gebhart/patrepeval huggingface dataset:
VEGF Inhibition and Renal Thrombotic Microangiopathy (2008)

The glomerular microvasculature is particularly susceptible to injury in thrombotic microangiopathy, but the mechanisms by which this occurs are unclear. We report the cases of six patients who were treated with bevacizumab, a humanized monoclonal antibody against vascular endothelial growth factor (VEGF), in whom glomerular disease characteristic of thrombotic microangiopathy developed. To show that local reduction of VEGF within the kidney is sufficient to trigger the pathogenesis of thrombotic microangiopathy, we used conditional gene targeting to delete VEGF from renal podocytes in adult mice; this resulted in a profound thrombotic glomerular injury. These observations provide evidence that glomerular injury in patients who are treated with bevacizumab is probably due to direct targeting of VEGF by antiangiogenic therapy.
Discovery of Siglec‐14, a novel sialic acid receptor undergoing concerted evolution with Siglec‐5 in primates (2006)

Immune receptors that show high mutual sequence similarity and have antagonizing signaling properties are called paired receptors, and are believed to fine-tune immune responses. Siglecs are sialic acid-recognizing receptors of the immunoglobulin (Ig) superfamily expressed on immune cells. Human Siglec-5, encoded by SIGLEC5 gene, has four extracellular Ig-like domains and a cytosolic inhibitory motif. We discovered human Siglec-14 with three Ig-like domains, encoded by the SIGLEC14 gene, adjacent to SIGLEC5. Human Siglec-14 has almost complete sequence identity with human Siglec-5 at the first two Ig-like domains, shows a glycan binding preference similar to that of human Siglec-5, and associates with the activating adapter protein DAP12. Thus, Siglec-14 and Siglec-5 appear to be the first glycan binding paired receptors. Near-complete sequence identity of the amino-terminal part of human Siglec-14 and Siglec-5 indicates partial gene conversion between SIGLEC14 and SIGLEC5. Remarkably, SIGLEC14 and SIGLEC5 in other primates also show evidence of gene conversions within each lineage. Evidently, balancing the interactions between Siglec-14, Siglec-5 and their common ligand(s) had selective advantage during the course of evolution. The "essential arginine" critical for sialic acid recognition in both Siglec-14 and Siglec-5 is present in humans but mutated in almost all great ape alleles.
Minimal sequence requirements for ribozyme activity. (1992)

The hammerhead ribozyme, as engineered by J. Haseloff and W. L. Gerlach [(1988) Nature (London) 334, 585-591], is an RNA molecule containing two regions of conserved nucleotides, a double helix, called helix II, which connects the two conserved regions, and flanking arms of variable sequence, which hybridize the ribozyme to its specific target. Here we show that this ribozyme may be reduced in size and still retain cleavage activity by replacing helix II with just a few nucleotides that cannot form Watson-Crick base pairs between themselves. Furthermore, the nucleotides replacing helix II and the nucleotides in the flanking arms may be substituted with DNA, and this small, DNA-containing ribozyme is fully as active as the original, full-size ribozyme. Cleavage activity of the minimized ribozyme depends on the number and sequence of the few nucleotides that replace helix II; optimal activity, thus far, is achieved by four or five deoxyribopyrimidines. The minimized ribozyme, or "minizyme," is active as a monomer, as shown by its nearly constant activity over a concentration range varying 25,000-fold, by the mobility of the minizyme-substrate complex in nondenaturing polyacrylamide gels as compared with other nucleic acid molecules of known size, and by other observations. These minizymes provide an excellent model system for studying the structure and mechanism of catalytic RNA; they might also be useful in a variety of biological applications.
Use of recombinant baculoviruses in synthesis of morphologically distinct viruslike particles of flock house virus, a nodavirus (1993)

