gebhart/patrepeval huggingface dataset:
Algae as an important environment for bacteria – phylogenetic relationships among new bacterial species isolated from algae (2013)

Bacteria are an inherent part of the biotic environment of algae. Recent investigations revealed that bacterial communities associated with algae were generally highly host specific. Several new bacterial species and genera were isolated from algae, which suggested that algae were an interesting environment for discovery of new bacterial taxa; however, the distribution of the different phylogenetic groups among those isolates remained unclear, and this information could help to explain specific associations. We conducted a phylogenetic study based on 16S rRNA gene sequences available in GenBank, including 101 validly described bacterial species that were isolated from eukaryotic macro- and micro-algae from marine and freshwater environments. These species were distributed among six bacterial phyla, including: Bacteroidetes (42 species), Proteobacteria (36 species), and Firmicutes, Actinobacteria, Verrucomicrobia and Planctomycetes (23 species). Bacterial species and strains that carried out similar metabolic functions were found to colonize similar algal taxa or algal groups. This assumption was supported by information available from bacterial species descriptions: (1) Most of the bacteria described from microalgae grouped into the Roseobacter clade (Alphaproteobacteria), which indicated that members of this group were well adapted for life in close association with phytoplankton; and (2) 32% of the bacterial species, mainly isolates from macroalgae, were able to decompose macroalgal polysaccharides. Because algal-bacterial association are still under-studied in various algal groups, we expect a great number of new bacterial taxa to be discovered in the future.
Lipoprotein-Associated Phospholipase A 2 , Platelet-Activating Factor Acetylhydrolase, Is Expressed by Macrophages in Human and Rabbit Atherosclerotic Lesions (1999)

We studied the expression of lipoprotein-associated phospholipase A(2) (Lp-PLA(2)), an enzyme capable of hydrolyzing platelet-activating factor (PAF), PAF-like phospholipids, and polar-modified phosphatidylcholines, in human and rabbit atherosclerotic lesions. Oxidative modification of low-density lipoprotein, which plays an important role in atherogenesis, generates biologically active PAF-like modified phospholipid derivatives with polar fatty acid chains. PAF is known to have a potent proinflammatory activity and is inactivated by its hydrolysis. On the other hand, lysophosphatidylcholine and oxidized fatty acids released from oxidized low-density lipoprotein as a result of Lp-PLA(2) activity are thought to be involved in the progression of atherosclerosis. Using combined in situ hybridization and immunocytochemistry, we detected Lp-PLA(2) mRNA and protein in macrophages in both human and rabbit atherosclerotic lesions. Reverse transcriptase-polymerase chain reaction analysis indicated an increased expression of Lp-PLA(2) mRNA in human atherosclerotic lesions. In addition, approximately 6-fold higher Lp-PLA(2) activity was detected in atherosclerotic aortas of Watanabe heritable hyperlipidemic rabbits compared with normal aortas from control rabbits. It is concluded that (1) macrophages in both human and rabbit atherosclerotic lesions express Lp-PLA(2), which could cleave any oxidatively modified phosphatidylcholine present in the lesion area, and (2) modulation of Lp-PLA(2) activity could lead to antiatherogenic effects in the vessel wall.
An introduction to GSM (1995)

From the Publisher:
Covering system architecture, implementation, and testing, this book provides you with an overview of GSM specifications and surveys competing cellular systems such as NADC and CDMA. Practical testing applications are explored in depth and compared with similar techniques used with analog cellular systems.
Macaque vision after magnocellular lateral geniculate lesions (1990)

