gebhart/patrepeval huggingface dataset:
Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1 (1997)

We report that Chlorella virus PBCV-1 encodes a 298-amino-acid ATP-dependent DNA ligase. The PBCV-1 enzyme is the smallest member of the covalent nucleotidyl transferase superfamily, which includes the ATP-dependent polynucleotide ligases and the GTP-dependent RNA capping enzymes. The specificity of PBCV-1 DNA ligase was investigated by using purified recombinant protein. The enzyme catalyzed efficient strand joining on a singly nicked DNA in the presence of magnesium and ATP (Km, 75 microM). Other nucleoside triphosphates or deoxynucleoside triphosphates could not substitute for ATP. PBCV-1 ligase was unable to ligate across a 2-nucleotide gap and ligated poorly across a 1-nucleotide gap. A native gel mobility shift assay showed that PBCV-1 DNA ligase discriminated between nicked and gapped DNAs at the substrate-binding step. These findings underscore the importance of a properly positioned 3' OH acceptor terminus in substrate recognition and reaction chemistry.
Level of Expression of Phospholipid Scramblase Regulates Induced Movement of Phosphatidylserine to the Cell Surface (1998)

We recently identified a 35-kDa erythrocyte membrane protein, phospholipid scramblase, that promotes Ca2+-dependent transbilayer movement of phosphatidylserine (PS) and other phospholipids (PL) in reconstituted proteoliposomes (Zhou, Q., Zhao, J., Stout, J. G., Luhm, R. A., Wiedmer, T., and Sims, P. J. (1997) J. Biol. Chem. 272, 18240-18244). To determine whether this same protein is responsible for the rapid movement of PS from inner-to-outer plasma membrane leaflets in other cells exposed to elevated cytosolic calcium concentration ([Ca2+]c), we analyzed how induced movement of PS to the cell surface related to expression of PL scramblase. Exposure to Ca2+ ionophore A23187 resulted in rapid PS exposure in those cell lines constitutively high in PL scramblase (HEL, Epstein-Barr virus-transformed B-lymphocytes, and Jurkat), whereas this response was markedly attenuated in cells expressing low amounts of this protein (Raji, HL60, and Dami). To confirm this apparent correlation between PL scramblase expression and PS egress at elevated [Ca2+]c, Raji cells were transfected with PL scramblase cDNA in pEGFP-C2, and stable transformants expressing various amounts of GFP-PL scramblase fusion protein were obtained. Clones expressing GFP-PL scramblase showed distinctly plasma membrane-localized fluorescence. When compared either with untransfected Raji cells or with transformants expressing GFP alone, clones expressing GFP-PL scramblase fusion protein showed increased exposure of PS at the cell surface in response to elevated [Ca2+]c, accompanied by increased expression of membrane catalytic function for the prothrombinase enzyme complex. These data indicate that transfection with PL scramblase cDNA promotes movement of PS to cell surfaces and suggest that this protein normally mediates redistribution of plasma membrane phospholipids in activated, injured, or apoptotic cells.
Complementary Metal Oxide Semiconductor Cantilever Arrays on a Single Chip:  Mass-Sensitive Detection of Volatile Organic Compounds (2002)

The sensing behavior of polymer-coated resonant cantilevers for mass-sensitive detection of volatile organic compounds was investigated. Industrial complementary metal oxide semiconductor (CMOS) technology combined with subsequent CMOS-compatible micromachining was used to fabricate a single-chip system comprising the transducers and all necessary driving and signal-conditioning circuitry. An analytical model was developed to describe the mass-sensing mechanism of polymer-coated resonant cantilevers. The model was validated by measurements of various gaseous analytes. As an exemplary application, the quantitative analysis of a binary mixture using an array of four cantilevers is described. Experimental results are given for the concentration prediction of a mixture of n-octane and toluene. Finally, it was established that the limit of detection achieved with cantilever sensors is comparable to that of other acoustic wave-based gas sensors.
In vitro studies on cellular and molecular mechanisms of arsenic trioxide (As2O3) in the treatment of acute promyelocytic leukemia: As2O3 induces NB4 cell apoptosis with downregulation of Bcl-2 expression and modulation of PML-RAR alpha/PML proteins (1996)

