gebhart/patrepeval huggingface dataset:
A form of anti-Tac(Fv) which is both single-chain and disulfide stabilized: comparison with its single-chain and disulfide-stabilized homologs (1997)

Disulfide-stabilized Fvs (dsFvs) are recombinant proteins composed of a heavy-chain variable domain (VH) of an antibody connected via a disulfide bond to the light-chain variable domain (VL). In single-chain Fvs (scFvs), a peptide connector links VH and VL. The dsFv form of the anti-Tac monoclonal antibody which reacts with the alpha subunit of the IL2 receptor was recently reported to be more stable and to aggregate less during renaturation than anti-Tac(scFv). In addition, it could be produced in a better yield owing to less aggregation. However, the yields are still too low to permit the production of material for clinical trials in which the dsFv will be used to image or treat IL2 receptor (CD25)-containing tumors. To increase the efficiency by which VH and VL associate and form a disulfide bond during renaturation, we have prepared an Fv form of anti-Tac which is both single chain and disulfide stabilized (scdsFv). The recombinant protein is expressed in Escherichia coli, where it accumulates in inclusion bodies. Using inclusion body protein as the reference point, the yield of purified anti-Tac(scdsFv) was 13% compared with 2% for anti-Tac(dsFv). Anti-Tac(scdsFv) has equivalent binding affinity, immunoreactivity after radiolabeling and stability. The results show that a linker between VH and VL facilitates heterodimer formation and leads to disulfide bond formation in a higher percentage of the molecules renatured. Thus anti-Tac(scdsFv) is the preferred form of anti-Tac(Fv) to be used for clinical studies. We anticipate that scdsFvs will be the optimum recombinant form of Fv to produce from bacteria.
Preparation and Properties of Amorphous Silicon Produced by a Consecutive, Separated Reaction Chamber Method (1982)

A new method of preparing a-Si film, in which each of the p, i, and n layers are deposited in consecutive, separated reaction chambers, is presented. It was confirmed experimentally that, in the conventional single reaction chamber method for a-Si film, the residual dopant gases which remain in the reaction chamber cause undesirable doping of the film, resulting in deterioration of the film quality. This undesirable doping can be avoided in the separated reaction chamber method. The photoconductivity of the i-layer prepared by this method was about 1×10 -3 (Ω -1 cm -1 ) in sunlight of AM–1 100 mW/cm -2 . The best conversion efficiency of p-i-n a-Si solar cells prepared by this method was 6.91%.
Focal Pulsed Field Ablation for Pulmonary Vein Isolation and Linear Atrial Lesions (2020)

The lattice-tip catheter can deliver focal PF to durably isolate veins and create linear lesions with excellent transmurality and without complications. The PF lesions did not damage the phrenic nerve, vessels, and the esophagus.
Phase I Study of Navitoclax (ABT-263), a Novel Bcl-2 Family Inhibitor, in Patients With Small-Cell Lung Cancer and Other Solid Tumors (2011)

Navitoclax is safe and well tolerated, with dose-dependent thrombocytopenia as the major adverse effect. Preliminary efficacy data are encouraging in SCLC. Efficacy in SCLC and the utility of pro-GRP as a marker of treatment response will be further evaluated in phase II studies.
Identification of a neutralization epitope on the envelope gp46 antigen of human T cell leukemia virus type I and induction of neutralizing antibody by peptide immunization (1991)

We have generated a number of mAb against various epitopes on the external envelope glycoprotein, gp46, of human T cell leukemia virus type I (HTLV-I) from a WKA rat immunized with a recombinant vaccinia virus containing the HTLV-I env gene. Among these mAb, one group of mAb, represented by a mAb designated LAT-27, could neutralize the infectivity of HTLV-I, as determined by a HTLV-I-mediated cell fusion inhibition assay. LAT-27 also interfered with transformation of normal T lymphocytes by HTLV-I in vitro. An antibody-binding assay using overlapping synthetic oligopeptides showed that LAT-27 bound specifically to 10-mer peptides that contained the gp46 amino acid sequence 191-196 (Leu-Pro-His-Ser-Asn-Leu). Antibodies from HTLV-I+ humans interfered with the binding of LAT-27 to gp46 Ag. Sera from rabbits immunized with a LAT-27-reactive peptide, 190-199, conjugated with OVA, but not sera from OVA-immunized rabbits, reacted with gp46 Ag and neutralized infectivity of HTLV-I. These results show that the HTLV-I neutralization epitope recognized by LAT-27 locates to the gp46 amino acids 191-196, and that immunization with a peptide containing the LAT-27 epitope can elicit an HTLV-I neutralizing antibody response.
Oxidative Stress Sensor Keap1 Functions as an Adaptor for Cul3-Based E3 Ligase To Regulate Proteasomal Degradation of Nrf2 (2004)

