gebhart/patrepeval huggingface dataset:
[Decellularization technology application in whole liver reconstruct biological scaffold]. (2009)

Perfusion with detergents through portal vein for liver decellularization was an efficient method to obtain a completely whole-liver scaffold which can be used for hepatic organ reconstruction.
Bioactive metabolites of symbiotic marine microorganisms (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBioactive metabolites of symbiotic marine microorganismsJunichi. Kobayashi and Masami. IshibashiCite this: Chem. Rev. 1993, 93, 5, 1753–1769Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/cr00021a005https://doi.org/10.1021/cr00021a005research-articleACS PublicationsRequest reuse permissionsArticle Views2276Altmetric-Citations277LEARN 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-Alertsclose Get e-Alerts
Repression of Acinetobacter vanillate demethylase synthesis by VanR, a member of the GntR family of transcriptional regulators (2000)

Vanillate is converted to protocatechuate by the action of vanillate demethylase encoded by vanAB. Convergent upon and overlapping Acinetobacter vanB is an open reading frame encoding a member of the gntR repressor family and designated vanR. This gene organization differs from that found in a Pseudomonas isolate. An Acinetobacter strain with a knockout mutation in vanR constitutively converted vanillate to protocatechuate. Reverse transcriptase-polymerase chain reaction was used to demonstrate that control of vanAB was exerted at the level of transcription.
Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs (2013)

Mammalian HELQ is a 3'-5' DNA helicase with strand displacement activity. Here we show that HELQ participates in a pathway of resistance to DNA interstrand crosslinks (ICLs). Genetic disruption of HELQ in human cells enhances cellular sensitivity and chromosome radial formation by the ICL-inducing agent mitomycin C (MMC). A significant fraction of MMC sensitivity is independent of the Fanconi anaemia pathway. Sister chromatid exchange frequency and sensitivity to UV radiation or topoisomerase inhibitors is unaltered. Proteomic analysis reveals that HELQ is associated with the RAD51 paralogs RAD51B/C/D and XRCC2, and with the DNA damage-responsive kinase ATR. After treatment with MMC, reduced phosphorylation of the ATR substrate CHK1 occurs in HELQ-knockout cells, and accumulation of G2/M cells is reduced. The results indicate that HELQ operates in an arm of DNA repair and signalling in response to ICL. Further, the association with RAD51 paralogs suggests HELQ as a candidate ovarian cancer gene.
Recent advances in nonlinear fiber optics (1995)

The objective of this paper is to provide an overview of the recent advances in the field of non linear fiber optics. The emphasis is placed on the generation, amplification and transmission of ultrashort optical pulses and their use in optical communication systems. Topics discussed include mode-locking of fiber lasers, chirped-pulse amplification and the importance of dispersion decreasing fibers for the generation and transmission of ultrashort solitons.
Direct conversion of pyranose anomeric OH→F→R in the artemisinin family of antimalarial trioxanes (1998)

Eleven examples form the basis of a short and effective synthetic method for replacement of an anomeric fluorine atom by saturated, unsaturated, aryl and heteroaryl carbon nucleophiles to prepare α- or β-oriented C10-R derivatives of the trioxane 10-deoxoartemisinin.
Expression and Function of the Progesterone Receptor in Human Prostate Stroma Provide Novel Insights to Cell Proliferation Control (2013)

Context:Like other tissues, the prostate is an admixture of many different cell types that can be segregated into components of the epithelium or stroma. Reciprocal interactions between these 2 types of cells are critical for maintaining prostate homeostasis, whereas aberrant stromal cell proliferation can disrupt this balance and result in diseases such as benign prostatic hyperplasia. Although the androgen and estrogen receptors are relatively well studied for their functions in controlling stromal cell proliferation and differentiation, the role of the progesterone receptor (PR) remains unclear.
Integration of model-based and sensor-based control for a two-link flexible robot arm (2002)

The experimental results of model-based and sensor-based control strategies for a two-link flexible planar robot arm are analyzed. Offline optimization determines a minimum-time straight-line tip trajectory which stays within the torque constraints of the motors and ends in a quiescent state, i.e., no vibrational transients. An efficient finite-element model is used in the optimization to approximate the flexible arm dynamics. Control schemes tested include an open-loop torque profile, a closed-loop proportional-derivative joint controller, and a feedforward controller. This last scheme uses the torque profile created from the optimization, along with PD feedback of the joint angles and proportional feedback of the strain gages, to correct for errors in the model. The results show that the best performance is achieved with this feedforward approach
GM‐CSF‐based cancer vaccines (2002)

