phenotypes of uniparentally hypomethylated seeds. The observation that development is less severely affected if gametes of both sexes (rather than just one) are 'neutralized' with respect to parent-of-origin effects supports the hypothesis that parental imprinting is not necessary to regulate development.
Developmental regulation of gene expression for the MPTPδ isoforms in the central nervous system and the immune system (1994)

MPTP delta is a murine transmembrane protein tyrosine phosphatase which has three isoforms, types A-C, differing in the structure of the extracellular regions. In this study, we examined MPTP delta isoform expression in the brain and the immune system at discrete developmental or differentiation stages. RT-PCR analysis demonstrated that another isoform, type D, is transcribed from the MPTP delta gene. In the brain, only type D was expressed until postnatal day 7 (P7), but after P14, all four isoforms were detected. In contrast, the spleen, thymus and all the hematopoietic cell lines examined express only types B and C isoforms. An in situ hybridization study showed that MPTP delta mRNA is diffusely expressed throughout the spleen, but its expression in the thymus is restricted to the medullary region.
Monodisperse Nanoparticles of Ni and NiO: Synthesis, Characterization, Self‐Assembled Superlattices, and Catalytic Applications in the Suzuki Coupling Reaction (2005)

Monodisperse spherical Ni nanoparticles with diameters of 2 nm, 5 nm, and 7 nm were synthesized from the thermal decomposition of a Ni–oleylamine complex. Ni nanocrystal superlattices were generated via the controlled evaporation of solvent (see Figure). The nanoparticles were successfully used as catalysts for the Suzuki coupling reaction, and were readily oxidized to produce NiO nanoparticles.
Evaluation of corn gluten meal extracted with supercritical carbon dioxide and other solvents: flavor and composition (1994)

Corn gluten meal is a 60% min. protein product derived from corn during the wet milling process. The undesirable flavour of corn gluten meal prevents its use in food. This research was undertaken to evaluate corn gluten meal after extraction with supercritical CO2 or hexane-ethanol (82:18, v/v) at various temp. [40, 60, 80-81°C], pressures [13.6-15.6, 40.8, 68 MPa], solvent-to-solid ratios, and particle sizes. Supercritical CO2 extraction of corn gluten meal at 68 MPa and 80°C significantly decreased fermented flavour, the predominant characteristic of unprocessed corn gluten meal. Hexane-ethanol extraction also significantly reduced fermented flavour. [It was concluded that] processing by supercritical CO2 extraction of hexane-ethanol extraction can significantly improve corn gluten meal flavour.
Blockade of phospholipid scramblase 1 with its N-terminal domain antibody reduces tumorigenesis of colorectal carcinomas in vitro and in vivo (2012)

Therefore, PLSCR1 may serve as a potential therapeutic target for CRC.
A Peptide Selected by Biopanning Identifies the Integrin αvβ6 as a Prognostic Biomarker for Nonsmall Cell Lung Cancer (2007)

The development of new modes of diagnosis and targeted therapy for lung cancer is dependent on the identification of unique cell surface features on cancer cells and isolation of reagents that bind with high affinity and specificity to these biomarkers. We recently isolated a 20-mer peptide which binds to the lung adenocarcinoma cell line, H2009, from a phage-displayed peptide library. We show here that the cellular receptor for this peptide, TP H2009.1, is the uniquely expressed integrin, alphavbeta6, and the peptide binding to lung cancer cell lines correlates to integrin expression. The peptide is able to mediate cell-specific uptake of a fluorescent nanoparticle via this receptor. Expression of alphavbeta6 was assessed on 311 human lung cancer samples. The expression of this integrin is widespread in early-stage nonsmall cell lung carcinoma (NSCLC). Log-rank test and Cox regression analyses show that expression of this integrin is significantly associated with poor patient outcome. Preferential expression is observed in the tumors compared with the surrounding normal lung tissue. Our data indicate that alphavbeta6 is a prognostic biomarker for NSCLC and may serve as a receptor for targeted therapies. Thus, cell-specific peptides isolated from phage biopanning can be used for the discovery of cell surface biomarkers, emphasizing the utility of peptide libraries to probe the surface of a cell.
Improving task reliability by fusion of redundant homogeneous modules using voting schemes (2002)