Ibotenic-acid lesions of the magnocellular portion of the macaque lateral geniculate nucleus were used to examine the role of the M-cell pathway in spatio-temporal contrast sensitivity. A lesion was placed in layer 1 of the lateral geniculate of each of two monkeys. Physiological mapping in one animal demonstrated that the visual-field locus of the lesion was on the horizontal meridian, approximately 6 deg in the temporal field. Visual thresholds were tested monocularly in the contralateral eye, and fixation locus was monitored with a scleral search coil to control the retinal location of the test target. Three threshold measures were clearly disrupted by the magnocellular lesions. Contrast sensitivity for a 1 cycle/deg grating that drifted at 10 Hz was reduced from about twofold greater than, to about the same as, that for 10-Hz counterphase modulated gratings. Sensitivity for a very low spatial frequency (Gaussian blob), 10-Hz flickering stimulus was reduced so severely that no threshold could be measured. In addition, flicker resolution was greatly reduced at lower modulation depths (0.22), but not at higher depths (1.0). Two of the measured thresholds were unaffected by the lesions. Contrast sensitivity for 2 cycle/deg stationary gratings remained intact, and little or no effect on sensitivity was found for 1 cycle/deg, 10-Hz counterphase modulated gratings. Together, these results suggest that the magnocellular pathway makes little contribution to visual sensitivity at low to moderate temporal frequencies. On the other hand, some contribution to detection sensitivity is evident at lower spatial and high temporal frequencies, especially for drifting stimuli.(ABSTRACT TRUNCATED AT 250 WORDS)
Purified hybrid insulin/insulin-like growth factor-I receptors bind insulin-like growth factor-I, but not insulin, with high affinity (1993)

Hybrid insulin/insulin-like growth factor-I (IGF-I) receptors have previously been described in human placenta, but it has not been possible to study their properties in the presence of classical insulin receptors and type I IGF receptors. To facilitate the purification of hybrids, we produced an anti-peptide monoclonal antibody IGFR 1-2, directed against the C-terminal peptide of the type I IGF receptor beta-subunit. The antibody bound native human and rat type I IGF receptors, and reacted specifically with the beta-subunit on immunoblots. Solubilized placental microsomal membranes were depleted of classical type I IGF receptors by incubation with an immobilized monoclonal antibody IGFR 24-55, which reacts well with type I receptors but very poorly with hybrid receptors. Residual hybrid receptors were then isolated by incubation with immobilized antibody IGFR 1-2, and recovered by elution with excess of synthetic peptide antigen. Binding properties of hybrids were compared with those of immuno-affinity-purified insulin receptors and type I IGF receptors, by using the radioligands 125I-IGF-I and 125I-insulin. Hybrids bound approx. 20 times as much 125I-IGF-I as 125I-insulin at tracer concentrations (approx. 0.1 nM). The binding of 125I-insulin, but not 125I-IGF-I, to hybrids increased after treatment with dithiothreitol to reduce disulphide bonds between the alpha-subunits. Hybrids behaved very similarly to type I receptors with respect to the inhibition of 125I-IGF-I binding by unlabelled IGF-I and insulin. By contrast, the affinity of hybrids for insulin was approx. 10-fold lower than that of classical insulin receptors, as assessed by inhibition of 125I-insulin binding by unlabelled hormone. It is concluded that the properties of insulin receptors, but not IGF receptors, are markedly affected by assembly as hybrid compared with classical structures, and that hybrids are more likely to be responsive to IGF-I than insulin under physiological conditions.
Extraintestinal pathogenicEscherichia coli: an update on antimicrobial resistance, laboratory diagnosis and treatment (2012)

Escherichia coli remains one of the most frequent causes of nosocomial and community-acquired bacterial infections including urinary tract infections, enteric infections and systemic infections in humans. Extraintestinal pathogenic E. coli (ExPEC) had emerged during the 2000s as an important player in the resistance to antibiotics, especially to the cephalosporins and fluoroquinolones. Most importantly, among ExPEC is the increasing recognition of isolates producing 'newer β-lactamases' that consist of plasmid-mediated AmpC β-lactamases (e.g., CMY), extended-spectrum β-lactamases (e.g., CTX-M) and carbapenemases (e.g., New Delhi metallo-β-lactamase, Klebsiella pneumonaie carbapenemase and OXA-48). This review will highlight recent aspects on antimicrobial resistance in ExPEC, including the laboratory detection of these isolates, and describe some treatment options for infections due to antimicrobial-resistant isolates.
HarpiaGrid: A Reliable Grid-based Routing Protocol for Vehicular Ad Hoc Networks (2008)

Vehicular ad hoc network (VANET) is a research field attracting growing attention. Current routing protocols in VANET usually use geographic information to forward data packets to the destination. Since geographic routing is stateless, during routing forwarding, route recovery processes would be continuously initiated if any topology hole exists, resulting in serious performance degradation. In addition, if vehicle density is low in the network, there might not be vehicles available to deliver the packet. This paper proposes HarpiaGrid, a reliable grid-based routing protocol for VANETs. The protocol utilizes in-car navigators to produce geographically logical routing paths, effectively trades route discovery network overhead with insignificant computation time. In addition, by taking advantage of the information provided by gridded geographic data, transmissions are made more efficient. Moreover, in the route maintenance, a fault-tolerance procedure is designed to avoid dead paths. Simulations were conducted, and the results demonstrated that the proposed scheme is indeed more efficient and reliable than other protocols.
Targeted electrode-based modulation of neural circuits for depression (2009)

