gebhart/patrepeval huggingface dataset:
Construction of Designed Protein Libraries Using Gene Assembly Mutagenesis (2003)

Whole genes, plasmids, and even viral genomes can be assembled from relatively short, synthetic, overlapping oligodeoxyribonucleotides (oligos) by DNA polymerase extension (,). Once the initial investment in a set of oligos spanning the length of a gene has been made, a mutation can be generated easily at any point in the gene merely by replacing two oligos and reassembling the gene. Swapping out the oligos encoding one or more amino acid residues (and their complementary overlapping oligos) with new degenerate oligos allows for libraries of mutants (see Fig. 1) (). By this method, multiple positions can be targeted in a single step with no limitations on their proximity, and every targeted position is guaranteed to be mutated in the product. Diversity is generated entirely in vitro, and the protocol, involving two rounds of PCR with no gel purifications, can be accomplished easily in less than one day, followed by cloning as one would for a traditional PCR product. Open image in new window Fig. 1. Schematic of gene assembly mutagenesis. A population of gene variants is assembled from short oligonucleotides encoding both strands of the gene and containing degenerate bases at the targeted positions (shown in bold). Following assembly PCR, the full length gene variants are amplified using the outside primers.
Intraventricular vortex properties in nonischemic dilated cardiomyopathy (2014)

Vortices may have a role in optimizing the mechanical efficiency and blood mixing of the left ventricle (LV). We aimed to characterize the size, position, circulation, and kinetic energy (KE) of LV main vortex cores in patients with nonischemic dilated cardiomyopathy (NIDCM) and analyze their physiological correlates. We used digital processing of color-Doppler images to study flow evolution in 61 patients with NIDCM and 61 age-matched control subjects. Vortex features showed a characteristic biphasic temporal course during diastole. Because late filling contributed significantly to flow entrainment, vortex KE reached its maximum at the time of the peak A wave, storing 26 ± 20% of total KE delivered by inflow (range: 1-74%). Patients with NIDCM showed larger and stronger vortices than control subjects (circulation: 0.008 ± 0.007 vs. 0.006 ± 0.005 m(2)/s, respectively, P = 0.02; KE: 7 ± 8 vs. 5 ± 5 mJ/m, P = 0.04), even when corrected for LV size. This helped confining the filling jet in the dilated ventricle. The vortex Reynolds number was also higher in the NIDCM group. By multivariate analysis, vortex KE was related to the KE generated by inflow and to chamber short-axis diameter. In 21 patients studied head to head, Doppler measurements of circulation and KE closely correlated with phase-contract magnetic resonance values (intraclass correlation coefficient = 0.82 and 0.76, respectively). Thus, the biphasic nature of filling determines normal vortex physiology. Vortex formation is exaggerated in patients with NIDCM due to chamber remodeling, and enlarged vortices are helpful for ameliorating convective pressure losses and facilitating transport. These findings can be accurately studied using ultrasound.
GDF-15 inhibits integrin activation and mouse neutrophil recruitment through the ALK-5/TGF-βRII heterodimer (2016)

Growth differentiation factor 15 (GDF-15) is the first cytokine known to counteract chemokine-induced activation of leukocyte integrins. We showed recently that this activity dampens neutrophil recruitment into inflamed tissue and is required for survival of myocardial infarction in mice. The receptor responsible for this GDF-15-triggered anti-inflammatory mechanism on myeloid cells is not known. Here, we identify this receptor as transforming growth factor β receptor I (TGF-βRI) (activin receptor-like kinase 5 [ALK-5]) and TGF-β receptor II (TGF-βRII). We show that interference with these receptors by small-molecule inhibitors, antibodies, or small interfering RNA, blocked the GDF-15 effect on leukocyte integrin activation. Likewise, gene inactivation of each of the 2 receptors in neutrophils isolated from conditional gene-deficient mice abolished the inhibitory effect of GDF-15 on CXCL1-induced β2-integrin activation and neutrophil diapedesis. Rapid neutrophil arrest induced by CXCL1 in vivo was inhibited by GDF-15 in an ALK-5 and TGF-βRII dependent way. As for GDF-15 gene-deficient mice, we found that extravasation of neutrophils deficient for ALK-5 or TGF-βRII was strongly increased in the interleukin-1β inflamed cremaster. The inhibitory effects of GDF-15 on neutrophil integrin activation and in vivo neutrophil arrest were also found for TGF-β1. Mechanistically, GDF-15 and TGF-β1 interfered with integrin activation by inhibiting the activation of Ras-related protein 1 (Rap-1), an effect that depended on CalDAG- guanine nucleotide exchange factor 1 (GEF1) and cell division control protein 42 homolog. We conclude that both GDF-15 and TGF-β1 counteract chemokine-induced integrin activation on neutrophils via the ALK-5/TGF-βRII heterodimer. This represents a novel, rapid anti-inflammatory activity of the 2 TGF-β receptors and of TGF-β1.
Protein array autoantibody profiles for insights into systemic lupus erythematosus and incomplete lupus syndromes (2006)

