gebhart/patrepeval huggingface dataset:
Synthesis of N-Terminally Linked Protein Dimers and Trimers by a Combined Native Chemical Ligation-CuAAC Click Chemistry Strategy (2009)

A novel method for the synthesis of N-terminally linked protein multimers is reported. Azide and alkyne thioesters were synthesized for the N-terminal modification of expressed proteins using native chemical ligation (NCL). Proteins modified by these moieties can be joined together to form homodimers and homotrimers via Cu(I)-catalyzed azide-alkyne [3 + 2] cycloaddition (CuAAC) click chemistry. The orthogonal nature of this reaction allows the production of protein heteromultimers, and this is demonstrated by synthesis of a protein heterodimer.
Structure of Recombinant Human CPP32 in Complex with the Tetrapeptide Acetyl-Asp-Val-Ala-Asp Fluoromethyl Ketone (1997)

The cysteine protease CPP32 has been expressed in a soluble form in Escherichia coli and purified to >95% purity. The three-dimensional structure of human CPP32 in complex with the irreversible tetrapeptide inhibitor acetyl-Asp-Val-Ala-Asp fluoromethyl ketone was determined by x-ray crystallography at a resolution of 2.3 A. The asymmetric unit contains a (p17/p12)2 tetramer, in agreement with the tetrameric structure of the protein in solution as determined by dynamic light scattering and size exclusion chromatography. The overall topology of CPP32 is very similar to that of interleukin-1beta-converting enzyme (ICE); however, differences exist at the N terminus of the p17 subunit, where the first helix found in ICE is missing in CPP32. A deletion/insertion pattern is responsible for the striking differences observed in the loops around the active site. In addition, the P1 carbonyl of the ketone inhibitor is pointing into the oxyanion hole and forms a hydrogen bond with the peptidic nitrogen of Gly-122, resulting in a different state compared with the tetrahedral intermediate observed in the structure of ICE and CPP32 in complex with an aldehyde inhibitor. The topology of the interface formed by the two p17/p12 heterodimers of CPP32 is different from that of ICE. This results in different orientations of CPP32 heterodimers compared with ICE heterodimers, which could affect substrate recognition. This structural information will be invaluable for the design of small synthetic inhibitors of CPP32 as well as for the design of CPP32 mutants.
[Hemodynamic structure of antiorthostatic reactions: relationship of mechanical activity of the heart and arterial pressure]. (1997)

In acute experiments with antiorthostatic rats tilt-induced changes in the parameters of cardiac activity (left ventricle systolic pressure (LVPs), its first derivative dp/dt, end-diastolic pressure (EDP) were compared in relation to the directionality and extent of systolic (sAP) and diastolic arterial pressure (dAP) shifts. Rise of the tilt angle by 15-45 degrees reduced sAP and dAP, increased LVPs and EDP and did not influence dp/dt. Changes in the cardiac parameters and AP were not unidirectional; sAP and dAP shifts were asynchronous. In a special experimental series, higher tilt angle was found to bring about opposite changes in cardiac ejection (CE) and total peripheral resistance (TPR). Growth in CE was concurrent to a progressive decline in TPR. Discussed is the response of the vascular system to antiorthostasis the unique character of which is vasodilatation.
Müllerian-Inhibiting Activity of Calf Fetal Testes: Relationship to Testosterone and Protein Synthesis (1975)

Müllerium-inhibiting activity was detected in incubation media of calf fetal testicular tissue. Dialysis of the medium did not modify its biological activity, but testosterone content of dialyzed medium was diminished by 92 percent. Four-fold concentration of incubation medium greatly enhanced its biological activity, which was destroyed by heat and blockage of sulphydryl groups by 0.5 M iodoacetic acid. Addition of cycloheximide to the medium during incubation decreased its biological activity, indicating that part of the activity is due to hormone newly synthesized during the incubation. These results prove that the anti-müllerian hormone is a macromolecule and suggest that it is probably a protein.
The logrank test (2004)

We often wish to compare the survival experience of two (or more) groups of individuals. For example, the table shows survival times of 51 adult patients with recurrent malignant gliomas1 tabulated by type of tumour and indicating whether the patient had died or was still alive at analysis—that is, their survival time was censored.2 As the figure shows, the survival curves differ, but is this sufficient to conclude that in the population patients with anaplastic astrocytoma have worse survival than patients with glioblastoma?

