gebhart/patrepeval huggingface dataset:
Novel Tricyclic Compounds Having Acetylene Groups at C-8a and Cyano Enones in Rings A and C:  Highly Potent Anti-inflammatory and Cytoprotective Agents (2007)

Novel C-8a functionalized tricyclic compounds having cyano enones in rings A and C have been synthesized and biologically evaluated. Among them, compounds with acetylene groups at C-8a show extremely high potency in in vitro and in vivo bioassays for anti-inflammatory and cytoprotective activities. Both in vitro and in vivo potencies are markedly higher than those of 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO), which is being evaluated as an anticancer drug in phase I clinical trials.
A New Photopolymerizable Blood Vessel Glue that Seals Human Vessel Anastomoses Without Augmenting Thrombogenicity (1995)

A new nonbiologic photopolymerizable glue, polyethyleneglycol 400 diacrylate, was studied with respect to its mechanical and biochemical interaction with human blood vessels. Using the human placental artery model, we tested the ability of polyethyleneglycol 400 diacrylate to prevent leakage of blood at the site of vascular anastomoses, which are made porous by the presence of tissue gaps and suture puncture sites. Fibrin glue is known to augment local vessel thrombogenicity through the presence of the coagulation enzyme thrombin. We tested the effect of externally applied polyethyleneglycol 400 diacrylate (which does not contain thrombin) on luminal thrombin activity and platelet deposition from flowing human blood. At a shear rate of 312 per second and a transmural pressure of 80 cm H2O, the leakage rate of saline from human placental artery anastomoses was 1.0 ± 1.2 ml/min (n = 8). When the same anastomoses were then glued, 7 of 8 of the anastomoses leaked less than 0.05 ml/min (p < 0.05). Platelet deposition to human vessels was not influenced by the external application of polyethyleneglycol 400 diacrylate either on intact vessels (no polyethyleneglycol 400 diacrylate, 0.51 ± 0.28 × 106 platelets/cm2; with polyethyleneglycol 400 diacrylate, 0.47 ± 0.26 × 106 platelets/ cm2; n = 7) or at anastomoses (no polyethyleneglycol 400 diacrylate, 0.69 ± 0.36 × 106 platelets/cm2; with polyethyleneglycol 400 diacrylate, 0.53 ± 0.33 × 106 platelets/ cm2; n = 8), p > 0.05. Luminal thrombin activity, measured as the rate of fibrinopeptide A formation, was similarly unchanged from control whether polyethyleneglycol 400 diacrylate was applied to intact vessels (no polyethyleneglycol 400 diacrylate, 19 ± 13 ng fibrinopeptide A/ml; with polyethyleneglycol 400 diacrylate, 15 ± 13 ng fibrinopeptide A/ml; n = 10) or to anastomoses (no polyethyleneglycol 400 diacrylate, 15 ± 12 ng fibrinopeptide A/ml; with polyethyleneglycol 400 diacrylate, 15 ± 14 ng fibrinopeptide A/ml; n = 10), p > 0.05. We conclude that polyethyleneglycol 400 diacrylate is able to effectively seal vessel puncture sites and anastomotic junctions without acutely augmenting local vascular thrombogenicity. The absence of biologic components and of a need for local delivery of thrombin (as occurs when fibrin glue is used) should prompt additional study of this novel glue. (Plast. Reconstr. Surg. 95: 901, 1995.)
Synovium-Derived Mesenchymal Stem Cells: A New Cell Source for Musculoskeletal Regeneration (2009)

Ever since synovium-derived mesenchymal stem cells (SMSCs) were first identified and successfully isolated in 2001, as a brand new member in MSC families, they have been increasingly regarded as a promising therapeutic cell species for musculoskeletal regeneration, particularly for reconstructions of cartilage, bones, tendons, and muscles. Besides the general multipotency in common among the MSC community, SMSCs excel other sourced MSCs in higher ability of proliferation and superiority in chondrogenesis. This review summarizes the latest advances in SMSC-related studies covering their specific isolation methodologies, biological insights, and practical applications in musculoskeletal therapeutics of which an emphasis is cast on engineered chondrogenesis.
Effect of Gene Dosage at High Amylose Loci on the Properties of the Amylopectin Fractions of the Starches (1980)