In this paper we present a technique that can help us design system components (behaviors) with reliability in mind. Our approach is similar to N-version programming. A team of functionally redundant behaviors vote for a set of possible actions. A voter then fuses the votes and selects the action which has received the maximum number of votes. We draw some design guidelines and show that with careful design, the selected action will have higher probability of success (reliability) than the reliability of each of the behaviors. A comprehensive set of experiments together with results are presented in which a team of tracking behaviors control a stereo camera head in the active vision task of smooth pursuit. The results show that the approach dramatically improves tracking performance.
A high-availability clustering architecture with data integrity guarantees (2001)

This paper discusses the design and implementation of a high-availability clustering solution.This solution provides data integrity guarantees and a simple and effective way for making services highly available.The implementation of the system design in a Linux environment on commodity hardware is documented.A proof-of-concept to provide a highly available NFS server is explained with caveats and their resolutions.
The Biochemical High-Risk Paradigm: Behavioral and Familial Correlates of Low Platelet Monoamine Oxidase Activity (1976)

A population of individuals potentially at risk for psychiatric disorders was identified by screening 375 college student volunteers for low platelet monoamine oxidase (MAO) activity levels. The lower and upper 10 per cent in MAO activity were interviewed and family history data were obtained. Low-MAO probands reported more frequent psychiatric or psychological counseling and problems with the law. Families of low MAO probands had an eightfold increase in the incidence of suicide or suicide attempts over those of high-MAO probands. This suggests that reduced MAO levels, reported previously in patients with affective disorders and chronic schizophrenia, may predict a vulnerability to psychiatric disorder.
Comparing and Combining Predictors of Mostly Disordered Proteins (2005)

Intrinsically disordered proteins and regions carry out varied and vital cellular functions. Proteins with disordered regions are especially common in eukaryotic cells, with a subset of these proteins being mostly disordered, e.g., with more disordered than ordered residues. Two distinct methods have been previously described for using amino acid sequences to predict which proteins are likely to be mostly disordered. These methods are based on the net charge-hydropathy distribution and disorder prediction score distribution. Each of these methods is reexamined, and the prediction results are compared herein. A new prediction method based on consensus is described. Application of the consensus method to whole genomes reveals that approximately 4.5% of Yersinia pestis, 5% of Escherichia coli K12, 6% of Archaeoglobus fulgidus, 8% of Methanobacterium thermoautotrophicum, 23% of Arabidopsis thaliana, and 28% of Mus musculus proteins are mostly disordered. The unexpectedly high frequency of mostly disordered proteins in eukaryotes has important implications both for large-scale, high-throughput projects and also for focused experiments aimed at determination of protein structure and function.
<title>Device-independent color in PostScript</title> (1993)

The PostScript language has long been known for very precise, device independent page descriptions of potentially very complex pages consisting of text, graphics, and images. However, in the past the description of color in PostScript has not done justice to the term device independence since the exact meaning of the colorants in a color space was not explicitly specified, but instead was left to the interpretation of each device receiving the given page description. Device independent color is the ability to describe color in a manner independent of the color forming properties of any particular device. Instead color is described based on the CIE system of color specification. PostScript has been extended to afford his manner of color specification.
Age-related macular degeneration and antioxidant vitamins: recent findings (2009)

Findings on the association of certain antioxidants and docosahexaenoic acid support a role for nutrition in a decreased risk of AMD. The inconsistent findings of an increased risk with increased intake of beta-carotene and vitamin E warrants continued investigation into these relationships.
Structural determination of Enzyme-Graphene Nanocomposite Sensor Material (2019)

State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.
Manipulating and understanding antibiotic production in Streptomyces coelicolor A3(2) with decoy oligonucleotides (2008)