Flock house virus (FHV) is a small icosahedral insect virus of the family Nodaviridae. Its genome consists of two messenger-sense RNA molecules, both of which are encapsidated in the same particle. RNA1 (3.1 kb) encodes proteins required for viral RNA replication; RNA2 (1.4 kb) encodes protein alpha (43 kDa), the precursor of the coat protein. When Spodoptera frugiperda cells were infected with a recombinant baculovirus containing a cDNA copy of RNA2, coat protein alpha assembled into viruslike precursor particles (provirions) that matured normally by autocatalytic cleavage of protein alpha into polypeptide chains beta (38 kDa) and gamma (5 kDa). The particles were morphologically indistinguishable from authentic FHV and contained RNA derived from the coat protein message. These results showed that RNA1 was required neither for virion assembly nor for maturation of provirions. Expression of mutants in which Asn-363 at the beta-gamma cleavage site of protein alpha was replaced by either aspartate, threonine, or alanine resulted in assembly of particles that were cleavage defective. For two of the mutants, unusual structural features were observed after preparation for electron microscopy. Particles containing Asp at position 363 were labile and showed a strong tendency to break into half-shells. Particles in which Asn-363 was replaced by Ala displayed a distinct hole in an otherwise complete shell. The third mutant, containing Thr at position 363, was indistinguishable in morphology from authentic FHV.
New miRNAs cloned from neuroblastoma (2008)

We provide evidence for 29 new miRNA and miRNA-like sequences (24 novel sequences and 5 miRNAs discovered initially in other species). Some of these newly identified sequences reside within frequently altered chromosomal regions in NB tumours and may play a role in NB biology.
A series of prostaglandin F2-like compounds are produced in vivo in humans by a non-cyclooxygenase, free radical-catalyzed mechanism. (1990)

Increasing attention has focused on the role of free radicals derived from oxygen in the pathophysiology of a wide variety of disorders. One of the well-recognized targets of free radical-induced injury is peroxidation of lipids. Using a variety of approaches, we have found that a series of prostaglandin F2-like compounds are produced in vivo in humans by a non-cyclooxygenase mechanism involving free radical-catalyzed peroxidation of arachidonic acid. Levels of these compounds in normal human plasma and urine range from 5 to 40 pg/ml and 500 to 4000 pg/mg of creatinine, respectively. In rats, their formation was found to increase as much as 200-fold in association with marked free radical-catalyzed lipid peroxidation induced by administration of CCl4 and diquat. To explore whether these prostanoids can exert biological activity, the effects of one of the compounds formed by this mechanism, 8-epi-prostaglandin F2 alpha, was examined in the kidney in the rat. Infusion of 8-epi-prostaglandin F2 alpha into a peripheral vein (5 micrograms/kg per min) or intrarenally (0.5-2.0 micrograms/kg per min) resulted in marked parallel reductions in renal blood flow and glomerular filtration rate. That the formation of these prostanoids is catalyzed by free radicals and that they can exert potent biological activity suggest that these prostanoids may participate as pathophysiological mediators in oxidant injury. Quantification of these compounds may also provide a noninvasive approach to assess oxidant status in humans. That the formation of these prostanoids occurs independent of the catalytic activity of the cyclooxygenase enzyme suggests that there may be limitations at times regarding the reliability of the use of cyclooxygenase inhibitors to assess the role of prostaglandins in certain pathophysiological processes.
Blood clearance kinetics and liver uptake of mononucleosomes in mice (1996)

Nucleosomes generated by apoptosis have become of considerable interest in relation to pathogenesis of systemic lupus erythematosus in mice and humans. Therefore, the fate of circulating mononucleosomes was examined in normal C57Bl/6J mice. The mononucleosomes were prepared from chicken erythrocytes and radiolabeled on the histone component. The removal of nucleosomes from circulation at doses less than 11 micrograms of injected mononucleosomes was rapid, but with increasing doses of injected nucleosomes, the slopes of the removal curves decreased. Liver was the major organ for removal of circulating nucleosomes, accounting for 71.0 to 84.7% of nucleosomes removed from circulation at 10 min. After i.v. injection of nucleosomes, 0.52 +/- 0.15% localized in kidneys. With prior i.v. injection of histones, the glomerular localization of mononucleosomes increased threefold. The clearance of mononucleosomes was decreased sixfold by concurrent injection of ssDNA. These studies show that in mice, circulating mononucleosomes are handled similar to DNA, and they do not avidly localize in glomeruli unless histones have already bound to renal glomeruli.
Constellation Shaping for Pragmatic Turbo-Coded Modulation With High Spectral Efficiency (2004)

