gebhart/patrepeval huggingface dataset:
Indole alkaloid biosynthesis in Catharanthus roseus: new enzyme activities and identification of cytochrome P450 CYP72A1 as secologanin synthase (2000)

The molecular characterization of CYP72A1 from Catharanthus roseus (Madagascar periwinkle) was described nearly a decade ago, but the enzyme function remained unknown. We now show by in situ hybridization and immunohistochemistry that the expression in immature leaves is epidermis-specific. It thus follows the pattern previously established for early enzymes in the pathway to indole alkaloids, suggesting that CYP72A1 may be involved in their biosynthesis. The early reactions in that pathway, i.e. from geraniol to strictosidine, contain several candidates for P450 activities. We investigated in this work two reactions, the conversion of 7-deoxyloganin to loganin (deoxyloganin 7-hydroxylase, DL7H) and the oxidative ring cleavage converting loganin into secologanin (secologanin synthase, SLS). The action of DL7H has not been demonstrated in vitro previously, and SLS has only recently been identified as P450 activity in one other plant. We show for the first time that both enzyme activities are present in microsomes from C. roseus cell cultures. We then tested whether CYP72A1 expressed in E. coli as a translational fusion with the C. roseus P450 reductase (P450Red) has one or both of these activities. The results show that CYP72A1 converts loganin into secologanin.
Thermal Atropisomerism of Aglucovancomycin Derivatives:  Preparation of (M,M,M)- and (P,M,M)-Aglucovancomycins (1998)

The degradation of vancomycin to a series of aglucovancomycin derivatives containing modifications in key functional groups and a study of their thermal atropisomerism are detailed. In all of the cases, selective isomerism of the DE ring system atropisomers was observed under conditions where the CD and AB stereochemistries were unaffected. Competitive retro aldol ring cleavage of the CD and DE ring systems (CD > DE) was observed but could be minimized by the choice of solvent and thermal conditions (DE ring system) or precluded by alcohol protection (CD ring system). Similarly, competitive main chain succinimide formation through the loss of ammonia from the Asn residue could be minimized by the choice of thermal conditions or prevented by carboxamide protection. Resynthesis of natural aglucovancomycin, (M,M,M)-2, and its unnatural DE atropisomer (P,M,M)-2 from 6 are described. The comparative antimicrobial activity of the key derivatives and their unnatural DE ring system P-diastereomers are disclosed.
A Symbolic Approach for Checking Functional and Timing Compatibility of Synthesized Designs (1993)

In a redesign situation, the compatibility of the replacement chips is critical. This can only be obtained by verifying both their functionality and timing. In this report, we will postulate that the general RTL verification problem is too difficult to be solved. Hence, it is necessary for a RTL verification system to trade off generality for usability. In fact, there is a real need for an automatic tool that can check the functional and timing compatibility of automatically synthesized chips quickly and effectively. We found that synthesized designs have several common properties that can be utilized to facilitate this task. By making use of the USC design data structure (DDS) graph models, we developed a hybrid symbolic approach that will not only verify functional compatibility but also take into account the timing and the interaction between the controller and the datapath. Experiments have been performed on two designs, an AR filter and a robot arm controller synthesized by the ADAM system. The results are very encouraging. In fact, these experiments helped to identify problems with the early version of the control signal generator (CSG) software.
Photoisomerization of Azobenzene Derivatives in Nanostructured Silica (2006)

A series of derivatized azobenzene molecules are synthesized such that one of the phenyl groups can be chemically bonded to mesostructured silica and the other, derivatized with dendrons, is free to undergo large-amplitude light-driven motion. The silica frameworks on which the motion takes place are either 150 nm thick films containing ordered hexagonal arrays of tubes (inner diameter about 2 nm) containing the bonded azobenzenes, or particles (about 500 nm in diameter) containing the same ordered arrays of functionalized tubes. The photoisomerization yields and the rate constants for the thermal cis to trans back-reaction of the azobenzenes in the tubes are measured and compared to those of the molecules in solution. The rate constants decrease with increasing size of the dendrons. Fluorescence spectra of the cis and trans isomers in the pores show that the photoisomerization in the nanostructured materials is selectively driven by specific wavelengths of light and is reversible.
Expression of thrombospondins by endothelial cells. Injury is correlated with TSP-1. (1995)

