gebhart/patrepeval huggingface dataset:
Complement-dependent cytotoxic antibodies to human T lymphotropic virus type I (HTLV-I)-infected cells in the sera of HTLV-I-infected individuals (1996)

Abstract To investigate whether HTLV-I induces the development of complement-dependent cytotoxic antibodies in humans, sera of asymptomatic HTLV-I carriers and of patients suffering from tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM) or adult T cell leukaemia (ATL) were used in a cytotoxicity assay against a panel of target cells. This panel included uninfected cell lines (CEM, Jurkat, Molt and H9), cell lines chronically infected with HTLV-I (MT2, MT4, C91PL and HUT102), as well as lines H36 (H9 infected with HTLV-I), H9-IIIB (H9 infected with HIVIIIB) and H9-MN (H9 infected with HIVMN). HTLV-I+ sera induced lysis of H36 and of lines expressing HTLV-I antigens in the presence of rabbit complement, but did not lyse cells in presence of human complement. The HTLV-I+ sera also failed to lyse the HTLV-I− lines and H9 cells, suggesting that lysis was specific for HTLV-I. H36 cell lysis was prevented by IgG depletion of the sera and by dialysis of rabbit complement against EGTA or EDTA. Rabbit complement-dependent cytotoxic antibodies were present in the sera of 14/14 HTLV-I-infected individuals; the highest titres were predominantly found in the sera of the TSP/HAM patients. Such antibodies were also detected in 5/5 individuals coinfected with HIV-1 and HTLV-I, although no cytotoxic antibody could be found against HIV-infected cells. Vice versa, sera of HIV-1-infected individuals did not exert a lytic effect in the presence of complement (of human or rabbit origin) against HIV-1- or HTLV-I-infected cells. Incubation of the sera of four HTLV-I-infected patients with HTLV-I env-specific synthetic peptides demonstrated that some of the complement-dependent cytotoxic antibodies recognized epitopes located on gp46 between amino acids 190 and 209. There is no correlation of rabbit complement-dependent cytotoxic HTLV-I antibodies with the development of disease.
Adhesion of Shewanella oneidensis MR-1 to Iron (Oxy)(Hydr)Oxides: Microcolony Formation and Isotherm (2010)

The adhesion of dissimilatory metal reducing bacteria (DMRB) to iron (oxy)(hydr)oxides may play an important role in their respiration on ferric iron-containing minerals, but few quantitative surface cell density measurements have been made thus far. We used confocal microscopy to examine the adhesion of a common DMRB species, Shewanella oneidensis MR-1, onto iron (oxy)(hydr)oxide particulate-coated glass slides across a broad range of bulk (i.e., solution phase) cell densities from 10(5) cells/mL to 2 x 10(9) cells/mL. At bulk cell densities less than 1 x 10(7) cells/mL, cells adhered to the slide surface formed an evenly distributed, homogeneous monolayer, while at the bulk cell densities higher than 2 x 10(8) cells/mL the adhered cells formed distinct microcolonies. As a result of this complex adhesion behavior, simple Langmuir or Freundlich adsorption isotherms do not capture the relationship between the surface cell density and the bulk cell density over the entire range of bulk cell densities. Thus a new, two-step isotherm was developed that incorporated both isolated attached cells at low cell densities as well as microcolonies at higher cell densities.
First measurement using a nuclear emulsion detector of theνμcharged-current cross section on iron around the 1 GeV energy region (2021)