View this table:

Weeks to death or censoring in 51 adults with recurrent gliomas1 (A=astrocytoma, G=glioblastoma)





Fig 1 
Survival curves for women with glioma by diagnosis



We could compute survival curves3 for each group and compare the proportions surviving at any specific time. The weakness of this approach is that it does not provide a comparison of the total survival experience of the two groups, but rather gives a comparison at some arbitrary time point(s). In the figure the difference in survival is greater at some times than others and eventually becomes …
Chemical screen identifies FDA-approved drugs and target pathways that induce precocious pancreatic endocrine differentiation (2011)

Pancreatic β-cells are an essential source of insulin and their destruction because of autoimmunity causes type I diabetes. We conducted a chemical screen to identify compounds that would induce the differentiation of insulin-producing β-cells in vivo. To do this screen, we brought together the use of transgenic zebrafish as a model of β-cell differentiation, a unique multiwell plate that allows easy visualization of lateral views of swimming larval fish and a library of clinical drugs. We identified six hits that can induce precocious differentiation of secondary islets in larval zebrafish. Three of these six hits were known drugs with a considerable background of published data on mechanism of action. Using pharmacological approaches, we have identified and characterized two unique pathways in β-cell differentiation in the zebrafish, including down-regulation of GTP production and retinoic acid biosynthesis.
Benzoate-Coenzyme A Ligase from Thauera aromatica : an Enzyme Acting in Anaerobic and Aerobic Pathways (2003)

In the denitrifying member of the beta-Proteobacteria Thauera aromatica, the anaerobic metabolism of aromatic acids such as benzoate or 2-aminobenzoate is initiated by the formation of the coenzyme A (CoA) thioester, benzoyl-CoA and 2-aminobenzoyl-CoA, respectively. Both aromatic substrates were transformed to the acyl-CoA intermediate by a single CoA ligase (AMP forming) that preferentially acted on benzoate. This benzoate-CoA ligase was purified and characterized as a 57-kDa monomeric protein. Based on V(max)/K(m), the specificity constant for 2-aminobenzoate was 15 times lower than that for benzoate; this may be the reason for the slower growth on 2-aminobenzoate. The benzoate-CoA ligase gene was cloned and sequenced and was found not to be part of the gene cluster encoding the general benzoyl-CoA pathway of anaerobic aromatic metabolism. Rather, it was located in a cluster of genes coding for a novel aerobic benzoate oxidation pathway. In line with this finding, the same CoA ligase was induced during aerobic growth with benzoate. A deletion mutant not only was unable to grow anaerobically on benzoate or 2-aminobenzoate, but also aerobic growth on benzoate was affected. This suggests that benzoate induces a single benzoate-CoA ligase. The product of benzoate activation, benzoyl-CoA, then acts as inducer of separate anaerobic or aerobic pathways of benzoyl-CoA, depending on whether oxygen is lacking or present.
??-blockers in heart failure (2003)

University of Florida, Gainesville, Florida, USA. Correspondence and requests for reprints to Julie A. Johnson, University of Florida, Box 100486, Gainesville, FL 32610-0486, USA. Tel: +1 352 846 2586; fax: +1 352 392 9388; e-mail: [email protected]
Salivary Cortisol: A Better Measure of Adrenal Cortical Function than Serum Cortisol (1983)

Salivary cortisol concentration was found to be directly proportional to the serum unbound cortisol concentration both in normal men and women and in women with elevated cortisol-binding globulin (CBG). The correlation was excellent in dynamic tests of adrenal function (dexamethasone suppression, ACTH stimulation), in normals and patients with adrenal insufficiency, in tests of circadian variation and randomly collected samples. Women in the third trimester of normal pregnancy exhibited elevated salivary cortisol throughout the day. The relationship between salivary and serum total cortisol concentration was markedly non-linear with a more rapid increase in salivary concentration once the serum CBG was saturated. The rate of equilibrium of cortisol between blood and saliva was very fast, being much less than 5 minutes. These data, combined with a simple, stress-free, non-invasive collection procedure, lead us to suggest that salivary cortisol is a more appropriate measure for the clinical assessment of adrenocortical function than is serum cortisol.
IGF-I is required for normal embryonic growth in mice. (1993)