The thrombospondins (TSP-1, -2, and -3) comprise a family of proteins that are homologous at the carboxy terminus but have unique sequences at the amino terminus that might be correlated with the regulation of cell behavior. To investigate the expression of TSP-1, -2, and -3 in endothelial cells, we examined developing murine blood vessels and human atherosclerotic plaques by in situ hybridization. The expression of TSP-1 was also characterized in cultured bovine aortic endothelial cells. Expression of TSP-2 was seen in the dorsal aorta as early as embryonic day 10; TSP-1 was not detected in endothelial cells until later stages, and TSP-3 was not apparent in the vasculature. In atherosclerotic specimens, TSP-1 mRNA was detected in many intraplaque microvessels and in the endothelium lining the atheromatous plaque; TSP-2 was absent from these regions. Cultured bovine aortic endothelial cells did not transcribe TSP-2 mRNA at detectable levels. There were high steady-state levels of TSP-1 mRNA in subconfluent bovine aortic endothelial cells before confluence and at the wound edge after injury of the cell monolayer, with maximal expression of TSP-1 in cultures at a time during which approximately 35% of the cells were in S phase. As the majority of these cells subsequently undergo mitosis, these data are consistent with TSP-1 as an inhibitor of endothelial cell proliferation that functions in G1. These results support the conclusion that, despite sequence homology, the TSPs have distinct functions in vascular biology.
Hypertriglyceridemia (2006)

Hypertriglyceridemia is a commonly encountered lipid abnormality frequently associated with other lipid and metabolic derangements. The National Cholesterol Education Program recommends obtaining a fasting lipid panel in adults over the age of 20. The discovery of hypertriglyceridemia should prompt an investigation for secondary causes such as high fat diet, excessive alcohol intake, certain medications, and medical conditions (eg, diabetes mellitus, hypothyroidism). In addition, patients should be evaluated for other components of the metabolic syndrome. These include abdominal obesity, insulin resistance, low high-density lipoprotein (HDL), high triglyceride, and hypertension. Hypertriglyceridemia is classified as primary hypertriglyceridemia when there are no secondary causes identified. Primary hypertriglyceridemia is the result of various genetic defects leading to disordered triglyceride metabolism. It is important to treat hypertriglyceridemia to prevent pancreatitis by reducing triglyceride levels to &lt;500 mg/dL. Furthermore, lowering triglycerides while treating other dyslipidemias and components of the metabolic syndrome will reduce coronary events. However, it is controversial how much isolated hypertriglyceridemia correlates directly with coronary artery disease and further studies are needed to clarify whether treatment for this condition leads to meaningful clinical outcomes. Therapeutic lifestyle changes (TLC) are the first line of treatment for hypertriglyceridemia. These changes include a low saturated fat, carbohydrate-controlled diet, combined with alcohol reduction, smoking cessation, and regular aerobic exercise. High doses of omega-3 fatty acids from fish and fish oil supplements will lower triglyceride levels significantly. When patients do not reach their goals by TLC, drug therapy should be started. In cases of isolated hypertriglyceridemia, fibrates are initially considered. When elevated low-density lipoprotein levels accompany hypertriglyceridemia, 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors are preferred. In patients with low HDL levels and hypertriglyceridemia, extended release niacin can be considered. A combination of the medicines may be necessary in recalcitrant cases.
The Immunoglobulin κ Gene Families of Human and Mouse: a Cottage Industry Approach (2000)

