gebhart/patrepeval huggingface dataset:
Acid-Catalyzed Oxidative Addition of a C–H Bond to a Square Planar d8 Iridium Complex (2014)

While the addition of C-H bonds to three-coordinate Ir(I) fragments is a central theme in the field of C-H bond activation, addition to square planar four-coordinate complexes is far less precedented. The dearth of such reactions may be attributed, at least in part, to kinetic factors elucidated in seminal work by Hoffmann. C-H additions to square planar carbonyl complexes in particular are unprecedented, in contrast to the extensive chemistry of oxidative addition of other substrates (e.g., H2, HX) to Vaska's Complex and related species. We report that Bronsted acids will catalyze the addition of the alkynyl C-H bond of phenylacetylene to the pincer complex (PCP)Ir(CO). The reaction occurs to give exclusively the trans-C-H addition product. Our proposed mechanism, based on kinetics and DFT calculations, involves initial protonation of (PCP)Ir(CO) to generate a highly active five-coordinate cationic intermediate, which forms a phenylacetylene adduct that is then deprotonated to give product.
Comparison of conventional and highly crosslinked UHMWPE patellae evaluated by a new in vitro patellofemoral joint simulator (2006)

A series of in vitro patella damage tests were developed using a knee simulator to investigate electron-beam-irradiated and -melted ultra-high molecular weight polyethylene and conventional ultra-high molecular weight polyethylene at the patellofemoral articulation. Three different simulations were created: (i) normal gait with optimal component alignment, (ii) stair climbing with optimal component alignment, and (iii) stair climbing with 4 degrees of femoral component internal rotation to simulate a component malalignment condition. In the last two simulations, all patellae were artificially aged. In normal gait, the unaged conventional and highly crosslinked patellae demonstrated similar behavior. In both stair climbing tests, unlike the aged highly crosslinked components, the aged conventional patellae developed cracks by 2 million cycles. These results demonstrate the potential advantage of highly crosslinked polyethylene for the patella.
Analysis of Paper-Based Colorimetric Assays With a Smartphone Spectrometer (2018)

We report on the adaptation of a smartphone's rear-facing camera to function as a spectrometer that measures the spectrum of light scattered by common paper-based assay test strips. We utilize a cartridge that enables a linear series of test pads in a single strip to be swiped past the read head of the instrument while the phone's camera records video. The strip is housed in a custom-fabricated cartridge that slides through the instrument to facilitate illumination with white light from the smartphone's flash LED that is directed through an optical fiber. We demonstrate the ability to detect subtle changes in the scattered spectrum that enables quantitative analysis of single-analyte and multi-analyte strips. The demonstrated capability can be applied to broad classes of paper-based assays in which visual observation of colored strips is not sufficiently quantitative, and for which analysis of red-green-blue pixel values of a camera image are not capable of measuring complex scattered spectra.
Wat het Nederlands ons kan leren over de Jespersencyclus (2012)

Amsterdam University Press is a leading publisher of academic books, journals and textbooks in the Humanities and Social Sciences. Our aim is to make current research available to scholars, students, innovators, and the general public. AUP stands for scholarly excellence, global presence, and engagement with the international academic community.
Characterization of the Flavoprotein Moieties of NADPH-Sulfite Reductase from Salmonella typhimurium and Escherichia coli (1989)