Transcription factor Nrf2 is a major regulator of genes encoding phase 2 detoxifying enzymes and antioxidant stress proteins in response to electrophilic agents and oxidative stress. In the absence of such stimuli, Nrf2 is inactive owing to its cytoplasmic retention by Keap1 and rapid degradation through the proteasome system. We examined the contribution of Keap1 to the rapid turnover of Nrf2 (half-life of less than 20 min) and found that a direct association between Keap1 and Nrf2 is required for Nrf2 degradation. In a series of domain function analyses of Keap1, we found that both the BTB and intervening-region (IVR) domains are crucial for Nrf2 degradation, implying that these two domains act to recruit ubiquitin-proteasome factors. Indeed, Cullin 3 (Cul3), a subunit of the E3 ligase complex, was found to interact specifically with Keap1 in vivo. Keap1 associates with the N-terminal region of Cul3 through the IVR domain and promotes the ubiquitination of Nrf2 in cooperation with the Cul3-Roc1 complex. These results thus provide solid evidence that Keap1 functions as an adaptor of Cul3-based E3 ligase. To our knowledge, Nrf2 and Keap1 are the first reported mammalian substrate and adaptor, respectively, of the Cul3-based E3 ligase system.
Unique precursor structure of an extracellular protease, aqualysin I, with NH2- and COOH-terminal pro-sequences and its processing in Escherichia coli. (1990)

Aqualysin I is a subtilisin-type serine protease which is secreted into the culture medium by Thermus aquaticus YT-1, an extremely thermophilic Gram-negative bacterium. The nucleotide sequence of the entire gene for aqualysin I was determined, and the deduced amino acid sequence suggests that aqualysin I is produced as a large precursor, consisting of at least three portions, an NH2-terminal pre-pro-sequence (127 amino acid residues), the protease (281 residues), and a COOH-terminal pro-sequence (105 residues). When the cloned gene was expressed in Escherichia coli cells, aqualysin I was not secreted. However, a precursor of aqualysin I lacking the NH2-terminal pre-pro-sequence (38-kDa protein) accumulated in the membrane fraction. On treatment of the membrane fraction at 65 degrees C, enzymatically active aqualysin I (28-kDa protein) was produced in the soluble fraction. When the active site Ser residue was replaced with Ala, cells expressing the mutant gene accumulated a 48-kDa protein in the outer membrane fraction. The 48-kDa protein lacked the NH2-terminal 14 amino acid residues of the precursor, and heat treatment did not cause any subsequent processing of this precursor. These results indicate that the NH2-terminal signal sequence is cleaved off by a signal peptidase of E. coli, and that the NH2- and COOH-terminal pro-sequences are removed through the proteolytic activity of aqualysin I itself, in that order. These findings indicate a unique four-domain structure for the aqualysin I precursor; the signal sequence, the NH2-terminal pro-sequence, mature aqualysin I, and the COOH-terminal pro-sequence, from the NH2 to the COOH terminus.
Second Harmonic Generation from a Nanopatterned Isotropic Nonlinear Material (2006)

Second harmonic generation (SHG) from a nanopatterned isotropic nonlinear material (GaAs) located inside the subwavelength gaps of a metallic coaxial array is demonstrated. The SHG results from the strong electromagnetic fields in the vicinity of the coaxial gaps; the signal strength is comparable to that from z-cut LiNbO3 even though the path length is much shorter (∼100 nm compared to 14 μm). Numerical simulations are in good agreement with the experimental data. The observation of a peak-wavelength blue shift between the SH spectrum and the linear transmission spectrum is explained.
Hepatitis delta virus replication in vitro is not affected by interferon- or - despite intact cellular responses to interferon and dsRNA (1994)

