gebhart/patrepeval huggingface dataset:
Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato (2020)

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.
A novel Dual String NOR (DuSNOR) memory cell technology scalable to the 256 Mbit and 1 Mbit flash memories (2002)

We have developed a novel NOR-type flash memory technology named Dual String NOR (DuSNOR). In the DuSNOR cell array, two adjacent cell strings share a source line and up to 128 cell transistors can be attached to a string. This makes the cell size of DuSNOR smaller than NAND, without sacrificing the advantages of the NOR-type cell. Both the program and erase operations utilize the Fowler-Nordheim tunneling. DuSNOR cells with a cell size of 1.60 /spl mu/m/sup 2/ was fabricated using 0.5 /spl mu/m design rules. It was found that the DuSNOR cell has a fast operating speed, reduced overprogram and disturb problems, and excellent endurance characteristics. DuSNOR is a promising technology for high density, high speed, and random-access flash memories with a small cell size, excellent device characteristics and simplicity in the fabrication process.
Inactivated hepatitis A vaccine: Reactogenicity, immunogenicity, and long‐term antibody persistence (1994)

This trial evaluated the reactogenicity, kinetics of antibody induction, and long-term immunogenicity of a 720 enzyme-linked immunosorbent assay units (EL.U.) antigen dose of an inactivated hepatitis A vaccine (Havrix, SmithKline Beecham Biologicals, Rixensart, Belgium). One hundred six healthy adult volunteers were enrolled to receive vaccine intramuscularly according to a 0, 1, and 6-month schedule. The vaccine was well tolerated. The most frequently reported local symptom was soreness, observed following 37.1% of all doses. Headache was the most frequently reported general symptom observed following 12.9% of documented vaccine doses. The administration of one vaccine dose induced seropositivity (anti-hepatitis A virus [HAV] > or = 20 mIU/ml) in 91% of all vaccinees 1 month later. The second vaccine dose resulted in seropositivity of the remaining vaccinees at month 2. All subjects remained seropositive for HAV antibodies at month 6, at which time the booster vaccine dose was given. At month 7, all vaccinees had anti-HAV titres > 200 mIU/ml. Serological results obtained at months 12, 18, 24, and 36 showed that antibodies against HAV induced by the vaccine booster dose persist for at least 30 months following its administration. All 49 subjects followed up until month 36 had antibody titres > or = 20 mIU/ml. The geometric mean titre (GMT) decreased by 60% from month 7 to month 12; between month 12 and 36, the GMT decreased by approximately 14% per period of 12 months. According to the vaccine-induced antibody kinetics and the magnitude of antibody level decrease over time, the predicted duration of antibody persistence is estimated to be at least 20 years.
P‐032: Differentiation between Alzheimer's disease patients and healthy controls is not possible with 2‐[18F]F‐A‐85380 pet imaging of nicotinic receptors (2007)

The cholinergic system and neuronal nicotinic acetylcholine receptors (nAChRs) are critical for higher order cognitive processes. Post-mortem studies suggest reductions in nAChRs (particularly the α4β2 subtype) with ageing and in Alzheimer's disease (AD), predominantly in frontal and temporal cortices. The radiotracer 2-[18F]F-A-85380 binds with high affinity at nAChRs and its uptake is consistent with the known distribution of the α4β2 nAChR subtype. This study aimed 1) to quantify the nAChR distribution in early AD patients compared to age-matched, normal elderly controls (HC) and 2) to correlate nAChR distribution with cognitive performance in AD and HC. Fourteen HC (MMSE 29 ± 1, aged 72 ± 9 years) and fifteen drug naı̈ve, early AD patients (MMSE 23 ± 2, aged 77 ± 10 years) all non-smokers, underwent neuropsychological testing designed to assess verbal learning, working memory, attention and psychomotor function along with a static 20-min PET scan acquired 100 min after injection of approximately 200MBq of 2-[18F]F-A-85380. Brain regional 2-[18F]F-A-85380 binding was assessed through a simplified estimation of Distribution Volume (DV(simplified)), defined as the ratio of regional activity to metabolite corrected venous plasma at apparent steady state (100–120min post-injection). Measures of cognition and DV(simplified) were analysed using t-tests and the relationship between DV(simplified) and measures of cognition were examined using correlational analysis. The AD group differed significantly from the HC group on all cognitive measures employed (p<.05 - p<.001). Statistical analysis showed no significant difference in nAChRs DV(simplified) between AD and HC. Furthermore, no significant correlations were found between cognitive measures and DV(simplified) for either group. Contrary to post-mortem research this in vivo study found no evidence of nAChR loss in early AD despite significant cognitive impairment. Furthermore, no correlation between nAChR and cognitive performance was found for either group. These results are in line with recent studies suggesting the stability of cholinergic markers during the early stages of AD.
The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet (2018)