We propose a new turbo-encoding scheme for high spectral efficiency with performance close to the Gaussian channel capacity. The scheme combines nonuniform signaling on a Gaussian channel with pragmatic turbo-coded modulation (TCM) for simple and flexible implementation. A variable-rate turbo code is followed by a Huffmann code mapping onto nonequiprobable points in a quadrature amplitude modulation constellation. The rate of the turbo code is matched to the Huffmann code by variable puncturing, such that both the input bit rate and the output symbol rate are constant. It is shown that the new scheme provides shaping gains of 0.6 and 0.9 dB, at rates 2 and 3 b/dimension, respectively, compared with the equiprobable pragmatic TCM, and reach about 1 dB from the continuous input Gaussian channel capacity.
In vivoelectrical conductivity measurements during and after tumor electroporation: conductivity changes reflect the treatment outcome (2009)

Electroporation is the phenomenon in which cell membrane permeability is increased by exposing the cell to short high-electric-field pulses. Reversible electroporation treatments are used in vivo for gene therapy and drug therapy while irreversible electroporation is used for tissue ablation. Tissue conductivity changes induced by electroporation could provide real-time feedback of the treatment outcome. Here we describe the results from a study in which fibrosarcomas (n = 39) inoculated in mice were treated according to different electroporation protocols, some of them known to cause irreversible damage. Conductivity was measured before, within the pulses, in between the pulses and for up to 30 min after treatment. Conductivity increased pulse after pulse. Depending on the applied electroporation protocol, the conductivity increase after treatment ranged from 10% to 180%. The most significant conclusion from this study is the fact that post-treatment conductivity seems to be correlated with treatment outcome in terms of reversibility.
Histone Modifications in Senescence-Associated Resistance to Apoptosis by Oxidative Stress (2013)

Aging and age-related diseases are associated with cellular senescence that results in variable apoptosis susceptibility to oxidative stress. Although fibroblast senescence has been associated with apoptosis resistance, mechanisms for this have not been well defined. In this report, we studied epigenetic mechanisms involving histone modifications that confer apoptosis resistance to senescent human diploid fibroblasts (HDFs). HDFs that undergo replicative senescence display typical morphological features, express senescence-associated β-galactosidase, and increased levels of the tumor suppressor genes, p16, p21, and caveolin-1. Senescent HDFs are more resistant to oxidative stress (exogenous H2O2)-induced apoptosis in comparison to non-senescent (control) HDFs; this is associated with constitutively high levels of the anti-apoptotic gene, Bcl-2, and low expression of the pro-apoptotic gene, Bax. Cellular senescence is characterized by global increases in H4K20 trimethylation and decreases in H4K16 acetylation in association with increased activity of Suv420h2 histone methyltransferase (which targets H4K20), decreased activity of the histone acetyltransferase, Mof (which targets H4K16), as well as decreased total histone acetyltransferase activity. In contrast to Bax gene, chromatin immunoprecipitation studies demonstrate marked enrichment of the Bcl-2 gene with H4K16Ac, and depletion with H4K20Me3, predicting active transcription of this gene in senescent HDFs. These data indicate that both global and locus-specific histone modifications of chromatin regulate altered Bcl-2:Bax gene expression in senescent fibroblasts, contributing to its apoptosis-resistant phenotype.
New Approaches to Olefin Cross-Metathesis (1999)

New methodology for the selective cross-metathesis (CM) of terminal olefins employing ruthenium benzylidene 1 is described.1 CM with symmetric internal olefins was found to provide a useful means for homologating terminal olefins to protected allylic alcohols, amines, and esters. Due to the limited commercial availability of symmetric internal olefins, a two-step CM procedure was developed in which terminal olefins were first homodimerized prior to the CM reaction. Terminal olefins with allylic methyl substituents were observed to provide CM products in diminished yield albeit with markedly improved trans-selectivity. Reaction rates were measured for CM reactions utilizing butenediol and allyl alcohol derivatives, and the results demonstrated distinct advantages in reaction rate and stereoselectivity for reactions employing the disubstituted olefins. In the course of studies of substrates with allylic oxygen substituents, a new CM application was discovered involving the metathesis of acrolein acetal derivatives with terminal olefins. Acrolein acetals, including asymmetric variants derived from tartaric acid, proved to be exceptionally robust and trans-selective CM substrates. In related work, a pinacol-derived vinyl boronate was also found to be a reactive CM partner, providing a novel means for converting terminal olefins into precursors for the Suzuki coupling reaction.
Different Patterns of Gene Expression in ras-Resistant and ras-Sensitive Cells (1991)

