gebhart/patrepeval huggingface dataset:
Transcriptional Activation of the <i>Pirb</i> Gene in B Cells by PU.1 and Runx3 (2011)

Cells in the immune system are regulated positively or negatively by sets of receptor pairs that conduct balanced, activating, or inhibitory intracellular signaling. One such receptor pair termed paired Ig-like receptor (PIR) is composed of the inhibitory PIR-B and its activating isoform, PIR-A. Upon binding to their shared ligand, MHC class I molecules, these receptors control the threshold for immune cell activation. Gene-targeting studies on PIR-B in mice revealed the importance of the inhibition mediated by the PIR-B-MHC interaction in the immune system. Recent studies also revealed the significance of the interaction of PIR-B with neurite outgrowth inhibitors, including Nogo in the CNS. The coordinated regulation by PIR-B and PIR-A is considered to be primarily dependent on their expression balance in cells. However, the mechanism underlying transcriptional control of the genes for PIR-B and PIR-A (Pirb and Pira, respectively) remains to be clarified. In this study, we identified the major cis-acting promoter segment for Pirb and Pira in B cells as the -212 to -117 region upstream from the translation initiation codon. PU.1 and Runx3 were found to bind to this Pirb promoter. Truncation of the PU.1-binding motif significantly reduced the promoter activity, whereas the influence of elimination of the Runx3 site was marginal in B lymphoma BCL1-B20 cells. Unexpectedly, PU.1, but not Runx3, knockdown reduced the levels of both the Pirb and Pira transcripts. We conclude that the major promoter of Pirb, and probably Pira as well, is activated dominantly by PU.1 and marginally by Runx3 in B cells.
Field testing a novel high residence positioning system for monitoring the fine‐scale movements of aquatic organisms (2018)

Acoustic telemetry is an important tool for studying the behaviour of aquatic organisms in the wild.VEMCO high residence (HR) tags and receivers are a recent introduction in the field of acoustic telemetry and can be paired with existing algorithms (e.g. VEMCO positioning system [VPS]) to obtain high-resolution two-dimensional positioning data.Here, we present results of the first documented field test of a VPS composed of HR receivers (hereafter, HR-VPS). We performed a series of stationary and moving trials with HR tags (mean HR transmission period = 1.5 s) to evaluate the precision, accuracy and temporal capabilities of this positioning technology. In addition, we present a sample of data obtained for five European perch <i>Perca fluviatilis</i> implanted with HR tags (mean HR transmission period = 4 s) to illustrate how this technology can estimate the fine-scale behaviour of aquatic animals.Accuracy and precision estimates (median [5th-95th percentile]) of HR-VPS positions for all stationary trials were 5.6 m (4.2-10.8 m) and 0.1 m (0.02-0.07 m), respectively, and depended on the location of tags within the receiver array. In moving tests, tracks generated by HR-VPS closely mimicked those produced by a handheld GPS held over the tag, but these differed in location by an average of ≈9 m.We found that estimates of animal speed and distance travelled for perch declined when positional data for acoustically tagged perch were thinned to mimic longer transmission periods. These data also revealed a trade-off between capturing real nonlinear animal movements and the inclusion of positioning error.Our results suggested that HR-VPS can provide more representative estimates of movement metrics and offer an advancement for studying fine-scale movements of aquatic organisms, but high-precision survey techniques may be needed to test these systems.
Immunohistochemical Analysis of Interleukin-1β–Converting Enzyme/Ced-3 Family Protease, CPP32/Yama/Caspase-3, in Hodgkin's Disease (1997)

