gebhart/patrepeval huggingface dataset:
The microbiological case for adjunctive therapy for periodontitis. (2004)

That chronic periodontitis is an infectious disease is now firmly established, and the primary role of Porphyromonas gingivalis, Tannerella forsythensis and Treponema denticola is generally accepted. Treatment by mechanical means such as scaling and root planing or surgery generally results in significant clinical improvement but may not arrest the progress or recurrence of disease. Several studies have shown that the probability of achieving lasting stability as measured by the arrest of progressive attachment loss and bone loss by primary mechanical therapy is a function, in major part, of whether pathogenic microorganisms are still present at local subgingival sites at the completion of active therapy. The infecting bacterial species are susceptible to killing by several antibiotics including, among others, tetracycline-class drugs, amoxicillin and metronidazole as well as by local exposure to chlorhexidine. Randomized clinical trials have shown that use of systemically administered antibiotics as an adjunct to mechanical therapies significantly enhances clinical outcomes and stability. Several slow-release devices that deliver anti-microbial drugs directly into periodontal pockets have been developed and are now on the market. Use of these devices permits local delivery of long-lasting, high concentrations of doxycycline (Atridox) minocycline (Arestin), and chlorhexidine (PerioChip) directly into periodontal pockets. Although these devices differ with regard to ease of use, concentration of drug delivered and length of time high drug concentrations can be maintained, randomized clinical trials have shown that their use as an adjunctive treatment to scaling and root planing results in a significantly greater reduction of periodontal pocket depth and an average increase in clinical periodontal attachment level of about 0.8 mm. Gain in clinical attachment is greater in deeper pockets than in shallower pockets. Locally delivered adjunctive anti-microbial therapy is an effective means to enhance therapeutic outcomes.
Development of a Duration Threshold for Modulating Evoked Neuronal Responses After Nerve Root Compression Injury (2011)

Cervical nerve roots are susceptible to compression injuries of various durations. The duration of an applied compression has been shown to contribute to both the onset of persistent pain and also the degree of spinal cellular and molecular responses related to nociception. This study investigated the relationship between peripherally-evoked activity in spinal cord neurons during a root compression and the resulting development of axonal damage. Electrically-evoked spikes were measured in the spinal cord as a function of time during and after (post-compression) a 15 minute compression of the C7 nerve root. Compression to the root significantly (p=0.035) reduced the number of spikes that were evoked over time relative to sham. The critical time for compression to maximally reduce evoked spikes was 6.6±3.0 minutes. A second study measured the post- compression evoked neuronal activity following compression applied for a shorter, sub-threshold time (three minutes). Ten minutes after compression was removed, the discharge rate remained significantly (p=0.018) less than baseline by 58±25% relative to sham after the 15 minute compression, but returned to within 3±33% of baseline after the three minute compression. Axonal damage was evident in the nerve root at day seven after nerve root compression only after a 15 minute compression. These studies demonstrate that even a transient mechanical insult to the nerve root is sufficient to induce sustained neuronal dysfunction and axonal pathology associated with pain, and results provide support that such minor neural tissue traumas can actually induce long-lasting functional deficits.
The Distribution of Concentrated Solar Radiation in Paraboloidal Collectors (1986)

A procedure is presented for calculating the distribution of concentrated flux in paraboloidal solar collectors and is applied to idealized and practical cases. This procedure is based on the firmly established concepts of the flux integral and radiant intensity but is implemented by simple geometrical constructions involving infinitesimal pyramids based on the reflecting surface. This procedure yields a formulation well suited for numerical evaluation.
Phosphorus Removal from Aerated Lagoons Using Alum, Ferric Chloride and Lime (1994)

Abstract Laboratory and on-site studies were conducted over a period of 18 months on two wastewater treatment plants. The main objective was the removal of phosphorus. Three coagulants were used: alum, ferric chloride and lime. In the precipitation process, alum was found to react preferentially with polyphosphates, but not with orthophosphates. Seasonal temperature variations in wastewater did not have a detrimental effect on the coagulation and flocculation processes. The molar capacity of alum for precipitating the orthophosphate fraction was greater at the secondary level of treatment than at the primary level. The phosphorus removal efficiency varied between 90 and 95% for all coagulants. For lime, the dosage was relatively high in order to achieve the same degree of dephosphatation, leading to sludge accumulation in the aerated lagoons.
Gamendazole, an Orally Active Indazole Carboxylic Acid Male Contraceptive Agent, Targets HSP90AB1 (HSP90BETA) and EEF1A1 (eEF1A), and Stimulates Il1a Transcription in Rat Sertoli Cells1 (2008)