We have shown previously that nontumorigenic NIH 3T3 cells can be made tumorigenic and metastatic by transfection and expression of activated ras, whereas in LTA cells, which are tumorigenic but nonmetastatic, the degree of malignancy is not altered by ras. To investigate possible mechanisms of natural ras resistance, we compared the expression patterns of several genes thought to be involved in ras-induced metastatic progression in LTA (ras-resistant) and NIH 3T3 (ras-sensitive) cells, before and after constitutive expression of transfected T24-H-ras. We examined the expression of the nuclear "early-response" genes jun and fos and the "tumor-suppressor" retinoblastoma (Rb) gene, as well as genes involved in invasion (major excreted protein [MEP], tissue inhibitor of metalloproteinases [TIMP]), and cell adhesion (secreted phosphoprotein 1 [SPP1; also known as osteopontin]). We found distinct differences in both the basal and ras-induced levels of expression of most of these genes in LTA versus NIH 3T3 cells. High levels of MEP and low levels of TIMP were induced in ras-transfected NIH 3T3 cells, whereas LTA cells showed intermediate levels of MEP and high levels of TIMP that were only marginally affected by the expression of transfected ras. Similarly, SPP1 expression was strongly induced by ras in NIH 3T3 cells but was repressed by ras in LTA cells. Enzymogram assays for functional gelatinase activity showed an increase in 67-kd and 62-kd bands in NIH 3T3 cells in the presence of ras. LTA cells showed no gelatinolytic activity in the presence or absence of ras. Data from an in vitro assay for chemoinvasiveness showed a pattern as predicted from the expression of invasion-related genes; chemoinvasiveness in ras-transfected NIH 3T3 was greater than in LTA and ras-transfected LTA cells, which was greater than in NIH 3T3 cells. Differences in expression of the genes examined are believed to contribute to the ras responsiveness of NIH 3T3 cells and the ras resistance of LTA cells.
CELL-CELL COMMUNICATION IN GRAM-POSITIVE BACTERIA (1997)

In gram-positive bacteria, many important processes are controlled by cell-to-cell communication, which is mediated by extracellular signal molecules produced by the bacteria. Most of these signaling molecules are peptides or modified peptides. Signal processing, in most cases, involves either transduction across the cytoplasmic membrane or import of the signal and subsequent interaction with intracellular effectors. Concentrations of signal in the nanomolar range or below are frequently sufficient for biological activity. The microbial processes controlled by extracellular signaling include the expression of virulence factors, the expression of gene transfer functions, and the production of antibiotics.
Problems and Solutions in Laboratory Testing for Hemophilia (2013)

A diagnosis of hemophilia A or hemophilia B begins with clinical assessment of the patient and is facilitated by laboratory testing. The influence of the latter on a diagnosis of hemophilia A or hemophilia B is clear-a diagnosis cannot be made without laboratory confirmation of a deficiency of factor FVIII (FVIII) or factor IX (FIX), respectively. Moreover, the degree of hemophilia severity is specifically characterized by laboratory test results. In turn, patient management, including choice and application of therapies, is influenced by the diagnosis, as well as by identification of respective disease severity. An incorrect diagnosis may lead to inappropriate management and unnecessary therapy, and thus to adverse outcomes. Moreover, identification of factor inhibitors in hemophilia will lead to additional and differential treatments, and incorrect identification of inhibitors or inhibitor levels may also lead to inappropriate management. Problems in hemophilia diagnosis or inhibitor detection can occur at any stage in the clinical diagnosis/laboratory interface, from the "pre-preanalytical" to "preanalytical" to "analytical" to "postanalytical" to "post-postanalytical." This report outlines the various problems in laboratory testing for hemophilia and provides various strategies or solutions to overcome these challenges. Although some outlined solutions are specific to the potential errors related to hemophilia, others are general in nature and can be applied to other areas of laboratory hemostasis. Key to improvement in this area is adoption of best practice by all involved, including clinicians, phlebotomists, and laboratories. Also key is the recognition that such errors may occur, and thus that clinicians should assess laboratory test results in the context of their patient's clinical history and follow-up any potential errors, thus avoid misdiagnoses, by requesting repeat testing on a fresh sample.
Use of frozen-thawed semen aggravates the summer-autumn infertility of artificially inseminated weaned sows in the Mediterranean region1 (2009)