Some aspects of the work of our group on the human and mouse immunoglobulin kappa genes are reviewed. The human kappa locus contains a large duplication: a 600 kb Ckappa-proximal copy with 40 Vkappa genes is found in the close vicinity of a 440 kb Ckappa-distal copy with 36 very similar, but not identical, Vkappa genes. The chimpanzee has only the Ckappa-proximal copy of the locus. The kappa locus of the mouse is close to 3.2 Mb in size, of which 3.1 Mb have been cloned in four contigs, leaving three small gaps of together about 90 kb; 140 Vkappa genes and pseudogenes were localized and sequenced. In parallel to the elucidation of the structure of the kappa loci, the mechanisms of the V-J rearrangement, somatic hypermutation and kappa gene expression were studied. Various polymorphisms were detected in the human population and a number of haplotypes defined. In addition to the Vkappa genes within the loci numerous Vkappa orphons were localized on different chromosomes. Comparing the kappa loci of different species allows some interesting conclusions as to the evolution of this multigene family. Finally our strategy of elucidating the structure and function of the kappa loci, which has been termed a 'cottage industry approach', is discussed in relation to the large-scale genome analysis as pursued today using automated methods.
Selective JAK Inhibitors (2014)

Consisting of four members, JAK1, JAK2, JAK3 and TYK2, the JAK kinases have emerged as important targets for proliferative and immune-inflammatory disorders. Recent progress in the discovery of selective inhibitors has been significant, with selective compounds now reported for each isoform. This article summarizes the current state-of-the-art with a discussion of the most recently described selective compounds. X-ray co-crystal structures reveal the molecular reasons for the observed biochemical selectivity. A concluding analysis of JAK inhibitors in the clinic highlights increased clinical trial activity and diversity of indications. Selective JAK inhibitors, as single agents or in combination regimens, have a very promising future in the treatment of oncology, immune and inflammatory diseases.
A guild of forty-five CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes (2005)

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. Four CRISPR-associated (Cas) protein families, designated Cas1 to Cas4, are strictly associated with CRISPR elements and always occur near a repeat cluster. Some spacers originate from mobile genetic elements and are thought to confer "immunity" against the elements that harbor these sequences. In the present study, we have systematically investigated uncharacterized proteins encoded in the vicinity of these CRISPRs and found many additional protein families that are strictly associated with CRISPR loci across multiple prokaryotic species. Multiple sequence alignments and hidden Markov models have been built for 45 Cas protein families. These models identify family members with high sensitivity and selectivity and classify key regulators of development, DevR and DevS, in Myxococcus xanthus as Cas proteins. These identifications show that CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a repeat cluster or filling the region between two repeat clusters. Distinctive subsets of the collection of Cas proteins recur in phylogenetically distant species and correlate with characteristic repeat periodicity. The analyses presented here support initial proposals of mobility of these units, along with the likelihood that loci of different subtypes interact with one another as well as with host cell defensive, replicative, and regulatory systems. It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated.
Novel molecular sensors for saccharides based on the interaction of boronic acid and amines: saccharide sensing in neutral water (1994)

The first known synthetic molecular colour sensor for saccharides is designed utilizing the boronic acid–amine interaction and visible colour changes were observed upon interaction with saccharides in neutral aqueous solutions.
Interleukin 10 (IL-10): an immunosuppressive factor and independent predictor in patients with metastatic renal cell carcinoma (1999)

Interleukin 10 (IL-10) is an immunosuppressive factor and has been detected in tumour cell cultures of renal cell carcinoma and of malignant melanoma. IL-10 has been described as a cytokine of the Th2 response; it is able to suppress antigen-presenting cells (APCs) and may lead to down-regulation of HLA class I and II molecules on dendritic cells and to anergy of T-lymphocytes. We evaluated pretreatment serum levels of soluble IL-10 and various clinical parameters to determine their prognostic value in 80 advanced renal cell carcinoma patients seen at our institution between May 1990 and April 1996. For statistical evaluation we used both univariate and multivariate Cox proportional hazards models. An elevated pretreatment serum level of IL-10 was a statistically independent predictor of unfavourable outcome (P < 0.0028), in addition to the well-known clinical and biochemical risk factors. These data support risk stratification for future therapeutic trials and identify a predictor which needs to be validated in prospective studies and may potentially influence decision making in palliative management of patients with metastatic renal cell carcinoma. These data also suggest a potential role of IL-10 in the development of advanced renal cell carcinoma and in the future design of therapeutic strategies.
IL-10 production differentially influences the magnitude, quality, and protective capacity of Th1 responses depending on the vaccine platform (2010)