Gamendazole was recently identified as an orally active antispermatogenic compound with antifertility effects. The cellular mechanism(s) through which these effects occur and the molecular target(s) of gamendazole action are currently unknown. Gamendazole was recently designed as a potent orally active antispermatogenic male contraceptive agent. Here, we report the identification of binding targets and propose a testable mechanism of action for this antispermatogenic agent. Both HSP90AB1 (previously known as HSP90beta [heat shock 90-kDa protein 1, beta]) and EEF1A1 (previously known as eEF1A [eukaryotic translation elongation factor 1 alpha 1]) were identified as binding targets by biotinylated gamendazole (BT-GMZ) affinity purification from testis, Sertoli cells, and ID8 ovarian cancer cells; identification was confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and Western blot analysis. BT-GMZ bound to purified yeast HSP82 (homologue to mammalian HSP90AB1) and EEF1A1, but not to TEF3 or HBS1, and was competed by unlabeled gamendazole. However, gamendazole did not inhibit nucleotide binding by EEF1A1. Gamendazole binding to purified Saccharomyces cerevisiae HSP82 inhibited luciferase refolding and was not competed by the HSP90 drugs geldanamycin or novobiocin analogue, KU-1. Gamendazole elicited degradation of the HSP90-dependent client proteins AKT1 and ERBB2 and had an antiproliferative effect in MCF-7 cells without inducing HSP90. These data suggest that gamendazole may represent a new class of selective HSP90AB1 and EEF1A1 inhibitors. Testis gene microarray analysis from gamendazole-treated rats showed a marked, rapid increase in three interleukin 1 genes and Nfkbia (NF-kappaB inhibitor alpha) 4 h after oral administration. A spike in II1a transcription was confirmed by RT-PCR in primary Sertoli cells 60 min after exposure to 100 nM gamendazole, demonstrating that Sertoli cells are a target. AKT1, NFKB, and interleukin 1 are known regulators of the Sertoli cell-spermatid junctional complexes. A current model for gamendazole action posits that this pathway links interaction with HSP90AB1 and EEF1A1 to the loss of spermatids and resulting infertility.
Funkčná analýza mikroRNA-21 na modely kolorektálného karcinomu. (2011)

Cilem studie bylo analyzovat vliv miR-21 na viabilitu, buněcný
cyklus, apoptozu a migraci buněk DLD-1.
ChemInform Abstract: Reaction of Tantalum Alkyne Complexes with Hydrazones. Stereoselective Synthesis of E‐Allylic Hydrazines. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Time-dependent Dynamical Reorientation Induced By CW Laser Beam In A Nematic Liquid Crystal Film (1990)

Liquid crystals in their mesophases are attractive materials for nonlinear optical devices because of their huge response to optical fields and their capability of being easily inserted in optically integrated structures. From the macroscopic point of view, we may consider a nematic liquid crystal as a fluid endowed with internal orientational degrees of freedom. These additional degrees of freedom, absent in ordinary fluids, may be accounted for by the director field n(r), a unit vector field attached at each point r in the medium. Unlike in the case of externally applied static fields, where n couples with the external field directly, in the case of optical fields n couples with the light polarization. As a consequence, n is driven by exchange of angular momentum between the light beam and the medium. This yields the appearance of various new nonlinear optical phenomena having no analogue in the static-field case. For instance, the molecular director n can be put into uniform precession about the beam propagation direction by transfer of intrinsic angular momentum (photon spin) from the beam to the liquid crystal. This effect can be observed only with circular polarization of the incident beam, for, in this case only, the deposition of angular momentum in the medium has a constant rate. With an elliptically polarized beam, the situation is far more intriguing. The main difference between circular and elliptical input polarization is that in the former case the molecular reorientation first breaks the azimutal symmetry of the whole system ( radiation + liquid crystal). This yields characteristic different results in the two cases: the elliptically polarized input can lead the system through various dynamic regimes: torsional oscillations, nonuniform precession, nutation of n superimposed on precession, and others.
Mechanism of amyloid peptide induced CCR5 expression in monocytes and its inhibition by siRNA for Egr-1 (2005)