NADPH-sulfite reductase flavoprotein (SiR-FP) was purified from a Salmonella typhimurium cysG strain that does not synthesize the hemoprotein component of the sulfite reductase holoenzyme. cysJ, which codes for SiR-FP, was cloned from S. typhimurium LT7 and Escherichia coli B, and both genes were sequenced. Physicochemical analyses and deduced amino acid sequences indicate that SiR-FP is an octamer of identical 66-kDa peptides and contains 4 FAD and 4 FMN per octamer. Potentiometric titrations of SiR holoenzyme, SiR-FP, and FMN-depleted SiR-FP yielded the following redox potentials for the prosthetic groups at pH 7.7: E'1 (FMNH./FMN) = -152 mV; E'2 (FMNH2/FMNH.) = -327 mV; E'3 (FADH./FAD) = -382 mV; E'4 (FADH2/FADH.) = -322 mV. Microcoulometric titration of SiR-FP at 25 degrees C yielded data which were in full agreement with these potentials. Spectroscopic and catalytic studies of native SiR-FP and of SiR-FP depleted of FMN support the following electron flow sequence: NADPH----FAD----FMN. FMN can then contribute electrons to the hemoprotein component of sulfite reductase, as well as to cytochrome c and various diaphorase acceptors. The FMN is postulated to cycle between the FMNH2 and FMNH. oxidation states during catalysis; in this sense SiR-FP shares a catalytic mechanism with NADPH-cytochrome P-450 oxidoreductase. SiR-FP domains involved in binding FMN, FAD, and NADPH are proposed from amino acid sequence homologies with Desulfovibrio vulgaris flavodoxin (Dubourdieu, M., and Fox, J.L. (1977) J. Biol. Chem. 252, 1453-1463) and spinach ferredoxin-NADP+ oxidoreductase (Karplus, P.A., Walsh, K.A., and Herriott, J. R. (1984) Biochemistry 23, 6576-6583). Comparison of the deduced amino acid sequences of SiR-FP and NADPH-cytochrome P-450 oxidoreductase (Porter, T. D., and Kasper, C.B. (1985) Proc. Natl. Acad. Sci. U. S.A. 82, 973-977) also showed identities that suggest these two proteins are descended from a common precursor, which contained binding regions for both FMN and FAD.
Prospective predictors of exacerbation status in severe asthma over a 3‐year follow‐up (2018)

Measurement of FeNO has a significant potential to predict future asthma exacerbation, which is independent of the "past exacerbation history."
Integration of a new alignment sensor for advanced technology nodes (2007)

In this paper alignment and overlay results of the advanced technology nodes are presented. These results were obtained on specially generated wafers as well as on regular manufacturing-type wafers. For this purpose, a new alignment sensor was integrated and evaluated in three generations of lithography tools, placed in R&D and mass manufacturing facilities. The capability of the sensor to align on marks with varying layout was evaluated. Long term overlay stability less than 11 nm was obtained on two different mark types: a standard ASML calibration mark and a flexible Toshiba mark design. The ability to align on low-contrast marks was validated by a dedicated experiment: typical alignment repeatability values of ~1 nm (3sigma) on shallow etch depth mark features of 25 nm are obtained for various mark designs, including flexible pitch alignment marks. From these results, design directions for improved mark detect ability were defined. The jointly developed mark designs were validated for their alignment robustness by an evaluation of manufacturing wafer alignment performance. On-product overlay results on manufacturing wafers were measured for three different process layers of the current technology node. The used alignment strategies were based on new mark capture and fine wafer alignment mark designs, thereby making optimal use of the mark design flexibility potential of the alignment sensor. Typical on-product overlay values obtained were less than 17 nm for the Active Area process layer, less than 12 nm for the Gate Conductor process layer, and less than 19 nm for the Metal-1 process layer; after applying batch corrections, as determined on a set of 2 send-ahead wafers. All results are based on full batch readout on an offline metrology tool. By applying optimal batch process corrections for linear terms, typical overlay values range between 10-14 nm, depending on the layer measured. Finally the sensor's infrared wavelengths were used to demonstrate a robust alignment solution for wafers containing a semi-transparent hard-mask layer.
Monoclonal antibodies against pools of mono- and polyacetylated peptides selectively recognize acetylated lysines within the context of the original antigen (2016)

Post-translational modifications (PTMs) strongly influence the structure and function of proteins. Lysine side chain acetylation is one of the most widespread PTMs, and it plays a major role in several physiological and pathological mechanisms. Protein acetylation may be detected by mass spectrometry (MS), but the use of monoclonal antibodies (mAbs) is a useful and cheaper option. Here, we explored the feasibility of generating mAbs against single or multiple acetylations within the context of a specific sequence. As a model, we used the unstructured N-terminal domain of APE1, which is acetylated on Lys27, Lys31, Lys32 and Lys35. As immunogen, we used a peptide mixture containing all combinations of single or multi-acetylated variants encompassing the 24-39 protein region. Targeted screening of the resulting clones yielded mAbs that bind with high affinity to only the acetylated APE1 peptides and the acetylated protein. No binding was seen with the non-acetylated variant or unrelated acetylated peptides and proteins, suggesting a high specificity for the APE1 acetylated molecules. MAbs could not finely discriminate between the differently acetylated variants; however, they specifically bound the acetylated protein in mammalian cell extracts and in intact cells and tissue slices from both breast cancers and from a patient affected by idiopathic dilated cardiomyopathy. The data suggest that our approach is a rapid and cost-effective method to generate mAbs against specific proteins modified by multiple acetylations or other PTMs.
C/EBPβ phosphorylation rescues macrophage dysfunction and apoptosis induced by anthrax lethal toxin (2007)

