gebhart/patrepeval huggingface dataset:
Isolation and characterization of a retinal pigment epithelial cell fluorophore: An <i>all-trans</i> -retinal dimer conjugate (2005)

Several lines of investigation suggest that the nondegradable fluorophores that accumulate as lipofuscin in retinal pigment epithelium (RPE) cells contribute to the etiology of macular degeneration. Despite evidence that much of this fluorescent material may originate as inadvertent products of the retinoid cycle, the enzymatic pathway by which the 11-cis-retinal chromophore of rhodopsin is generated, the only fluorophores of the RPE to be characterized as yet have been A2E and its isomers. Here, we report the isolation and structural characterization of an additional RPE lipofuscin fluorophore that originates as a condensation product of two molecules of all-trans-retinal (ATR) dimer and forms a protonated Schiff base conjugate with phosphatidylethanolamine (PE), the latter conjugate (ATR dimer-PE) having UV-visible absorbance maxima at 285 and 506 nm. ATR dimer was found to form natively in bleached rod outer segments in vitro and when rod outer segments were incubated with ATR. HPLC analysis of eye-cups that included RPE and isolated neural retina from Abcr-/- mice and RPE isolated from human donor eyes revealed the presence of a pigment with the same UV-visible absorbance and retention time as synthetic ATR dimer-PE conjugate. Evidence that ATR dimer undergoes a photooxidation process involving the addition of oxygens at double bonds as well as an aromatic demethylation also may indicate a role for this molecule, or its derivatives, in the photoreactivity of RPE lipofuscin.
<title>Architecture And Applications Of The HEP Multiprocessor Computer System</title> (1982)

The HEP computer system is a large scale scientific parallel computer employing shared-resource MIMD architecture. The hardware and software facilities provided by the system are described, and techniques found to be useful in programming the system are also discussed.
Molecular Characterization of<i>Campylobacter jejuni</i>Clones: A Basis for Epidemiologic Investigation (2002)

A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region. We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.
Hydrophobicity of protein surfaces: Separating geometry from chemistry (2008)

To better understand the role of surface chemical heterogeneity in natural nanoscale hydration, we study via molecular dynamics simulation the structure and thermodynamics of water confined between two protein-like surfaces. Each surface is constructed to have interactions with water corresponding to those of the putative hydrophobic surface of a melittin dimer, but is flattened rather than having its native "cupped" configuration. Furthermore, peripheral charged groups are removed. Thus, the role of a rough surface topography is removed, and results can be productively compared with those previously observed for idealized, atomically smooth hydrophilic and hydrophobic flat surfaces. The results indicate that the protein surface is less hydrophobic than the idealized counterpart. The density and compressibility of water adjacent to a melittin dimer is intermediate between that observed adjacent to idealized hydrophobic or hydrophilic surfaces. We find that solvent evacuation of the hydrophobic gap (cavitation) between dimers is observed when the gap has closed to sterically permit a single water layer. This cavitation occurs at smaller pressures and separations than in the case of idealized hydrophobic flat surfaces. The vapor phase between the melittin dimers occupies a much smaller lateral region than in the case of the idealized surfaces; cavitation is localized in a narrow central region between the dimers, where an apolar amino acid is located. When that amino acid is replaced by a polar residue, cavitation is no longer observed.
Interaction and presentation techniques for shake menus in tangible augmented reality (2009)

Menus play an important role in both information presentation and system control. We explore the design space of shake menus, which are intended for use in tangible augmented reality. Shake menus are radial menus displayed centered on a physical object and activated by shaking that object. One important aspect of their design space is the coordinate system used to present menu options. We conducted a within-subjects user study to compare the speed and efficacy of several alternative methods for presenting shake menus in augmented reality (world-referenced, display-referenced, and object-referenced), along with a baseline technique (a linear menu on a clipboard). Our findings suggest tradeoffs amongst speed, efficacy, and flexibility of interaction, and point towards the possible advantages of hybrid approaches that compose together transformations in different coordinate systems. We close by describing qualitative feedback from use and present several illustrative applications of the technique.
Characterization, localization and distribution of alpha1 adrenoceptor subtype in male rabbit urethra. (1998)