In Alzheimer's disease (AD), one finds increased presence of monocytes/macrophages and activated microglial cells in the brain. Immunohistochemical studies show increased expression of chemokine receptor 5 (CCR5) on reactive microglia associated with amyloid deposits in AD, suggesting that CCR5 may play a role in the regulation of the immune response in AD. In this study, we used peripheral blood monocytes and human monocytic THP-1 cell line as a model of microglia to delineate the cellular signaling mechanism of Abeta-induced CCR5 expression and the latter's role in the chemotaxis of monocytes. We observed that Abeta peptides at pathophysiological concentrations (125 nM) increased CCR5 mRNA and cell surface protein expression. The cellular signaling involved activation of c-Raf, ERK-1/ERK-2, and c-Jun NH(2)-terminal kinase. Analysis of some transcription factors associated with CCR5 promoter revealed that Abeta increased DNA binding activity of Egr-1 and AP-1. In addition, we show that CCR5 promoter contains an Egr-1 like consensus sequence GCGGGGGTG as demonstrated by 1) electrophoretic mobility shift assay, 2) transfection studies with truncated CCR5 gene promoter construct, and 3) chromatin immunoprecipitation analysis. Moreover, transfection of Egr-1 siRNA, but not of scrambled Egr-1 siRNA, in THP-1 cells resulted in >75% reduction in both Abeta-mediated CCR5 expression and concomitant chemotaxis to its ligands. We suggest that inhibition of Egr-1 by either Egr-1 siRNA or pharmacological agents may reduce activation of monocytes/microglia and possibly ameliorate the inflammation and progression of AD.
Anal, Penile, and Oral High-Risk HPV Infections and HPV Seropositivity in HIV-Positive and HIV-Negative Men Who Have Sex with Men (2014)

The effects of single or multiple concordant HPV infections at various anatomical sites on type-specific HPV seropositivity are currently unknown. In this cross-sectional study we assessed whether high-risk HPV infections at various anatomical sites (i.e., anal canal, penile shaft, and oral cavity), as well as concordant infections at multiple anatomical sites, were associated with type-specific seropositivity in HIV-positive and HIV-negative MSM. MSM aged ≥ 18 years were recruited in Amsterdam, the Netherlands (2010-2011). Baseline anal, penile, and oral samples were analyzed for HPV DNA and genotyped using a highly sensitive PCR and reverse line blot assay. Virus-like particle (VLP) based multiplex immunoassay was used to asses HPV-specific serum antibodies against L1 VLPs. The associations between HPV infections and type-specific seropositivity of seven high-risk HPV types (7-hrHPV: types 16, 18, 31, 33, 45, 52, 58) were estimated using logistic regression analyses with generalized estimating equations. We found that 86% of 306 HIV-positive MSM and 62% of 441 HIV-negative MSM were seropositive for at least one 7-hrHPV type. 69% of HIV-positive and 41% of HIV-negative MSM were infected with at least one 7-hrHPV type at the anus, penis, or oral cavity. In multivariable analyses, 7-hrHPV seropositivity was associated with type-specific anal (and not penile) 7-hrHPV infection, and did not significantly increase with a higher number of infected anatomical sites. Oral 7-hrHPV infection showed a positive, albeit non-significant, association with seropositivity. In conclusion, seropositivity among MSM appears to be largely associated with anal HPV infection, irrespective of additionally infected anatomical sites.
Temperature dependence of carrier lifetime and Auger recombination in 1.3 μm InGaAsP (1985)

Carrier lifetime has been measured by the luminescence decay of a 1.3-μm-InGaAsP layer excited by a mode locked YAG laser at 1.06 μm. The measurements have been done as a function of excitation intensity for nearly three orders of magnitude of carrier concentration (4×1016–2×1019 cm−3) and for different temperatures (between 32 and 346 K). At low and moderate carrier density, the lifetime τ follows the variation with excitation of the theoretical radiative lifetime. At high carrier density (above 1018 cm−3) the carrier decay rate increases more rapidly than the radiative one and around room temperature this can be accounted for by an additional recombination mechanism whose variation with excitation is typical of an Auger process. The Auger coefficient (Ca=2.6×10−29 cm6 s−1) does not vary with temperature within experimental uncertainty. This suggests that though Auger recombination is for a large part responsible for the low T0 value of 1.3-μm InGaAsP lasers, the temperature dependence of the Auger coefficient does not contribute to it.
Metabolites from the purple heartwoods of the mimosoideae. Part 4. Acacia fasciculifera F. Muell ex. Benth: fasciculiferin, fasciculiferol, and the synthesis of 7-aryl- and 7-flavanyl-peltogynoids (1981)

