gebhart/patrepeval huggingface dataset:
Purification and characterization of methionine γ-lyase from Trichomonas vaginalis (1991)

Methionine gamma-lyase (EC 4.4.1.11) was purified to homogeneity from the anaerobic protozoan parasite Trichomonas vaginalis by a series of f.p.l.c. procedures. The enzyme catalyses alpha gamma- and alpha beta-elimination reactions of a number of derivatives of methionine and cysteine. It also catalyses gamma-replacement reactions of the thiomethyl group of methionine, homocysteine and ethionine to yield the corresponding S-substituted homocysteine derivative. The enzyme is pyridoxal 5'-phosphate-dependent, has a native molecular mass of approx. 160 kDa and consists of four apparently identical subunits of molecular mass 43-45 kDa. The absorption spectrum of the enzyme is typical of those obtained for other pyridoxal 5'-phosphate-dependent enzymes, and the holoenzyme can be resolved to the apoenzyme by incubation with hydroxylamine and reconstituted by addition of the cofactor. The enzyme activity is significantly affected by carbonyl and thiol reagents, is competitively inhibited by a number of substrate analogues and is completely inactivated by the suicide inhibitor DL-propargylglycine. The T. vaginalis enzyme is similar, in terms of activity and properties, to the enzymes found in a number of species of bacteria that metabolize methionine under anaerobic conditions. It is suggested that methionine catabolism may be of particular importance to the survival of T. vaginalis under microaerophilic conditions in its host.
Tetrahedral Zinc Blende Tin Sulfide Nano‐ and Microcrystals (2006)

Entering a new phase: Tin sulfide (SnS) nano- and microcrystals were synthesized by a seedless, solution procedure. Three-dimensional tetrahedral particles crystallized in the zinc blende (ZB) structure (see SEM image) while two-dimensional platelike particles crystallized in the orthorhombic phase. The optical properties of the orthorhombic plates were similar to bulk SnS, but the absorption edge of the ZB tetrahedra was blue-shifted by around 300 nm compared to that of bulk SnS. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2006/z500460_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Physical and functional interactions of protein tyrosine kinases, p59fyn and ZAP-70, in T cell signaling (1996)

The src family protein tyrosine kinases participate in signaling through cell surface receptors that lack intrinsic tyrosine kinase domains. One of the src family kinases, p59fyn (Fyn), plays an important role in the TCR-mediated signaling. Here we report that Fyn becomes associated with the zeta-associated tyrosine kinase, ZAP-70, in a T cell hybridoma upon stimulation. The association was transient; it occurred as early as 10 s after stimulation and disappeared after 10 min. The two proteins were also associated with each other when coexpressed in COS cells. Coexpression of the zeta-chain was not required for their interaction. Mutational analysis of Fyn and ZAP-70 revealed that their kinase activities were relevant to the association. Deletion of both the SH2 and SH3 domains of Fyn resulted in the decrease of the association with ZAP-70. Consistently, Fyn-SH2 and Fyn-SH3 fused to glutathione S-transferase were able to bind to ZAP-70. These data suggest that multiple sites of Fyn and ZAP-70 are involved in the association. Furthermore, coexpression of the wild-type of both kinases in COS cells enhanced tyrosine phosphorylation of the helix-turn-helix-containing protein, HS1. HS1 was also tyrosine phosphorylated upon TCR stimulation. Thus, we propose that Fyn phosphorylates and activates ZAP-70 and that both kinases cooperate in TCR signaling.
MANET: Empirical Analysis of Security Issue of Routing Protocol using NS-3.29 (2019)

MANETs are open and cooperative networks and can be formed quickly and without any complex infrastructure. These are very useful characteristics for fast and easy connectivity, however this poses severe security threats. In this paper, we only focus on the security threats posed to most popular MANET routing protocol AODV by black hole and flooding attacks. A Simulation study has been conducted in ns-3.29 to compare the performance of preventive schemes FAP and AMTT in case of flooding and black hole attacks on MANET’s. The performance is analyzed based on throughput, message delay and routing overhead. In trust management security scheme, the trust model has two components: direct observation and indirect observation. In direct observation, trust value is calculated from an observer node to observed node. On the other hand, indirect observation is also referred as secondhand information which is obtained from neighbor nodes of the observer node; the trust value is calculated between them. By combining these two components in the trust model, a more accurate trust value is obtained. This will help to improve throughput and packet delivery ratio in the network.
Life span of multipotential hematopoietic stem cells in vivo. (1990)