Abstract The effect of gene dosage at the amylose‐extender (ae) locus of maize and the rigosus‐a ( r a ) locus of peas on the amylopectin fraction of endosperm and cotyledon starch were examined. Amylopectin fractions were isolated by gel filtration, butanol complexing and a combination of the two methods. In general, increasing doses of the recessive allele at either locus resulted in amylopectin fractions with iodine spectra with absorption maxima at higher wavelengths and greater absorptivity. Starches from endosperm of differing ae dosage but homozygous waxy were found to contain no amylose by gel filtration. By debranching with pullulanase, these starches were shown to have increasing average chain length with increasing ae dosage. Additional data suggested that increasing dosage at the ae locus (regardless of the genotype at the waxy locus) or the r a locus resulted in amylopectin with increasing linearity. In addition, short chained amylose (approximately 100 glucose units) was observed in all ae genotypes in a homozygous Waxy background and all r a genotypes.
Small Molecule Kinase Inhibitors for LRRK2 and Their Application to Parkinson's Disease Models (2012)

Parkinson's disease (PD) is the second most common neurodegenerative disorder. Several single gene mutations have been linked to this disease. Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) indicate LRRK2 as promising therapeutic target for the treatment of PD. LRRK2 mutations were observed in sporadic as well as familial PD patients and have been investigated intensively. LRRK2 is a large and complex protein, with multiple enzymatic and protein-interaction domains, each of which is effected by mutations. The most common mutation in PD patients is G2019S. Several LRRK2 inhibitors have been reported already, although the crystal structure of LRRK2 has not yet been determined. This review provides a summary of known LRRK2 inhibitors and will discuss recent in vitro and in vivo results of these inhibitors.
Regulation of intestinal epithelial cell growth by transforming growth factor type beta. (1989)

A nontransformed rat jejunal crypt cell line (IEC-6) expresses transforming growth factor type beta 1 (TGF-beta 1) mRNA, secretes latent 125I-labeled TGF-beta 1 competing activity into culture medium, and binds 125I-labeled TGF-beta 1 to specific, high-affinity (Kd = 3.7 pM) cell surface receptors. IEC-6 cell growth is markedly inhibited by TGF-beta 1 and TGF-beta 2 with half-maximal inhibition occurring between 0.1 and 1.0 ng of TGF-beta 1 per ml. TGF-beta 1-mediated growth inhibition is not associated with the appearance of biochemical markers of enterocyte differentiation such as alkaline phosphatase expression and sucrase activity. TGF-beta 1 (10 ng/ml) increases steady-state levels of its own mRNA expression within 8 hr of treatment of rapidly growing IEC-6 cells. In freshly isolated rat jejunal enterocytes that are sequentially eluted from the crypt villus axis, TGF-beta 1 mRNA expression is most abundant in terminally differentiated villus tip cells and least abundant in the less differentiated, mitotically active crypt cells. We conclude that TGF-beta 1 is an autoregulated growth inhibitor in IEC-6 cells that potentially functions in an autocrine manner. In the rat jejunal epithelium, TGF-beta 1 expression is most prominently localized to the villus tip--i.e., the region of the crypt villus unit that is characterized by the terminally differentiated phenotype. These data suggest that TGF-beta 1 may function in coordination of the rapid cell turnover typical for the intestinal epithelium.
Solid-Phase Synthesis of Alkyl Aryl Ethers via the Ullmann Condensation (2002)

Alkyl aryl ether formation is a frequently employed reaction in organic synthesis. Ullmann condensation is an alternative method to the widely used Mitsunobu reaction and is very useful in situations where application of the Mitsunobu reaction is limited. By application of this reaction to solid-phase synthesis of a series of alkyl aryl ethers, reaction conditions (catalyst, solvent, temperature, time, etc.) for a sterically hindered class of alcohols were investigated and optimized. A range of aryl halides was used to explore the scope of the reaction in solid phase.
A Distributed Intelligent Agent-Based Spatial Decision Support System (1998)

GIS usage has resulted in large volumes of spatial data, and organizations see the need for incorporating this data into their analysis and decision making. Managers are beginning to understand the potential of using DSS and EIS that are enhanced with spatial and temporal capabilities in addressing issues related to marketing, demographics, routing, etc. Traditional GIS have lagged behind in providing tools that support upper management in decision making and cooperative problem solving. As pointed out by Keenan (1997), and Mennecke (1997), there are ample opportunities for cross fertilization of ideas from IS and GIS research in this regard.
Imperfect Gold Standards for Kidney Injury Biomarker Evaluation (2011)