During the last 20 years of neuroscience research, we have witnessed a fundamental shift in the conceptualization of psychiatric disorders, with the dominant psychological and neurochemical theories of the past now complemented by a growing emphasis on developmental, genetic, molecular, and brain circuit models. Facilitating this evolving paradigm shift has been the growing contribution of functional neuroimaging, which provides a versatile platform to characterize brain circuit dysfunction underlying specific syndromes as well as changes associated with their successful treatment. Discussed here are converging imaging findings that established a rationale for testing a targeted neuromodulation strategy, deep brain stimulation, for treatment-resistant major depression.
ALBIPUNCTATE RETINOPATHY WITH CONE DYSFUNCTION AND NO ABNORMALITY IN THE RDH5 OR RLBP1 GENES (2003)

MARMOR, MICHAEL F. MD*; HAESELEER, FRANCOISE PhD†; PALCZEWSKI, KRZYSZTOF PhD†‡§ Author Information
von Hippel-Lindau Syndrome: Target for Anti-Vascular Endothelial Growth Factor (VEGF) Receptor Therapy (2000)

von Hippel-Lindau (VHL) syndrome is a familial cancer syndrome caused by germline mutations in the VHL tumor suppressor gene. Mutations in the VHL gene result in the constitutive stabilization of transcription factors hypoxia-inducible factors 1α and 2α, which bind to specific enhancer elements in the vascular endothelial growth factor (VEGF) gene and stimulate angiogenesis. This increase in angiogenesis under normoxic conditions in key target organs such as the brain, kidney, and eye leads to high morbidity and reduced life expectancy. Drugs designed to block the VEGF signaling pathway may prevent the long-term complications of the disease. To test this hypothesis, a clinical study was initiated to evaluate the effect of the VEGF tyrosine kinase receptor inhibitor SU5416 in patients with VHL syndrome. Preliminary data on SU5416 indicate that it is well tolerated when administered chronically in such patients. However, since little is known about the long-term use of such inhibitors, patients will need careful monitoring. Data obtained from monitoring these patients will provide valuable information for adjuvant treatment trials in cancer patients.
Effect of intracranial pressure on bridging veins in rats (1987)

The behavior of bridging veins at their entrance into the superior sagittal sinus during elevated intracranial pressure (ICP) was investigated in rats using a cranial window and infusion of mock cerebrospinal fluid. The bridging veins became slightly smaller as the ICP rose (maximum reduction 17%). Compression or collapse of the veins was not observed, even at an ICP level of 100 mm Hg, and there was no cuffing of bridging veins upstream of the entrance. Both the scanning electron microscopic investigation based on resin vessel casts and the histological examination of whole-head coronal sections indicated that the narrowest points of the bridging veins are at their entrance to the superior sagittal sinus, caused by the oval aperture with thickened wall structure in the lateral sinus wall to which the bridging veins are connected. The present data thus support the concept that cerebral blood flow during intracranial hypertension is not reduced by venous cuffing or compression of the lateral lacunae and bridging veins; by contrast, the arteriovenous pressure difference seems to remain the determining factor even at high ICP. Thus, blood flow through the brain stops when ICP approaches the level of blood pressure.
1083 nm ytterbium doped fibre amplifier for opticalpumping of helium (1997)

A combination of a narrow linewidth, tunable DBR diode laser and high power ytterbium fibre amplifier in a master oscillator power fibre amplifier (MOPFA) configuration is demonstrated for efficient optical pumping of helium. A compact and efficient diode pumped prototype system is shown to compare favourably with alternative laser sources for production of hyperpolarised 3He using direct pumping for medical application in MRI.
An intelligent clustering forecasting system based on change-point detection and artificial neural networks: application to financial economics (2005)