Abstract We have carried out $\nu_{\mu}$ charged-current interaction measurement on iron using an emulsion detector exposed to the T2K neutrino beam in the J-PARC neutrino facility. The data samples correspond to $4.0 \times 10^{19}$ protons on target, and the neutrino mean energy is 1.49 GeV. The emulsion detector is suitable for precision measurements of charged particles produced in neutrino–iron interactions with a low momentum threshold thanks to a thin-layered structure and sub-$\mu$m spatial resolution. The charged particles are successfully detected, and their multiplicities are measured using the emulsion detector. The cross section was measured to be $\sigma^{\mathrm{Fe}}_{\mathrm{CC}} = (1.28 \pm 0.11({\mathrm{stat.}})^{+0.12}_{-0.11}({\mathrm{syst.}})) \times 10^{-38} \, {\mathrm{cm}}^{2}/{\mathrm{nucleon}}$. The cross section in a limited kinematic phase space of induced muons, $\theta_{\mu} &amp;lt; 45^{\circ}$ and $p_{\mu} &amp;gt; 400 \, {\rm MeV}/c$, on iron was $\sigma^{\mathrm{Fe}}_{\mathrm{CC \hspace{1mm} phase \hspace{0.5mm} space}} = (0.84 \pm 0.07({\mathrm{stat.}})^{+0.07}_{-0.06}({\mathrm{syst.}})) \times 10^{-38} \, {\mathrm{cm}}^{2}/{\mathrm{nucleon}}$. The cross-section results are consistent with previous values obtained via different techniques using the same beamline, and they are reproduced well by current neutrino interaction models. These results demonstrate the capability of the detector in the detailed measurement of neutrino–nucleus interactions around the 1 GeV energy region.
Polypharmacologicalin SilicoBioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat (2017)

In this work, we describe the computational ("in silico") mode-of-action analysis of CNS-active drugs, which is taking both multiple simultaneous hypotheses as well as sets of protein targets for each mode-of-action into account, and which was followed by successful prospective in vitro and in vivo validation. Using sleep-related phenotypic readouts describing both efficacy and side effects for 491 compounds tested in rat, we defined an "optimal" (desirable) sleeping pattern. Compounds were subjected to in silico target prediction (which was experimentally confirmed for 21 out of 28 cases), followed by the utilization of decision trees for deriving polypharmacological bioactivity profiles. We demonstrated that predicted bioactivities improved classification performance compared to using only structural information. Moreover, DrugBank molecules were processed via the same pipeline, and compounds in many cases not annotated as sedative-hypnotic (alcaftadine, benzatropine, palonosetron, ecopipam, cyproheptadine, sertindole, and clopenthixol) were prospectively validated in vivo. Alcaftadine, ecopipam cyproheptadine, and clopenthixol were found to promote sleep as predicted, benzatropine showed only a small increase in NREM sleep, whereas sertindole promoted wakefulness. To our knowledge, the sedative-hypnotic effects of alcaftadine and ecopipam have not been previously discussed in the literature. The method described extends previous single-target, single-mode-of-action models and is applicable across disease areas.
ChemInform Abstract: Towards Tumor Targeting with Copper‐Radiolabeled Macrocycle‐Antibody Conjugates: Synthesis, Antibody Linkage, and Complexation Behavior. (1990)

Abstract A set of four macrocyclic ligands (I) and (II) bearing aminomethylphenyl units to facilitate linkage to a monoclonal antibody via acylation with the thiol‐specific vinyl‐pyridine linker molecule (III) is prepared.
Data from Synergistic Targeting of PI3K/AKT Pathway and Androgen Receptor Axis Significantly Delays Castration-Resistant Prostate Cancer Progression <i>In Vivo</i> (2023)

&lt;div&gt;Abstract&lt;p&gt;The progression to castration-resistant prostate cancer (CRPC) correlates with gain-of-function of the androgen receptor (AR) and activation of AKT. However, as single agents, AR or AKT inhibitors result in a reciprocal feedback loop. Therefore, we hypothesized that combination of an AKT inhibitor with an antiandrogen might result in a more profound, long-lasting remission of CRPC. Here, we report that the AKT inhibitor AZD5363 potently inhibits proliferation and induces apoptosis in prostate cancer cell lines expressing the AR and has anticancer activity &lt;i&gt;in vivo&lt;/i&gt; in androgen-sensitive and castration-resistant phases of the LNCaP xenograft model. However, we found that the effect of castration-resistant tumor growth inhibition and prostate-specific antigen (PSA) stabilization is transient and resistance occurs with increasing PSA after approximately 30 days of treatment. Mechanistically, we found that single agent AZD5363 induces increase of AR binding to androgen response element, AR transcriptional activity, and AR-dependent genes such as PSA and NKX3.1 expression. These effects were overcome by the combination of AZD5363 with the antiandrogen bicalutamide, resulting in synergistic inhibition of cell proliferation and induction of apoptosis &lt;i&gt;in vitro&lt;/i&gt;, and prolongation of tumor growth inhibition and PSA stabilization in CRPC &lt;i&gt;in vivo&lt;/i&gt;. This study provides a preclinical proof-of-concept that combination of an AKT inhibitor with antiandrogen results in prolonged disease stabilization in a model of CRPC. &lt;i&gt;Mol Cancer Ther; 12(11); 2342–55. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
SPAD imagers for super resolution localization microscopy enable analysis of fast fluorophore blinking (2017)