The crafting of genetic and biochemical techniques to identify cancer antigens yielded the unexpected discovery that immune recognition of tumors regularly accompanies cancer development. The failure of the host to suppress tumor formation or attenuate disease progression may thus reflect the limited immunogenicity of nascent tumors. One critical determinant of host immunity is the mixture of cytokines produced in the tumor microenvironment. We have compared a large number of secreted and surface molecules for their relative abilities to augment tumor immunity following gene transfer into cancer cells. In multiple murine models, granulocyte-macrophage colony stimulating factor (GM-CSF) proved to be the most potent immunostimulatory product. Vaccination with irradiated tumor cells engineered to secrete GM-CSF involves enhanced tumor antigen presentation by recruited dendritic cells (DCs) and macrophages; the coordinated functions of CD4+ and CD8+ T cells, CD1d-restricted NKT cells and antibodies mediate protective immunity. The evaluation of this vaccination strategy in patients with advanced melanoma revealed the consistent induction of cellular and humoral antitumor responses capable of effectuating substantial necrosis of distant metastases. The formulation of simplified methods for manufacturing autologous, GM-CSF-secreting tumor cells has enabled more extensive clinical testing in diverse patient settings.
Maternal immunization of mice with group B streptococcal type III polysaccharide-beta C protein conjugate elicits protective antibody to multiple serotypes. (1994)

Group B streptococcal infection is a major cause of neonatal mortality. Antibody to the capsular polysaccharide protects against invasive neonatal disease, but immunization with capsular polysaccharides fails to elicit protective antibody in many recipients. Conjugation of the polysaccharide to tetanus toxoid has been shown to increase immune response to the polysaccharide. In animal models, C proteins of group B streptococci are also protective determinants. We examined the ability of the beta C protein to serve in the dual role of carrier for the polysaccharide and protective immunogen. Type III polysaccharide was covalently coupled to beta C protein by reductive amination. Immunization of rabbits with the polysaccharide-protein conjugate elicited high titers of antibody to both components, and the serum induced opsonophagocytic killing of type III, Ia/C, and Ib/C strains of group B streptococci. Female mice were immunized with the conjugate vaccine and then bred; 93% of neonatal pups born to these dams vaccinated with conjugate survived type III group B streptococcal challenge and 76% survived type Ia/C challenge, compared with 3% and 8% survival, respectively, in controls (P < 0.001). The beta C protein acted as an effective carrier for the type III polysaccharide while simultaneously induced protective immunity against beta C protein--containing strains of group B streptococci.
Automatic thesaurus construction supporting fuzzy retrieval of reusable components (1995)

Effective access to repositories of reusable: components should rely on retrieval functionalities based also on imprecise queries. This paper presents a fuzzy retrieval model based on keywords describing the functionalities of reusable components. Fuzzy weights are assigned to these keywords automatically. Retrieval is supported by a Thesaurus where a fuzzy synonymia relationship is used to c:ompute adaptability of reusable components to the needs expressed by the user fuzzy query. The adaptability index is ameliorated along time via a quality function reporting feedback on the system usage.
Tricarboxylic Acid Cycle Activity Regulates Tomato Root Growth via Effects on Secondary Cell Wall Production (2010)

Transgenic tomato (Solanum lycopersicum 'Moneymaker') plants independently expressing fragments of various genes encoding enzymes of the tricarboxylic acid cycle in antisense orientation have previously been characterized as exhibiting altered root growth. In this study, we evaluate the rates of respiration of roots from these lines in addition to determining their total dry weight accumulation. Given that these features were highly correlated, we decided to carry out an evaluation of the cell wall composition in the transformants that revealed a substantial reduction in cellulose. Since the bulk of cellulose is associated with the secondary cell walls in roots, we reasoned that the transformants most likely were deficient in secondary wall cellulose production. Consistent with these findings, cross-sections of the root collar (approximately 15 mm from the junction between root and stem) displayed reduced lignified secondary cell walls for the transformants. In contrast, cell and cell wall patterning displayed no differences in elongating cells close to the root tip. To further characterize the modified cell wall metabolism, we performed feeding experiments in which we incubated excised root tips in [U-(14)C]glucose in the presence or absence of phosphonate inhibitors of the reaction catalyzed by 2-oxoglutarate dehydrogenase. Taken together, the combined results suggest that restriction of root respiration leads to a deficit in secondary cell wall synthesis. These data are discussed in the context of current models of biomass partitioning and plant growth.
Self-regulation of procoagulant events on the endothelial cell surface. (1985)