<b>Background:</b> Berberine (BBR) has been extensively reported to inhibit colorectal cancer (CRC) development, though its bioavailability is poor. Nowadays, an increasing number of studies have shown that BBR significantly accumulates in the intestines and could regulate gut microbiota in obesity. The purpose of this study was to further explore the effects of BBR on gut microbiota in Apc <sup>min/+</sup> mice receiving a high fat diet (HFD). <b>Methods:</b> Apc <sup>min/+</sup> mice received either HFD alone or HFD and BBR for 12 weeks. The intestinal tissues were collected to evaluate the efficiency of BBR on neoplasm development by hematoxylin and eosin staining. Meanwhile, immunohistochemistry was conducted to investigate the effects of BBR on cyclin D1 and β-catenin in colon tissues. Fecal samples were subjected to 16S rRNA sequencing. <b>Results:</b> BBR significantly reduced intestinal tumor development and altered the structure of gut microbiota in Apc <sup>min/+</sup> mice fed with an HFD. At the phylum level, it was able to significantly inhibit the increase in <i>Verrucomicrobia</i>. At the genus level, it was able to suppress <i>Akkermansia</i> and elevate some short chain fat acid (SCFA)-producing bacteria. <b>Conclusions:</b> BBR significantly alleviated the development of CRC in Apc <sup>min/+</sup> mice fed with HFD and restored the enteric microbiome community.
Overlapping but Nonidentical Binding Sites on CD2 for CD58 and a Second Ligand CD59 (1992)

The interaction of the T cell glycoprotein CD2 with one ligand, CD58, contributes to T cell function. We have identified CD59, a glycoprotein with complement-inhibitory function, as a second physiological ligand for CD2. Antibodies to CD59 inhibit CD2-dependent T cell activation in murine T cell hybridomas expressing human CD2. In an in vitro binding assay with purified CD58 and CD59, CD2+ cells bind not only immobilized CD58 but also CD59. With two complementary approaches, it was demonstrated that the binding sites on CD2 for CD58 and CD59 are overlapping but nonidentical. These observations suggest that direct interactions between CD2 and both CD58 and CD59 contribute to T cell activation and adhesion.
ChemInform Abstract: Estimation of Lipophilicity by Reversed‐Phase Thin‐Layer Chromatography (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
<title>Miniaturized sequential injection analyzer for the monitoring and quantitation of chemical weapons degradation compounds</title> (2002)

The ability to monitor and detect chemical warfare agents and their degradation compounds continues to be of utmost importance. Remote on-site field analysis of these compounds is also extremely important as it relates to treaty verification for the Chemical Weapons Convention, as well as the minimization and elimination of human exposure. A portable instrument has been developed and miniaturized that allows for the detection of these compounds in the field with better quantitative results and higher reproducibility than traditional field test kits. All sample and reagent manipulations are conducted in a completely automated fashion. Quantitative results may be determined colorimetrically using the molybdenum blue reaction for the final degradation product of phosphonic acid based chemical warfare agents with a detection limit of 0.05 ppm. The instrument is based on the flow analysis technique of sequential injection analysis (SIA). The benefits of this approach are that the method provides rapid response, high reproducibility of results, high sensitivity and minimal waste production.
Development of an Ion Chromatography–Inductively Coupled Plasma–Mass Spectrometry Method To Determine Inorganic Arsenic in Liver from Chickens Treated with Roxarsone (2012)