Clinicians have used serum creatinine in diagnostic testing for acute kidney injury for decades, despite its imperfect sensitivity and specificity. Novel tubular injury biomarkers may revolutionize the diagnosis of acute kidney injury; however, even if a novel tubular injury biomarker is 100% sensitive and 100% specific, it may appear inaccurate when using serum creatinine as the gold standard. Acute kidney injury, as defined by serum creatinine, may not reflect tubular injury, and the absence of changes in serum creatinine does not assure the absence of tubular injury. In general, the apparent diagnostic performance of a biomarker depends not only on its ability to detect injury, but also on disease prevalence and the sensitivity and specificity of the imperfect gold standard. Assuming that, at a certain cutoff value, serum creatinine is 80% sensitive and 90% specific and disease prevalence is 10%, a new perfect biomarker with a true 100% sensitivity may seem to have only 47% sensitivity compared with serum creatinine as the gold standard. Minimizing misclassification by using more strict criteria to diagnose acute kidney injury will reduce the error when evaluating the performance of a biomarker under investigation. Apparent diagnostic errors using a new biomarker may be a reflection of errors in the imperfect gold standard itself, rather than poor performance of the biomarker. The results of this study suggest that small changes in serum creatinine alone should not be used to define acute kidney injury in biomarker or interventional studies.
Live Cell Refractometry Using Hilbert Phase Microscopy and Confocal Reflectance Microscopy (2009)

Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ.
NF-κB Function in Growth Control: Regulation of Cyclin D1 Expression and G 0 /G 1 -to-S-Phase Transition (1999)

Nuclear factor kappa B (NF-kappaB) has been implicated in the regulation of cell proliferation, transformation, and tumor development. We provide evidence for a direct link between NF-kappaB activity and cell cycle regulation. NF-kappaB was found to stimulate transcription of cyclin D1, a key regulator of G1 checkpoint control. Two NF-kappaB binding sites in the human cyclin D1 promoter conferred activation by NF-kappaB as well as by growth factors. Both levels and kinetics of cyclin D1 expression during G1 phase were controlled by NF-kappaB. Moreover, inhibition of NF-kappaB caused a pronounced reduction of serum-induced cyclin D1-associated kinase activity and resulted in delayed phosphorylation of the retinoblastoma protein. Furthermore, NF-kappaB promotes G1-to-S-phase transition in mouse embryonal fibroblasts and in T47D mammary carcinoma cells. Impaired cell cycle progression of T47D cells expressing an NF-kappaB superrepressor (IkappaBalphaDeltaN) could be rescued by ectopic expression of cyclin D1. Thus, NF-kappaB contributes to cell cycle progression, and one of its targets might be cyclin D1.
Conversion of hydroxycinnamic acids into volatile phenols in a synthetic medium and in red wine by Dekkera bruxellensis (2012)

The conversion of p-coumaric acid, ferulic acid, and caffeic acid into 4-ethylphenol, 4-ethylguaiacol and 4-ethylcatechol was studied in Dekkera bruxellensis ISA 1791 under defined conditions in a synthetic medium and in a red wine. Liquid chromatography (HPLC-DAD) was used to quantify the phenolic acids, and gas chromatography (GC) coupled to a FID detector was used to quantify volatile phenols using a novel analytical methodology that does not require sample derivatization. Identification was achieved by gas chromatography-mass detection (GC-MS). The results show that phenolic acids concentration decreases while volatile phenols concentration increases. The proportion of caffeic acid taken up by Dekkera bruxellensis is lower than that for p-coumaric or ferulic acid; therefore less 4-ethylcatechol is formed. More important, 4-ethylcathecol synthesis by Dekkera bruxellensis in wine has never been demonstrated so far. These results contribute decisively to a better understanding of the origin of the volatile phenols in wines. The accumulation of these compounds in wine is nowadays regarded as one of the key factors of quality control.
Tim-3 Expression Defines Regulatory T Cells in Human Tumors (2013)