IGF-I is a pleiotropic hormone reported to affect linear growth, glucose metabolism, organ homeostasis, and the immune and neurologic systems. In contrast to IGF-II, IGF-I is expressed at low levels embryonically and has been thought to be more important for postnatal growth and development. To investigate the role of IGF-I in normal development we generated mice with an inactive IGF-I gene by homologous recombination in ES cells. Heterozygous mice are healthy and fertile, but they are 10-20% smaller than wild-type littermates and have lower than normal levels of IGF-I. The size reduction is attributable to a decrease in organs and muscle and bone mass. However, all tissues appear histologically normal. At birth homozygous mutant mice (IGF-I-/-) are < 60% body weight of wild type. Greater than 95% of IGF-I-/- pups die perinatally. Histopathology is characterized by underdevelopment of muscle tissue. Lungs of late embryonic and neonates also appeared less organized with ill-defined alveolae. IGF-I appears to be essential for correct embryonic development in mice.
Optimized strategy for in vivo Cas9-activation in Drosophila (2017)

While several large-scale resources are available for in vivo loss-of-function studies in <i>Drosophila</i>, an analogous resource for overexpressing genes from their endogenous loci does not exist. We describe a strategy for generating such a resource using Cas9 transcriptional activators (CRISPRa). First, we compare a panel of CRISPRa approaches and demonstrate that, for in vivo studies, dCas9-VPR is the most optimal activator. Next, we demonstrate that this approach is scalable and has a high success rate, as >75% of the lines tested activate their target gene. We show that CRISPRa leads to physiologically relevant levels of target gene expression capable of generating strong gain-of-function (GOF) phenotypes in multiple tissues and thus serves as a useful platform for genetic screening. Based on the success of this CRISRPa approach, we are generating a genome-wide collection of flies expressing single-guide RNAs (sgRNAs) for CRISPRa. We also present a collection of more than 30 Gal4 > UAS:dCas9-VPR lines to aid in using these sgRNA lines for GOF studies in vivo.
Reorganization Energies of Ferrocene-Peptide Monolayers (2007)

To deepen understanding of the electron transfer through a peptide backbone, we have investigated a series of noncyclic and cyclic ferrocene-peptide (Fc-peptide) cystamine conjugates immobilized on the gold microelectrode. Interaction of the ferrocenium group with BF4-, ClO4-, and PF6- as counterions was explored and the electron-transfer rates and reorganization energies were determined by variable temperature cyclic voltammetry. The highest reorganization energy was observed for the BF4- counterion, which has the weakest ability to associate with the ferrocenium cation. In addition, the more rigid cyclic Fc-peptide conjugates have a smaller reorganization energy ranging from 0.3 to 0.5 eV compared to less rigid noncyclic Fc-peptide cystamine conjugates which have higher reorganization energies in the range of 0.5-1.0 eV, which suggests that the dynamic properties of the conjugate play a role in mediating electron transfer in these systems.
A Novel Approach for Directing Transgene Expression in Drosophila: T2A-Gal4 In-Frame Fusion (2011)

In Drosophila, the Gal4-UAS system permits a transgene to be expressed in the same pattern as a gene of interest by placing the Gal4 transcription factor under control of the gene's DNA regulatory elements. If these regulatory elements are not known, however, expression of Gal4 in the desired pattern may be difficult or impossible. To solve this problem, we have developed a method for co-expressing Gal4 with the endogenous gene by exploiting the "ribosomal skipping" mechanism of the viral T2A peptide. This method requires explicit knowledge only of the endogenous gene's open reading frame and not its regulatory elements.
Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis (2013)