Structural examination of the heartwood metabolites of Acacia fasciculifera revealed the presence of fasciculiferin, a novel peltogynoid, and fasciculiferol, a dibenzo-α-pyrone, in addition to known flavonoids, peltogynoids, and biflavanoids.Synthesis of 7-aryl- and 7-flavanyl-peltogynoids as model tannins from peltogynol requires increasingly drastic conditions with decrease of nucleophilicity of the substrate. These condensations come progressively under thermodynamic control and proceed with greater difficulty than those involving the flavan-3,4-diol analogue.
On the digestive coefficients of roughages in the Japanese polled breed of cattle (1952)

1 無角和種が粗悪な飼料の利用性に富むものかどうかをみるために,粗飼料の消化率を求め,有角の和牛のそれと此較してみた。有角の和牛は2頭でそのうち1頭は黒毛和種であり,他は豚尻牛であつた。2 無角和種は黒毛和種及び豚尻牛に比して一般に粗飼料の消化率が高かつた。ことに粗飼料の質の良好でない時にこの差は判然と現われるようである。3 粗飼料の質が悪化した場合,無角和種における各飼料成分の消化率低下の割合は豚尻牛に比して少かつた。これは無角和種が粗悪な飼料をもよく利用する能力があることを示すものかと思われる。4 豚尻牛の消化率は一般に無角和種に比して低いが,粗飼料における粗脂肪の消化率のみはやゝ高かつた。それにも拘わらず豚尻牛が体脂肪蓄積の能力に乏しいとすればそれは,豚尻牛の脂肪代謝における生理異常の問題と関連しているものと思われ,興味ある事実といゝうるであろう。
Silicon at the nanoscale using lithography control: Nanowires, nanopores and quantum dots (2016)

Nanostructures of silicon are becoming increasingly important as they may combine new opto-electronic features or devices with CMOS technology. This enables the integration of e.g. nanowire sensors with readout electronics or nanoscale LEDs grown directly on Si wafers. A problem here is that nanostructures are often fabricated using a bottom-up approach necessitating a second deposition step of random nature or involving a tedious alignment procedure. This is because current lithography techniques do not allow sub 10 nm precision for direct top-down fabrication. In this presentation I will show examples of fabricating some generic silicon structures such as nanowires, nanopores and quantum dots using optical or e-beam lithography where a second process step is used to shrink feature sizes in a controlled way. Thus, the lithography step for positioning of nanostructures and the size determining process step become decoupled, as shown by three examples from our work: (i) Silicon nanowires were fabricated using a top-down approach using optical lithography. Thinning of the device layer to ∼20 nm enabled picomolar sensitivity for detection of biomolecules, avoiding traditional CVD growth of nanowires. These “nanoribbons” allows multiple parallel detection and direct electrical readout. (ii) Nanopores are interesting for single molecule detection and DNA sequencing. We have fabricated silicon membranes with arrays of nanopores down to sub 10 nm diameter. Electro-chemical etching was used as the final size control. This allows multiple optical detection of DNA translocation. (iii) Finally, individual Si quantum dots have been fabricated using e-beam lithography and a final tuning of the core by oxidation in a “self-limiting” regime. This has allowed single-dot spectroscopy revealing quantum confined exciton recombination with ultra-sharp emission lines. Many other features such as blinking and spectral diffusion have been observed, similar to direct bandgap quantum dots. Recent data indicate that very high quantum yields are possible enabling new applications.
Luminescent, Freestanding Composite Films of Au<sub>15</sub> for Specific Metal Ion Sensing (2012)

A highly luminescent freestanding film composed of the quantum cluster, Au(15), was prepared. We studied the utility of the material for specific metal ion detection. The sensitivity of the red emission of the cluster in the composite to Cu(2+) has been used to make a freestanding metal ion sensor, similar to pH paper. The luminescence of the film was stable when exposed to several other metal ions such as Hg(2+), As(3+), and As(5+). The composite film exhibited visual sensitivity to Cu(2+) up to 1 ppm, which is below the permissible limit (1.3 ppm) in drinking water set by the U.S. environmental protection agency (EPA). The specificity of the film for Cu(2+) sensing may be due to the reduction of Cu(2+) to Cu(1+)/Cu(0) by the glutathione ligand or the Au(15) core. Extended stability of the luminescence of the film makes it useful for practical applications.
Use of near-infrared luminescent gold nanoclusters for detection of macrophages (2012)