The Caenorhabditis elegans cell death gene, Ced-3, encodes a protein homologous to mammalian interleukin-1beta-converting enzyme (ICE), a cysteine protease implicated in programmed cell death (PCD). CPP32, also known as Yama, apopain, and Caspase-3, is a member of this family, has substrate specificities similar to Ced-3, and has been shown to have an active role in PCD. Evidence suggests that these proteases act downstream of inhibitors of PCD such as Bcl-2 and Bcl-x(L), which are frequently expressed in Reed-Sternberg (RS) cells of Hodgkin's disease (HD). To date there have been no studies examining the role of the ICE/Ced-3 family of proteins, in particular CPP32, in HD. We examined 24 cases of HD with a classical immunophenotype and 6 cases of nodular lymphocyte predominant HD (NLPHD) for the expression of CPP32 in the RS cells and lymphohistiocytic (L&H) cells as detected by immunohistochemistry. Twenty two of 24 cases (92%) of HD expressed the protein in the RS cells, whereas the L&H cells in all 6 cases of NLPHD lacked expression of CPP32. These results provide further evidence that NLPHD is a phenotypically different disease distinct from classical forms of HD. The differential expression of the cell death protein CPP32 may be an important factor contributing to the apparently different clinical behaviour of NLPHD in contrast to classical HD. The lack of expression of CPP32 in NLPHD shares similarities with low-grade B-cell non-Hodgkin's lymphomas and may explain their common clinical course. Further studies are required to elucidate the significance of CPP32 in HD.
Assessment of dementia risk in aging adults using both FDG‐PET and FDDNP‐PET imaging (2012)

The FDG-PET data provided independent validation that different patterns of FDDNP-PET binding in non-demented individuals may be associated with differential dementia risk.
Loop Length Model of Fillet Structure (2016)

The loop configuration that is obtained in the knit depends on both qualitative and quantitative factors, the most important of which is the loop length. Thus, it is necessary to have a geometrical model of knitted loop configuration. The aim of this research is to develop loop model for net knit structure with hexagonal cell which is formed by alternation of tricot and chain courses. Vertical ribs of such net structure consist of tricot closed loops of identical configuration while diagonal ribs consist of tricot and chain loops of different type, shape and form. In this study each loop is presented as sum of planar and spatial lines, the length of which can be easily calculated by the well-known formulas. Numerical dependences for loop length calculation are determined as a result of mathematical transformations. To verify the suggested model few variants of fillet warp knit structures were produced from polyester yarn. The investigation showed that theoretical average loop length of repeat corresponds to experimental value. It is concluded that the model can predict geometrical properties of half set two guide bar warp knitted fabric.
Analysis and Optimization of an Adsorption Air Conditioner for Electric Vehicle Applications (1994)

Abstract This paper shows an analysis of the applicability of an adsorption system for electric vehicle (EV) air conditioning. Adsorption systems are designed and optimized to provide the required cooling for four combinations of vehicle characteristics and driving cycles. The resulting adsorption systems are compared with vapor compression air conditioners that can satisfy the cooling load. The objective function is the overall system weight, which includes the cooling system weight and the weight of the battery necessary to provide energy for air conditioner operation. The system with the minimum overall weight is considered to be the best. The results show the optimum values of all the variables, as well as temperatures and amounts adsorbed, for the adsorption and desorption processes. The results indicate that, for the conditions analyzed in this paper, vapor compression air conditioners are superior to adsorption systems, not only because they are lighter, but also because they have a higher COP and are more compact.
Ketone Supplementation Reduces Superoxide Production in Cultured Primary Human Dermal Fibroblasts: Comparison of Young vs Aged Cells (2013)

In the United States, it is estimated that there are 1.8 million new cases of chronic wounds annually, with the majority occurring in the elderly. Reactive oxygen species (ROS) damage is augmented in aged patients leading to redox imbalance and is a key characteristic in impaired wound healing. Ketones are an energy substrate that reduce ROS production in the brain and heart, and thus may augment wound healing. We hypothesized that Beta‐Hydroxybutyrate (BHB; 5mM) would reduce cytosolic and mitochondrial ROS production in both young and aged primary human dermal fibroblasts. Primary human dermal fibroblasts (HDFs, passaged 2–8) from young and aged donors (24 to 88 years) were incubated in the absence or presence of BHB for 72 hours prior to stress with 100uM tert‐buytl‐hydrogen peroxide for 3 hours. ROS production was measured fluorescently with dihydroethidium (DHE, cytosolic) and Mitosox Red (mitochondrial) in triplicate, N=6. In the cytosol, aged HDFs produced 28% (p=&lt;0.001)) more ROS basally compared to their young counterparts. When incubated in BHB for 72 hours, ROS production in the young HDFs decreased by 40% (p=&lt;0.0001) and by 41% (p=&lt;0.0001) in the aged. In the mitochondria, aged HDFs produced 27% (p=&lt;0.0001) more ROS at baseline than the young HDFs, consistent with observations in cytosol. When incubated in BHB, ROS production was reduced in the young by 29% (p&lt;0.0001) and in the aged by 51% (p&lt;0.0001); the aged ROS production was no longer significantly different from the young. Ketone supplementation did not significantly change proliferation in the HDFs, but did increase migration in both young and aged HDFs. We conclude that ketone supplementation may protect against redox stress and augment wound healing, shifting redox homeostasis in HDFs, especially in the elderly. Funding: ONR, VA Merit Review.
Proposition de géométrie d’acquisition de données radar de sol pour la localisation et la caractérisation de réflecteurs plans. Approche 3D en milieu hétérogène (2012)