The objective of this study was to investigate the prevalence and clinical significance of a spectrum of autoantibodies in systemic lupus erythematosus and incomplete lupus syndromes using a proteome microarray bearing 70 autoantigens. Microarrays containing candidate autoantigens or control proteins were printed on 16-section slides. These arrays were used to profile 93 serum samples from patients with systemic lupus erythematosus (SLE (n = 33), incomplete LE (ILE; n = 23), first-degree relatives (FDRs) of SLE patients (n = 20) and non-autoimmune controls (NC; n = 17). Data were analysed using the significance analysis of microarray (SAM) and clustering algorithms. Correlations with disease features were determined. Serum from ILE and SLE patients contained high levels of IgG autoantibodies to 50 autoantigens and IgM autoantibodies to 12 autoantigens. Elevated levels of at least one IgG autoantibody were detected in 26% of SLE and 19% of ILE samples; elevated IgM autoantibodies were present in 13% of SLE and 17% of ILE samples. IgG autoantibodies segregated into seven clusters including two specific for DNA and RNA autoantigens that were correlated with the number of lupus criteria. Three IgG autoantibody clusters specific for collagens, DNA and histones, were correlated with renal involvement. Of the four IgM autoantibody clusters, two were correlated negatively with the number of lupus criteria; none were correlated with renal disease. The IgG : IgM autoantibody ratios generally showed a stepwise increase in the groups following disease burden from NC to SLE. Insights derived from the expanded autoantibody profiling made possible with the antigen array suggest differences in autoreactivity in ILE and SLE. Determining whether the IgM aurotreactivity that predominates in ILE represents an early stage prior to IgG switching or is persistent and relatively protective will require further longitudinal studies.
Nitriles as Solvents in Glycosylation Reactions: Highly Selective β-Glycoside Synthesis1 (1990)

Treatment of glycosyl trichloroacetimidates in nitriles as solvent at low temperatures with trimethylsilyl trifluoro-methanesulfonate (SN1-type conditions) leads under α-face attack to fast nitrilium-nitrile conjugate formation. These intermediates are converted rapidly in the presence of various acceptors into β-disaccharides in high yields and diastereoselectivities.
Fluorescent Probes for Sensing Processes in Polymers (2005)

Fluorescence spectroscopy is an important analytical technique that has been widely used in a variety of applications, such as biomedicine, biology, and science of materials, because it presents some properties which makes it unique, that is, extraordinary sensitivity and selectivity, short delay time (<10(-9) s), and it is neither invasive nor destructive, so it can be used for in situ measurements. Generally, intrinsic fluorescence of many materials, like polymers, is unspecific so it is not useful to analyse their properties or to be correlated to changes in their microenvironment. The incorporation of additives with fluorescent groups would be necessary. When the fluorescence emission of these molecules is sensitive to changes of properties, such as polarity, fluidity, order, molecular mobility, pH, or electric potential, they can be used for detecting such changes in their microenvironment, and they are called fluorescent probes. As long as these probes can follow processes of practical interest, they can be employed as sensors, if the information given by the measure of fluorescence adequately reflects the changes in the system. In addition, a sensor must fulfil some other requirements in order to make them of practical use, the most important being that the material support in which the sensor molecule is inserted. This support should permit a rapid detection of the process and should allow easy processing in a variety of forms. Polymers are well-known systems in which estimation of local parameters are possible by means of fluorimetric techniques. It allows the study of dynamic processes of interest, such as polymerization kinetics and mechanisms, thermal transitions, photodegradation, swelling morphology changes, and so forth.
Study of the effects of centrifugal instabilities on flow in a 40 to 1 aspect ratio rectangular curved channel, for Dean numbers from 35 to fully turbulent conditions (1990)