We have adapted and extended the decoy oligonucleotide technique for use in prokaryotes. To identify cis-acting regulatory elements within a promoter, we developed a DNase I/T7 exonuclease footprinting technique and applied it to actII-orf4 from Streptomyces coelicolor A3(2), which encodes the pathway-specific activator for production of the antibiotic actinorhodin. Our in vivo mapping data allowed us to create decoy oligonucleotides incorporating the identified regulatory elements and to test whether their introduction into S. coelicolor affected antibiotic production. We mapped the promoter region when in a transcriptionally inactive state before the onset of actinorhodin production with the aim of designing decoy oligonucleotides capable of interfering with potential repressor binding and so stimulate actinorhodin production. Mapping identified five candidates for decoy oligonucleotides, and these were tested in a plate-based assay to rapidly validate their activity. A transfection protocol was developed for liquid cultures that enabled efficient uptake of decoys, and quantitative real-time PCR demonstrated decoy persistence for >70 h. Measurement of the effects on growth, expression of actII-orf4, and antibiotic production demonstrated that one of the decoys, in concordance with the plate assay, was more efficacious than the others in increasing actinorhodin production. Two of the identified regulatory elements occurred upstream of gene SCO5812, deletion of which reduced actinorhodin production, confirming that experimental analysis of regulatory motifs can provide new insights into factors influencing antibiotic production in streptomycetes.
Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity. (1988)

The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk- cells was determined. We tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR confirmed by monitoring Ecogpt expression in stably transfected Ltk- cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the 3'U3/R region determines the basal level of transcription, whereas sequences within the 5'U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.
Isolation of a cytokinin gene, ZOG1 , encoding zeatin O -glucosyltransferase from Phaseolus lunatus (1999)

Zeatin is the most active and ubiquitous of the naturally occurring cytokinins. The O-glucoside of zeatin, found in all plants examined, is considered to be important in cytokinin transport, storage, and protection against cytokinin oxidases. The enzyme UDPglucose:zeatin O-glucosyltransferase (EC 2.4.1.203) was previously isolated from Phaseolus lunatus seeds. Immunoscreening of an expression library with monospecific antibody resulted in the isolation of a cDNA encoding the enzyme. The recombinant protein efficiently converts labeled zeatin to O-glucosylzeatin and has properties similar to the native enzyme. The cDNA of 1.5 kb contains an ORF encoding a 51. 4-kDa polypeptide of 459 amino acids. The sequence is unique based on a BLAST search of data bases. The genomic sequence, isolated with PCR using specific primers based on the cDNA sequence, does not contain introns. The cloning of this gene provides the tools for further study of the regulation of cytokinin metabolism and analysis of the precise role of O-glucosylzeatin in plant development.
A Small Molecule Inhibitor, 1,2,4,5-Benzenetetraamine Tetrahydrochloride, Targeting the Y397 Site of Focal Adhesion Kinase Decreases Tumor Growth (2008)

Focal adhesion kinase (FAK) is a nonreceptor kinase that is overexpressed in many types of tumors. We developed a novel cancer-therapy approach, targeting the main autophosphorylation site of FAK, Y397, by computer modeling and screening of the National Cancer Institute (NCI) small molecule compounds database. More than 140,000 small molecule compounds were docked into the N-terminal domain of the FAK crystal structure in 100 different orientations that identified 35 compounds. One compound, 14 (1,2,4,5-benzenetetraamine tetrahydrochloride), significantly decreased viability in most of the cells to the levels equal to or higher than control FAK inhibitor 1a (2-[5-chloro-2-[2-methoxy-4-(4-morpholinyl)phenylamino]pyrimidin-4-ylamino]-N-methylbenzamide, TAE226) from Novartis, Inc. Compound 14 specifically and directly blocked phosphorylation of Y397-FAK in a dose- and time-dependent manner. It increased cell detachment and inhibited cell adhesion in a dose-dependent manner. Furthermore, 14 effectively caused breast tumor regression in vivo. Thus, targeting the Y397 site of FAK with 14 inhibitor can be effectively used in cancer therapy.
Demineralization of Dentin by <i>Streptococcus mutans</i> Biofilms Grown in the Constant Depth Film Fermentor (2003)

