gebhart/patrepeval huggingface dataset:
The Herpes Simplex Virus Type-1 Single-strand DNA-binding Protein (ICP8) Promotes Strand Invasion (2003)

ICP8, the herpes simplex virus type-1 single-strand DNA-binding protein, was recently shown to promote strand exchange in conjunction with the viral replicative helicase (Nimonkar, A. V., and Boehmer, P. E. (2002) J. Biol. Chem. 277, 15182-15189). Here we show that ICP8 also catalyzes strand invasion in an ATP-independent manner. Thus, ICP8 promotes the assimilation of a single-stranded donor molecule into a homologous plasmid, resulting in the formation of a displacement loop. Invasion of a homologous duplex by single-stranded DNA requires homology at either 3' or 5' end of the invading strand. The reaction is dependent on the free energy of supercoiling and alters the topology of the acceptor plasmid. Hence, strand invasion products formed by ICP8 are resistant to the action of restriction endonucleases that cleave outside of the area of pairing. The ability to catalyze strand invasion is a novel activity of ICP8 and the first demonstration of a eukaryotic viral single-strand DNA-binding protein to promote this reaction. In this regard ICP8 is functionally similar to the prototypical prokaryotic recombinase RecA and its eukaryotic homologs. This strand invasion activity of ICP8 coupled with DNA synthesis may explain the high prevalence of branched DNA structures during viral replication.
Synthetic oligonucleotide tails inhibitin vitroandin vivotranslation of SP6 transcripts of maize zein cDNA clones (1986)

A maize zein cDNA clone was used to synthesize mRNA with the SP6 in vitro transcription system. Although we obtained full-length transcripts of the cDNA sequence, these were inefficient templates for protein synthesis. Removal of the 5' oligo(G) sequence that was synthesized during the cDNA cloning procedure allowed efficient translation of the mRNAs in a wheat germ cell-free protein synthesis system or in Xenopus laevis oocytes. The alteration in translational efficiency did not result from an interaction of the 5' oligo(G) homopolymer tail with the 3' oligo(C) sequence, as transcripts with or without the oligo(C) tail were translated similarly in both protein synthesis systems. Ribosome interaction with the mRNA may be affected due either to the secondary structure of the oligo(G) sequence itself, or an unusual secondary structure between the oligo(G) sequence and another region in the mRNA. Synthetic oligonucleotides at the 5' end of cloned cDNA sequences may generally be inhibitory for translation of mRNAs transcribed in vitro.
Several genes encoding ribosomal proteins are over-expressed in prostate-cancer cell lines: Confirmation of L7a and L37 over-expression in prostate-cancer tissue samples (1998)

A cDNA library specific for mRNA over-expressed in prostate cancer was generated by subtractive hybridization of transcripts originating from prostatic hyperplasia and cancer tissues. cDNA encoding ribosomal proteins L4, L5, L7a, L23a, L30, L37, S14 and S18 was found to be present among 100 analyzed clones. Levels of ribosomal mRNA were significantly higher at least in one of the prostate-cancer cell lines, LNCaP, DU-145 and PC-3, than in hyperplastic tissue, as determined by slot-blot hybridization. Furthermore, L23a- and S14-transcript levels were significantly elevated in PC-3 cells as compared with those in the normal prostate epithelial cell line PrEC. Generally, dramatic changes in the mRNA content of the ribosomal proteins were not detected, the most evident over-expression being that of L37 mRNA, which was 3.4 times more abundant in LNCaP cells than in hyperplastic prostate tissue. The over-expression of L7a and L37 mRNA was confirmed in prostate-cancer tissue samples by in situ hybridization. Elevated cancer-related expression of L4 and L30 has not been reported, but levels of the other ribosomal proteins are known to be increased in several types of cancers. These results therefore suggest that prostate cancer is comparable with other types of cancers, in that a larger pool of some ribosomal proteins is gained during the transformation process, by an unknown mechanism.
REVOLUTA regulates meristem initiation at lateral positions (2001)