The development and structure of Dean vortices in a high aspect ratio curved channel were measured and studied for Dean numbers from 35 to fully turbulent conditions. Mean vorticity components were determined from measurements of the three components of mean velocity, which were measured using a miniature five-hole pressure probe. Streamwise, radial and spanwise vorticity components measured 120 deg from the start of curvature, show evidence of Dean vortices in the time-averaged flow field. Peak streamwise and peak spanwise vorticity, as well as streamwise circulation, generally increase as the Dean number increases from 60 to 240. Peak radial vorticity increases as Dean numbers vary from 60 to about 160. Spectra obtained from hot-wire probes show evidence of different frequency events, including twisting and undulation. Twisting is apparent for Dean numbers of 135 to 160 while undulation is observed at lower Dean numbers. Flow visualization results illustrate a variety of time dependent events in the channel.
Cisplatin plus Gemcitabine versus Gemcitabine for Biliary Tract Cancer (2010)

As compared with gemcitabine alone, cisplatin plus gemcitabine was associated with a significant survival advantage without the addition of substantial toxicity. Cisplatin plus gemcitabine is an appropriate option for the treatment of patients with advanced biliary cancer. (ClinicalTrials.gov number, NCT00262769.)
cIAP-2 block apoptotic events in bladder cancer cells. (2003)

cIAP-2 is an important regulator of apoptosis in bladder cancer and its overexpression may make tumours less susceptible to therapy involving apoptosis. The combination of immunotherapy and chemotoxic agents may represent a valid strategy to potentiate anti-tumour therapy, in particular treating tumours resisting conventional chemotherapy.
GLUT1 mutations are a rare cause of familial idiopathic generalized epilepsy (2012)

Our study shows that GLUT1 defects are a rare cause of classic IGE. SLC2A1 screening should be considered in IGE featuring absence epilepsies with onset from early childhood to adult life, because this diagnosis may have important implications for treatment and genetic counseling.
Pesticide chemistry and bioscience, the food-environment challenge (1999)

Plenary lectures synthesis and structure-activity relationships delivery natural products mode of action and resistance metabolism environmental fate residues in food and the environment regulation and risk assessment.
Gemtuzumab Ozogamicin, A Potent and Selective Anti-CD33 Antibody−Calicheamicin Conjugate for Treatment of Acute Myeloid Leukemia (2001)

CD33 is expressed by acute myeloid leukemia (AML) cells in >80% of patients but not by normal hematopoietic stem cells, suggesting that elimination of CD33(+) cells may be therapeutically beneficial. A conjugate of a calicheamicin hydrazide derivative attached via hydrazone formation to the oxidized carbohydrates of the anti-CD33 murine antibody P67.6 had been chosen for use in AML prior to humanization of this antibody. However, the CDR-grafted humanized P67.6 could not be used to make the carbohydrate conjugate because of the unexpected sensitivity of this antibody to periodate oxidation. Exploration of a series of bifunctional linkers resulted in a new class of calicheamicin conjugates, termed the hybrid conjugates, that allows for the attachment of the calicheamicin to lysines but incorporates the site of hydrolytic release, a hydrazone, previously shown to be required for activity. The optimized conjugate chosen for clinical trials, gemtuzumab ozogamicin ("gem-ozo", Mylotarg, formerly designated CMA-676), was significantly more potent and selective than the carbohydrate conjugate it replaced. It was selectively cytotoxic to HL-60 leukemia cells in tissue culture with an IC(50) in the low to sub-pg cal/mL range (cal = calicheamicin equivalents). Doses of gem-ozo as low as 50 microg cal/kg given three times to mice bearing HL-60 xenografts routinely resulted in long-term, tumor-free survivors, while a nonbinding control conjugate was relatively inactive. Gem-ozo at a concentration of 2 to 10 ng cal/mL selectively inhibited leukemia colony formation by marrow cells from a significant proportion of AML patients. Gem-ozo has also shown significant activity against AML in Phase II trials and is the first antibody-targeted chemotherapeutic agent approved by the FDA.
CMP‐N‐acetylneuraminic acid hydroxylase from mouse liver and pig submandibular glands (1994)