International audience
Individually Dispersing Single-Walled Carbon Nanotubes with Novel Neutral pH Water-Soluble Chitosan Derivatives (2008)

Chitosan and its various neutral pH water-soluble derivatives were investigated for dispersing single-walled carbon nanotubes (SWNTs). Chitosan (CS) can produce good dispersion of SWNTs, but only in acidic pH condition. Our two novel derivatives, O-carboxymethylchitosan (OC) and OC modified by poly(ethylene glycol) at the −COOH position (OPEG), were able to produce highly effective debundling and dispersion of SWNTs in neutral pH aqueous solution. Atomic force microscopy (AFM), transmission electron microscopy (TEM), photoluminescence, UV−vis−NIR spetroscopy, and Raman spectroscopy confirmed that SWNTs are present as individual nanotubes in the dispersions. The solubilities of individually dispersed SWNTs in neutral water are 0.021 and 0.032 g/L for OC and OPEG, respectively, which are comparable to 0.038 g/L for SWNTs using CS in acetic acid. Further, OC and OPEG aqueous solutions (1 wt %) do not significantly lower the surface tensions (65−67 mN/m). From the Fourier transform infrared spectroscopic results, we conclude that the free electron pair in the pendant amine groups of OC and OPEG plays a vital role in finely dispersing the SWNTs; the −NH2 contributes to the adsorption of these two chitosan derivatives on the nanotubes. Quaternary ammonium chitosan (QC), with alkyl substitution at the protonated amine, was found to be unable to disperse SWNTs; possibly cation−π interaction with nanotubes is diminished due to steric hindrance.
The influence of sialylation on glycan negative ion dissociation and energetics (2006)

For the analysis of native glycans using tandem mass spectrometry (MS), it is desirable to choose conditions whereby abundances of cross-ring cleavages indicative of branch positions are maximized. Recently, negative ion tandem mass spectrometry has been shown to produce significantly higher abundances of such ions in glycans compared to the positive ion mode. Much of this prior work has concerned fragmentation patterns in asialo glycans. The present work compares the abundances of critical cross-ring cleavage ions using negative mode tandem mass spectrometry for milk oligosaccharides and N-linked glycans. For comparison, product ion formation was studied for deprotonated and nitrated ions formed from asialo glycans and deprotonated ions from sialylated glycans. Breakdown profiles demonstrate clearly that more energy was required to fragment sialylated compounds to the same extent as either their asialo or nitrate adducted counterparts. The extraction of a proton from a ring hydroxyl group during the ionization process may be viewed, qualitatively, as imparting significantly more energy to the ion than would that from a molecule bearing an acidic group, so that acidic glycans are more stable in the gas phase, as the negative charge resides on the carboxyl group. These results have strong practical implications because a major portion of glycans released from mammalian proteins will be sialylated.
Multidisciplinary observations at an expandable sub-marine cabled station off the Hatsushima island, the Sagami bay, Japan (2007)