The pharmacological characterization demonstrates the predominance of alpha1A or alpha1A + alpha1B adrenoceptor subtype(s) in male rabbit urethral smooth muscle. Furthermore, the autoradiographic and immunohistochemical studies show a heterogeneous distribution of alpha1 adrenoceptors along the longitudinal axis of the urethra, within the smooth muscle fibers, with the receptors being localized more densely in the proximal than in the distal urethra.
Vascular wall von Willebrand factor in human diabetic retinopathy. (1994)

These observations are compatible with the occurrence in diabetes of the slow release of endothelial vWf through the pathway of vWf secretion not linked to synthesis, ie, the regulated pathway.
L-663,536 (MK-886) (3-[1-(4-chlorobenzyl)-3-<i>t</i>-butyl-thio-5-isopropylindol-2-yl]-2,2-dimethylpropanoic acid), a novel, orally active leukotriene biosynthesis inhibitor (1989)

L-663,536 (3-[1-(4-chlorobenzyl)-3-t-butyl-thio-5-isopropylindol-2-yl]-2, 2-dimethylpropanoic acid) is a potent inhibitor of leukotriene (LT) biosynthesis in intact human polymorphonuclear leukocytes (PMN) (IC50, 2.5 nM). Similarly, L-663,536 inhibited A23187-induced LTB4 formation by rat peripheral blood and elicited PMN. At concentrations where inhibition of leukotriene biosynthesis occurred in human whole blood (1.1 microM), no effect was seen on cyclooxygenase or 12-lipoxygenase, an effect also observed in washed human platelets. The compound had no effect on rat or porcine 5-lipoxygenase indicating that L-663,536 is not a direct 5-lipoxygenase inhibitor. When administered in vivo L-663,536 was a potent inhibitor of antigen-induced dyspnea in inbred rats pretreated with methysergide (ED50, 0.036 mg/kg p.o.) and of Ascaris-induced bronchoconstriction in squirrel monkeys (1 mg/kg p.o.). The compound inhibited leukotriene biosynthesis in vivo in a rat pleurisy model (ED50, 0.2 mg/kg p.o.), an inflamed rat paw model (ED50, 0.8 mg/kg), a model of leukotriene excretion in rat bile following antigen provocation, and a model in the guinea-pig ear where leukotriene synthesis was induced by topical challenge with ionophore A23187 (ED50, 2.5 mg/kg p.o. and 0.6 micrograms topically). The results indicate that L-663,536 is a potent inhibitor of leukotriene biosynthesis both in vitro and in vivo indicating that the compound is suitable for studying the role of leukotrienes in a variety of pathological situations.
Pamidronate and 1,24(S)-dihydroxyvitamin D2 synergistically inhibit the growth of myeloma, breast and prostate cancer cells. (2005)

Combined dosing of pamidronate and 1,24(OH)2D2 may have therapeutic value for the treatment of multiple myeloma, prostate and breast cancers.
A nondestructive integrity test for membrane filters based on air-coupled ultrasonic spectroscopy (2003)

This work describes the application of an ultrasonic air-coupled characterization technique to membrane filters. Coefficient of transmission of sound at normal incidence through each membrane in the frequency range 0.55 MHz-2.4 MHz was measured. For all cases, at least one thickness resonance was observed. From these measurements density, velocity, and attenuation of ultrasonic longitudinal waves are calculated and compared to available filtration data such as water flux measurements and bubble point data, both provided by manufacturers. Results show that velocity of ultrasonic waves in membrane filters depends on the membrane grade and can be correlated to filtration properties; attenuation per wavelength is independent of membrane grade but sensitive to moisture content. Advantages of this technique over other conventional membrane tests are pointed out.
Volatile organic compounds emitted after leaf wounding: On‐line analysis by proton‐transfer‐reaction mass spectrometry (1999)