While the shoot apical meristem (SAM) is indirectly responsible for the initiation of all above-ground postembryonic organs, in most plants the vast majority of these organs are directly initiated by lateral meristems. In Arabidopsis thaliana, the lateral meristems include flower meristems (FMs), which form on the flanks of the SAM, and lateral shoot meristems (LSMs), which develop in leaf axils. While significant progress has been made on the molecular genetic basis of SAM initiation during embryo development, relatively little is known about the initiation of meristems at lateral positions. Here we have characterized the phenotypic consequences and genetic interactions of mutations in the REVOLUTA (REV) gene, with an emphasis on the role of REV in lateral meristem initiation. Our observations indicate that REV is required for initiation of both LSMs and FMs, and likely acts in the same pathway as, and upstream of, known meristem regulators. We identified the REV gene and found it encodes a predicted homeodomain/leucine zipper transcription factor that also contains a START sterol-lipid binding domain. REV is the same as the IFL gene. REV was expressed at the earliest stages of LSM and FM formation. Within the inflorescence shoot meristem, REV expression appeared to predict 3--5 incipient flower primordia on the flanks of the SAM, and REV expression at stage 1 and stage 2 matched that of WUS and STM, respectively. We propose that REV acts at lateral positions to activate the expression of known meristem regulators.
Efficient Isolation of Novel Human Monoclonal Antibodies with Neutralizing Activity Against HIV-1 from Transgenic Mice Expressing Human Ig Loci (2002)

Despite considerable interest in the isolation of mAbs with potent neutralization activity against primary HIV-1 isolates, both for identifying useful targets for vaccine development and for the development of therapeutically useful reagents against HIV-1 infection, a relatively limited number of such reagents have been isolated to date. Human mAbs (hu-mAbs) are preferable to rodent mAbs for treatment of humans, but isolation of hu-mAbs from HIV-infected subjects by standard methods of EBV transformation of B cells or phage display of Ig libraries is inefficient and limited by the inability to control or define the original immunogen. An alternative approach for the isolation of hu-mAbs has been provided by the development of transgenic mice that produce fully hu-mAbs. In this report, we show that immunizing the XenoMouse G2 strain with native recombinant gp120 derived from HIV(SF162) resulted in robust humoral Ab responses against gp120 and allowed the efficient isolation of hybridomas producing specific hu-mAbs directed against multiple regions and epitopes of gp120. hu-mAbs possessing strong neutralizing activity against the autologous HIV(SF162) strain were obtained. The epitopes recognized were located in three previously described neutralization domains, the V2-, V3- and CD4-binding domains, and in a novel neutralization domain, the highly variable C-terminal region of the V1 loop. This is the first report of neutralizing mAbs directed at targets in the V1 region. Furthermore, the V2 and V3 epitopes recognized by neutralizing hu-mAbs were distinct from those of previously described human and rodent mAbs and included an epitope requiring a full length V3 loop peptide for effective presentation. These results further our understanding of neutralization targets for primary, R5 HIV-1 viruses and demonstrate the utility of the XenoMouse system for identifying new and interesting epitopes on HIV-1.
LF-Net: Learning Local Features from Images (2018)

We present a novel deep architecture and a training strategy to learn a local feature pipeline from scratch, using collections of images without the need for human supervision. To do so we exploit depth and relative camera pose cues to create a virtual target that the network should achieve on one image, provided the outputs of the network for the other image. While this process is inherently non-differentiable, we show that we can optimize the network in a two-branch setup by confining it to one branch, while preserving differentiability in the other. We train our method on both indoor and outdoor datasets, with depth data from 3D sensors for the former, and depth estimates from an off-the-shelf Structure-from-Motion solution for the latter. Our models outperform the state of the art on sparse feature matching on both datasets, while running at 60+ fps for QVGA images.
Synthesis and Biological Activity of Ribose-5‘-Carbamate Derivatives of Vitamin B12 (1999)