Bacillus anthracis lethal toxin (LT) impairs innate and adaptive immunity. Anthrax lethal factor stimulates cleavage of MAPK kinases, which prevents the activation of antiapoptotic MAPK targets. However, these MAPK targets have not been yet identified. Here, we found that LT induces macrophage apoptosis by enhancing caspase 8 activation and by preventing the activation of ribosomal S6 kinase-2 (RSK), a MAPK target, and the phosphorylation of CCAAT/enhancer binding protein-beta (C/EBPbeta) on T(217), a RSK target. Expression of the dominant positive, phosphorylation mimic C/EBPbeta-E(217) rescued macrophages from LT-induced apoptosis by blocking the activation of procaspase 8. LT inhibited macrophage phagocytosis and oxidative burst and induced apoptosis in normal mice but not in C/EBPbeta-E(217) transgenic mice. These findings suggest that C/EBPbeta may play a critical role in anthrax pathogenesis, at least in macrophages.
Effects of the experimental manipulation of Fourier components of naturalistic imagery on search performance and eye-tracking behavior (2015)

Historically, visual search experiments used artificial stimuli (simple shapes) as targets and distractors arranged in an imaginary array of cells on a blank background. Little research on search behavior has been conducted with naturalistic stimuli and a frequency-domain framework. With the common metric provided by Fourier analysis, it is possible to compare the effects of various frequency-domain components on search efficiency.<sup>1</sup> In the current study, we experimentally manipulated the spectral content of target and distractor (background) cells filled with spatially filtered segments of real-life scenes. Our experimental design included two types of spatial filters, orientation (some frequency overlap between target and distractor) and spatial frequency (no overlap), and uniform distractor (target and distractors filtered similarly) and mixed distractor (only half distractors filtered like the target) conditions. Generally, observers found the target more quickly and were more confident in their performance in the mixed condition. Observers were faster, more accurate, and more confident in the spatial filter condition than in the orientation filter condition. Overall, observers spent less time (fixation duration) and effort (fixation frequency) examining dissimilar distractors. The effect with the fixation frequency measure was magnified when the spatial frequency filter was used.
Macro- to Nanoscale Wear Prevention via Molecular Adsorption. (2007)

Abstract not provided.
Emerging memory technologies for reconfigurable routing in FPGA architecture (2010)

Emerging non-volatile resistive memories such as Phase Change Memories (PCMs) are promising candidates to replace Flash and SRAM memories in some applications. This paper introduces a novel memory node for Field-Programmable Gate Arrays (FPGAs). We propose an elementary circuit storing the reconfiguration signals by means of two resistive memories and one programming transistor. The area and write time of the proposed node are investigated and their impact on complex circuits is assessed. We show that the elementary memory node yields an improvement in area and write time of 3.4× and 16× respectively vs. a regular Flash implementation. We use the designed memory node to reconfigure the switchbox in the routing part of FPGAs, and we demonstrate a delay reduction up to 50% on a benchmark of logic circuits that we mapped on an FPGA architecture thanks to the area saving and especially to the low on-resistance of PCMs.
Quantitative evaluation of the inactivation effect of ozonated water on SARS-CoV-2 based on corrected CT values (2022)

There are many issues in the evaluation protocols based on CT (mg min/L) values, which have been used to assess the germicidal effect of highly oxidative and unstable ozonated water. The major problems include the carryover of culture medium components in virus inactivation assays and the reaction volume ratio between the virus suspension and ozonated water. Furthermore, it is essential to correct the CT value with the decay curve of dissolved ozone under the same conditions as the inactivation assay. In this study, these concerns were reexamined to obtain quantitative CT values. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) inactivation test using ozonated water prepared from pure water was assessed by determining the corrected concentration time (CCT) values. Moreover, a possible inactivation mechanism of SARS-CoV-2 was discussed with the aid of findings from this study and previous reports. The findings revealed that the CCT value required for 99.95% inactivation of SARS-CoV-2 with ozonated water was 0.97 mg·min/L. To quantitatively evaluate the SARS-CoV-2 inactivation test, the virus purification procedure during the pretreatment and the CT value correction using a dissolved ozone decay curve obtained under the same condition as the inactivation test were demonstrated to be essential.We proposed a possible mechanism of SARS-CoV-2 inactivation with ozonated water. Amino acids such as tyrosine, tryptophan, methionine, cysteine, and histidine in the SARS-CoV-2 spike protein are susceptible to oxidative attack by the ozone dissolved in water. This attack may induce structural destruction of the spike protein and inhibit its binding to the angiotensin converting enzyme 2 (ACE2) receptor, an essential host receptor for viral infection, resulting in viral inactivation and contributing to infection suppression.
Interactive Video Retrieval System Integrating Visual Search with Textual Search (2002)