The findings reported in this study highlight several important features of the development of hematopoietic stem cells after transplantation into irradiated recipients. First, they demonstrate the existence of a class of primitive multipotential stem cells that can function for a significant portion of the lifetime of a mouse (15 mo). In addition, they clearly show that these primitive stem cells can be infected with recombinant retroviruses and thus would be appropriate targets for gene therapy in somatic tissues. Second, our data indicate that the progeny of some, but not all, of the primitive stem cells have fully expanded into the various hematopoietic lineages by 2 mo after reconstitution. Finally, our analysis of the secondary recipients provides strong evidence suggesting that the primitive stem cell population can actually clonally expand. Our current experiments are aimed at determining the extent to which this expansion can occur and whether or not this expansion can be influenced by exogenous factors.
Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine (2006)

Single-stranded DNA-binding proteins (SSBs) are required for repair, recombination and replication in all organisms. Eukaryotic SSBs are regulated by phosphorylation on serine and threonine residues. To our knowledge, phosphorylation of SSBs in bacteria has not been reported. A systematic search for phosphotyrosine-containing proteins in Streptomyces griseus by immunoaffinity chromatography identified bacterial SSBs as a novel target of bacterial tyrosine kinases. Since genes encoding protein-tyrosine kinases (PTKs) have not been recognized in streptomycetes, and SSBs from Streptomyces coelicolor (ScSSB) and Bacillus subtilis (BsSSB) share 38.7% identity, we used a B.subtilis protein-tyrosine kinase YwqD to phosphorylate two cognate SSBs (BsSSB and YwpH) in vitro. We demonstrate that in vivo phosphorylation of B.subtilis SSB occurs on tyrosine residue 82, and this reaction is affected antagonistically by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation of SSBs is a conserved process of post-translational modification in taxonomically distant bacteria.
Expansion and Characterization of T Cells Transduced with a Chimeric Receptor against Ovarian Cancer (2000)

Adoptive immunotherapy with genetically modified T lymphocytes is being utilized in clinical trials for the treatment of a broad range of diseases including cancer and HIV infection. To improve on these treatments, and to better understand their mechanisms of action, it is necessary to develop techniques to generate large numbers of cells and characterize the functional heterogeneity of the cells produced. In this study, patient peripheral blood lymphocytes were transduced with a chimeric antigen receptor (MOv-γ) derived from a mouse monoclonal antibody against folate-binding protein, which is overexpressed on many ovarian cancers. Thus, irrespective of their original specificity, normal human T lymphocytes were redirected to react against ovarian cancer cells. Lymphocytes from five patients were transduced and grown to large numbers, with a median expansion of more than 7000-fold. When proliferation was inadequate, the cells were expanded by stimulation utilizing anti-CD3, IL-2, and irradiated allogeneic PBMCs. The cells maintained their functional ability to recognize ovarian cancer over several months. Cloning of transduced cells was undertaken to determine the level of gene expression and function of individual cells making up the bulk population. Transduced CD4+ and CD8+ cell clones were isolated from the bulk and demonstrated antitumor activity. These clones had a diverse repertoire with respect to secretion of cytokines, and individual clones maintained their cytokine profile on subsequent expansion. These studies establish the feasibility of consistently generating large numbers of gene-modified tumor-reactive lymphocytes, with a stable and diverse cytokine repertoire, that could be utilized for patient treatment.
Comparison of 5-aminosalicylic acid and N-acetylaminosalicylic acid uptake by the isolated human colonic epithelial cell. (1992)

