gebhart/patrepeval huggingface dataset:
BAFF binding to T cell‐expressed BAFF‐R costimulates T cell proliferation and alloresponses (2004)

Binding of the TNF family member, B cell activating factor (BAFF), to its receptor (BAFF-R, TNFRSF13C) is required for generation and maintenance of mature B cells, but there are no data as to any role for the BAFF/BAFF-R pathway in T cell functions. We report that the binding of BAFF to BAFF-R expressed by a subset of primarily CD4(+) T cells costimulates T cell activation and allo-proliferation in vitro and in vivo, and that mice with a mutation in the BAFF-R, or with a targeted deletion of BAFF, show prolonged cardiac allograft survival as compared to wild-type or transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI)(-/-) controls. Taken together, these data indicate the BAFF/BAFF-R pathway contributes to both T and B cell responses and may be an attractive target for control of acute and chronic allograft rejection.
α1,3‐Fucoslytransferase IX (Fuc‐TIX) is very highly conserved between human and mouse; molecular cloning, characterization and tissue distribution of human Fuc‐TIX (1999)

The amino acid sequence of Fuc-TIX is very highly conserved between mouse and human. The number of non-synonymous nucleotide substitutions of the Fuc-TIX gene between human and mouse was strikingly low, and almost equivalent to that of the alpha-actin gene. This indicates that Fuc-TIX is under a strong selective pressure of preservation during evolution. The human Fuc-TIX (hFuc-TIX) showed a unique characteristics, i.e. hFuc-TIX was not activated by Mn2+ and Co2+, whereas hFuc-TIV and hFuc-TVI were activated by the cations. The hFuc-TIX transcripts were abundantly expressed in brain and stomach, and interestingly were detected in spleen and peripheral blood leukocytes.
Physical and electrical characterization of ultrathin yttrium silicate insulators on silicon (2001)

This article describes the oxidation of yttrium on silicon to form yttrium silicate films for application as high dielectric constant insulators. The high reactivity of yttrium metal with silicon and oxygen is utilized to form amorphous yttrium silicate films with a minimal interfacial silicon dioxide layer. Yttrium silicate films (∼40 Å) with an equivalent silicon dioxide thickness of ∼11 Å and k∼14 are formed by oxidizing yttrium on silicon. The physical properties of yttrium silicate films on silicon are investigated using x-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. The oxidation of yttrium silicide results in films nearly identical, although with a higher silicon fraction, to films formed by oxidation of yttrium on silicon. The oxidation of yttrium on silicon results in a competition for yttrium between silicide formation and oxidation. This competition yields yttrium silicate films for thin (&amp;lt;40 Å) initial metal thickness and a Y2O3/silicate bilayer for thick (&amp;gt;80 Å) initial metal thickness. Annealing yttrium films on silicon in vacuum to form yttrium silicide and then oxidizing the silicide is used to eliminate the competition and control the yttrium/silicon reaction. Analysis of the oxidation of yttrium on silicon reveals fast oxidation during silicate formation and a slow rate during oxidation of the silicon substrate to form SiO2. Oxidation of other metals, such as Hf, Zr, and La, on silicon is expected to result in metal silicate films through a similar simultaneous (or controlled sequential) silicide/oxidation reactions.
Linear PADRE T Helper Epitope and Carbohydrate B Cell Epitope Conjugates Induce Specific High Titer IgG Antibody Responses (2000)