Melanoma brain metastasis (MBM) represents a frequent complication of cutaneous melanoma. Despite aggressive multi-modality therapy, patients with MBM often have a survival rate of <1 year. Alteration in DNA methylation is a major hallmark of tumor progression and metastasis; however, it remains largely unexplored in MBM. In this study, we generated a comprehensive DNA methylation landscape through the use of genome-wide copy number, DNA methylation and gene expression data integrative analysis of melanoma progression to MBM. A progressive genome-wide demethylation in low CpG density and an increase in methylation level of CpG islands according to melanoma progression were observed. MBM-specific partially methylated domains (PMDs) affecting key brain developmental processes were identified. Differentially methylated CpG sites between MBM and lymph node metastasis (LNM) from patients with good prognosis were identified. Among the most significantly affected genes were the HOX family members. DNA methylation of HOXD9 gene promoter affected transcript and protein expression and was significantly higher in MBM than that in early stages. A MBM-specific PMD was identified in this region. Low methylation level of this region was associated with active HOXD9 expression, open chromatin and histone modifications associated with active transcription. Demethylating agent induced HOXD9 expression in melanoma cell lines. The clinical relevance of this finding was verified in an independent large cohort of melanomas (n = 145). Patients with HOXD9 hypermethylation in LNM had poorer disease-free and overall survival. This epigenome-wide study identified novel methylated genes with functional and clinical implications for MBM patients.
SpaceFold and PhysicLenses (2014)

Many tasks performed in multiscale visual spaces require the user to have several foci. Using bimanual interaction, multitouch devices can facilitate the simultaneous definition and exploration of several foci. However, multitouch is rarely used for multifocus navigation, and may limit the interaction to a sequential definition of areas of interest. We introduce two novel navigation techniques that combine multiple foci and bimanual touch, and therefore enable the isochronic definition of areas of interest, leading to simultaneous multifocus navigation. SpaceFold folds the visual space in the third dimension, allowing users to bring objects closer to each other. Our technique enables a direct, bimanual manipulation of a folded space and therefore provides high flexibility. PhysicLenses uses multiple magnification lenses to compare objects. Using a physics model, PhysicLenses introduces a general solution for the arrangement of multiple lenses within the viewport. We conducted a controlled experiment with 24 participants to compare the techniques with split screen. The results show that SpaceFold significantly outperformed all other techniques, whereas PhysicLenses was just as fast as split screen.
Software for C1 interpolation (1977)

The problem of mathematically defining a smooth surface, passing through a finite set of given points is studied. Literature relating to the problem is briefly reviewed. An algorithm is described that first constructs a triangular grid in the (x,y) domain, and first partial derivatives at the modal points are estimated. Interpolation in the triangular cells using a method that gives C sup.1 continuity overall is examined. Performance of software implementing the algorithm is discussed. Theoretical results are presented that provide valuable guidance in the development of algorithms for constructing triangular grids.
Synthesis and characterization of conducting polymers and their composites (1997)

Blends of conducting polymers polypyrrole and polyaniline, in the insulating host polymers, polybisphenol A carbonate, polyamide and polyamide have been prepared electrochemically. Composite homogeneity and a possible chemical interaction between the host matrices and the conducting polymers were searched. Several spectroscopic and thermal analyses of free standing films suggest such an interaction.
A Fluorescent Reporter Assay for the Detection of Ligands Acting Through GIProtein-Coupled Receptors (2000)

Accompanying the advances in basic biology of G protein-coupled receptors (GPCRs) is the practical need among biopharmaceutical companies for sensitive assays to assess GPCR function, particularly formats that are compatible with high-throughput drug screening. Here we describe a novel cell-based assay format for the high-throughput detection of ligands for G, protein-coupled receptors. Two Gi-GPCRs, μ-opioid receptor (μ-OPR) and 5-hydroxytryptamine receptor la (5HTlaR) are employed as model receptor targets. The key feature of this assay system is the isolation of stable, clonal Chinese hamster ovary (CHO) cell lines that carry three separate expression plasmids: (1) a chimeric Gq/i5 protein (which re-directs a negative Gi-type signal to a positive Gq-type response), (2) a given Gi-GPCR, and (3) a β-lactamase (βla) reporter gene responsive to Gi-GPCR signaling. Cell-based assays built using this format show appropriate rank order of potency among a reference set of receptor agonist and antagonist compounds. Such assays are also robust, reliable, and can be used for industrial-scale applications such as high-throughput screening for drug leads.
Gastrin regulates growth of human pancreatic cancer in a tonic and autocrine fashion (1996)