Volatile organic compounds (VOCs) released from vegetation, including wound‐induced VOCs, can have important effects on atmospheric chemistry. The analytical methods for measuring wound‐induced VOCs, especially the hexenal family of VOCs (hexenals, hexenols, and hexenyl esters), are complicated by their chemical instability and the transient nature of their formation after leaf and stem wounding. Here we demonstrate that formation and emission of hexenal family compounds can be monitored on‐line using proton‐transfer‐reaction mass spectrometry (PTR‐MS), avoiding the need for preconcentration or chromatography. These measurements allow direct analysis of the rapid emission of the parent compound, ( Z )‐3‐hexenal, within 1–2 s of wounding of aspen leaves and then its disappearance and the appearance of its metabolites including ( E )‐2‐hexenal, hexenols, and hexenyl acetates. Similar results were seen in wounded beech leaves and clover. The emission of hexenal family compounds was proportional to the extent of wounding, was not dependent on light, occurred in attached or detached leaves, and was greatly enhanced as detached leaves dried out. Emission of ( Z )‐3‐hexenal from detached drying aspen leaves averaged 500 μg C g −1 (dry leaf weight). Leaf wound compounds were not emitted in a nitrogen atmosphere but were released within seconds of reintroduction of oxygen; this indicates that there are not large pools of hexenyl compounds in leaves. The PTR‐MS method also allows the simultaneous detection of less abundant hexanal family VOCs including hexanal, hexanol, and hexyl acetate and VOCs formed in the light (isoprene) or during anoxia (acetaldehyde). PTR‐MS may be a useful tool for the analysis of VOC emissions resulting from grazing, herbivory, and other physical damage to vegetation, from harvesting of crops, and from senescing leaves.
Effect of neoadjuvant chemotherapy on tumor-infiltrating lymphocytes and PD-L1 expression in breast cancer and its clinical significance (2017)

Increase in stromal TILs in residual cancer compared to pretreatment tissue is associated with improved recurrence-free survival. Despite a trend for increasing TIL counts, PD-L1 expression decreased in residual disease compared to pretreatment samples.
Reduced oxygen availability during high intensity intermittent exercise impairs performance (1994)

This study examined the influence of reduced oxygen availability on the ability to perform repeated bouts of high intensity exercise on a cycle ergometer. Seven male physical education students performed 10 exercise bouts (of 6 s each), interspersed with 30-s recovery periods, under hypoxic and normoxic conditions. The hypoxic condition was carried out in a low pressure chamber at 526 mmHg. Subjects were instructed to try to maintain a target pedalling speed of 140 rev min-1 during each exercise period. The mean power output of the first exercise bout was approximately 950 W. In both experimental conditions, all subjects were able to maintain the target speed for the first 3 s of each of the 10 exercise bouts. During the last 3-s interval of each exercise period the target speed was not maintained in both conditions over the 10 sprints. However, the reduction was greater in the hypoxic condition (P < 0.05). Post-exercise blood lactate accumulation was higher with hypoxia [10.3 (0.7) vs. 8.5 (0.8) mmol l-1, P < 0.05]. Oxygen uptake, measured during the exercise and recovery periods of sprints 6-9, was lower in the hypoxic condition [3.03 (0.2) vs. 3.19 (0.2) 1 min-1, P < 0.05]. These results indicate that a reduction in oxygen availability during high intensity intermittent exercise results in a higher accumulation of blood lactate and a lower oxygen uptake. The ability to maintain a high power output is impaired.
Analysis of Flavin Oxidation and Electron-Transfer Inhibition in <i>Plasmodium falciparum</i> Dihydroorotate Dehydrogenase (2008)

Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH) is a flavin-dependent mitochondrial enzyme that provides the only route to pyrimidine biosynthesis in the parasite. Clinically significant inhibitors of human DHODH (e.g., A77 1726) bind to a pocket on the opposite face of the flavin cofactor from dihydroorotate (DHO). This pocket demonstrates considerable sequence variability, which has allowed species-specific inhibitors of the malarial enzyme to be identified. Ubiquinone (CoQ), the physiological oxidant in the reaction, has been postulated to bind this site despite a lack of structural evidence. To more clearly define the residues involved in CoQ binding and catalysis, we undertook site-directed mutagenesis of seven residues in the structurally defined A77 1726 binding site, which we term the species-selective inhibitor site. Mutation of several of these residues (H185, F188, and F227) to Ala substantially decreased the affinity of pfDHODH-specific inhibitors (40-240-fold). In contrast, only a modest increase in the Kmapp for CoQ was observed, although mutation of Y528 in particular caused a substantial reduction in kcat (40-100-fold decrease). Pre-steady-state kinetic analysis by single wavelength stopped-flow spectroscopy showed that the mutations had no effect on the rate of the DHO-dependent reductive half-reaction, but most reduced the rate of the CoQ-dependent flavin oxidation step (3-20-fold decrease), while not significantly altering the Kdox for CoQ. As with the mutants, inhibitors that bind this site block the CoQ-dependent oxidative half-reaction without affecting the DHO-dependent step. These results identify residues involved in inhibitor binding and electron transfer to CoQ. Importantly, the data provide compelling evidence that the binding sites for CoQ and species-selective site inhibitors do not overlap, and they suggest instead that inhibitors act either by blocking the electron path between flavin and CoQ or by stabilizing a conformation that excludes CoQ binding.
Content Contribution for Revenue Sharing and Reputation in Social Media: A Dynamic Structural Model (2012)

This study examines the incentives for content contribution in social media. We propose that exposure and reputation are the major incentives for contributors. Besides, as more and more social media Web sites offer advertising-revenue sharing with some of their contributors, shared revenue provides an extra incentive for contributors who have joined revenue-sharing programs. We develop a dynamic structural model to identify a contributor's underlying utility function from observed contribution behavior. We recognize the dynamic nature of the content-contribution decision—that contributors are forward-looking, anticipating how their decisions affect future rewards. Using data collected from YouTube, we show that content contribution is driven by a contributor's desire for exposure, revenue sharing, and reputation and that the contributor makes decisions dynamically.
Chromophore-Labeled Dendrons as Light Harvesting Antennae (1996)

A novel series of polyether dendrimer segments (dendrons) end-capped with pyrenyl, naphthyl, or methyl groups has been prepared by a convergent growth method. Steady-state fluorescence measurements indicate the absence of intramolecular naphthalene excimer in the naphthyl-capped dendrons. However, in the pyrenyl-capped dendrons, excimer emission predominates. Fluorescence from both the naphthyl monomer and pyrenyl excimer are quenched when a suitable electron donor (e.g., a 3-[dimethylamino]phenoxy group) is covalently attached at the dendron focal point. No sensitized emission from the dendron backbone is observed in the chromophore-labeled dendrons, although the control methyl-capped dendron fluoresces weakly at 310 nm when excited at 284 nm. Absorption and fluorescence spectra, fluorescence quantum yields, and fluorescence lifetimes for the chromophore-labeled dendrons are reported.
Preparation of Encapsulated Microbial Cells for Environmental Applications (1992)

An improved method for the encapsulation of bacteria into microspheres of alginate, agarose, or polyurethane is described. Cell suspensions were passed through a low-pressure nozzle into an aqueous phase where matrix polymerization or gelation yielded beads 2 to 50 mum in diameter. Trials with a chlorophenol-degrading Flavobacterium species showed that cells entrapped by these procedures were as catabolically active as free cells. These types of beads should have numerous applications in the fields of environmental science and engineering.
Criteria for Cure of Acromegaly: A Consensus Statement  (2000)

In February 1999, a workshop was held in Cortina, Italy to develop a consensus defining the criteria for cure of acromegaly. The workshop was sponsored by the University of Brescia and hosted by the Italian Society of Endocrinology. Invited international participants included endocrinologists, neurosurgeons, and radiotherapists skilled in the management of acromegaly. This statement summarizes the consensus achieved in these discussions.
Impact of chemokine receptor CXCR3 on tumor-infiltrating lymphocyte recruitment associated with favorable prognosis in advanced gastric cancer. (2015)