The quality of a Th1 response can be a prospective correlate of vaccine-mediated protection against certain intracellular pathogens. Using two distinct vaccine platforms, we evaluate the influence of interleukin (IL) 10 production on the magnitude, quality, and protective capacity of CD4(+) T cell responses in the mouse model of Leishmania major infection. Multiparameter flow cytometry was used to delineate the CD4(+) T cell production of interferon (IFN) gamma, IL-2, tumor necrosis factor (TNF), and IL-10 (or combinations thereof) after vaccination. Immunization with a high dose of adenovirus (ADV) expressing leishmanial proteins (MML-ADV) elicited a limited proportion of multifunctional IFN-gamma(+)IL-2(+)TNF(+) Th1 cells, a high frequency of IL-10-producing CD4(+) T cells, and did not protect against subsequent challenge. Surprisingly, in the absence of IL-10, there was no change in the magnitude, quality, or protective capacity of the Th1 response elicited by high-dose MML-ADV. In contrast, after immunization with MML protein and CpG (MML + CpG), IL-10 limited the production of IL-12 by DCs in vivo, thereby decreasing the generation of multifunctional Th1 cells. Consequently, three immunizations with MML + CpG were required for full protection. However, inhibiting IL-10 at the time of immunization enhanced the magnitude and quality of the Th1 response sufficiently to mediate protection after only a single immunization. Overall, we delineate distinct mechanisms by which vaccines elicit protective Th1 responses and underscore the importance of multifunctional CD4(+) T cells.
Technological advances in adoptive immunotherapy (2005)

Adoptive immunotherapy is an attractive and elegant strategy for treating a variety of life-threatening diseases. Several approaches have been developed to generate antigen-specific CD4+ and CD8+ T cells for adoptive T-cell therapy in cancer and infectious diseases. Currently, many approaches are based on either the use of autologous peptide pulsed dendritic cells as antigen-presenting cells or nonspecific expansion of T cells. Unfortunately, current approaches lack the ability to serve as reproducible and economically viable methods. Several groups are developing new artificial approaches to overcome problems associated with dendritic cells and the nonspecific expansion of T-cell clones in order to make adoptive immunotherapy more feasible and effective. Thus, by increasing the availability of adoptive immunotherapy, we will be able to better determine the efficacy of the approaches in the treatment of a variety of diseases. In this review, we focus on technological advances that will facilitate adoptive immunotherapy. Specifically, we summarize current strategies which are either based on artificial antigen-presenting cells or on T-cell receptor gene transfer.
Visualization of glucocorticoid receptor translocation and intranuclear organization in living cells with a green fluorescent protein chimera. (1996)

A highly fluorescent mutant form of the green fluorescent protein (GFP) has been fused to the rat glucocorticoid receptor (GR). When GFP-GR is expressed in living mouse cells, it is competent for normal transactivation of the GR-responsive mouse mammary tumor virus promoter. The unliganded GFP-GR resides in the cytoplasm and translocates to the nucleus in a hormone-dependent manner with ligand specificity similar to that of the native GR receptor. Due to the resistance of the mutant GFP to photobleaching, the translocation process can be studied by time-lapse video microscopy. Confocal laser scanning microscopy showed nuclear accumulation in a discrete series of foci, excluding nucleoli. Complete receptor translocation is induced with RU486 (a ligand with little agonist activity), although concentration into nuclear foci is not observed. This reproducible pattern of transactivation-competent GR reveals a previously undescribed intranuclear architecture of GR target sites.
A homogeneous method for genotyping with fluorescence polarization (1997)