The hepatitis delta virus (HDV) genome consists of circular ssRNA which has extensive intramolecular complementarity and can form a dsRNA rod-like structure. If such RNA species were to exist in an unmasked form in cells, they would be expected to induce interferon (IFN) expression and activate two IFN-inducible dsRNA-dependent enzymes with anti-viral activity, namely the dsRNA-dependent protein kinase (PKR) and 2',5' oligoadenylate (2',5' A) synthetase. Since the virus replicates to high copy number for prolonged periods in infected cells it is apparently able to evade these antiviral mechanisms. The RNA genome may be masked and fail to induce or activate the antiviral response, or the virus may inhibit such a response. Treatment of a hepatoma cell line, Huh7, and a fibrosarcoma cell line, HT1080, stably transfected with a trimeric HDV cDNA construct, with IFN-alpha or IFN-gamma for up to seven days failed to influence the level of expression of genomic or antigenomic HDV RNA, or delta antigen (Ag). This is consistent with either failure of activation or inhibition of the IFN response. However the induction of several IFN-responsive genes, including PKR, 2',5' A synthetase and class I MHC is normal and cotransfection of a construct expressing delta Ag did not affect expression from an IFN-inducible chloramphenicol acetyltransferase construct. In addition, the activation of PKR is not inhibited in HDV-expressing cells and antiviral assays suggest that the ability of these cells to mount an antiviral response to at least two cytopathic viruses is unaffected. IFN-beta is inducible normally by dsRNA in cells transfected with the delta cDNA trimer. We conclude that HDV replication is not inhibited by IFN-alpha or IFN-gamma, even though the responses of cells expressing HDV RNA and antigen to IFN and dsRNA are intact.
Maximum likelihood training of probabilistic neural networks (1994)

A maximum likelihood method is presented for training probabilistic neural networks (PNN's) using a Gaussian kernel, or Parzen window. The proposed training algorithm enables general nonlinear discrimination and is a generalization of Fisher's method for linear discrimination. Important features of maximum likelihood training for PNN's are: 1) it economizes the well known Parzen window estimator while preserving feedforward NN architecture, 2) it utilizes class pooling to generalize classes represented by small training sets, 3) it gives smooth discriminant boundaries that often are "piece-wise flat" for statistical robustness, 4) it is very fast computationally compared to backpropagation, and 5) it is numerically stable. The effectiveness of the proposed maximum likelihood training algorithm is assessed using nonparametric statistical methods to define tolerance intervals on PNN classification performance.
Interleukin 1 protects from cytosine arabinoside‐induced alopecia in the rat model (1991)

Protection from cytosine arabinoside-induced alopecia by ImuVert has recently been reported in a rat model. ImuVert, a biologic response modifier, is capable of activating mononuclear cells causing release of various cytokines. In the present study, using the young rat model, recombinant human IL 1 beta produced excellent protection from cytosine arabinoside-induced alopecia. Mouse recombinant tumor necrosis factor gave definite but modest protection whereas human tumor necrosis factor gave none. It is concluded that the protection from alopecia by ImuVert is mediated by cytokines, primarily IL 1.
Fabrication of a gold microelectrode for amperometric detection on a polycarbonate electrophoresis chip by photodirected electroless plating (2006)

A novel method of photoresist-free micropatterning coupled with electroless gold plating is described for the fabrication of an integrated gold electrode for electrochemical detection (ED) on a polycarbonate (PC) electrophoresis microchip. The microelectrode layout was photochemically patterned onto the surface of a PC plate by selective exposure of the surface coated without photoresist to 254 nm UV light through a chromium/quartz photomask. Thus, the PC plate was selectively sensitized by formation of reactive chemical moieties in the exposed areas. After a series of wet chemistry reactions, the UV-exposed area was activated with a layer of gold nanoparticles that served as a seed to catalyze the electroless plating. The gold microelectrode was then selectively plated onto the activated area by using an electroless gold plating bath. Nonselective gold deposition on the unwanted areas was eliminated by sonication of the activated PC plate in a KSCN solution before electroless plating, and the adhesion of the plated electrodes to the PC surface was strengthened with thermal annealing. Compared with the previously reported electroless plating technique for fabrication of microelectrodes on a microchip, the present method avoided the use of a membrane stencil with an electrode pattern to restrict the area to be wet-chemically sensitized. The CE with integrated ED (CE-ED) microchip was assembled by thermal bonding an electrode-plated PC cover plate to a microchannel-embossed PC substrate. The novel method allows one to fabricate low-cost, electrode-integrated, complete PC CE-ED chips with no need of a clean room. The fabricated CE-ED microchip was demonstrated for separation and detection of model analytes, including dopamine (DA) and catechol (CA). Detection limits of 0.65 and 1.03 microM were achieved for DA and CA, respectively, and theoretical plate number of 1.4 x 10(4) was obtained for DA. The plated gold electrode can be used for about 4 h, bearing usually more than 100 runs before complete failure.
Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains (2011)