Interleukin 1 (IL-1) is a potent mediator of inflammatory and immunologic phenomena. In addition, IL-1 may be intimately involved in the regulation of hemostasis, since interaction of IL-1 with endothelial cells has been reported to induce tissue factor activity. We demonstrate that perturbation of the endothelial cell induces augmented IL-1 release. Human umbilical vein endothelial cells perturbed by treatment with lipopolysaccharide produced enhanced amounts of IL-1 activity. IL-1 activity from lipopolysaccharide-treated endothelial cell supernatants could be absorbed by an antibody to IL-1 coupled to Sepharose. Elaboration of IL-1 activity was dependent on the dose of lipopolysaccharide and occurred in a time-dependent manner. Addition of cycloheximide blocked generation of IL-1 activity. A physiological vessel wall perturbant, the coagulation enzyme thrombin, induced comparable amounts of IL-1 activity in endothelial cell cultures. This effect was specific for the enzyme, since active site-blocked thrombin and prothrombin had no effect on IL-1. In addition, IL-1-containing supernatants from thrombin-stimulated endothelial cells induced tissue factor procoagulant activity in fresh endothelial cell cultures. Thus, in contrast to the multiple, known inhibitory mechanisms that block thrombin procoagulant activity, these data suggest a circle of interaction in which thrombin induces endothelial cell elaboration of IL-1, a mediator of endothelial cell procoagulant activity. Endothelial cell production of IL-1 in response to perturbation allows these cells to play an integral role in the regulation of the inflammatory and coagulation systems.
States of Tyrosyl Residues and Circular Dichroism of Kunitz Trypsin Inhibitor<xref ref-type="fn" rid="fn1"><sup>*</sup></xref> (1969)

In order to clarify the origin of the side chain Cotton effects of Kunitz trypsin inhibitor, effects of acetylation of the tyrosyl residues with N-acetylimidazole, oxidation of the tryptophyl residues with N-bromosuccinimide (NBS) and of pH on the circular dichroism (CD) were studied. Spectrophotometric titration of the tyrosyl groups and the change in the inhibitor activity accompanying acetylation were also examined. Spectrophotometric titration and acetylation with N-acetylimidazole demonstrate that one of the four tyrosyl residues of Kunitz trypsin inhibitor is free on the surface of the molecule and the remaining three are buried in the interior. Acetylation of all the tyrosyl residues which is achieved in 8 or 10 M urea at 50°G prevents the refolding of the inhibitor molecule on removal of urea. The CD spectrum of native Kunitz trypsin inhibitor has negative maxima at 294, 287, 280, 271, 263, and 245 mμ and a positive maximum at 226 mμ, in addition to a negative maximum at 203 mμ which arises from the peptide conformation. The negative band at around 280 mμ decreased proportionally with the increase in the degree of acetylation. A slight change in the CD band at 226 mμ was observed with acetylation of the one free tyrosyl residue. Acetylation in 8 M urea at 50°C, followed by removal of urea, modified the buried tyrosyl residues and abolished the band at 226 mμ, indicating a large contribution of the protein conformation to this band. The negative maximum at 294 mμ is originated from the tryptophyl residues. A new peak due to ionized tyrosyl residues appeared at 247 mμ with increasing pH. From the pH dependence of the CD spectrum, it was found that Kunitz trypsin inhibitor undergoes a confonnational change below pH7 and above pH 11.5. It is noteworthy that oxidation of tryptophyl residues with NBS generates new bands due to the oxidized product.
RNA integrity number (RIN) - towards standardization of RNA quality assessment (2004)

1649 RNA quality assessment has been identified as one of the most critical elements in order to obtain meaningful gene expression data via microarray or real-time PCR experiments. Current advances in microfluidics have improved RNA quality measurements tremendously by allowing a more detailed look at RNA degradation patterns by providing electrophoretic traces of RNA samples. However, the interpretation of such electropherograms still requires a certain level of experience and can vary from one researcher to the next. A so-called “RNA integrity number” (RIN) algorithm is introduced that assigns a user-independent integrity number to each RNA sample. The RIN has been developed using neural networks by “teaching” this algorithm with a large number of RNA integrity data. It was found that the RIN is more reliable than the ribosomal ratio, when assessing the integrity of RNA samples. The RIN is shown to be largely independent of RNA concentration, instrument (Agilent 2100 bioanalyzer), and most importantly, the origin of the RNA sample. Using the RIN, researchers can work towards standardization of the important RNA integrity measurement ensuring reproducibility and reliability of gene expression experiments.
Increased Cholesterol Content in Gammadelta (γδ) T Lymphocytes Differentially Regulates Their Activation (2013)