Western part of Sagami Bay is one of the active tectonic areas in Japan. In this area, Teishi Knoll, volcanic scamount, erupted in 1989 and the earthquake swarms occurs repeatedly every few years in the eastern coast of the Izu Peninsula. The real-time deep sea floor observatory was deployed about 7 km off Hatsushima Island, Sagami Bay, at a depth of 1174 m in 1993 to monitor seismic activities, underwater pressure, water temperature and deep currents. The video camera and lights were also mounted in the observatory to monitor the relations among biological activities associated with the tectonic activities. The observation system including submarine electro-optical cable with a length of 8 km was completely renewed in 2000. The several underwater-mateable connectors are installed in the new observatory for additional observation instruments. An ocean bottom electro-magnetic meter(OBEM), precise pressure sensor and ocean bottom gravity meter were installed using ROV Hyper-Dolphin in the cruise of R/V Natsushima from January 9 to 14, 2005. We started to operate them at February 10, 2005 after checking those of data qualities. Observed data have been sent to Yokohama institute, JAMSTEC. Around the Sagami bay, seismic activity is very high. A large earthquake (M5.4) occurred off Izu peninsula at April 21, 2006, and submarine land slide was then generated. Generated mud flow reached to the Hatsushima station, and moved positions of some sensors. The video camera was able to take a movie of mud flow. An OBEM and other sensors also detected some distinctive changes with the mud flow.
Relative Bioavailability of Apixaban Solution or Crushed Tablet Formulations Administered by Mouth or Nasogastric Tube in Healthy Subjects (2015)

Comparable Frel was observed for oral apixaban solution, tablet, NGT administration of solution flushed with D5W and infant formula, and NGT administration of crushed tablet suspension. Exposure was less when oral solution was administered via NGT with nutritional supplement. These results support several alternative methods of administering apixaban that may be useful in certain clinical situations. ClinicalTrials.gov identifiers: NCT02034565, NCT02034578, and NCT02034591.
Steric and Electronic Effects on the Interaction of Xe and Kr with Functionalized Zirconia Metal–Organic Frameworks (2021)

The separation of xenon and krypton from their mixtures has been an enduring and complex venture due to their similar sizes and unreactive nature. Metal–organic frameworks (MOFs) have shown the potential to complete these challenging separations by utilizing pressure-swing adsorption (PSA) as a sustainable alternative to current cryogenic distillation techniques. To rationally design materials to better realize this goal, two main approaches have emerged: pore-size optimized and polarizability-based separations. To ascertain the efficacy of these strategies, we designed a series of UiO-type MOFs with terphenyl linkers that systematically varied their steric and electronic properties, including −Me, −F, −TMS, and −I functionalities, to assess their interactions with xenon and krypton. The prepared MOFs are all isoreticular and have similar pore size distributions, allowing us to directly evaluate the effects imposed by the functional groups. We found that the xenon uptake could be increased with greater polarizability of the functional group (−F < −Me ≈ −TMS < −I), whereas the selectivities seem to follow a trend more related to pore-steric effects (−TMS < −I < −Me < −F).
Calibration of areal surface topography measuring instruments (2017)

The ISO standards which are related to the calibration of areal surface topography measuring instruments are the ISO 25178-6xx series which defines the relevant metrological characteristics for the calibration of different measuring principles and the ISO 25178-7xx series which defines the actual calibration procedures. As the field of areal measurement is however not yet fully standardized, there are still open questions to be addressed which are subject to current research. Based on this, selected research results of the authors in this area are presented. This includes the design and fabrication of areal material measures. For this topic, two examples are presented with the direct laser writing of a stepless material measure for the calibration of the height axis which is based on the Abbott- Curve and the manufacturing of a Siemens star for the determination of the lateral resolution limit. Based on these results, as well a new definition for the resolution criterion, the small scale fidelity, which is still under discussion, is presented. Additionally, a software solution for automated calibration procedures is outlined.
Homotropic Cooperativity from the Activation Pathway of the Allosteric Ligand-Responsive Regulatory <i>trp</i> RNA-Binding Attenuation Protein (2013)