Crimean Congo hemorrhagic fever virus (CCHFV) is a deadly human pathogen that evades innate immune responses by efficiently interfering with antiviral signaling pathways mediated by NF-κB, IRF3, and IFNα/β. These pathways rely on protein ubiquitination for their activation, and one outcome is the modification of proteins with the ubiquitin (Ub)-like modifier interferon-stimulated gene (ISG)15. CCHFV and related viruses encode a deubiquitinase (DUB) of the ovarian tumor (OTU) family, which unlike eukaryotic OTU DUBs also targets ISG15 modifications. Here we characterized the viral OTU domain of CCHFV (vOTU) biochemically and structurally, revealing that it hydrolyzes four out of six tested Ub linkages, but lacks activity against linear and K29-linked Ub chains. vOTU cleaved Ub and ISG15 with similar kinetics, and we were able to understand vOTU cross-reactivity at the molecular level from crystal structures of vOTU in complex with Ub and ISG15. An N-terminal extension in vOTU not present in eukaryotic OTU binds to the hydrophobic Ile44 patch of Ub, which results in a dramatically different Ub orientation compared to a eukaryotic OTU-Ub complex. The C-terminal Ub-like fold of ISG15 (ISG15-C) adopts an equivalent binding orientation. Interestingly, ISG15-C contains an additional second hydrophobic surface that is specifically contacted by vOTU. These subtle differences in Ub/ISG15 binding allowed the design of vOTU variants specific for either Ub or ISG15, which will be useful tools to understand the relative contribution of ubiquitination vs. ISGylation in viral infection. Furthermore, the crystal structures will allow structure-based design of antiviral agents targeting this enzyme.
Reconstitution of Ancestral Green Visual Pigments of Zebrafish and Molecular Mechanism of Their Spectral Differentiation (2005)

We previously reported that zebrafish have four tandemly duplicated green (RH2) opsin genes (RH2-1, RH2-2, RH2-3, and RH2-4). Absorption spectra vary widely among the four photopigments reconstituted with 11-cis retinal, with their peak absorption spectra (lambda(max)) being 467, 476, 488, and 505 nm, respectively. In this study, we inferred the ancestral amino acid (aa) sequences of the zebrafish RH2 opsins by likelihood-based Bayesian statistics and reconstituted the ancestral opsins by site-directed mutagenesis. The ancestral pigment (A1) to the four zebrafish RH2 pigments and that (A3) to RH2-3 and RH2-4 showed lambda(max) at 506 nm, while that (A2) to RH2-1 and RH2-2 showed a lambda(max) at 474 nm, indicating that a spectral shift had occurred toward the shorter wavelength on the evolutionary lineages A1 to A2 by 32 nm, A2 to RH2-1 by 7 nm, and A3 to RH2-3 by 18 nm. Pigment chimeras and site-directed mutagenesis revealed a large contribution (approximately 15 nm) of glutamic acid to glutamine substitution at residue 122 (E122Q) to the A1 to A2 and A3 to RH2-3 spectral shifts. However, the remaining spectral differences appeared to result from complex interactive effects of a number of aa replacements, each of which has only a minor spectral contribution (1-3 nm). The four zebrafish RH2 pigments cover nearly an entire range of lambda(max) distribution among vertebrate RH2 pigments and provide an excellent model to study spectral tuning mechanisms of RH2 in vertebrates.
Fog computing and its role in the internet of things (2012)

Fog Computing extends the Cloud Computing paradigm to the edge of the network, thus enabling a new breed of applications and services. Defining characteristics of the Fog are: a) Low latency and location awareness; b) Wide-spread geographical distribution; c) Mobility; d) Very large number of nodes, e) Predominant role of wireless access, f) Strong presence of streaming and real time applications, g) Heterogeneity. In this paper we argue that the above characteristics make the Fog the appropriate platform for a number of critical Internet of Things (IoT) services and applications, namely, Connected Vehicle, Smart Grid, Smart Cities, and, in general, Wireless Sensors and Actuators Networks (WSANs).
Characterization and Comparison of Local Onset and Remote Propagated Electrographic Seizures Recorded with Intracranial Electrodes (1998)