Linear carbohydrate-peptide constructs based on the 13 amino acid nonnatural pan DR epitope (PADRE) and carbohydrate B cell epitopes are demonstrated to be potent immunogens. These data support our belief that PADRE should be considered as an alternative to more complex carriers for use in prophylaxis and therapeutic vaccines. Two model carbohydrate-PADRE glycoconjugates were used to demonstrate that PADRE could effectively provide T cell help for carbohydrate-specific Ab responses. Conjugates of PADRE covalently linked to the human milk oligosaccharide, lacto-N-fucopentose II or a dodecasaccharide derived from Salmonella typhimurium O-Ag induced high titer IgG Ab responses in mice, which were comparable to glycoconjugates employing human serum albumin (HSA) as the carrier protein. Different adjuvants, in combination with PADRE conjugates, allowed for the modulation of the isotype profile with alum supporting an IgG1 profile; QS-21 an IgG2a, 2b profile, while an alum/QS-21 mixture generated a balanced IgG1/IgG2b isotype profile. As defined by binding to synthetic glycoconjugates, dodecasaccharide-specific Abs exhibited fine specificity similar to protective polyclonal Ab responses previously reported for dodecasaccharide-protein conjugates. The same Abs bound to intact S. typhimurium cells, suggesting that biologically relevant specificities were produced. The affinity of the dodecasaccharide-specific Abs was further shown to be comparable to that of a well-characterized, high affinity monoclonal anti-carbohydrate Ab recognizing the same epitope.
Noninvasive Fetal Sex Determination Using Cell-Free Fetal DNA (2011)

Despite interstudy variability, performance was high using maternal blood. Sensitivity and specificity for detection of Y chromosome sequences was greatest using RTQ-PCR after 20 weeks' gestation. Tests using urine and tests performed before 7 weeks' gestation were unreliable.
Single molecule force spectroscopy by AFM indicates helical structure of poly(ethylene-glycol) in water (1999)

We elongated individual poly(ethylene-glycol) (PEG) molecules tethered at one end to an AFM cantilever. We observed the resistive force as a function of elongation in different solvents. In all cases the molecular response was found to be fully reversible and thus in thermodynamic equilibrium. In hexadecane the stretched PEG acts like an ideal entropy spring and can be well described as a freely jointed chain. In water we observed marked deviations in the transition region from entropic to enthalpic elasticity, indicating the deformation of a supra-structure within the polymer. An analysis based on elastically coupled Markovian two-level systems agrees well with recent ab initio calculations predicting that PEG in water forms a non-planar supra-structure which is stabilized by water bridges. We obtained a binding free energy of 3.0±0.3 kT.
GAS6 Mediates Adhesion of Cells Expressing the Receptor Tyrosine Kinase Axl (1997)

Axl is a receptor tyrosine kinase that contains both immunoglobulin and fibronectin III repeats in its extracellular domain reminiscent of cell adhesion molecules. Expression of the receptor tyrosine kinase Axl in the 32D myeloid cell line permits aggregation of cells in response to treatment with the native ligand GAS6; this aggregation was not observed in untreated 32D-Axl cells nor in treated parental cells. This aggregation can be blocked by the addition of excess Axl extracellular domain peptide and does not require intracellular Axl kinase activity. Cell surface binding activity of GAS6 was mapped to distinct plasma membrane interacting domains that are separate from the GAS6 motifs that engage the Axl receptor. This suggests that aggregation is mediated by a heterotypic intercellular mechanism whereby cell-bound GAS6 interacts with Axl receptor on an adjacent cell. This mechanism is supported by our observation that GAS6 binds to 32D parental cells which then permits their aggregation with untreated 32D-Axl cells. We have recently demonstrated that the GAS6-Axl interaction does not initiate mitogenesis in 32D cells. When considered with the adhesion results, these data suggest that an important biological function of the Axl-GAS6 interaction is to mediate cell-cell binding.
High-Power ZBLAN Glass Fiber Lasers: Review and Prospect (2010)

ZBLAN (ZrF 4 -BaF 2 -LaF 3 -AlF 3 -NaF), considered as the most stable heavy metal fluoride glass and the excellent host for rare-earth ions, has been extensively used for efficient and compact ultraviolet, visible, and infrared fiber lasers due to its low intrinsic loss, wide transparency window, and small phonon energy. In this paper, the historical progress and the properties of fluoride glasses and the fabrication of ZBLAN fibers are briefly described. Advances of infrared, upconversion, and supercontinuum ZBLAN fiber lasers are addressed in detail. Finally, constraints on the power scaling of ZBLAN fiber lasers are analyzed and discussed. ZBLAN fiber lasers are showing promise of generating high-power emissions covering from ultraviolet to mid-infrared considering the recent advances in newly designed optical fibers, beam-shaped high-power pump diodes, beam combining techniques, and heat-dissipating technology.
Pituitary-Specific and Hormonally Regulated Gene Expression Directed by the Rat Proopiomelanocortin Promoter in Transgenic Mice (1990)