Twelve biologically active derivatives of vitamin B(12) (cyanocobalamin) have been synthesized in which spacers were attached to the ribose-5'-hydroxyl group of vitamin B(12). Their potential to act as oral delivery agents for proteins, nanospheres, or immunogens using the vitamin B(12) uptake system was evaluated by determining their affinity for intrinsic factor (IF) and non-IF. The ribose-5'-hydroxyl group of vitamin B(12) was activated through the use of 1,1'-carbonyldiimidazole (CDI), 1,1'-carbonyldi(1,2, 4-triazole) (CDT), or di(1-benzotriazolyl) carbonate (DBTC). Subsequent addition of an aminoalkane, diaminoalkane, or alkane diacid dihydrazide gave rise to vitamin B(12) derivatives suitable for attachment to various proteins, peptides, or nanospheres to enable oral delivery utilizing the vitamin B(12) uptake system. The ribose-5'-carbamate derivatives were found to possess similar affinity for intrinsic factor as that of the e-monocarboxylic acid of vitamin B(12). The affinity for non-IF was similar to cyanocobalamin or even higher for some of the smaller derivatives. Polysciences nanoparticles derivatized with vitamin B(12) 5'-carbamate adipic dihydrazide into CaCo-2 cells showed significantly higher levels of transport of the particles, when compared to unmodified particles.
The terminal peptides of insulin (1949)

While this work was in progress an outline of a fluorimetric method for the determination of N- methyl-2-pyridone-5-carboxylamide in urine was reported by Rosen, Perlzweig & Handler (1948). The authors considered that their values for normal urines (5.0-13.2 mg./day) may have been somewhat low, but it is obvious that they are of the same order as those obtained by the present colorimetric method (see Table SUMMARY 1. Methods are described for the determination of N-methyl-2-pyridone-5-carboxylamide and N- methyl-2-pyridone-3-carboxylamideinhuman urine. The methods are based on the nitration of the com- pounds, after isolation from urine by adsorption on Lloyd's reagent followed by extraction with chloro- form, and on their colorimetric determination by means of the yellow colours given by the nitro derivatives in alkaline solution.
Drawing Lithography: Three‐Dimensional Fabrication of an Ultrahigh‐Aspect‐Ratio Microneedle (2009)

Drawing lithography is a novel fabrication technique in which a thermosetting polymer is directly drawn from a two-dimensional solid surface without the need for a mask and light irradiation (see figure). Drawing lithography differs from traditional lithography techniques, such as photolithography, in that it is based on the inherently planar geometries of a two-dimensional substrate in a three-dimensional microstructure.
Performance evaluation of the transmission of image data over digital networks involving mobile terminals (1989)

Presents further investigations carried out into the performance evaluation of transmitted line diagram graphics images such as street maps, building plans, etc., through a mobile channel at data rates of 2400 and 4800 bit/s. The essential features of a suitable source code are identified and the geometric encoding, designed to meet these specifications, is presented. Computer simulation is used for modelling the mobile channel and the results are used as an error source for evaluating the performance of the transmitted images. Subjective tests based on the CCIR 5-grade scale are carried out to assess the quality and the usefulness of the received images for various mobile channel parameters. Under normal conditions, line diagram graphics, such as the campus map and the floor plan used as an example in this paper can be transmitted to mobiles in under 5 seconds.
The mechanism of activation of IRAK1 and IRAK4 by interleukin-1 and Toll-like receptor agonists (2017)

We have developed the first assays that measure the protein kinase activities of interleukin-1 receptor-associated kinase 1 (IRAK1) and IRAK4 reliably in human cell extracts, by employing Pellino1 as a substrate in conjunction with specific pharmacological inhibitors of IRAK1 and IRAK4. We exploited these assays to show that IRAK4 was constitutively active and that its intrinsic activity towards Pellino1 was not increased significantly by stimulation with interleukin-1 (IL-1) in IL-1R-expressing HEK293 cells, Pam<sub>3</sub>CSK<sub>4</sub>-stimulated human THP1 monocytes or primary human macrophages. Our results, in conjunction with those of other investigators, suggest that the IL-1-stimulated <i>trans</i>-autophosphorylation of IRAK4 is initiated by the myeloid differentiation primary response gene 88-induced dimerization of IRAK4 and is not caused by an increase in the intrinsic catalytic activity of IRAK4. In contrast with IRAK4, we found that IRAK1 was inactive in unstimulated cells and converted into an active protein kinase in response to IL-1 or Pam<sub>3</sub>CSK<sub>4</sub> in human cells. Surprisingly, the IL-1-stimulated activation of IRAK1 was not affected by pharmacological inhibition of IRAK4 and not reversed by dephosphorylation and/or deubiquitylation, suggesting that IRAK1 catalytic activity is not triggered by a covalent modification but by an allosteric mechanism induced by its interaction with IRAK4.
Enhanced production of succinic acid by overexpression of phosphoenolpyruvate carboxylase in Escherichia coli (1996)