The initial ictal discharge pattern recorded with intracranial electrodes can assist in differentiating local onset and remote propagated electrographic seizures, with rhythmic round theta-delta activity being unique to distant propagated sites. Nevertheless, the initial discharge of a subclass of remote propagated electrographic seizures consists of an independent pattern indistinguishable from that observed at local onset sites.
The cell-specific enhancer of the mouse transthyretin (prealbumin) gene binds a common factor at one site and a liver-specific factor(s) at two other sites. (1988)

We previously defined two distinct cell-specific DNA elements controlling the transient expression of the transthyretin gene in Hep G2 (human hepatoma) cells: a proximal promoter region (-202 base pairs [bp] to the cap site), and a far-upstream cell-specific enhancer located between 1.6 and 2.15 kilobases (kb) 5' of the cap site (R. H. Costa, E. Lai, and J. E. Darnell, Jr., Mol. Cell. Biol. 6:4697-4708, 1986). In this report, we located the effective transthyretin enhancer element within a 100-bp region between 1.96 and 1.86 kb 5' to the mRNA cap site. In Hep G2 nuclear extracts, three protein-binding sites within this minimal enhancer element were identified by gel mobility and methylation protection experiments. Each binding site was required for full enhancer activity in Hep G2 transient expression assays. Competition experiments in protein-binding assays suggested that two of the three sites were recognized by a similar factor and that the protein interaction with the third site was different. The nuclear protein(s) which bound to the two homologous sites was found mainly or only in cells of hepatic origin, suggesting an involvement of this region in the cell-specific function of this enhancer. The nuclear protein(s) recognizing the third enhancer region was also found in HeLa and spleen cells.
Arginine-specific ADP-ribosyltransferases in leukocytes (1998)

The posttranslational modification of proteins by the addition of an ADP-ribose group is mediated by ADP-ribosyltransferases, which are expressed widely in many eukaryotic tissues, including leukocytes. DNA encoding arginine-specific ADP-ribosyltransferases has been cloned from both polymorphonuclear neutrophil leukocytes and lymphocytes, and their primary structures are widely conserved, particularly in those domains of the enzyme implicated in NAD+ binding and catalysis. In most cases the enzymes are tethered to the outer aspect of the cell surface or are released directly from the cell surface. The protein substrates of some of the ADP-ribosyltransferases have been identified and the catalytic activity of these enzymes has been implicated in several immune responses as well as white cell chemotaxis. This review describes recent significant advances in this field, and it seems likely that additional leukocyte functions, most particularly those linked to the activity of surface integrins, will be assigned to this class of enzymes.
Dietary behaviours during pregnancy: findings from first-time mothers in southwest Sydney, Australia (2010)

HBT is registered with the Australian Clinical Trial Registry (ACTRNO12607000168459).
A fat-specific enhancer is the primary determinant of gene expression for adipocyte P2 in vivo. (1990)

The murine gene for adipocyte P2 encodes an adipocyte-specific member of the family of intracellular lipid binding proteins. The region upstream from the start of transcription of this gene has been found to contain binding sites for the transcription factors c-jun/c-fos and C/EBP (CCAAT/enhancer binding protein) and several short sequence elements found in other adipocyte gene promoters, termed fat-specific elements. To identify DNA sequences that were responsible for the high level of transcription of the gene for adipocyte P2 in vivo, we made a series of transgenic mice containing 168 base pairs (bp), 247 bp, 1.7 kilobases (kb), and 5.4 kb of 5' flanking sequence linked to the bacterial gene chloramphenicol acetyltransferase. Although plasmids containing only 168 bp of 5' sequence including the C/EBP and AP-1 (activation protein 1) binding sites were expressed well in cultured adipocytes, high levels of chloramphenicol acetyltransferase activity in the adipose tissue of transgenic mice were not observed until the 5' flanking region was extended to kb -54. An enhancer mapping between kb -4.9 and kb -5.4 upstream from the start of transcription was identified by transfection of further deletions into cultured adipocytes. This enhancer, when linked to a bp -63 promoter fragment from the gene for adipocyte P2, directed very high level chloramphenicol acetyltransferase expression specifically to adipose tissue in transgenic mice. These results identify a functional adipose-specific enhancer and indicate that it is the major determinant of tissue specificity of the gene for adipocyte P2. These results also demonstrate that the proximal-promoter binding sites for AP-1 and C/EBP are not sufficient or necessary to give adipose-tissue-specific expression in vivo, though they may play an important role in the response of this promoter to glucocorticoids.