In this report, the nature of the protein components involved in the functioning of cytidine-5'-monophosphate-N-acetylneuraminic acid (CMP-Neu5 Ac) hydroxylase in high-speed supernatants of mouse liver has been investigated. Fractionation and reconstitution experiments showed that this enzyme system consists of NADH-cytochrome b5 reductase, cytochrome b5 and a 56-kDa terminal electron acceptor having the CMP-Neu5 Ac hydroxylase activity. This enzyme system is extracted in a soluble protein fraction; however, the amphipathic, usually membrane-associated, forms of cytochrome b5 and the reductase were found to predominate and are presumably the forms which support the turnover of the hydroxylase in vivo. Although the majority of cellular cytochrome b5 and cytochrome b5 reductase is membrane-bound, the addition of intact microsomes elicited no significant increase in the hydroxylase activity of supernatants. Detergent-solubilised microsomes, however, potently activated the hydroxylase, probably due to the greater accessibility of the cytochrome b5. Accordingly, in reconstitution experiments, pure hydrophilic cytochrome b5 interacts more effectively with the hydroxylase than isolated amphipathic cytochrome b5. Studies on the CMP-Neu5 Ac hydroxylase system in fractionated porcine submandibular glands and bovine liver suggest that the composition of this enzyme system is conserved in all mammals possessing sialoglycoconjugates containing N-glycolylneuraminic acid.
Overview of Protein Structural and Functional Folds (2004)

This overview provides an illustrated, comprehensive survey of some commonly observed protein-fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web-based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein-structure databases, protein-structure-classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon-diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
A real-time, multichannel system with parallel digital signal processors (2002)

A high-performance parallel signal processing system for use in a real-time environment is described. The system includes analog input and output conditioners and data converters, digital signal processing (DSP) elements, and a system control computer. Expanding requirements and advances in DSP technology have resulted in the evolution of several generations of the system, each more powerful than the previous one. The hallmark of the newest system is an ensemble of DSP boards, each containing eight AT&T DSP32C processors. Custom architectures and algorithms were developed to allow the DSP chips to execute filters with more taps per second than processor cycles.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken β-tropomyosin pre-mRNA (1995)

Computer analysis of human intron sequences have revealed a 50 nucleotide (nt) GC-rich region downstream of the 5' splice site; the trinucleotide GGG occurs almost four times as frequently as it would in a random sequence. The 5' part of a beta-tropomyosin intron exhibits six repetitions of the motif (A/U)GGG. In order to test whether these motifs play a role in the splicing process we have mutated some or all of them. Mutated RNAs show a lower in vitro splicing efficiency when compared with the wild-type, especially when all six motifs are mutated (> 70% inhibition). Assembly of the spliceosome complex B and, to a lesser extent, of the pre-spliceosome complex A also appears to be strongly affected by this mutation. A 55 kDa protein within HeLa cell nuclear extract is efficiently cross-linked to the G-rich region. This protein is present in the splicing complexes and its cross-linking to the pre-mRNA requires the presence of one or several snRNP. Altogether our results suggest that the G-rich sequences present in the 5' part of introns may act as an enhancer of the splicing reaction at the level of spliceosome assembly.
Evolution of influenza A viruses in wild birds (2007)

The emergence of highly pathogenic (HP) H5 influenza A viruses in Asia and the increase of HP H7 viruses in Europe and the Americas focused greater attention on the ecology of influenza in wild birds. Influenza virus surveillance studies in wild bird populations in the Americas, Europe, and Asia confirmed that wild aquatic birds are the reservoir for all known influenza A viruses. Phylogenetic analysis groups the influenza viruses in wild aquatic birds into two distinct superfamilies-one in the Americas and one in Eurasia. The separation of viruses into American and Eurasian clades implies that transmission of HP H5 into the Americas by wild birds is likely to be a rare event. The rapid evolution of the Eurasian H5N1 viruses makes them a continued threat to poultry and humans worldwide.
Galactose catabolism in Caulobacter crescentus (1978)