It has been shown recently in China that arsenic trioxide (As2O3) is a very effective treatment for acute promyelocytic leukemia (APL). APL patients resistant to all-trans retinoic acid (ATRA) and conventional chemotherapy can still respond to AS2O3. In this study, we addressed the possible cellular and molecular mechanisms of this treatment by using NB4 cells as a model. The results show that: (1) As2O3 triggers relatively specific NB4 cell apoptosis at micromolar concentration, as proved by morphology, histogramic related nuclear DNA contents, and DNA gel eletrophoresis. (2) As2O3 does not influence bax, bcl-x, c-myc, and p53 gene expression, but downregulates bcl-2 gene expression at both mRNA and protein levels. (3) As2O3 induces a significant modulation of the PML staining pattern in NB4 cells and HL-60 cells. The micropunctates characteristic of PML-RAR alpha in NB4 cells dissappear after treatment with As2O3, whereas a diffuse PML staining occurs in the perinuclear cytoplasmic region. In addition, a low percentage of untreated NB4 cells exhibits an accumulation of PML positive particles in a compartment of cytoplasm. The percentage of these cells can be significantly increased after As2O3 treatment. A similar PML staining pattern is observed in apoptotic cells. (4) ATRA pretreatment does not influence As2O3-induced apoptosis. These results suggest that induction of cell apoptosis can be one of the mechanisms of the therapeutic effect of As2O3. Moreover, this apoptosis induction occurs independently of the retinoid pathway and may be mediated, at least partly, through the modulation of bcl-2, as well as PML-RAR alpha and/ or PML proteins.
Surface‐modified mutants of cytochrome P450cam: enzymatic properties and electrochemistry (1999)

We report the electrochemistry of genetic variants of the haem monooxygenase cytochrome P450cam. A surface cysteine-free mutant (abbreviated as SCF) was prepared in which the five surface cysteine residues Cys-58, Cys-85, Cys-136, Cys-148 and Cys-334 were changed to alanines. Four single surface cysteine mutants with an additional mutation, R72C, R112C, K344C or R364C, were also prepared. The haem spin-state equilibria, NADH turnover rates and camphor-hydroxylation properties, as well as the electrochemistry of these mutants are reported. The coupling of a redox-active label, N-ferrocenylmaleimide, to the single surface cysteine mutant SCF-K344C, and the electrochemistry of this modified mutant are also described.
Identification of glucocorticoid-inducible cytochromes P-450 in the intestinal mucosa of rats and man. (1987)

We used monoclonal antibodies and complementary DNAs (cDNAs) to glucocorticoid-inducible liver cytochromes P-450 in rats (P-450p) and in man (HLp) to search for related cytochromes in intestinal mucosa. In rat enterocytes, we found two dexamethasone-inducible proteins related to the steroid-inducible liver cytochromes P-450. Induction of these proteins in enterocytes was associated with increases in the amount of a P-450p-related messenger RNA and of erythromycin demethylase, an activity highly characteristic of P-450p and HLp. Similar studies on human jejunal enterocytes revealed a microsomal protein indistinguishable from HLp on immunoblots and an abundance of RNA hybridizing with HLp cDNA. In human enterocytes the specific concentration of the HLp-related cytochrome (measured immunochemically or as erythromycin demethylase activity) was similar to that found in human liver and could account for all of the CO-binding hemo-protein detected. We conclude that the intestinal mucosa contains prominent form(s) of cytochromes P-450 similar to liver cytochrome P-450p in their structure, function, and some regulatory characteristics.
Rational Design of α‐Helical Antimicrobial Peptides to Target Gram‐negative Pathogens, Acinetobacter baumannii and Pseudomonas aeruginosa: Utilization of Charge, ‘Specificity Determinants,’ Total Hydrophobicity, Hydrophobe Type and Location as Design Parameters to Improve the Therapeutic Ratio (2011)

The rapidly growing problem of increased resistance to classical antibiotics makes the development of new classes of antimicrobial agents with lower rates of resistance urgent. Amphipathic cationic α-helical antimicrobial peptides have been proposed as a potential new class of antimicrobial agents. The goal of this study was to take a broad-spectrum, 26-residue, antimicrobial peptide in the all-D conformation, peptide D1 (K13) with excellent biologic properties and address the question of whether a rational design approach could be used to enhance the biologic properties if the focus was on Gram-negative pathogens only. To test this hypothesis, we used 11 and 6 diverse strains of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. We optimized the number and location of positively charged residues on the polar face, the number, location, and type of hydrophobe on the non-polar face and varied the number of 'specificity determinants' in the center of the non-polar face from 1 to 2 to develop four new antimicrobial peptides. We demonstrated not only improvements in antimicrobial activity, but also dramatic reductions in hemolytic activity and unprecedented improvements in therapeutic indices. Compared to our original starting peptide D1 (V13), peptide D16 had a 746-fold improvement in hemolytic activity (i.e. decrease), maintained antimicrobial activity, and improved the therapeutic indices by 1305-fold and 895-fold against A. baumannii and P. aeruginosa, respectively. The resulting therapeutic indices for D16 were 3355 and 895 for A. baumannii and P. aeruginosa, respectively. D16 is an ideal candidate for commercialization as a clinical therapeutic to treat Gram-negative bacterial infections.
Vascular morphogenesis: tales of two syndromes (2003)