To develop a bacterial demineralization model, we grew Streptococcus mutans biofilms in a constant depth film fermentor (CDFF) and studied the effects of sucrose pulsing frequency (SPF) in time on dentin demineralization. S. mutans biofilms were grown in dentin specimens with grooves and on dentin surface specimens for 20 days. During the experiments, 2% sucrose was pulsed either 4 or 8 times per day for periods of 30 min. Diluted brain-heart infusion medium containing 25 mM PIPES buffer and 1.5 mM CaCl2 was pulsed as the alternative growth medium. Specimens with intact biofilms were taken out on days 5, 12 and 20. The model was assessed by viable counts of the biofilm, mineral loss and lesion depth in the dentin specimens (by transversal microradiography) and pH measurements in the groove (by pH microelectrode). The results showed that biofilms formed on the dentin surface specimens were constant in viable counts for the low SPF, while this parameter tended to increase with time under the high SPF. Lesions with intact surfaces were formed and the lesion size increased significantly over time and increased significantly with increasing SPF. Typical Stephan curves were found after sucrose pulsing. The pH inside the groove returned to neutral under low SPF, but remained below 6.5 under high SPF. With the CDFF S. mutans biofilm model, lesions can be created in dentin within reasonable experimental time periods, as a result of the presence of a biofilm and in response to carbohydrate challenges.
Structural Determinants of MALT1 Protease Activity (2012)

The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.
Research Progress on Preparation Methods of PMIA Fiber (2012)

PMIA is a functional fiber with superior heat-resistance, flame resistance, high temperature dimensional stability and electrical insulation. In PMIA crystal structure, there exist hydrogen bonds between two planes in the crystal and they are arranged in grid. The strong interactions between hydrogen bonds result in a very stable chemical structure of PMIA. Owing to lower internal rotation potential energy than PPTA, PMIA molecular chains are flexible structures and its elastic modulus is in the same level as other flexible macromolecules. In this paper, the structure character of molecular chain and performance of PMIA have been introduced. Additionally, the common used polymerization techniques for PMIA have been described in detail. These synthesis techniques include low-temperature solution polymerization, interfacial polymerization and emulsion polymerization.
MMP Inhibition and Downregulation by Bisphosphonates (1999)

Bisphosphonates are a group of drugs capable of inhibiting bone resorption, and are thus used for the treatment of bone diseases, such as Paget's disease, osteoporosis, and for bone metastases of malignant tumors. Their primary cellular target is considered to be the osteoclast. The molecular mechanisms responsible for the downregulation of bone resorption by bisphosphonates have remain unclear. We have discovered that various matrix metalloproteinases (MMPs) are inhibited in vitro by several bisphosphonates. This novel finding may, in part, explain the efficacy of bisphosphonates in their current indications in humans. In enzyme activity tests using purified and recombinant enzymes, we have observed the inhibition of MMP-1, -2, -3, -7, -8, -9, -12, -13, and -14 by clondronate, alendronate, pamidronate, zolendronate, nedrinate, and clodrinate. The IC50s range from 50 to 150 microM. We have also shown that clodronate can downregulate the expression of MT1-MMP protein and mRNA in several cell lines. Additionally, several bisphosphonates decrease the degree of invasion of malignant melanoma (C8161) and fibrosarcoma (HT1080) cells through artificial basement membrane (Matrigel) in cell cultures at IC50s of 50-150 microM and below. Having low toxicity and proven to be well tolerated after several years in human use, bisphosphonates have the potential to become one of the main MMP-inhibitors for MMP-related human soft and hard tissue-destructive diseases in the near future.
Increased telomerase activity and elevated hTERT mRNA expression during multistage carcinogenesis of squamous cell carcinoma of the lung (2001)

These results suggest that an increase in telomerase activity and hTERT mRNA expression are features of the early stages of the development of squamous cell carcinoma of the lung, with strong telomerase activity and hTERT mRNA expression being prominent during the latter stages.
Assessment of Renal Hemodynamics and Function in Pigs with 64-Section Multidetector CT: Comparison with Electron-Beam CT (2007)

The clinical multidetector CT scanner provides reliable measurements of single-kidney hemodynamics and function, which are similar to those obtained with previously validated electron-beam CT.