All aspects of POMC biosynthesis exhibit tissue-specific regulation. The single copy gene is highly expressed in anterior lobe (AL) corticotrophs and intermediate lobe (IL) melanotrophs of the pituitary gland and in the arcuate nucleus of the hypothalamus. POMC gene transcription in corticotrophs is induced by hypothalamic CRH and vasopressin and inhibited by adrenal glucocorticoids, while in melanotrophs it is predominantly regulated by beta-adrenergic neural input and dopamine. To identify the rat POMC (rPOMC) gene sequences necessary and sufficient to target expression and hormonal regulation in corticotrophs and melanotrophs, we generated 13 transgenic mice carrying rPOMC fusion genes. The genes consisted of 706 or 480 basepairs of rPOMC 5' flanking sequences ligated to either the E. coli LacZ gene encoding beta-galactosidase or the K1 mutant of the SV40 large T-antigen gene. Overall, half of the transgenic lines had reporter gene expression in their AL and IL in a pattern indistinguishable from ACTH immunohistochemistry. In three of these lines, beta-galactosidase or K1 T-antigen was localized by double immunofluorescence exclusively to ACTH-positive corticotrophs and melanotrophs. Transcriptional regulation of the rPOMC-LacZ fusion gene in response to hormonal manipulation was quantified by a fluorescence assay for beta-galactosidase enzyme activity in pituitary extracts. There was a 15-fold increase in AL enzyme activity after adrenalectomy and a 3-fold increase in IL activity after haloperidol treatment. X-gal histochemistry of pituitaries from hormonally treated mice confirmed the cellular specificity of these effects.(ABSTRACT TRUNCATED AT 250 WORDS)
Identification and sequencing of a gene encoding a hydantoin racemase from the native plasmid of Pseudomonas sp. strain NS671 (1992)

DNA fragments containing the genes involved in the conversion of 5-substituted hydantoins to their corresponding L-amino acids have been cloned from the 172-kb native plasmid (pHN671) of Pseudomonas sp. strain NS671. The largest recombinant plasmid, designated pHPB14, encoded the ability to convert D-5-substituted hydantoins to the corresponding L-amino acids, whereas the smallest one, designated pHPB12, encoded the ability to convert them to their corresponding N-carbamyl-D-amino acids. Restriction analysis suggested that the inserts of both recombinant plasmids are derived from the identical portion in pHN671 and that the insert of pHPB14, compared with that of pHPB12, has an extra 5.3 kb in length. DNA sequencing revealed that pHPB14 contains two additional complete open reading frames, designated ORF5 and hyuE. Analysis of deletion derivatives of pHPB14 indicated that hyuE is required for the ability to produce L-amino acids from the corresponding D-5-substituted hydantoins, but ORF5 is not. Cells of Escherichia coli transformed with a plasmid containing hyuE were capable of racemizing different 5-substituted hydantoins, indicating that hyuE is a gene encoding a hydantoin racemase.
Iron Oxyfluorides as High Capacity Cathode Materials for Lithium Batteries (2009)

Nanostructure iron oxyfluoride compounds of tunable oxygen content were fabricated by a solution process utilizing iron metal and fluorosilicic acid solutions as precursors. Simple adjustment of the synthesis atmosphere, temperature, and time enabled the fabrication of iron oxyfluoride materials with compositions spanning over the entire range from pure to FeOF. Nanocomposites were fabricated from iron oxyfluorides of various oxygen content and activated carbon in order, for the first time, to evaluate the impact of oxygen on the iron fluoride electrochemical performance. The introduction of oxygen proved beneficial to cycling stability but at the expense of reversible capacity. A combination of electrochemical and structural characterization analyses was performed to identify the iron oxyfluoride reaction mechanism.
Left Ventricular Assist Device Inflow Cannula Angle and Thrombosis Risk (2018)