Roxarsone, (4-hydroxy-3-nitrophenyl)arsonic acid, is an arsenic-containing compound that has been approved as a feed additive for poultry and swine since the 1940s; however, little information is available regarding residual arsenic species present in edible tissues. We developed a novel method for the extraction and quantification of arsenic species in chicken liver. A strongly basic solution solubilized the liver, and ultrafiltration removed macromolecules and particulate material. Ion chromatography separated the species [arsenite, arsenate, monomethylarsonic acid, dimethylarsinic acid, (4-hydroxy-3-aminophenyl)arsonic acid, (4-hydroxy-3-acetaminophenyl)arsonic acid, and roxarsone] in the extracts, which were then detected by inductively coupled plasma-mass spectrometry. The extraction oxidized most arsenite to arsenate. For fortification concentrations at 2 μg kg(-1) and above, recoveries ranged from 70 to 120%, with relative standard deviations from 7 to 34%. We detected roxarsone, its 3-amino and 3-acetamido metabolites, inorganic arsenic, and additional unknown arsenic species in livers from roxarsone-treated chickens. Both the originating laboratory and a second laboratory validated the method.
Surface elastic modulus of barnacle adhesive and release characteristics from silicone surfaces (2004)

The properties of barnacle adhesive on silicone surfaces were studied by AFM indentation, imaging, and other tests and compared to the barnacle shear adhesion strength. A multilayered structure of barnacle adhesive plaque is proposed based on layered modulus regions measured by AFM indentation. The fracture of barnacles from PDMS surfaces was found to include both interfacial and cohesive failure of barnacle adhesive plaque, as determined by protein staining of the substratum after forced barnacle release from the substrate. Data for freshly released barnacles showed that there was a strong correlation between the mean Young's modulus of the outermost (softest) adhesive layer (E<0.3 MPa) and the shear strength of adhesion, but no correlation for other higher modulus regions. Linear, quadratic, and Griffith's failure criterion (based on rough estimate of crack length) regressions were used in the fit, and showed significance.
Flavin Chemical Models for Monoamine Oxidase Inactivation by Cyclopropylamines, .alpha.-Silylamines, and Hydrazines (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFlavin Chemical Models for Monoamine Oxidase Inactivation by Cyclopropylamines, .alpha.-Silylamines, and HydrazinesJong-Man Kim, Susan E. Hoegy, and Patrick S. MarianoCite this: J. Am. Chem. Soc. 1995, 117, 1, 100–105Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ja00106a012https://doi.org/10.1021/ja00106a012research-articleACS PublicationsRequest reuse permissionsArticle Views371Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Canon's development status of EUVL technologies (2008)

We developed a small field exposure tool (SFET) in collaboration with EUVA (Extreme Ultraviolet Lithography System Development Association). SFET was installed at SELETE (Semiconductor Leading Edge Technologies; Japanese Consortium) in 2006. SFET is positioned as a cornerstone of the manufacturing technologies for EUVL Full- Field tools as well as tool for resist and mask development. We started the system design of the Full-Field tool and fabrication of the six-mirror projection optics based on the experience of the SFET. In this paper, we introduce the outline of Canon's activities for the full-field tool. EUVL is requested to resolve the sub 30 nm features. The studies of the resolution for higher NA EUV projection optics is also presented.
Identification of Novel HLA-A2-Restricted Human Immunodeficiency Virus Type 1-Specific Cytotoxic T-Lymphocyte Epitopes Predicted by the HLA-A2 Supertype Peptide-Binding Motif (2001)