Gammadelta (γδ) T lymphocytes respond quickly upon antigen encounter to produce a cytokine response. In this study, we sought to understand how functions of γδ T cells are differentially regulated compared to αβ T cells. We found that cholesterol, an integral component of the plasma membrane and a regulator of TCR signaling, is increased in γδ T cells compared to αβ T cells, and modulates their function. Higher levels of activation markers, and increased lipid raft content in γδ cells suggest that γδ T cells are more activated. Cholesterol depletion effectively decreased lipid raft formation and activation of γδ T cells, indicating that increased cholesterol content contributes to the hyper-activated phenotype of γδ T cells, possibly through enhanced clustering of TCR signals in lipid rafts. TCR stimulation assays and western blotting revealed that instead of a lower TCR threshold, enhanced TCR signaling through ERK1/2 activation is likely the cause for high cholesterol-induced rapid activation and proliferation in γδ T cells. Our data indicate that cholesterol metabolism is differentially regulated in γδ T cells. The high intracellular cholesterol content leads to enhanced TCR signaling and increases activation and proliferation of γδ T cells.
Macrophage in chronic kidney disease (2016)

Chronic kidney disease (CKD) has become a major health problem worldwide. This review describes the role of macrophages in CKD and highlights the importance of anti-inflammatory M2 macrophage activation in both renal fibrosis and wound healing processes. Furthermore, the mechanisms by which M2 macrophages induce renal repair and regeneration are still under debate and currently demand more attention. The M1/M2 macrophage balance is related to the renal microenvironment and could influence CKD progression. In fact, an inflammatory renal environment and M2 plasticity can be the major hurdles to establishing macrophage cell-based therapies in CKD. M2 macrophage cell-based therapy is promising if the M2 phenotype remains stable and is 'fixed' by <i>in vitro</i> manipulation. However, a greater understanding of phenotype polarization is still required. Moreover, better strategies and targets to induce reparative macrophages <i>in vivo</i> should guide future investigations in order to abate kidney diseases.
Thermal evolution of amorphous tricalcium phosphate (2003)

Amorphous calcium phosphate (ACP) is one of the major components of biological mineralisation and plays a crucial role in several biomaterials. However, due to their instability, the thermochemical characteristics of ACP and of the derived metastable phases are still unknown. The thermal transformations affecting ACP, with a Ca/P atomic ratio close to 1.50, were studied in the range 373–1173 K. The samples were examined by X-ray diffraction, FTIR spectroscopy and BET measurements. The thermal behaviour was analysed by thermogravimetric and differential thermal analysis. The dissolution enthalpies of the products, in 9 wt% aqueous nitric acid solution, were determined using an isoperibolic calorimeter. The samples remained amorphous up to 773 K. The evolution of the dissolution enthalpy between 298 and 573 K was attributed to the irreversible loss of adsorbed water. The adsorption enthalpy at 298 K of liquid water on ACP was estimated at −12.3 kJ mol−1. At 673 K, the variation of the dissolution enthalpy corresponded to the occurrence in the amorphous phase of a more stable ionic organisation. The nucleation of the crystalline phase was believed to begin at 773 K. At 873 K and above, the ACP crystallised mainly into metastable α-tricalcium phosphate (α-TCP). Though the enthalpy of dissolution of the formed α-TCP varied with temperature, it remained lower than that of the most stable tricalcium phosphate crystalline structure: β-TCP. This phase was formed at 1173 K. The thermal measurements confirm the high instability of ACP compared to other calcium phosphates, including apatites. These properties, plus the very high specific surface area, explain the very fast transformation of ACP into apatite in aqueous media and justify its use in new types of self-setting cements.
Infarct scar: a dynamic tissue (2000)

Infarct scar, a requisite to the rebuilding of necrotic myocardium following myocardial infarction (MI), has long been considered inert. Earlier morphologic studies suggested healing at the infarct site was complete within 6-8 weeks following MI and resultant scar tissue, albeit necessary, was acellular and simply fibrillar collagen. Utilizing molecular and cellular biologic technologies, recent studies indicate otherwise. Infarct scar is composed of phenotypically transformed fibroblast-like cells, termed myofibroblasts (myoFb) because they express alpha-smooth muscle actin (alpha-SMA) and these microfilaments confer contractile behavior in response to various peptides and amines. These cells are nourished by a neovasculature and are persistent at the MI site, where they are metabolically active expressing components requisite to angiotensin (Ang) peptide generation, including converting enzyme, receptors for AngII and transforming growth factor (TGF)-beta1. They continue to elaborate fibrillar type I collagen. Their generation of these peptides contribute to ongoing scar tissue collagen turnover and to fibrous tissue formation of noninfarcted myocardium. Infarct scar contraction accounts for its thinning and its tonus may contribute to abnormal ventricular chamber stiffness with diastolic dysfunction. Infarct scar is a dynamic tissue: cellular, vascularized, metabolically active and contractile. Pharmacologic interventions with angiotensin converting enzyme inhibitor or AT1 receptor antagonist has proven effective in attenuating scar tissue metabolic activity and minimizing adverse accumulation of fibrous tissue in noninfarcted myocardium.