Advances in our understanding of fundamental biological processes can be made by the analysis of defects manifested in inherited diseases. The genes responsible for these genetic syndromes often encode proteins that act at critical points of the pathways that control biological processes such as cell proliferation, cell-cell communication, cellular differentiation, and cell death. This approach has lead to the discovery of novel gene products and/or biochemical pathways involved in disease, genes that in turn play a fundamental role in normal biological processes. This forward genetic approach, focusing on Mendelian disorders of vascular anomalies, has been particularly fruitful for the study of genetic regulation of angiogenesis. This review summarizes the ongoing saga of two genetic syndromes involving disruption of normal vascular morphogenesis. Each inherited disorder involves the focal development of a distinct vascular anomaly. In hereditary hemorrhagic telangiectasia (HHT), the hallmark vascular lesion is termed an arteriovenous malformation, which involves the direct communication of an artery with a vein (arteriovenous shunt), without an intervening capillary bed. For cerebral cavernous malformations (CCM), the lesions are grossly-dilated, closely-packed, capillary-like sinusoidal chambers. The autosomal dominant mode of inheritance of each of these distinct syndromes suggested that the underlying genes might regulate critical aspects of vascular morphogenesis. Emerging but intriguing tales are being told by the genes (and their protein products) mutated in these disorders.
Anti-TAPA-1 antibodies induce protein tyrosine phosphorylation that is prevented by increasing intracellular thiol levels. (1993)

We studied the signal induced by the anti-TAPA-1 antibody and compared it to the signal induced by anti-IgM antibodies in a human B cell line, OCl-LY8. We found that exposure of these cells to either antibody resulted in a rapid increase in protein tyrosine phosphorylation which was prevented by inhibitors of tyrosine kinases. Tyrosine phosphorylation was an early event in the cascase leading to the antiproliferative effect of the anti-TAPA-1 antibody. However, 2-ME, a reducing agent that is not an inhibitor of tyrosine kinases, prevented both tyrosine phosphorylation and the antiproliferative effect of the antibody. Cells grown in low concentrations of 2-ME did not exhibit an increase in tyrosine phosphorylation in response to the anti-TAPA-1 antibody and were insensitive to the antiproliferative effect of the antibody. In contrast, the same cells maintained in 2-ME were able to induce tyrosine phosphorylation in response to anti-IgM. The use of 2-ME resulted in an increase in intracellular thiols, mostly glutathione. Moreover, compounds that block glutathione synthesis rendered cells susceptible to the antibody, even in the presence of 2-ME. These experiments demonstrate that tyrosine kinases are involved in propagating the antiproliferative signal initiated by the anti-TAPA-1 antibody and suggest that this signal is dependent upon the level of intracellular thiols.
Epitope Mapping of the Transforming Growth Factor-β Superfamily Protein, Macrophage Inhibitory Cytokine-1 (MIC-1):  Identification of at Least Five Distinct Epitope Specificities (2000)

Macrophage inhibitory cytokine-1 (MIC-1) is a divergent member of the transforming growth factor-beta (TGF-beta) superfamily whose increased expression is associated with macrophage activation and which is expressed highly in placenta as compared to other tissues. There are two known allelic forms of human MIC-1 due an amino acid substitution at position 6 of the mature protein. We have raised four monoclonal antibodies (MAbs) and one polyclonal antiserum to the mature protein region of human MIC-1 and have used an extensive panel of MIC-1 relatives, mutants, and chimeras to map their epitopes. None of the MAbs were able to cross-react with either the murine homologue of MIC-1 or with hTGF-beta1, and all of the MAb epitopes were conformation-dependent. A distinct cross-reactivity pattern with the various antigens was observed for each of the monoclonal and polyclonal antibodies suggesting the presence of at least five immunogenic regions on the MIC-1 surface. One of the MAbs is directed against the amino terminus of the protein and can distinguish between the two allelic forms of MIC-1. The epitopes for the other three MAbs were located near the tips of the so-called "fingers" of the protein and appeared to be partially overlapping as each involved amino acids in the region 24-37. In one case, it was possible to mutate murine MIC-1 so that it could be recognized by one of the MAbs. Finally, the use of another mutant in which Cys 77 was replaced by serine enabled confirmation of the location of the MIC-1 interchain disulfide bond.
Assessing pain in critically ill sedated patients by using a behavioral pain scale (2001)

These results indicate that the expression of pain can be scored validly and reliably by using the BPS in sedated, mechanically ventilated patients. Further studies are warranted regarding the utility of the BPS in making clinical decisions about the use of analgesic drugs in the intensive care unit.
Human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) DNA in Kaposi's sarcoma lesions, AIDS Kaposi's sarcoma cell lines, endothelial Kaposi's sarcoma simulators, and the skin of immunosuppressed patients. (1996)