Fermentative production of succinic acid from glucose by Escherichia coli was significantly increased by overexpression of phosphoenolpyruvate carboxylase. In contrast, overexpression of phosphoenolpyruvate carboxykinase had no effect. Under optimized conditions, induction of the carboxylase resulted in a 3.5-fold increase in the concentration of succinic acid, making succinic acid the major fermentation product by weight.
Interleukin 12 and tumor necrosis factor alpha are costimulators of interferon gamma production by natural killer cells in severe combined immunodeficiency mice with listeriosis, and interleukin 10 is a physiologic antagonist. (1993)

Listeriosis in mice with the severe combined immunodeficiency (SCID) mutation is an established model in vivo and in vitro of interferon gamma (IFN-gamma)-dependent macrophage activation by natural killer (NK) cells during the development of natural immunity. We demonstrate that IFN-gamma production from SCID splenocytes is stimulated by interleukin (IL) 12, tumor necrosis factor alpha (TNF-alpha), and IL-2 but is inhibited by IL-10, IL-10, IL-12, and TNF are induced by heat-killed Listeria monocytogenes (hk-LM) from SCID splenocytes and peritoneal macrophages. IL-12 production is necessary for hk-LM to stimulate IFN-gamma production by SCID splenocytes since neutralization of IL-12 totally blocks IFN-gamma production in this system. TNF-alpha and IL-2 act synergistically with IL-12 to augment IFN-gamma production. Also, exogenous IL-2 increases the response of NK cells to hk-LM or to IL-12 and TNF-alpha. In contrast, IL-10 inhibits hk-LM-induced IFN-gamma production at two levels: (i) by inhibiting TNF and IL-12 production from these cultures (presumably from the macrophage) and (ii) by inhibiting the stimulatory effects of IL-12 and TNF-alpha on NK-cell IFN-gamma production. Thus, these data indicate that macrophage production of TNF-alpha and IL-12 stimulates the release of IFN-gamma by NK cells and that IL-10 produced in response to hk-LM inhibits this response at the level of the macrophage and the NK cell.
Changing colors in mice: an inducible system that delivers: Figure 1. (2001)

Expression of exogenous genes in mammalian systems can be extremely informative for deciphering the function of an encoded protein or determining the role of a putative regulatory region. In many instances it is desirable or even essential to employ a system that has the ability to be controlled by the experimenter. For example, embryonic lethality that results from expression of an exogenous transgene or disruption of an endogenous gene can be problematic as it precludes examination of the phenotypic consequence in the organism under study. In these cases the use of an inducible gene expression system would be advantageous so that gene expression could be turned on or off at will. Inducible systems would not only be useful for analyzing the function of exogenous genes, but may also be implemented in gene disruption experiments or in gene therapy protocols in which a therapeutic gene is delivered. Many laboratories have designed systems that aim to achieve inducible gene expression. However, even the best laid plans often yield disappointing results in vivo. This is attributable to an incomplete understanding of regulatory mechanisms that orchestrate mammalian gene expression. Exacerbating this problem is the fact that bacterial or viral genes and regulatory elements that are often implemented in the scheme may be rendered nonfunctional in mammalian systems, further decreasing the chance of success and increasing the chance of frustration.
Classification and Characterization of Therapeutic Antibody Aggregates (2011)

A host of diverse stress techniques was applied to a monoclonal antibody (IgG(2)) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134-25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG(1) and IgG(2) subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced.
Birefringent photosensitivity in monomode optical fibre: application to external writing of rocking filters (1991)