Isolated human colonic epithelial cell suspensions were incubated with either 0.1 mM 5-aminosalicylic acid (5-ASA) or 0.1 mM acetylaminosalicylic acid (Ac-ASA) for up to two hours. Intra- and extracellular 5-ASA and Ac-ASA were measured by high performance liquid chromatography. Mean 5-ASA uptake in one hour was 160.5 nmol/g dry weight, compared with an Ac-ASA uptake of only 5.75 nmol/g dry weight. No unchanged 5-ASA was detected inside the cell. Repeated washing had no effect on the intracellular Ac-ASA concentration. This discrepancy in drug uptake may explain why Ac-ASA seems to be ineffective when given to patients with ulcerative colitis.
Type 1 diabetes immunotherapy using polyclonal regulatory T cells (2015)

Autologous regulatory T cells can be expanded and are well tolerated in patients with recent-onset type 1 diabetes.
Rigidly linking cyclometallated Ir(iii) and Pt(ii) centres: an efficient approach to strongly absorbing and highly phosphorescent red emitters (2017)

The synthesis and photophysical properties of an unprecedented tetranuclear complex are described, in which a fac-tris-cyclometallated Ir(iii) centre is rigidly connected to three cyclometallated Pt(ii) centres. The complex absorbs strongly up to ∼600 nm and emits red light with unusually high efficiency.
A reporter gene assay to assess the molecular mechanisms of xenobiotic-dependent induction of the human CYP3A4 genein vitro (1999)

1. A plasmid containing 1 kb of the CYP3A4 regulatory (promoter) region coupled to a reporter gene for secretary placental alkaline phosphatase (SPAP) was transfected into HepG2 cells. Transfected cells were dosed with several known inducers of CYP3A4 and the levels of SPAP were measured. The effect of co-transfecting a plasmid encoding the human glucocorticoid receptor on reporter gene activity was also examined. 2. Dexamethasone induced CYP3A4-dependent reporter gene expression in a concentration-dependent manner and induction was approximately doubled in the presence of the glucocorticoid receptor. Dexamethasone-dependent induction was blocked by RU-486 (a glucocorticoid receptor antagonist), in the presence of the co-transfected glucocorticoid receptor. 3. Induction of CYP3A4-dependent reporter gene expression and enhancement of the induction by the glucocorticoid receptor was also observed with pregnenolone-16alpha-carbonitrile (PCN), rifampicin, phenytoin, carbamazepine, phenylbutazone and phenobarbitone, all known in vivo inducers of CYP3A4 in man. 4. Metyrapone and sulfinpyrazone induced CYP3A4-dependent reporter gene expression, but induction was not enhanced by the glucocorticoid receptor. 5. Clotrimazole, erythromycin and triacetyloleandomycin (TAO) did not induce CYP3A4-dependent reporter gene expression, consistent with the observation that these inducers act through post-transcriptional mechanisms. 6. These results highlight differences in the molecular mechanisms of induction of CYP3A4 by the xenobiotics studied and indicate that the glucocorticoid receptor is involved in the induction of the CYP3A4 gene by some, but not all, CYP3A4 inducers. 7. We propose that the approach described here provides a useful in vitro approach for the identification of transcriptional regulators of the CYP3A4 gene.
Chronic cutaneous lupus erythematosus treated with thalidomide (1993)

<h3>REPORT OF A CASE</h3> A 38-year-old woman presented with extensive scarring alopecia diagnosed as chronic cutaneous lupus erythematosus (CCLE) at age 21 years. A skin biopsy specimen confirmed the diagnosis, and repeated studies failed to reveal anti-nDNA (double-stranded or native), anti-Ro (SSA), or anti-La (SS-B) antibodies. She denied photosensitivity, arthralgias, pericarditis, pleurisy, renal or hematologic disease, or psychiatric disorders. Half of the scalp was involved, with an extensive atrophic scarring alopecia that demonstrated patchy hyperpigmentation, hypopigmentation, and erythema (<b>Figure 1</b>). Scattered follicular plugs were also present. The patient received quinacrine (Atabrine) (100 mg twice daily) from October 1983 through May 1987. In October 1985, hydroxychloroquine (Plaquenil Sulfate) was added to therapy, with the dose increasing from 200 to 400 mg/d. Hydroxychloroquine therapy was discontinued in April 1989, and dapsone (50 mg/d) was substituted in June 1989 for 8 weeks. Isotretinoin (Accutane)
An efficient text input method for pen-based computers (1998)