Chemokine receptor CXCR3 has been proved to play an important role in tumorigenesis and tumor progression in many malignancies, but its precise efficacy on gastric cancer (GC) has not been evaluated yet. The present study was aimed to explore the correlation of chemokine receptor CXCR3 with tumor-infiltrating lymphocytes (TILs) and prognosis in advanced gastric cancer (GC). Expression of CXCR3 and CD4+, CD8+ TILs was conducted in 192 advanced GC specimens and 48 corresponding paracancerous tissues by immunohistochemical (IHC) analysis. CXCR3 expression in GC tissues was significantly higher than that in paracancerous tissues (P<0.001) and CD8+, CD4+ TILs infiltration increased with high CXCR3 expression (P=0.032 and P<0.001, respectively). Our study showed significantly lower CXCR3 expression in patients with greater tumor invasion depth and lymph node metastasis compared with patients with lesser tumor invasion depth and without lymph node metastasis (P=0.002 and P=0.001, respectively). Univariate analysis indicated that patients with high CXCR3 expression and high CD8+ TILs infiltration had longer overall survival (OS) (log-rank test, P<0.001 and P=0.002, respectively). Univariate and multivariate analyses indicated that CXCR3 expression was an independent prognostic factor for OS (P=0.002). The present study suggested that CXCR3 expression was upregulated in advanced GC and was associated with increased CD4+, CD8+ TILs infiltration and improved OS. Therefore, CXCR3 overexpression is implicated as a favorable prognostic biomarker in human advanced GC.
HIV-1 Tat Alters Neuronal Autophagy by Modulating Autophagosome Fusion to the Lysosome: Implications for HIV-Associated Neurocognitive Disorders (2015)

Antiretroviral therapy has increased the life span of HIV+ individuals; however, HIV-associated neurocognitive disorder (HAND) occurrence is increasing in aging HIV patients. Previous studies suggest HIV infection alters autophagy function in the aging CNS and HIV-1 proteins affect autophagy in monocyte-derived cells. Despite these findings, the mechanisms leading to dysregulated autophagy in the CNS remain unclear. Here we sought to determine how HIV Tat dysregulates autophagy in neurons. Tat caused a dose-dependent decrease in autophagosome markers, microtubule-associated protein-1 light chain β II (LC3II), and sequestosome 1(SQSTM1), in a membrane-enriched fraction, suggesting Tat increases autophagic degradation. Bafilomycin A1 increased autophagosome number, LC3II, and SQSTM1 accumulation; Tat cotreatment diminished this effect. Tat had no effect when 3-methyladenine or knockdown of beclin 1 blocked early stages of autophagy. Tat increased numbers of LC3 puncta and resulted in the formation of abnormal autophagosomes in vitro. Likewise, in vivo studies in GFAP-Tat tg mice showed increased autophagosome accumulation in neurons, altered LC3II levels, and neurodegeneration. These effects were reversed by rapamycin treatment. Tat colocalized with autophagosome and lysosomal markers and enhanced the colocalization of autophagosome with lysosome markers. Furthermore, co-IP studies showed that Tat interacts with lysosomal-associated membrane protein 2A (LAMP2A) in vitro and in vivo, and LAMP2A overexpression reduces Tat-induced neurotoxicity. Hence, Tat protein may induce autophagosome and lysosome fusion through interaction with LAMP2A leading to abnormal neuronal autophagy function and dysregulated degradation of critical intracellular components. Therapies targeting Tat-mediated autophagy alterations may decrease neurodegeneration in aging patients with HAND.
MATERIAL AND THERMAL ANALYSIS OF LASER SINTERTED PRODUCTS (2013)

Abstract Thermal analysis of laser processes can be used to predict thermal stresses and consequently deformation in a completed part. Analysis of temperature is also the basic for feedback of laser processing parameters in manufacturing. The quality of laser sintered parts greatly depends on proper selection of the input processing parameters, material properties and support creation. In order to relatively big heat stress in the built part during sintering process, the thermal simulation and thermal analysis, which could help better understand and solve the issue of parts deformations is very important. Main aim of presented work is to prepare input parameters for thermal simulations by the use of RadTherm software (Thermoanalytics Inc., USA), directly during the sintering process and after the process and find out the impact of the heat stress on a final shape and size of the prototype. Subsequently, an annealing process of constructed products after DMLS could be simulated and specified.