Caulobacter crescentus wild-type strain CB13 is unable to utilize galactose as the sole carbon source unless derivatives of cyclic AMP are present. Spontaneous mutants have been isolated which are able to grow on galactose in the absence of exogenous cyclic nucleotides. These mutants and the wild-type strain were used to determine the pathway of galactose catabolism in this organism. It is shown here that C. crescentus catabolizes galactose by the Entner-Duodoroff pathway. Galactose is initially converted to galactonate by galactose dehydrogenase and then 2-keto-3-deoxy-6-phosphogalactonate aldolase catalyzes the hydrolysis of 2-keto-3-deoxy-6-phosphogalactonic acid to yield triose phosphate and pyruvate. Two enzymes of galactose catabolism, galactose dehydrogenase and 2-keto-3-deoxy-6-phosphogalactonate aldolase, were shown to be inducible and independently regulated. Furthermore, galactose uptake was observed to be regulated independently of the galactose catabolic enzymes.
MUC18, a marker of tumor progression in human melanoma, shows sequence similarity to the neural cell adhesion molecules of the immunoglobulin superfamily. (1989)

The MUC18 antigen is an integral membrane glycoprotein of 113 kDa whose expression on primary human melanomas correlates with poor prognosis and the development of metastatic disease. MUC18 is expressed only sporadically in benign melanocytic nevi and thin primary melanomas that have a low probability of metastasizing. However, with increasing tumor thickness, MUC18 expression becomes more frequent and it is found on 80% of advanced primary tumors and metastases. MUC18-encoding cDNA clones were obtained by screening a human melanoma phage lambda expression library with monoclonal antibodies produced against the denatured antigen. The deduced sequence of 603 amino acids consists of a signal peptide, five immunoglobulin-like domains, a transmembrane region, and a short cytoplasmic tail. The highest sequence similarity is with a group of nervous system cell adhesion molecules, which includes neural cell adhesion molecule (N-CAM). The close structural relationship with these molecules suggests that MUC18 may also be a developmentally regulated cell adhesion molecule.
Genes, Enzymes, and Regulation of para -Cresol Metabolism in Geobacter metallireducens (2007)

In aerobic and facultatively anaerobic bacteria, the degradation of para-cresol (p-cresol) involves the initial hydroxylation to p-hydroxybenzyl alcohol by water catalyzed by the soluble, periplasmatic flavocytochrome p-cresol methylhydroxylase (PCMH; alpha(2)beta(2) composition). In denitrifying bacteria the further metabolism proceeds via oxidation to p-hydroxybenzoate, the formation of p-hydroxybenzoyl-coenzyme A (CoA), and the subsequent dehydroxylation of the latter to benzoyl-CoA by reduction. In contrast, the strictly anaerobic Desulfobacterium cetonicum degrades p-cresol by addition to fumarate, yielding p-hydroxybenzylsuccinate. In this work, in vitro enzyme activity measurements revealed that the obligately anaerobic Geobacter metallireducens uses the p-cresol degradation pathway of denitrifying bacteria. Surprisingly, PCMH, which is supposed to catalyze both p-cresol hydroxylation and p-hydroxybenzyl alcohol oxidation to the corresponding aldehyde, was located in the membrane fraction. The alpha subunit of the enzyme was present in two isoforms, suggesting an alphaalpha'beta(2) composition. We propose that the unusual asymmetric architecture and the membrane association of PCMH might be important for alternative electron transfer routes to either cytochrome c (in the case of p-cresol oxidation) or to menaquinone (in the case of p-hydroxybenzyl alcohol oxidation). Unusual properties of further enzymes of p-cresol metabolism, p-hydroxybenzoate-CoA ligase, and p-hydroxybenzoyl-CoA reductase were identified and are discussed. A proteomic approach identified a gene cluster comprising most of the putative structural genes for enzymes involved in p-cresol metabolism (pcm genes). Reverse transcription-PCR studies revealed a different regulation of transcription of pcm genes and the corresponding enzyme activities, suggesting the presence of posttranscriptional regulatory elements.