sCMOS imagers are currently utilized (replacing EMCCD imagers) to increase the acquisition speed in super resolution localization microscopy. Single-photon avalanche diode (SPAD) imagers feature frame rates per bit depth comparable to or higher than sCMOS imagers, while generating microsecond 1-bit-frames without readout noise, thus paving the way to in-depth time-resolved image analysis. High timing resolution can also be exploited to explore fluorescent dye blinking and other photophysical properties, which can be used for dye optimization. We present the methodology for the blinking analysis of fluorescent dyes on experimental data. Furthermore, the recent use of microlenses has enabled a substantial increase of SPAD imager overall sensitivity (12-fold in our case), reaching satisfactory values for sensitivity-critical applications. This has allowed us to record the first super resolution localization microscopy results obtained with a SPAD imager, with a localization uncertainty of 20 nm and a resolution of 80 nm.
Micromachined relay which utilizes single crystal silicon electrostatic actuator (1999)

A MMR which utilizes a single crystal silicon based electrostatic actuator is presented in this paper. The MMR is fabricated by critical-dimensions-controllable SOI-A/B (Anodic bonding) process. Size of the MMR is 2.0 mm/spl times/2.5 mm and driving voltage is 24 V. Hot-switching tests with 10 V-10 mA resistive load were performed 10/sup 6/ cycles with around 0.5 ohm relay resistance (sum. of signal line resistance, contact resistance and package resistance). Breakdown voltage (stand off voltage) is larger than 200 V. Switching time was around 03 msec and power consumption was less than 0.05 mW.
Leveraging complexity in software for cybersecurity (2009)

A method for assessing statistically quantifiable improvements in security for software vulnerabilities is presented. Drawing on concepts in complexity theory, undecidability, and previous work in high-reliability systems, we show that ensembles of similar implementations have statistical value even though each by itself is inscrutable. Research questions are identified that may allow practical application of these concepts.
Remote Substitution on N-Heterocyclic Carbenes Heightens the Catalytic Reactivity of Their Palladium Complexes (2011)

A new series of exceptionally bulky N-heterocyclic carbene (NHC) ligands is based on 1,3-bis-2′,6′-diisopropylphenylimidazol-2-ylidene (IPr), through substitution of large groups at the para (4′) position of the aryl rings. π-Cinnamylpalladium chloride complexes with these ligands are precatalysts for Suzuki–Miyaura coupling. Large triarylmethyl substituents at the 4′ position of the NHC give significantly greater catalyst activity. Although the %Vbur parameter has been proposed as a general measure of the size of bulky ligands, the sterically induced enhancement of the catalytic rate does not correlate with the %Vbur parameter; instead, solid angles are more useful in quantifying the differences between ligands because they account for bulk more distant from the metal. Overall, these results show that the use of distant steric hindrance can have a distinct positive influence on catalytic ability.
[Determination of ecdysterone in Achyranthes bidentata Bl. and its activity promoting proliferation of osteoblast-like cells]. (2000)

Ecdysterone was screened quickly by cultivating with OB-like cells together in vitro. The HPLC method is accurate, fast and reproducible for the determination of ecdysterone in AB.
Pulmonary uptake of liposomal phosphatidylcholine upon intratracheal administration to rats. (1982)

Liposomes composed of dipalmitoylphosphatidylcholine (DPPC) labeled with L-α-[dipalmitoyl-1-<SUP>14</SUP>C]-phosphatidylcholine ([<SUP>14</SUP>C]-DPPC) and cholesterol (molar ratio 7 : 2) were injected into rats intratracheally. The lungs took up about 90% of administered [<SUP>14</SUP>C]-DPPC and 50% of liposomal DPPC was retained for over 24 h. In contrast, uptake by the liver and kidney after intravenous administration was high and uptake by the lung was negligible. Uptake of [<SUP>14</SUP>C]-DPPC by lung lamellar bodies was higher than that by other lung subcellular fractions (mitochondria, microsomes and soluble fractions). From the results of histochemical investigation, it was found that the liposomes were taken up uniformly by the lung.
[A case report of pleural involvement in primary macroglobulinemia]. (1990)