We combined the amplification refractory mutation system (ARMS) and fluorescence polarization (FP) to give a homogeneous genomic DNA genotype analysis method. Oligonucleotide probes labeled with the fluorescein dyes fluorescein isothiocyanate and 5-([4,6-dichlorotriazin-2-yl]amino)fluorescein and the rhodamine dye 6-carboxyrhodamine were included in amplification mixes and were annealed to PCR products after amplification. Hybridization was accompanied by an increase in the FP of the probe. We demonstrated homogeneous genotyping by analyzing human DNA samples for delta F508 mutation status of the cystic fibrosis transmembrane conductance regulator gene. The genotypes determined with the method described herein were in full agreement with those obtained by the conventional application of ARMS. We also demonstrated the simultaneous detection of two PCR products in a single reaction. The assay method described is homogeneous and so obviates the necessity to open reaction vessels after amplification. This therefore eliminates PCR carryover contamination.
Polynomial-based optical true-time delay devices with microelectromechanical mirror arrays (2002)

We previously reported optical true-time delay devices, based on the White cell, to support phased-array radars. In particular, we demonstrated a quadratic device, in which the number of delays obtainable was proportional to the square of the number of times the light beam bounced in the cell. Here we consider the possibilities when a microelectromechanical (MEM) tip/tilt mirror array with multiple stable states is used. We present and compare designs for quadratic, quartic, and octic cells using MEM mirror arrays with two, three, and five micro-mirror tilt angles. An octic cell with a three-state MEM can produce 6,339 different delays in just 17 bounces.
5-Hydroxymethylfurfural (HMF) as a building block platform: Biological properties, synthesis and synthetic applications (2011)

The biorefinery is an important approach for the current needs of energy and chemical building blocks for a diverse range of applications, that gradually may replace current dependence on fossil-fuel resources. Among other primary renewable building blocks, 5-hydroxymethylfurfural (HMF) is considered an important intermediate due to its rich chemistry and potential availability from carbohydrates such as fructose, glucose, sucrose, cellulose and inulin. In recent years, considerable efforts have been made on the transformation of carbohydrates into HMF. In this critical review we provide an overview of the effects of HMF on microorganisms and humans, HMF production and functional group transformations of HMF to relevant target molecules by taking advantage of the primary hydroxyl, aldehyde and furan functionalities.
Pointing in Intelligent Environments with the WorldCursor. (2003)

Abstract: We introduce the WorldCursor, a pointing device and cursor designed for intelligent environments. The WorldCursor is analogous to the mouse and cursor used in traditional GUIs: the user may select and interact with a physical device by positioning the cursor on the device and clicking. We use the XWand (Wilson, 2003) as a physical pointing mechanism, and couple it with the WorldCursor device which projects a cursor on the physical environment. The WorldCursor improves upon the XWand by removing the need for external positioning technology such as video cameras. We detail the device and signal processing algorithms, and discuss its application in intelligent environments.
Enzyme-Catalyzed Polymerization of Phenols within Polyelectrolyte Microcapsules (2004)

Enzyme-catalyzed synthesis of a phenolic polymer within layer-by-layer (LbL) constructed polyelectrolyte microcapsules has been introduced. This approach is based on selective permeability of capsule walls for monomer molecules, while biocatalyst and forming polymeric chains cannot leave capsules interior because of high molecular weight. Horseradish peroxidase was encapsulated into four bilayer poly(styrenesulfonate)/poly(allylamine hydrochloride) capsules with an average diameter of 5 μm using pH-driven pore opening. 4-(2-Aminoethyl)phenol hydrochloride (tyramine) was used as a monomer giving easily detectable fluorescent polymeric products after addition of hydrogen peroxide into the system. Filling of the capsules with polymer was confirmed by different methods (AFM, quartz crystal microbalance, and confocal microscopy).
MIB-1 as a proliferative marker in transitional cell carcinoma of the bladder (2000)

MIB-1 immunostaining in transitional cell carcinoma of the bladder correlated well with grade, stage, and clinical outcome. In multivariate analysis, proliferation fraction had prognostic value in predicting recurrence free survival for patients with Ta and T1 tumors, whereas stage and age appeared to be predictors of progression free survival.