Efficient, narrowband rocking filters have been made in polarisation-maintaining monomode optical fibre by photoinducing periodic birefringent gratings along the length of the fibre. These gratings, fabricated with a period chosen to provide synchronous coupling between the two principal states of polarisation of the LP01 mode at a preselected wavelength, gently rock to and fro along the principal polarisation axes of the fibre. To photoinduce the grating, the fibre is exposed periodically along its length to a UV light beam which is incident at right angles to the geometrical axis of the fibre and is directed π/A rad with respect to the principal polarisation axes. Efficient polarisation mode conversion at 1.3 μm with the birefringent fibre grating is demonstrated.
A Combination of Rifaximin and Neomycin Is Most Effective in Treating Irritable Bowel Syndrome Patients With Methane on Lactulose Breath Test (2010)

The combination of rifaximin and neomycin is more effective in treating methane-producing subjects-in both clinical response and methane elimination.
The voltage‐dependent activity of Escherichia coli porins in different planar bilayer reconstitutions (1989)

Because of conflicting results from differing techniques, the degree of voltage sensitivity of Escherichia coli porins in planar bilayers is still a matter of debate. In order to provide the first comparative study, OmpF porin was purified in three ways; firstly as native outer membrane vesicles, secondly as salt-extracted porin trimers in sodium dodecyl sulphate and thirdly as solubilised trimers extracted with octyl-polyoxyethylene (Octyl-POE). These methods represent the major approaches to porin isolation and purification. All three were reconstituted into Schindler-type bilayers. Detergent-solubilised OmpF was also reconstituted into Montal-Mueller- and Mueller-Rudin-type bilayers. In all cases voltage-dependent closing of OmpF was observed. Octyl-POE-extracted PhoE porin was similarly investigated in all three types of planar bilayer. Two membrane-formation techniques appeared genuinely to alter the voltage sensitivity of the porins they contained. Firstly, porins in membranes formed by the Montal-Mueller technique sometimes showed an increase in voltage sensitivity during the first 30 min after bilayer formation. Secondly, membranes formed by the Mueller-Rudin technique on thick polyethylene septa showed both poor solvent drainage and a significantly reduced porin voltage sensitivity.
NK inhibitory-receptor blockade for purging of leukemia: Effects on hematopoietic reconstitution (2002)

One of the obstacles of BMT that limits its efficacy is failure to eradicate the original tumor. The incidence of tumor relapse is particularly high after autologous BMT. Natural killer (NK) cells comprise various subsets that can express inhibitory receptors for MHC class I determinants. We have recently demonstrated that blockade of NK-cell inhibitory receptors can augment antitumor effects in vitro and in vivo. However, breakdown of tolerance and autoreactivity may occur as a result of the inhibition of NK-cell inactivation to self MHC determinants. We have utilized F(ab')2 fragments of monoclonal antibody, 5E6, against Ly49C/I inhibitory receptors, which are expressed on 35% to 60% of NK cells in H2b strains of mice and are specific for H2Kb, to investigate the effect of inhibitory-receptor blockade on syngeneic bone marrow cell (BMC) and tumor cell growth. We show that treatment of interleukin 2-activated C57BL/6 (B6, H2b) SCID-mouse NK cells with 5E6 F(ab')2 fragments during 48-hour coculture resulted in autoreactivity against syngeneic BMCs as demonstrated by suppression of myeloid reconstitution on day 14 post-BMT. However, this suppressive effect was transient and normalized by day 21 post-BMT. In contrast, blockade of inhibitory receptors during 24-hour coculture had no adverse effects on myeloid reconstitution after BMT. Furthermore, under the same coculture conditions, NK cell-mediated purging of C1498 leukemia cells contaminating syngeneic BMCs was more effective with inhibitory-receptor blockade, leading to a significantly higher proportion of animals with long-term survival compared to the control recipients. These results demonstrate that short-term in vitro blockade of inhibitory receptors can augment antitumor activity without long-term inhibitory effects on BMCs and thus may be of potential use in the purging of contaminating tumor cells prior to autologous BMT.Biol Blood Marrow Transplant 2002;8(1):17-25.