Virus-specific cytotoxic T-lymphocyte (CTL) responses are critical in the control of human immunodeficiency virus type 1 (HIV-1) infection and will play an important part in therapeutic and prophylactic HIV-1 vaccines. The identification of virus-specific epitopes that are efficiently recognized by CTL is the first step in the development of future vaccines. Here we describe the immunological characterization of a number of novel HIV-1-specific, HLA-A2-restricted CTL epitopes that share a high degree of conservation within HIV-1 and a strong binding to different alleles of the HLA-A2 superfamily. These novel epitopes include the first reported CTL epitope in the Vpr protein. Two of the novel epitopes were immunodominant among the HLA-A2-restricted CTL responses of individuals with acute and chronic HIV-1 infection. The novel CTL epitopes identified here should be included in future vaccines designed to induce HIV-1-specific CTL responses restricted by the HLA-A2 superfamily and will be important to assess in immunogenicity studies in infected persons and in uninfected recipients of candidate HIV-1 vaccines.
Effect of nitrogen on the microstructure and mechanical properties of Co–33Cr–9W alloys prepared by dental casting (2017)

The effect of nitrogen concentration on the mechanical properties of Co-33Cr-9W alloy dental castings fabricated using the "high-Cr and high-N" concept was investigated. Microstructural analysis was performed on the alloys, and findings were discussed in relation to the mechanical properties. Owing to their high nitrogen concentrations (0.25-0.35wt%), all alloys prepared exhibited face-centered cubic (fcc) γ-phase matrices with a-few-millimeter grains consisting of dendritic substructures. Strain-induced martensitic transformations to produce hexagonal close-packed (hcp) ε-phases were not identified under tensile deformation. The precipitation of the intermetallic σ-phase was identified at the interdendritic regions where solidification segregation of Cr and W occurred. The size and chemical composition of this σ-phase did not vary with the bulk nitrogen concentration. Adding nitrogen to the alloys did not alter their tensile yield stress or Vickers hardness values significantly, suggesting that the nitrogen strengthening effect is affected by the manufacturing route as well as local chemistry that is involved in the microstructural evolution during solidification. The tensile ductility, on the other hand, increased with an increase in nitrogen concentration; the alloy with 0.35wt% nitrogen exhibited 21% elongation with a high 0.2% proof stress (589MPa). This significant improvement in ductility was likely caused by the reduction in the amount of σ-phase precipitates at the interdendritic regions following the addition of nitrogen.
Reinvestigation of the formation of a mononuclear Fe(iii) hydroperoxido complex using high pressure kinetics (2010)

Previous stopped flow kinetic experiments suggested an interchange associative mechanism for the ligand substitution reaction, [Fe(bztpen)(OMe)](2+) + H(2)O(2)--> {[Fe(bztpen)(OMe)(HOOH)](2+)}(++)--> [Fe(bztpen)(OOH)](2+) + MeOH (bztpen = N-benzyl-N, N',N'tris(2-methylpyridyl)-ethylenediamine). Thus a seven-coordinate transition state containing both the leaving methoxide and the incoming hydrogen peroxide ligands was proposed. On the basis of high pressure kinetic data we can now conclude that this is not the case since the rate of the reaction is independent of pressure for the formation of the purple low spin transient hydroperoxido complex, [Fe(bztpen)(OOH)](2+). [Fe(bztpen)(OOH)](2+) has so far proved to be too short-lived for solid state isolation. As part of our ongoing pursuit of this elusive species we have structurally characterised the nitrosyl and acetate iron(II) complexes, [Fe(bztpen)(NO)](OTf)(2) and [Fe(bztpen)(OAc)](BPh(4)), as well as the air stable Co(II) complexes [Co(bztpen)Cl)]BF(4), [Co(metpen)Cl]SbF(6) and [Co(bztpen)(OAc)]BPh(4). We did not realise our aim of accessing stable Co(III) hydroperoxido or peroxido complexes by reaction of the cobalt complexes with H(2)O(2).
CVD diamond wafers as large-area thermoluminescence detectors for measuring the spatial distribution of dose (2003)