Angulation of the inflow cannula >7° from the apical axis (axis connecting mitral valve and ventricular apex) leads to markedly unfavorable hemodynamics as determined by computational fluid dynamics. Computational hemodynamic simulations incorporating Lagrangian and Eulerian metrics are a powerful tool for studying optimization of LVAD implantation strategies, with the long-term potential of improving outcomes.
Construction and characterization of a potential live oral carrier-based vaccine against Vibrio cholerae O139 (1996)

The rfb region from Vibrio cholerae O139 strain MO45 was cloned from cosmid gene banks established in Escherichia coli HB101, using an immunoblot assay for screening of the correct clones. Immunoblot analysis of lipopolysaccharide (LPS) preparations revealed the presence of two types of positive clones: (i) those expressing only a short core-linked O polysaccharide (SOPS) and (ii) those also expressing a highly polymerized capsular polysaccharide (CPS) not bound to the E. coli K-12 LPS core. In addition, the latter clones appear to contain a locus which may encode a putative regulator of SOPS and CPS chain length. Further characterization in E. coli showed that CPS constitutes a barrier against large particles such as the bacteriophage Ffm but not against bacteriophage lambda or P1. In addition, a portion of the K-12 LPS core may not be substituted with SOPS. Loci associated with the two clonal types were transferred into V. cholerae CH19, an rfbAB deletion mutant of CVD103-HgR deficient in the production of the homologous Inaba O polysaccharide. This resulted in the stable expression of SOPS, alone or together with CPS, that was indistinguishable from that of wild-type V. cholerae O139. Strains CH25 and CH26, which correspond to CH19 bearing the V. cholerae O139 rfb region integrated into the chromosome, were found to be genetically stable and essentially identical to the parent CVD103-HgR with respect to physiological properties such as cell motility, mercury resistance, toxicity, and production of the cholera toxin B subunit. Rabbits immunized with CH25 elicited high titers of anti-O139 SOPS- and CPS-specific serum antibodies. These strains possess characteristics desirable in candidate live oral vaccines against V. cholerae O139.
Xanalogical structure, needed now more than ever (1999)

article Free Access Share on Xanalogical structure, needed now more than ever: parallel documents, deep links to content, deep versioning, and deep re-use Author: Theodor Holm Nelson Project Xanadu, Keio University Project Xanadu, Keio UniversityView Profile Authors Info & Claims ACM Computing SurveysVolume 31Issue 4esDec. 1999 pp 33–eshttps://doi.org/10.1145/345966.346033Published:01 December 1999Publication History 50citation2,161DownloadsMetricsTotal Citations50Total Downloads2,161Last 12 Months117Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Fast-Degrading Tissue-Engineered Vascular Grafts Lead to Increased Extracellular Matrix Cross-Linking Enzyme Expression (2021)