Improvement of farrowing rate (FR) and litter size (LS) of sows that are AI with frozen-thawed (FT) semen can hardly be reached without identification of the factors behind the high variability seen among trials. Three experiments using weaned (4-d wean-to-estrus interval) multiparous (parity 2 to 7) sows were conducted to evaluate the effect of period of the year on FR and LS of FT-inseminated sows in southern Spain. Sows were grouped into 2 periods of the year: winter-spring (November to April; WS) and summer-autumn (May to October; SA). Ovarian status was monitored by transrectal ultrasonography to record how long before or after ovulation AI was performed (pre-, peri-, or postovulatory AI) and to determine the onset of estrus-to-ovulation interval (EOI). Inseminations were performed using deep intrauterine AI with 1.5 x 10(9) FT sperm per dose. The first experiment was designed to determine the influence of the period of the year on FR and LS of FT semen. Sows (116 in WS and 100 in SA) were AI at 33 and 39 h after the onset of estrus. The period of the year influenced the FR and LS (P < 0.01). Farrowing rate and LS were least in SA (P < 0.05). This pattern of annual variation was similar to that shown by sows on the same farm currently undergoing AI with liquid semen (cervical AI at 12 and 36 h after the onset of estrus with 3 x 10(9) sperm per dose). However, the FR reduction in SA respect to WS was more substantial in sows artificially inseminated with FT (77.6 vs. 50%, P < 0.001) than those artificially inseminated with liquid semen (83.9 vs. 71.8%, P < 0.05). More pre- and less periovulatory AI were performed in SA sows than in WS sows (P <or= 0.05). Experiment 2 was designed to evaluate whether the period of the year influenced EOI. Ovarian status was transrectal ultrasonography scanned every 6 h after the onset of estrus until the end of ovulation (WS: 30; SA: 31 sows). There were more sows with long EOI (>48 h) in SA than in WS (P <or= 0.05). Experiment 3 aimed to improve the reduced FR and LS recorded in SA sows when using FT semen (Exp. 1) by inducing ovulation with eCG + hCG. A single AI with FT semen was performed 5 h before the expected ovulation (55 sows). As a control, spontaneously ovulating sows (n = 53) were FT-inseminated as in Exp. 1. Hormonal induction of ovulation did not improve FR and LS (P > 0.05). In the Spanish Mediterranean area, a longer EOI during SA negatively influenced the FR and LS of weaned sows after AI. This effect was particularly evident when FT semen was used. These findings were not ameliorated by hormonal induction of ovulation.
Expression, Purification and Properties of Shikimate Dehydrogenase from Mycobacterium Tuberculosis (2005)

Tuberculosis, caused by Mycobacterium tuberculosis, continues to be one of the main diseases to mankind. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. The shikimate pathway is considered as an attractive target for the discovery of novel antibiotics for its essentiality in bacteria and absence in mammalian cells. The Mycobacterium tuberculosis aroE-encoded shikimate dehydrogenase was cloned, expressed and purified. Sequence alignment analysis shows that shikimate dehydrogenase of Mycobacterium tuberculosis exhibit the pattern of G-X-(N/S)-V-(T/S)-X-PX-K, which is highly conserved within the shikimate dehydrogenase family. The recombinant shikimate dehydrogenase spectrum determined by CD spectroscopy showed that the percentages for alpha-helix, beta-sheet, beta-turn, and random coil were 29.2 %, 9.3 %, 32.7 %, and 28.8 %, respectively. The enzymatic characterization demonstrates that it appears to be fully active at pH from 9.0 to 12, and temperature 63(o)C. The apparent Michaelis constant for shikimic acid and NADP(+) were calculated to be about 29.5 microM and 63 microM. The recombinant shikimate dehydrogenase catalyzes the substrate in the presence of NADP(+) with an enzyme turnover number of 399 s(-1). Zymological studies suggest that the cloned shikimate dehydrogenase from M. tuberculosis has a pretty activity, and the work should help in the discovery of enzyme inhibitors and further of possible antimicrobial agents against Mycobacterium tuberculosis.