has not yet taken off, partly because of the lack of fast and easy text input methods. The situation is even worse for people using East Asian languages, where thousands of characters are used and handwriting recognition is extremely difficult. In this paper, we propose a new fast text input method for pen-based computers, where text is not composed by entering characters one by one, but by selecting words from a menu of candidates created by filtering the dictionary and predicting from context. Using our approach, users can enter Japanese text more than hvice as fast as recognition-based and other existing text input methods. User studies and detailed analysis of the method are also given.
An investigation of the binding of protein proteinase inhibitors to trypsin by electrospray ionization mass spectrometry (1996)

The binding of BPTI and SBTI with trypsin has been investigated by ESI MS, using the mutant K15V-BPTI and the chemically modified RcamBPTI as controls. Although high cone voltages (+80 V) produce sharp spectra of BPTI, RcamBPTI, SBTI and trypsin alone, the complexes of BPTI, RcamBPTI and SBTI with trypsin undergo partial dissociation due to collisional activation. At lower cone voltages (+40 V) these non-covalent complexes are stable. The charge distribution on the trypsin and the inhibitors produced by gas phase dissociation of the complexes are markedly different from those of the components alone, indicating that ESI MS provides a novel probe for exploring the ionic interactions at the contact surface of proteins. Moreover, by determining the cone voltage at which the gas phase dissociation of complexes occurs it may be possible to use ESI MS to compare the binding energies of closely related complexes.
Illustrating smooth surfaces (2000)

We present a new set of algorithms for line-art rendering of smooth surfaces. We introduce an efficient, deterministic algorithm for finding silhouettes based on geometric duality, and an algorithm for segmenting the silhouette curves into smooth parts with constant visibility. These methods can be used to find all silhouettes in real time in software. We present an automatic method for generating hatch marks in order to convey surface shape. We demonstrate these algorithms with a drawing style inspired by A Topological Picturebook by G. Francis.
The synthesis and photophysics of tris-heteroleptic cyclometalated iridium complexes (2011)

Herein we report the synthesis and photophysical study of tris-heteroleptic complexes of the general formula IrLL'(acac), where L and L' are two differently substituted 2-phenylpyridines (ppyH) and acacH is 2,4-pentanedione, using a combinatorial approach that could be employed for many ligand combinations. The tris-heteroleptic complexes and the analogous bis-heteroleptic complexes of the form IrL(2)(acac) have been studied by a combination of absorption and photoluminescence spectroscopies in conjunction with modelling by DFT and TD-DFT to elucidate the nature and location of the excited state in the novel species.
Quantification of pH gradients and implications in insulator‐based dielectrophoresis of biomolecules (2011)

Direct current (DC) insulator-based dielectrophoretic (iDEP) microdevices have the potential to replace traditional alternating current dielectrophoretic devices for many cellular and biomolecular separation applications. The use of large DC fields suggest that electrode reactions and ion transport mechanisms can become important and impact ion distributions in the nanoliters of fluid in iDEP microchannels. This work tracked natural pH gradient formation in a 100 μm wide, 1 cm-long microchannel under applicable iDEP protein manipulation conditions. Using fluorescence microscopy with the pH-sensitive dye FITC Isomer I and the pH-insensitive dye TRITC as a reference, pH was observed to drop drastically in the microchannels within 1 min in a 3000 V/cm electric field; pH drops were observed in the range of 6-10 min within a 100 V/cm electric field and varied based on the buffer conductivity. To address concerns of dye transport impacting intensity data, electrokinetic mobilities of FITC were carefully examined and found to be (i) toward the anode and (ii) 1 to 2 orders of magnitude smaller than H⁺ transport which is responsible for pH drops from the anode toward the cathode. COMSOL simulations of ion transport showed qualitative agreement with experimental results. The results indicate that pH changes are severe enough and rapid enough to influence the net charge of a protein or cause aggregation during iDEP experiments. The results also elucidate reasonable time periods over which the phosphate buffering capacity can counter increases in H⁺ and OH⁻ for unperturbed iDEP manipulations.
XBF-1, a winged helix transcription factor with dual activity, has a role in positioning neurogenesis in Xenopus competent ectoderm (1998)