Tissue-engineered vascular grafts (TEVGs) require adequate extracellular matrix (ECM) to withstand arterial pressure. Tissue transglutaminase (TG2) and lysyl oxidase (LOX) are enzymes that cross-link ECM proteins and play a pivotal role in the development of vascular stiffness associated with aging. The purpose of this study is to investigate the expression of ECM cross-linking enzymes and mechanisms of scaffold degeneration leading to vascular stiffness in TEVG remodeling. Fast- and slow-degrading electrospun TEVGs were fabricated using polydioxanone (PDO) and poly(L-lactide-co-caprolactone) (PLCL) copolymer, with a PDO/PLCL ratio of 9:1 for fast-degrading and 1:1 for slow-degrading graft. These grafts were implanted in rats (<i>n</i> = 5/group) as abdominal aortic interposition conduits. The grafts were harvested at 1 month to evaluate patency, mechanical properties, vascular neotissue formation, and the expression of ECM cross-linking enzymes. All TEVGs were patent without any aneurysmal formation at 1 month. ECM area, TG2-positive area, and LOX-positive area were significantly greater in fast-degrading TEVGs compared to slow-degrading TEVGs, with significantly less remaining scaffold. The mechanical properties of fast-degrading TEVGs were similar to that of native aorta, as demonstrated by strain-stress curve. In conclusion, at 1 month, fast-degrading TEVGs had rapid and well-organized ECM with greater TG2 and LOX expression and native-like mechanical properties, compared to slow-degrading TEVGs. Impact statement Around 1.4 million patients in the United States require arterial prostheses each year due to cardiovascular diseases. Current synthetic vascular grafts suffer from increased risk of infection, thrombosis, a lack of endothelialization, and compliance mismatch to the native vasculature. Tissue-engineered vascular graft (TEVGs) presented in this study exhibited tunable biodegradation profiles by controlling the polymer ratio of polydioxanone/poly(L-lactide-co-caprolactone). One month after implantation, the fast-degrading TEVGs exhibited mechanical properties similar to that of native aorta, formation of endothelium, and well-organized extracellular matrix (ECM) with increased expression of tissue transglutaminase and lysyl oxidases, which are critical to the ECM remodeling process.
Ovine-Based Collagen Matrix Dressing: Next-Generation Collagen Dressing for Wound Care (2016)

<b>Significance:</b> Broad-spectrum metalloproteinase (MMP) reduction along with inherent aspects of an extracellular matrix (ECM) dressing can bring about improved wound healing outcomes and shorter treatment duration. Initial reports of clinical effectiveness of a new ovine-based collagen extracellular matrix (CECM) dressing demonstrate benefits in chronic wound healing. <b>Recent Advances:</b> CECM dressings are processed differently than oxidized regenerated cellulose/collagen dressings. CECM dressings consist primarily of collagens I and III arranged as native fibers that retain the three-dimensional architecture present in tissue ECM. As such, ovine-based ECM dressings represent a new generation of collagen dressings capable of impacting a broad spectrum of MMP excess known to be present in chronic wounds. <b>Critical Issues:</b> While MMPs are essential in normal healing, elevated presence of MMPs has been linked to wound failure. Collagen has been shown to reduce levels of MMPs, acting as a sacrificial substrate for excessive proteases in a chronic wound. Preserving collagen dressings in a more native state enhances bioactivity in terms of the ability to affect the chronic wound environment. Clinical observation and assessment may not be sufficient to identify a wound with elevated protease activity that can break down ECM, affect wound fibroblasts, and impair growth factor response. <b>Future Directions:</b> Collagen dressings that target broad-spectrum excessive MMP levels and can be applied early in the course of care may positively impact healing rates in difficult wounds. Next-generation collagen dressings offer broader MMP reduction capacity while providing a provisional dermal matrix or ECM.
AAV Genome Loss From Dystrophic Mouse Muscles During AAV-U7 snRNA-mediated Exon-skipping Therapy (2013)

In the context of future adeno-associated viral (AAV)-based clinical trials for Duchenne myopathy, AAV genome fate in dystrophic muscles is of importance considering the viral capsid immunogenicity that prohibits recurring treatments. We showed that AAV genomes encoding non-therapeutic U7 were lost from mdx dystrophic muscles within 3 weeks after intramuscular injection. In contrast, AAV genomes encoding U7ex23 restoring expression of a slightly shortened dystrophin were maintained endorsing that the arrest of the dystrophic process is crucial for maintaining viral genomes in transduced fibers. Indeed, muscles treated with low doses of AAV-U7ex23, resulting in sub-optimal exon skipping, displayed much lower titers of viral genomes, showing that sub-optimal dystrophin restoration does not prevent AAV genome loss. We also followed therapeutic viral genomes in severe dystrophic dKO mice over time after systemic treatment with scAAV9-U7ex23. Dystrophin restoration decreased significantly between 3 and 12 months in various skeletal muscles, which was correlated with important viral genome loss, except in the heart. Altogether, these data show that the success of future AAV-U7 therapy for Duchenne patients would require optimal doses of AAV-U7 to induce substantial levels of dystrophin to stabilize the treated fibers and maintain the long lasting effect of the treatment.