A case of primary macroglobulinemia with pleural and gastric involvement was presented. A 48-year-old female was admitted with productive cough. On physical examination neither lymphoadenopathy nor hepatosplenomegaly were found. In addition, no bleeding tendency nor disturbance of the visual acuity were detected. Her chest roentgenogram showed a moderate amount of pleural effusion in the left pleural cavity without infiltration in the lung fields and no evidence of swollen hilar or mediastinal lymphnodes. A monoclonal M-band of to IgM-kappa type was observed in her serum and the pleural effusion. The diffuse ulcerative lesion in the gastric mucosa was detected by gastrofiberscopy. The lymphoid cells taken from the pleural effusion and the gastric mucosa stained positively with fluorescein-conjugated antiserum to u or the kappa chain. Pleural effusion and gastric infiltration of lymphoid cells improved remarkably following ACOP therapy.
Parámetros genéticos y respuesta a la selección en una población de gallinas de raza castellana negra (2006)

Se presentan los resultados de un programa de mejora genética en tres generaciones de una población de gallinas de la raza Castellana Negra, encaminado a la posible obtención de productos diferenciados. La selección se ha realizado para el peso vivo, la puesta y el peso del huevo. La heredabilidad aparece elevada para el peso vivo (0,83) y el peso del huevo (0,69) y baja para la puesta (0,21). La correlación genética es alta y positiva para el peso vivo con el peso del huevo (0,68), bajas y negativas para el peso vivo con la puesta (-0,15) y para la puesta con el peso del huevo (-0,18). El progreso genético se estima positivo en todos los caracteres, siendo el peso vivo el carácter con mayor progreso genético (198,44 g).
Conidial Dihydroxynaphthalene Melanin of the Human Pathogenic Fungus Aspergillus fumigatus Interferes with the Host Endocytosis Pathway (2011)

Aspergillus fumigatus is the most important air-borne fungal pathogen of humans. The interaction of the pathogen with the host's immune system represents a key process to understand pathogenicity. For elimination of invading microorganisms, they need to be efficiently phagocytosed and located in acidified phagolysosomes. However, as shown previously, A. fumigatus is able to manipulate the formation of functional phagolysosomes. Here, we demonstrate that in contrast to pigmentless pksP mutant conidia of A. fumigatus, the gray-green wild-type conidia inhibit the acidification of phagolysosomes of alveolar macrophages, monocyte-derived macrophages, and human neutrophil granulocytes. Therefore, this inhibition is independent of the cell type and applies to the major immune effector cells required for defense against A. fumigatus. Studies with melanin ghosts indicate that the inhibitory effect of wild-type conidia is due to their dihydroxynaphthalene (DHN)-melanin covering the conidia, whereas the hydrophobin RodA rodlet layer plays no role in this process. This is also supported by the observation that pksP conidia still exhibit the RodA hydrophobin layer, as shown by scanning electron microscopy. Mutants defective in different steps of the DHN-melanin biosynthesis showed stronger inhibition than pksP mutant conidia but lower inhibition than wild-type conidia. Moreover, A. fumigatus and A. flavus led to a stronger inhibition of phagolysosomal acidification than A. nidulans and A. terreus. These data indicate that a certain type of DHN-melanin that is different in the various Aspergillus species, is required for maximal inhibition of phagolysosomal acidification. Finally, we identified the vacuolar ATPase (vATPase) as potential target for A. fumigatus based on the finding that addition of bafilomycin which inhibits vATPase, led to complete inhibition of the acidification whereas the fusion of phagosomes containing wild-type conidia and lysosomes was not affected.
Getting clever about shared services (2012)

Reduced costs and increased efficiency are the big sell of public sector Shared Services, but the benefits can fast evaporate when leadership and cultural obstacles arise. Former senior public servant Greg Field opens the bonnet to examine what works well - and what doesn't.
<title>Crack and damage assessment in concrete and polymer matrices using liquids released internally from hollow optical fibers</title> (1996)