The gastrointestinal peptides gastrin and cholecystokinin (CCK) stimulate growth of human pancreatic cancer through a CCK-B/gastrin- like receptor. In the present study we evaluated whether growth of human pancreatic cancer is endogenously regulated by gastrin. Immunohistomical examination of BxPC-3 cells and tumor xenografts revealed specifc gastrin immunoreactivity. Gastrin was detected by radioimmunoassay in pancreatic cancer cell extracts and in pancreatic cancer cell extracts and in the growth media. With use of reverse-transcriptase polymerase chain reaction gastrin gene expression was detected in both cultured BxPC-3 cancer cells and transplanted tumors, as well as seven addition human pancreatic cancer cell lines. Growth of BxPC-3 human pancreatic cancer cell in serum-free medium was inhibited by the addition of the CCK-B/gastrin receptor antagonist L-365,260, and gastrin treatment reversed the inhibitory effect of the antagonist. A selective gastrin antibody (Ab repressed growth of BxPC-3 cells. Gastrin immunoreactivity was detected in fresh human pancreatic cancer specimens but not in normal human pancreatic tissue. These data provide the first evidence that growth of a human pancreatic cancer is tonically stimulated by the autocrine production of gastrin. Evidence for the ubiquity of this system was provided by the detection of gastrin gene expression in multiple human pancreatic cancer cell lines and detection of gastrin in cell lines and fresh pancreatic tumors.
Murine Mammary Carcinoma Exosomes Promote Tumor Growth by Suppression of NK Cell Function (2006)

Many tumor cells shed specialized membrane vesicles known as exosomes. In this study, we show that pretreatment of mice with exosomes produced by TS/A or 4T.1 murine mammary tumor cells resulted in accelerated growth of implanted tumor cells in both syngeneic BALB/c mice and nude mice. As implanted TS/A tumor cells grew more rapidly in mice that had been depleted of NK cells, we analyzed the effects of the tumor-derived exosomes on NK cells. The tumor-derived exosomes inhibit NK cell cytotoxic activity ex vivo and in vitro as demonstrated by chromium release assays. The treatment of mice with TS/A tumor exosomes also led to a reduction in the percentages of NK cells, as determined by FACS analysis, in the lungs and spleens. Key features of NK cell activity were inhibited, including release of perforin but not granzyme B, as well as the expression of cyclin D3 and activation of the Jak3-mediated pathways. Human tumor cell lines also were found to produce exosomes that were capable of inhibiting IL-2-stimulated NK cell proliferation. Exosomes produced by dendritic cells or B cells did not. The presentation of tumor Ags by exosomes is under consideration as a cancer vaccine strategy; however, we found that pretreatment of mice with tumor exosomes blunted the protective effect of syngeneic dendritic cells pulsed ex vivo with tumor exosomes. We propose that tumor exosomes contribute to the growth of tumors by blocking IL-2-mediated activation of NK cells and their cytotoxic response to tumor cells.
Inhibition of collagen IV deposition promotes regeneration of injured CNS axons (1999)

Scarring impedes axon regrowth across the lesion site and is one major extrinsic constraint to effective regeneration in the adult mammalian central nervous system. In the present study we determined whether specific biochemical or immunochemical modulation of one major component of the scar, the basal membrane (BM), would provide a means to stimulate axon regeneration in the mechanically transected postcommissural fornix of the adult rat. Basal membrane developed within the first 2 weeks after transection in spatiotemporal coincidence with the abrupt growth arrest of spontaneously regrowing axons. Local injection of anticollagen IV antibodies or alpha, alpha'-dipyridyl, an inhibitor of collagen triple helix formation and synthesis, significantly reduced lesion-induced BM deposition. This treatment allowed massive axon elongation across the lesion site. Anterograde tracing provided unequivocal evidence that regenerating axons follow their original pathway, reinnervate the appropriate target, the mammillary body, and become remyelinated with compact myelin. Presynaptic electrophysiological recordings of regenerated fibre tracts showed recovery to nearly normal conduction properties. Our results indicate that lesion-induced BM is an impediment for successful axonal regeneration and its reduction is a prerequisite and sufficient condition for regrowing axons to cross the lesion site.