Suggests a new clustering forecasting system to integrate change-point detection and artificial neural networks. The basic concept of the proposed model is to obtain intervals divided by change points, to identify them as change-point groups, and to involve them in the forecasting model. The proposed models consist of two stages. The first stage (the clustering neural network modeling stage) detects successive change points in a data set and forecasts the change-point group with backpropagation neural networks (BPN). In this stage, three change-point detection methods are applied and compared: (1) the parametric method, (2) the nonparametric approach, and (3) the model-based approach. The next stage is to forecast the final output with a BPN. Through an application to financial economics, we compare the proposed models with a neural network model alone and, in addition, determine which of the three change-point detection methods can perform better. This article then examines the predictability of the integrated neural network model based on change-point detection.
Catalytic antibodies: mechanistic and practical considerations (1993)

J. D. Stewart and S. J. Benkovic, Chem. Soc. Rev., 1993, 22, 213 DOI: 10.1039/CS9932200213
Human Umbilical Cord Perivascular (HUCPV) Cells: A Source of Mesenchymal Progenitors (2005)

We describe the isolation of a nonhematopoietic (CD45-, CD34-, SH2+, SH3+, Thy-1+, CD44+) human umbilical cord perivascular (HUCPV) cell population. Each HUCPV cell harvest (2-5 x 10(6), depending on the length of cord available) gave rise to a morphologically homogeneous fibroblastic cell population, which expressed alpha-actin, desmin, vimentin, and 3G5 (a pericyte marker) in culture. We determined the colony-forming unit-fibro-blast (CFU-F) frequency of primary HUCPV cells to be 1:333 and the doubling time, which was 60 hours at passage 0 (P0), decreased to 20 hours at P2. This resulted in a significant cell expansion, producing over 10(10) HUCPV cells within 30 days of culture. Furthermore, HUCPV cells cultured in nonosteogenic conditions contained a subpopulation that exhibited a functional osteogenic phenotype and elaborated bone nodules. The frequency of this CFU-osteogenic subpopulation at P1 was 2.6/10(5) CFU-F, which increased to 7.5/10(5) CFU-F at P2. Addition of osteogenic supplements to the culture medium resulted in these frequencies increasing to 1.2/10(4) and 1.3/10(4) CFU-F, respectively, for P1 and P2. CFU-O were not seen at P0 in either osteogenic or non-osteogenic culture conditions, but P0 HUCPV cells did contain a 20% subpopulation that presented neither class I nor class II cell-surface major histocompatibility complexes (MHC-/-). This population increased to 95% following passage and cryopreservation (P5). We conclude that, due to their rapid doubling time, high frequencies of CFU-F and CFU-O, and high MHC-/- phenotype, HUCPV cells represent a significant source of cells for allogeneic mesenchymal cell-based therapies.
Peptide Sugar Mimetics Prevent HIV Type 1 Replication in Peripheral Blood Mononuclear Cells in the Presence of HIV-Positive Antiserum (2010)

Cells of the immune system express a number of receptors that bind carbohydrate ligands. We questioned whether peptide mimetics of these ligands will activate phagocytic cells and thereby enhance an antiviral response. Short peptide sequences were identified by computational modeling of docking to glycan-specific lectins, selected as receptor analogs, and incorporated into quadravalent structures by peptide synthesis. A peptide with the sequence HPSLK bound to several lectins specific for monosaccharides and to lectins specific for Neu5Ac-Gal-containing complex glycans, whereas a longer sequence, NPSHPLSG, bound only lectins specific for the more complex glycans. In cultures of peripheral blood mononuclear cells (PBMCs) these peptides stimulated phagocytosis of opsonized microspheres. The peptides inhibited replication of HIV-1 in PBMC cultures by 20-80% at concentrations between 1 nM and 1 muM but inhibited replication 100% in the presence of diluted HIV-positive antiserum that alone inhibited replication by 30%. HPSLK caused about 50% loss of viability of cells at 1 mM, a concentration 10(6)-fold higher than an effective inhibitory concentration, but no toxicity was observed with NPSHPLSG. These results demonstrated that peptidomimetics of glycan ligands of cellular receptors are effective in activating phagocytosis, which may be a factor in providing complete inhibition of HIV-1 replication in vitro.
A complementary study of surface-enhanced Raman scattering and metal nanorod arrays (2000)