The applicability of large-area CVD diamond wafers (diameter about 5 cm, thickness about 0.1 mm), read out as thermoluminescence (TL) detectors, for assessing two-dimensional (2-D) dose distribution over their area, was investigated. To obtain 2-D TL images, a special TL reader equipped with large-area planchet and a CCD camera instead of the usual PM tube was developed. Several 2-D TL images: of an alpha source (Am-241), a Ra-226 needle source and a Ru-106 ophthalmic applicator, were measured and high-resolution digital images obtained. Our preliminary results demonstrate the potential capability of large-area CVD diamond wafers, read out as TL detectors, in 2-D dosimetry for medical applications. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Intracellular Eukaryotic Parasites Have a Distinct Unfolded Protein Response (2011)

Insult to the endoplasmic reticulum (ER) activates the Unfolded Protein Response (UPR), a set of signaling pathways that protect the cell from the potential damage caused by improperly folded proteins. Accumulation of misfolded proteins in the ER lumen initiates a series of signal transduction events via activation of three transmembrane ER proteins: Ire1, Atf6 and PERK. Activation of these proteins results in the transcriptional up-regulation of the components of the folding, trafficking and degradation machinery in the ER. PERK further reduces the load on the ER via the phosphorylation of eIF2α, attenuating general protein translation. It is believed that the UPR evolved as a transcriptional response that up-regulates protein folding machinery in the ER and later gained the ability to decrease ER load by attenuating general protein translation in metazoa. However, our in silico analyses of protozoan parasites revealed an absence of proteins involved in the transcriptionally mediated UPR and the presence of both PERK and its target eIF2α. Consistent with these observations, stimulation of the UPR in Leishmania donovani identified an absence of up-regulation of the ER chaperone BiP, the canonical ER chaperone modulated by the UPR in higher eukaryotes, while exhibiting increased phosphorylation of eIF2α which has been shown to attenuate protein translation. We further observed that L. donovani is more sensitive to UPR inducing agents than host macrophages, suggesting that the less evolved stress response could provide a new avenue for therapeutic treatment of parasitic infections.
Effect of structure on properties of polyols and polyurethanes based on different vegetable oils (2004)

Abstract We synthesized six polyurethane networks from 4,4′‐diphenylmethane diisocyanate and polyols based on midoleic sunflower, canola, soybean, sunflower, corn, and linseed oils. The differences in network structures reflected differences in the composition of fatty acids and number of functional groups in vegetable oils and resulting polyols. The number average molecular weights of polyols were between 1120 and 1300 and the functionality varied from 3.0 for the midoleic sunflower polyol to 5.2 for the linseed polyol. The functionality of the other four polyols was around 3.5. Canola, corn, soybean, and sunflower oils gave polyurethane resins of similar crosslinking density and similar glass transitions and mechanical properties despite somewhat different distribution of fatty acids. Linseed oil–based polyurethane had higher crosslinking density and higher mechanical properties, whereas midoleic sunflower oil gave softer polyurethanes characterized by lower T g and lower strength but higher elongation at break. It appears that the differences in properties of polyurethane networks resulted primarily from different crosslinking densities and less from the position of reactive sites in the fatty acids. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 809–819, 2004
Assessment of Endoscopic Mucosal Healing of Ulcerative Colitis Using Linked Colour Imaging, a Novel Endoscopic Enhancement System (2017)

Endoscopic LCI classification and LCI index can subdivide samples with the same Mayo endoscopic subscore. LCI may be a novel approach for evaluating colonic mucosal inflammation and for predicting outcome in UC patients.