We used the polymerase chain reaction on 63 tissue specimens of histologically staged classic Kaposi's sarcoma (KS) from 40 patients, 14 specimens from 14 acquired immune deficiency syndrome (AIDS)-KS cases (all from the same geographic area over a 10-year period), and peripheral blood mononuclear cells from 1 of the non-AIDS KS patients to amplify a specific 210-bp genomic sequence of the newly discovered KS-associated herpesvirus (KSHV). Also tested were 86 benign and malignant endothelial lesions, which potentially simulated each KS histological stage and were further matched by age approximation and by sex with a classical KS specimen. The lesions included hemangioma, lymphangioma, pyogenic granuloma, and angiosarcoma. KSHV was also sought in multiple well characterized vascular endothelial cell lines from AIDS-KS lesions and in 20 mainly cutaneous benign and malignant lesions from 15 immunosuppressed transplant patients. Overall, 92% of KS tissue specimens, representing 88% of classical KS and 100% of AIDS-KS patients, and in addition the sample of peripheral blood mononuclear cell DNA, were positive as visualized on ethidium bromide gels and confirmed by Southern blot hybridization (only 1 case was negative on gell visualization but positive on Southern blot), thus confirming the close association of KSHV with KS of different clinical forms. None of the various other endothelial lesion, skin lesions in immunosuppressed patients, or AIDS-KS endothelial cell lines contained amplifiable KSHV DNA, which indicates that reactivation of KSHV is not present in the skin lesions of immunosuppressed patients and probably is not a ubiquitous agent that secondarily infects proliferative endothelium. The absence of amplifiable virus DNA in the cultured endothelium of KS suggests that the stimulus for angioproliferation originates in another host cell or under conditions not reproduced in culture. The polymerase chain reaction is a specific and sensitive means of verifying KS in the differential diagnosis of angioproliferative lessons.
Tuning Peptoid Secondary Structure with Pentafluoroaromatic Functionality:  A New Design Paradigm for the Construction of Discretely Folded Peptoid Structures (2006)

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.
Topical antifungal treatments for tinea cruris and tinea corporis (2014)

The pooled data suggest that the individual treatments terbinafine and naftifine are effective. Adverse effects were generally mild and reported infrequently. A substantial number of the studies were more than 20 years old and of unclear or high risk of bias; there is however, some evidence that other topical antifungal treatments also provide similar clinical and mycological cure rates, particularly azoles although most were evaluated in single studies.There is insufficient evidence to determine if Whitfield's ointment, a widely used agent is effective.Although combinations of topical steroids and antifungals are not currently recommended in any clinical guidelines, relevant studies included in this review reported higher clinical cure rates with similar mycological cure rates at the end of treatment, but the quality of evidence for these outcomes was rated very low due to imprecision, indirectness and risk of bias. There was insufficient evidence to confidently assess relapse rates in the individual or combination treatments.Although there was little difference between different classes of treatment in achieving cure, some interventions may be more appealing as they require fewer applications and a shorter duration of treatment. Further, high quality, adequately powered trials focusing on patient-centred outcomes, such as patient satisfaction with treatment should be considered.
Electroanatomical mapping of atrial fibrillation: Review of the current techniques and advances. (2014)

The number of atrial fibrillation (AF) catheter ablations performed annually has been increasing exponentially in the western countries in the last few years. This is clearly related to technological advancements, which have greatly contributed to the improvements in catheter ablation of AF. In particular, state-of-the-art electroanatomical mapping systems have greatly facilitated mapping processes and have enabled complex AF ablation strategies. In this review, we outline contemporary and upcoming electroanatomical key technologies focusing on new mapping tools and strategies in the context of AF catheter ablation.
Method for navigation and control of a magnetically guided capsule endoscope in the human stomach (2012)

The use of flexible endoscopes is the standard screening method for the upper gastrointestinal tract today. Disadvantages for the patient, due to the insertion process and often applied sedation, can be overcome with wireless capsule endoscopy (WCE). But WCE is not suited for the stomach as it can not guarantee a complete screening having no active guidance. With the magnetically guided capsule endoscopy (MGCE) a novel minimal invasive screening method for the gastrointestinal tract is being developed. With its current focus on the human stomach comes the need for a navigation and control method that is specialized for this application and its constraints. We present a new method for screening a water-filled stomach with 10 functions for basic capsule movements, special maneuvers and mode-changes. Its evaluation was done in a clinical study consisting of 53 patient and volunteer cases. The individual evaluation of each function included a statistical analysis and an operators' survey. The functions proved sufficient to reach all parts of the stomach and to acquire close-up views of the mucosa.