This was an investigation into the feasibility of using liquid core optical fibers for the detection and self repair of cracking in cement or polymer materials generated by dynamic or static loading. These experiments relied on our current research sponsored by the National Science Foundation. That work on the concept of internal adhesive delivery from hollow fibers for repair was here combined with the nondestructive fiber optic analysis of crack location and volume. The combination of the ability to remotely measure crack occurrence in real time and determine the location and volume of crack damage in the matrix is unique in the field of optic sensors. The combination of this with crack repair, rebonding of any detached or broken fibers, and replenishment of liquid core chemicals, when necessary, make this a potentially powerful sensing and repair tool. Work on this research topic was sponsored by the University of Illinois.
Highly efficient video compression using quadtree structures and improved techniques for motion representation and entropy coding (2010)

This paper describes a novel video coding scheme that can be considered as a generalization of the block-based hybrid video coding approach of H.264/AVC. While the individual building blocks of our approach are kept simple similarly as in H.264/AVC, the flexibility of the block partitioning for prediction and transform coding has been substantially increased. This is achieved by the use of nested and pre-configurable quadtree structures, such that the block partitioning for temporal and spatial prediction as well as the space-frequency resolution of the corresponding prediction residual can be adapted to the given video signal in a highly flexible way. In addition, techniques for an improved motion representation as well as a novel entropy coding concept are included. The presented video codec was submitted to a Call for Proposals of ITU-T VCEG and ISO/IEC MPEG and was ranked among the five best performing proposals, both in terms of subjective and objective quality.
Factors affecting the open-circuit voltage and electrode kinetics of some iron/titanium redox flow cells (1977)

Performance of the iron-titanium redox flow cell was studied as a function of acid concentration. Anion permeable membranes separated the compartments. Electrodes were graphite cloth. Current densities ranged up to 25 mA/square centimeter. Open-circuit and load voltages decreased as the acidity was increased on the iron side as predicted. On the titanium side, open-circuit voltages decreased as the acidity was increased in agreement with theory, but load voltages increased due to decreased polarization with increasing acidity. High acidity on the titanium side coupled with low acidity on the iron side gives the best load voltage, but such cells show voltage losses as they are repeatedly cycled. Analyses show that the bulk of the voltage losses are due to diffusion of acid through the membrane.
Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma (2017)

A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both infants and adults, but in different proportions. OTUs from the five genera highlighted (*) above defined the nasopharyngeal core microbiome at the 95% level. No significant differences in alpha- and beta-diversity were observed between seasons, but bacterial mean relative proportions of Haemophilus, Moraxella, Staphylococcus and Corynebacterium varied significantly between summer-fall and age groups (inter-patient variation). Additionally, OTUs varied significantly within patients between time points in 35 of the 40 patients analyzed. Future cross-sectional studies should be mindful of the temporal dynamics of the nasopharyngeal microbiota.
Turbulence Organization and Mean Profile Shapes in the Stably Stratified Boundary Layer: Zones of Uniform Momentum and Air Temperature (2022)

Abstract A persistent spatial organization of eddies is identified in the lowest portion of the stably stratified planetary boundary layer. The analysis uses flow realizations from published large-eddy simulations (Sullivan et al. in J Atmos Sci 73(4):1815–1840, 2016) ranging in stability from near-neutral to almost z-less stratification. The coherent turbulent structure is well approximated as a series of uniform momentum zones (UMZs) and uniform temperature zones (UTZs) separated by thin layers of intense gradients that are significantly greater than the mean. This pattern yields stairstep-like instantaneous flow profiles whose shape is distinct from the mean profiles that emerge from long-term averaging. However, the scaling of the stairstep organization is closely related to the resulting mean profiles. The differences in velocity and temperature across the thin gradient layers remain proportional to the surface momentum and heat flux conditions regardless of stratification. The vertical thickness of UMZs and UTZs is proportional to height above the surface for near-neutral and weak stratification, but becomes thinner and less dependent on height as the stability increases. Deviations from the logarithmic mean profiles for velocity and temperature observed under neutral conditions are therefore predominately due to the reduction in eddy size with increasing stratification, which is empirically captured by existing Monin–Obukhov similarity relations for momentum and heat. The zone properties are additionally used to explain trends in the turbulent Prandtl number, thus providing a connection between the eddy organization, mean profiles, and turbulent diffusivity in stably stratified conditions.