Neuronal differentiation in the vertebrate nervous system is temporally and spatially controlled by mechanisms which are largely unknown. Here we investigate the role of XBF-1, an anterior neural plate-specific winged helix transcription factor, in controlling the pattern of neurogenesis in Xenopus ectoderm. We show that, in the anterior neural plate of normal embryos, prospective neurogenesis is positioned at the anterior boundary of the XBF-1 expression domain. By misexpressing XBF-1 in the posterior neural plate we show that a high dose of XBF-1 has a dual effect; it suppresses endogenous neuronal differentiation in high expressing cells and induces ectopic neuronal differentiation in adjacent cells. In contrast, a low dose of XBF-1 does not suppress but instead, expands the domain of neuronal differentiation in the lateral and ventral sides of the embryo. XBF-1 regulates the expression of XSox3, X-ngnr-1, X-Myt-1 and X-&Dgr;-1 suggesting that it acts early in the cascade leading to neuronal differentiation. A fusion of XBF-1 to a strong repressor domain (EnR) mimics most of the XBF-1 effects suggesting that the wild type XBF-1 is a transcriptional repressor. However, fusion of XBF-1 to a strong activation domain (E1A) specifically suppresses neuronal differentiation suggesting that XBF-1 may also work as a transcriptional activator. Based on these findings, we propose that XBF-1 is involved in positioning neuronal differentiation by virtue of its concentration dependent, dual activity, as a suppressor and an activator of neurogenesis.
Cell adhesion and proliferation mediated through the G1 domain of versican (1999)

We have demonstrated previously that versican stimulated cell proliferation through the G3 domain. In these experiments, we show that versican mini-gene-transfected cell lines exhibited decreased cell-substratum interaction and increased cell proliferation. Exogenous addition of growth medium containing the versican gene product produced the same results. Because the G1 domain of versican is structurally similar to the G1 domain of aggrecan and to link protein, both of which play role in cell adhesion, we hypothesized that versican's proliferative effects may be a consequence of its ability to reduce cell adhesion, and may be mediated through the G1 domain. To investigate this, we expressed a G1 construct in NIH3T3 cells and showed that it reduced cell adhesion and enhanced cell proliferation. We then demonstrated that deletion of the G1 domain from versican greatly, but not completely, reversed the effects of versican: G1-deletion mutants of versican show slightly reduced amounts of cell adhesion and slightly increased rates of proliferation. We concluded that versican can stimulate cell proliferation via two mechanisms: through two EGF-like motifs in the G3 domain which play a role in stimulating cell growth, and through the G1 domain, which destabilizes cell adhesion and facilitates cell growth. We purified the G1 product with an affinity column and demonstrated that it reduced cell adhesion and enhanced cell proliferation.
The colicin G, H and X determinants encode microcins M and H47, which might utilize the catecholate siderophore receptors FepA, Cir, Fiu and IroN (2003)

The colicin G producer Escherichia coli CA46, the colicin H producer E. coli CA58 and E. coli Nissle 1917 (DSM 6601) were shown to produce microcin H47 and the newly described microcin M. Both microcins were exported like colicin V by an RND-type export system, including TolC. The gene cluster encoding microcins H47 and M in strains CA46 and CA58 is nearly identical to that in strain DSM 6601, except that two additional genes are included. A Fur box identified in front of the microcin-encoding genes explained the observed iron regulation of microcin production. The catecholate siderophore receptors Fiu, Cir and FepA from E. coli and IroN, Cir and FepA from Salmonella were identified as receptors for microcins M, H47 and E492. IroN takes up the glucose-containing catecholate siderophore salmochelin, whose synthesis is encoded in the iro gene cluster found in Salmonella and certain, often uropathogenic, E. coli strains. A gene in this iro cluster, iroB, which encodes a putative glycosyltransferase, was also found in the microcin H47/M and microcin E492 gene clusters. These microcins could aid the producing strain in competing against enterobacteria that utilize catecholate siderophores.