Abstract The two-dimensional arrays of various metal nanowires with diameters ranging from 15 to 70 nm have been fabricated by electrodepositing metals of Cu, Ag, Au, Ni, and Co into the nanoholes of the anodic aluminum oxide (AAO) films, followed by partial removal of the film. The strong surface-enhanced Raman scattering (SERS) effects were observed from the metal nanowire arrays including Ni, Co metals that were normally considered to be non-SERS active substrates. It has been shown that metal nanowire arrays can serve as very good SERS active substrates, especially for transition metals. The SERS intensity of the probe molecule adsorbed at the nanowires depends critically on the length of the nanowires explored at the surface. And the band frequency is very sensitive to the diameter, which reflects the change in the electronic property of metal nanowires. Applying this probe molecule strategy, SERS could develop into a diagnostic tool of metal nanowires (nanorods).
Synthesis of a gene for human serum albumin and its expression inSaccharomyces cerevisiae (1990)

A 1761 base pairs long artificial gene coding for human serum albumin (HSA) has been prepared by a newly developed synthetic approach, resulting in the largest synthetic gene so far described. Oligonucleotides corresponding to only one strand of the HSA gene were prepared by chemical synthesis, while the complementary strand was obtained by a combination of enzymatic and cloning steps. 24 synthetic, 69-85 nucleotides long oligonucleotides covering the major part of the HSA gene (41-1761 nucleotides) were used as building blocks. Generally, four groups of 6-6 such oligonucleotides were successively cloned in pUC19 Escherichia coli vector to obtain about quarters of the gene as large fragments. Joining of these four fragments resulted in a cloned DNA coding for the 13-585 amino acid region of HSA, which was further supplemented with a double-stranded linker sequence coding for the amino terminal 12 amino acids. The completed structural gene composed of frequently used codons in the highly expressed yeast genes was then supplied with yeast regulatory sequences and the HSA expression cassette so obtained was inserted into an Escherichia coli-Saccharomyces cerevisiae shuttle vector. This vector was shown to direct the expression in Saccharomyces cerevisiae of correctly processed, mature HSA which was recognized by antiserum to HSA, and possessed the correct N-terminal amino acid sequence.
COMPARISON OF ACID NEUTRALIZING AND NON-ACID NEUTRALIZING STRESS ULCER PROPHYLAXIS IN THERMALLY INJURED PATIENTS (1994)

We have compared the effectiveness of non-acid neutralizing stress ulcer prophylaxis (SUC) with sucralfate (n = 48) with that of acid neutralizing prophylaxis (AN) utilizing antacids and cimetidine (n = 48) in the prevention of stress ulcer bleeding and nosocomial pneumonia (PN) in thermally injured patients. In the subset of intubated patients, the incidence of PN was 17.8% and 42.8% in the AN and SUC groups, respectively (p < 0.05) despite a similar postburn time of onset of pneumonia. Ten patients in each group died. Three patients in the SUC group developed upper GI bleeding with one requiring gastrectomy. Bacterial colonization of the upper airway occurred in virtually all patients, whereas 83% (SUC) and 96% (AN) had colonization of gastric contents. Gram-negative colonization rates for the upper airway were not different (70%) whereas 48% of SUC patients compared with 60% of AN patients had gram-negative gastric colonization. In conclusion, SUC therapy was efficacious in the prevention of stress ulcer bleeding but did not alter the rate of bacterial colonization of the airway or gastric contents, and was associated with a higher incidence of nosocomial pneumonia in intubated patients.
Time sequence of changes in the responsiveness of glycogen breakdown to adrenergic agonists in perfused liver of rats with insulin-induced hypoglycemia (2000)

The time-course changes of the responsiveness of glycogen breakdown to alpha- and ss-adrenergic agonists during insulin-induced hypoglycemia (IIH) were investigated. Blood glucose levels were decreased prior to the alteration in the hepatic responsiveness to adrenergic agonists. The activation of hepatic glucose production and glycogenolysis by phenylephrine (2 microM) and isoproterenol (20 microM) was decreased in IIH. The changes in the responsiveness of glycogen catabolism were first observed for isoproterenol and later for phenylephrine. Hepatic ss-adrenergic receptors showed a higher degree of adrenergic desensitization than did alpha-receptors. Liver glycogen synthase activity, glycogen content and the catabolic effect of dibutyryl cyclic AMP (the ss-receptor second messenger) were not affected by IIH.