Tim-3, a member of the novel Tim (T cell immunoglobulin and mucin domain) family, has been reported to negatively regulate the immune responses against viral infection and had implications for autoimmune disease. However, the nature and role of Tim-3(+) CD4 T cells in human tumors remain largely unknown. In the present study, we characterized Tim-3(+) CD4 T cells in 100 specimens from human hepatocellular, cervical, colorectal and ovarian carcinoma patients. Compared with peripheral blood and nontumor-infiltrating lymphocytes, the lymphocytes isolated from the corresponding tumor tissues of hepatocellular, cervical, colorectal and ovarian carcinoma patients contained significantly greater proportion of Tim-3(+) CD4 T cells. The majority of tumor-derived Tim-3(+) CD4 T cells exhibited an impaired capacity to produce IFN-γ and IL-2, but expressed higher levels of CD25, Foxp3, CTLA-4 and GITR than their Tim-3(-) CD4 T cell counterparts. In contrast, most Tim-3(+) CD4 T cells isolated from the paired nontumor tissues and peripheral blood did not express these molecules. Moreover, tumor-derived Tim-3(+) CD4 T cells, but not tumor-derived Tim-3(-) CD4 T cells, significantly suppressed the proliferation of autologous CD8(+) T cells in vitro. Notably, multi-color immunofluorescence and confocal microscopy demonstrated that Tim-3(+)Foxp3(+)CD4(+) cells were preferentially distributed in the tumor nest rather than the peritumoral stroma of hepatocellular carcinoma. Together, our data indicate that Tim-3-expressing CD4 T cells in human tumors could represent the functional regulatory T cells which contribute to the formation of the immune-suppressive tumor micromilieu.
Direct interaction of Gβγ with a C-terminal Gβγ-binding domain of the Ca 2+ channel α 1 subunit is responsible for channel inhibition by G protein-coupled receptors (1997)

Several classes of voltage-gated Ca2+ channels (VGCCs) are inhibited by G proteins activated by receptors for neurotransmitters and neuromodulatory peptides. Evidence has accumulated to indicate that for non-L-type Ca2+ channels the executing arm of the activated G protein is its betagamma dimer (Gbetagamma). We report below the existence of two Gbetagamma-binding sites on the A-, B-, and E-type alpha1 subunits that form non-L-type Ca2+ channels. One, reported previously, is in loop 1 connecting transmembrane domains I and II. The second is located approximately in the middle of the ca. 600-aa-long C-terminal tails. Both Gbetagamma-binding regions also bind the Ca2+ channel beta subunit (CCbeta), which, when overexpressed, interferes with inhibition by activated G proteins. Replacement in alpha1E of loop 1 with that of the G protein-insensitive and Gbetagamma-binding-negative loop 1 of alpha1C did not abolish inhibition by G proteins, but the exchange of the alpha1E C terminus with that of alpha1C did. This and properties of alpha1E C-terminal truncations indicated that the Gbetagamma-binding site mediating the inhibition of Ca2+ channel activity is the one in the C terminus. Binding of Gbetagamma to this site was inhibited by an alpha1-binding domain of CCbeta, thus providing an explanation for the functional antagonism existing between CCbeta and G protein inhibition. The data do not support proposals that Gbetagamma inhibits alpha1 function by interacting with the site located in the loop I-II linker. These results define the molecular mechanism by which presynaptic G protein-coupled receptors inhibit neurotransmission.
Boronate-Based Fluorescent Probes for Imaging Cellular Hydrogen Peroxide (2005)

The syntheses, properties, and biological applications of the Peroxysensor family, a new class of fluorescent probes for hydrogen peroxide, are presented. These reagents utilize a boronate deprotection mechanism to provide high selectivity and optical dynamic range for detecting H2O2 in aqueous solution over similar reactive oxygen species (ROS) including superoxide, nitric oxide, tert-butyl hydroperoxide, hypochlorite, singlet oxygen, ozone, and hydroxyl radical. Peroxyresorufin-1 (PR1), Peroxyfluor-1 (PF1), and Peroxyxanthone-1 (PX1) are first-generation probes that respond to H2O2 by an increase in red, green, and blue fluorescence, respectively. The boronate dyes are cell-permeable and can detect micromolar changes in H2O2 concentrations in living cells, including hippocampal neurons, using confocal microscopy and two-photon microscopy. The unique combination of ROS selectivity, membrane permeability, and a range of available excitation/emission colors establishes the potential value of PR1, PF1, PX1, and related probes for interrogating the physiology and pathology of cellular H2O2.
Facing the future: challenges and opportunities in adoptive T cell therapy in cancer (2019)