We determined the effect of aggregation and coating thickness of gold on the luminescence of nanoparticles engulfed by macrophages and in gelatin phantoms. Thin gold-coated iron oxide nanoclusters (nanoroses) have been developed to target macrophages to provide contrast enhancement for near-infrared optical imaging applications. We compare the brightness of nanoroses luminescent emissions in response to 635 nm laser excitation to other nanoparticles including nanoshells, nanorods, and Cy5 conjugated iron oxide nanoparticles. Luminescent properties of all these nanoparticles were investigated in monomeric and aggregated form in gelatin phantoms and primary macrophage cell cultures using confocal microscopy. Aggregation of the gold nanoparticles increased luminescence emission and correlated with increased surface mass of gold per nanoparticle (nanoshells 37 ± 14.30 × 10(-3) brightness with 1.23 × 10(-4) wt of gold (g)/nanoparticle versus original nanorose 1.45 ± 0.37 × 10(-3) with 2.10 × 10(-16) wt of gold/nanoparticle, p<0.05). Nanoshells showed greater luminescent intensity than original nanoroses or Cy5 conjugated iron oxide nanoparticles when compared as nanoparticles per macrophage (38 ± 10 versus 11 ± 2.8 versus 17 ± 6.5, p<0.05, respectively, ANOVA), but showed relatively poor macrophage uptake (1025 ± 128 versus 7549 ± 236 versus 96,000 nanoparticles/cell, p<0.05, student t-test nanoshells versus nanoroses). Enhancement of gold fluorescent emissions by nanoparticles can be achieved by reducing the thickness of the gold coating, by clustering the gold on the surface of the nanoparticles (nanoshells), and by clustering the gold nanoparticles themselves.
Numerical Taxonomy Analysis of Bacteria Isolated from the Completed ‘Most Probable Numbers’ Test for Coliform Bacilli (1981)

Lactose‐fermenting bacteria were isolated from oyster, water and sediment samples tested to determine the Most Probable Number (MPN) of coliforms present. The completed test series was used to enumerate the total number of coliforms. The strains from the completed tests of the MPN analysis were compared with named reference cultures, for which 100 phenotypic characters were recorded and the taxonomic data analysed by methods of numerical taxonomy. The isolates were recovered in 13 phenetic groups, defined at or above the 80% similarity level. Nine phena were identified as Acinetobacter calcoaceticus, Chromobacterium violaceum, Citrobacter freundii, Erwinia herbicola, Escherichia coli, Hafnia alvei, Klebsiella pneumoniae, Serratia liquefaciens , and Ser. marcescens. Of these, Ac. calcoaceticus and C. violaceum were isolated exclusively from oyster tissue samples and strains of the other taxa from both water and oyster samples. Some strains of Esch. coli, Er. herbicola, H. alvei and bacteria that were not Enterobacteriaceae were found to lose the ability to ferment lactose, following storage on laboratory media. Identifications from diagnostic keys, rapid identification systems and IMViC patterns were not always in agreement.
Synthesis of Lanopylin B<sub>1</sub> (2005)

Phase-transfer alkylation of diethyl 2-oxopropylphosphonate (9) with 2-iodoalkyl azide afforded 40% of azido phosphonate 6, which underwent a phase-transfer Horner-Emmons Wittig reaction with heptadecanal to provide 80% of azido enone 5. An intramolecular aza-Wittig reaction with polymer-bound Ph(3)P in toluene at reflux completed the first synthesis of lanopylin B(1) in 76% yield.
Flow Induced Bifurcations to Three-Dimensional Oscillatory Motions in Continuous Tubes (1984)

Three-dimensional motions of a cantilever tube carrying an incompressible fluid and having rotational symmetry about the vertical axis are examined for bifurcating oscillatory solutions. The system behavior depends on two parameters, $\rho $, the flow velocity and $\beta$, the mass ratio of the fluid and the tube. As the flow rate is increased past a critical value, the zero solution becomes unstable by a double pair of complex conjugate eigenvalues of the linearized operator crossing the imaginary axis. Using ideas from the center manifold theory and the method of integral averaging, the governing partial differential equations are reduced to a set of four nonlinear ordinary differential equations. It is then shown that the system bifurcates into two qualitatively distinct oscillatory motions. These oscillatory solutions themselves, for some values of the mass ratio $\beta$, bifurcate into more complex amplitude modulated oscillations.