The trp RNA-binding attenuation protein (TRAP) assembles into an 11-fold symmetric ring that regulates transcription and translation of trp-mRNA in bacilli via heterotropic allosteric activation by the amino acid tryptophan (Trp). Whereas nuclear magnetic resonance studies have revealed that Trp-induced activation coincides with both microsecond to millisecond rigidification and local structural changes in TRAP, the pathway of binding of the 11 Trp ligands to the TRAP ring remains unclear. Moreover, because each of 11 bound Trp molecules is completely surrounded by protein, its release requires flexibility of Trp-bound (holo) TRAP. Here, we used stopped-flow fluorescence to study the kinetics of Trp binding by Bacillus stearothermophilus TRAP over a range of temperatures and observed well-separated kinetic steps. These data were analyzed using nonlinear least-squares fitting of several two- and three-step models. We found that a model with two binding steps best describes the data, although the structural equivalence of the binding sites in TRAP implies a fundamental change in the time-dependent structure of the TRAP rings upon Trp binding. Application of the two-binding step model reveals that Trp binding is much slower than the diffusion limit, suggesting a gating mechanism that depends on the dynamics of apo TRAP. These data also reveal that dissociation of Trp from the second binding mode is much slower than after the first Trp binding mode, revealing insight into the mechanism for positive homotropic allostery, or cooperativity. Temperature-dependent analyses reveal that both binding modes imbue increases in bondedness and order toward a more compressed active state. These results provide insight into mechanisms of cooperative TRAP activation and underscore the importance of protein dynamics for ligand binding, ligand release, protein activation, and allostery.
An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype (2013)

The DNA methylation patterns include anomalies in key genes implicated in the pathogenesis of RA and are stable for multiple cell passages. Persistent epigenetic alterations could contribute to the aggressive phenotype of RA synoviocytes and identify potential therapeutic targets that could modulate the pathogenic behavior.
Toxicological Evaluation of Realistic Emission Source Aerosols (TERESA)—Power plant studies: assessment of breathing pattern (2011)

Our approach to study multi-pollutant aerosols isolates a single emissions source, evaluates the toxicity of primary and secondary particles derived from this source, and simulates chemical reactions that occur in the atmosphere after emission. Three U.S. coal-fired power plants utilizing different coals and with different emission controls were evaluated. Secondary organic aerosol (SOA) derived from α-pinene and/or ammonia was added in some experiments. Male Sprague-Dawley rats were exposed for 6 h to filtered air or different atmospheric mixtures. Scenarios studied at each plant included the following: primary particles (P); secondary (oxidized) particles (PO); oxidized particles + SOA (POS); and oxidized and neutralized particles + SOA (PONS); additional control scenarios were also studied. Continuous respiratory data were obtained during exposures using whole body plethysmography chambers. Of the 12 respiratory outcomes assessed, each had statistically significant changes at some plant and with some of the 4 scenarios. The most robust outcomes were found with exposure to the PO scenario (increased respiratory frequency with decreases in inspiratory and expiratory time); and the PONS scenario (decreased peak expiratory flow and expiratory flow at 50%). PONS findings were most strongly associated with ammonium, neutralized sulfate, and elemental carbon (EC) in univariate analyses, but only with EC in multivariate analyses. Control scenario O (oxidized without primary particles) had similar changes to PO. Adjusted R(2) analyses showed that scenario was a better predictor of respiratory responses than individual components, suggesting that the complex atmospheric mixture was responsible for respiratory effects.
Design and Prototype of Auto-Track Long-Range Free-Space Optical Communication (2022)

We present a free-space optical communication module for the NSF PAWR program with an auto-tracking over ±6.5° angle of arrival with &lt;1 μrad resolution. The module is designed to work for rural area deployment.
Separation of Benzoic and Unconjugated Acidic Components of Leonardite Humic Material Using Sequential Solid-Phase Extraction at Different pH Values as Revealed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Correlation Nuclear Magnetic Resonance Spectroscopy (2018)

Here, we report on sequential solid-phase extraction of leonardite hymatomelanic acid (CHM) on a non-ionic sorbent at four steadily lowered pH values: 7, 5, 3, and 2, yielding fractions with different acidic properties. Using nuclear magnetic resonance (NMR) spectroscopy and ultrahigh-resolution mass spectrometry, we revealed a gradual shift of dominating scaffolds in the fractions of CHM from reduced saturated to oxidized aromatic compounds. An increase on the average aromaticity of the CHM fractions was accompanied by a red shift in fluorescence spectra. These results were supported by heteronuclear single quantum coherence and heteronuclear multiple bond correlation NMR experiments. We have demonstrated that the CHM fraction isolated at pH 5 was dominated by aliphatic carboxyl carriers, while the pH 3 fraction was dominated by aromatic carboxyl acids. The developed fractionation technique will enable deeper insight on structure-property relationships and the design of the humic-based materials with tailored reactive properties.