The immunotherapy toolbox is rapidly expanding and improving, and the future promises further breakthroughs in the T cell ACT field. The heterogeneity of the tumor microenvironment and the multiplicity of tumor immune escape mechanisms pose formidable challenges to successful T cell immunotherapy in solid tumors, however. Individualized approaches and strategies combining treatments targeting different immunotherapeutic aspects will be needed in order to expand the applicability and improve the response rates in future.
Efficient chemoenzymatic synthesis of an N-glycan isomer library (2015)

Quantification, characterization and biofunctional studies of N-glycans on proteins remain challenging tasks due to complexity, diversity and low abundance of these glycans. The availability of structurally defined N-glycans (especially isomers) libraries is essential to help on solving these tasks. We reported herein an efficient chemoenzymatic strategy, namely Core Synthesis/Enzymatic Extension (CSEE), for rapid production of diverse N-glycans. Starting with 5 chemically prepared building blocks, 8 N-glycan core structures containing one or two terminal N-acetyl-D-glucosamine (GlcNAc) residue(s) were chemically synthesized via consistent use of oligosaccharyl thioethers as glycosylation donors in the convergent fragment coupling strategy. Each of these core structures was then extended to 5 to 15 N-glycan sequences by enzymatic reactions catalyzed by 4 robust glycosyltransferases. Success in synthesizing N-glycans with Neu5Gc and core-fucosylation further expanded the ability of enzymatic extension. High performance liquid chromatography with an amide column enabled rapid and efficient purification (>98% purity) of N-glycans in milligram scales. A total of 73 N-glycans (63 isomers) were successfully prepared and characterized by MS<sup>2</sup> and NMR. The CSEE strategy provides a practical approach for "mass production" of structurally defined N-glycans, which are important standards and probes for Glycoscience.
The human 18S ribosomal RNA gene: evolution and stability. (1986)

We report the 1,870-base-pair primary sequence of a human 18S rRNA gene and propose a secondary structure based on this sequence and the general mammalian structure. A basic secondary structure for the small subunit rRNA has been preserved throughout evolution by compensatory and neutral base changes in double-stranded regions. The molecule contains eight regions that can vary in structure and that comprise 432 bases, while 1,438 bases belong to regions of conserved structure among all species tested. The conserved regions show a remarkably low sequence divergence rate of 0.1% between the human and mouse genes over the approximately 80 million years since the mammalian radiation. This value may make the small subunit rDNA the most highly conserved sequence known. Sequence conservation in higher eukaryotes with multiple copies of the gene is probably achieved by the combination of strong selection and the correction of tandem genes by unequal homologous exchange.
Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family (2006)

Haloacid dehalogenase (HAD)-like hydrolases are a vast superfamily of largely uncharacterized enzymes, with a few members shown to possess phosphatase, beta-phosphoglucomutase, phosphonatase, and dehalogenase activities. Using a representative set of 80 phosphorylated substrates, we characterized the substrate specificities of 23 soluble HADs encoded in the Escherichia coli genome. We identified small molecule phosphatase activity in 21 HADs and beta-phosphoglucomutase activity in one protein. The E. coli HAD phosphatases show high catalytic efficiency and affinity to a wide range of phosphorylated metabolites that are intermediates of various metabolic reactions. Rather than following the classical "one enzyme-one substrate" model, most of the E. coli HADs show remarkably broad and overlapping substrate spectra. At least 12 reactions catalyzed by HADs currently have no EC numbers assigned in Enzyme Nomenclature. Surprisingly, most HADs hydrolyzed small phosphodonors (acetyl phosphate, carbamoyl phosphate, and phosphoramidate), which also serve as substrates for autophosphorylation of the receiver domains of the two-component signal transduction systems. The physiological relevance of the phosphatase activity with the preferred substrate was validated in vivo for one of the HADs, YniC. Many of the secondary activities of HADs might have no immediate physiological function but could comprise a reservoir for evolution of novel phosphatases.