In children <10 years with sTBI, the present clinical management regarding ICP monitoring deviates from the current German national and international guidelines. The reasons remain unclear, with the low level of evidence in the field of ICP monitoring and the recency of changes in guideline recommendations as potential contributors. Prospective interventional studies should elucidate the benefit of ICP monitoring and ICP directed therapies to provide evidence-based recommendations on ICP monitoring.
A facile method for direct determination of phospholipase A2 activity in intact cells. (1987)

The fluorescent phospholipid analogue 1-acyl-2-(N-4-nitrobenzo-2-oxa-1,3- diazole)aminocaproylphosphatidylcholine (C6-NBD-PC), which incorporates into cell membranes, is employed as a substrate for phospholipase A2 (PLA2) in intact cells. The interaction of this substrate with the cells produces only one fluorescent product; the fatty acid C6-NBD-FA, which does not incorporate into other lipids, and is not further metabolized. The product, a hydrophilic fatty acid, is separated from the substrate by aqueous: organic solvent phase separation. Using this method, the fatty acid produced is fully recovered and its amount, as measured by its fluorescence intensity, is a direct measure of the cell membrane PLA2 activity.
Phase transitions and domain structures in strained pseudocubic (100)SrTiO3thin films (2006)

The mutual interactions between a structural transition and a ferroelectric transition are analyzed for different strain states in a pseudocubic (100) $\mathrm{Sr}\mathrm{Ti}{\mathrm{O}}_{3}$ film by examining the equilibrium solutions of the total free energy as a function of polarization, strain and structural order parameter. The range of possible ferroelectric transition temperatures and the possible ferroelectric states of a strained $\mathrm{Sr}\mathrm{Ti}{\mathrm{O}}_{3}$ film are determined with respect to the variation in the reported properties of bulk $\mathrm{Sr}\mathrm{Ti}{\mathrm{O}}_{3}$ single crystals. The ferroelectric and structural domain morphologies at a biaxial tensile strain ${e}_{0}=0.94%$ were predicted using phase-field simulations. It is shown that variations in the reported values of bulk properties and in the Landau energy coefficients from different literature sources lead not only to a wide range of possible transition temperatures at a given strain, but also to different ferroelectric states (e.g., polarization along the pseudocubic ⟨110⟩ vs ⟨100⟩ directions) thus different domain structures under a biaxial tensile strain. Both optical second harmonic generation and confocal scanning optical microscopy measurements demonstrate that the domain states in $\mathrm{Sr}\mathrm{Ti}{\mathrm{O}}_{3}$ films strained at ${e}_{0}=0.94%$ and 1.16% exhibit polar directions along the pseudocubic ⟨110⟩ directions within the pseudocubic (001) plane of the film.
Abstract 4690: Inhibition of PI3K-AKT signaling causes a FOXO-dependent induction of receptor tyrosine kinase expression and phosphorylation in cancer (2011)

Abstract Hyperactivation of the PI3K-AKT-mTOR pathway is a common mechanism for oncogenic signaling in tumors and multiple inhibitors of this pathway are now in clinical development. As the PI3K-AKT-mTOR pathway is known to be tightly regulated by negative feedback, we hypothesized that these drugs might relieve feedback inhibition, reactivate upstream signaling and limit their antitumor effects. We tested the effects of inhibitors of PI3K and AKT kinase on receptor tyrosine kinase signaling in a panel of cell lines derived from multiple tumor types. PI3K-AKT pathway inhibition resulted in increased expression and phosphorylation of a common set of receptor tyrosine kinases, including IGF-1R and insulin receptor and HER3. Induction of RTK expression was dependent on activation of members of the Forkhead transcription factor family in response to AKT inhibition. We found that depletion of FOXO proteins blocked the rise in HER3, IGF-1R, and insulin receptor protein and phosphorylation caused by AKT inhibition. Expression of a constitutively activated form of one of the FOXO proteins resulted in increased expression of these receptors. Moreover, immunoprecipitation of FOXO proteins revealed that they are preferentially associated with the promoters of these receptors upon AKT inhibition. To determine the consequences of induction of these RTKs, we utilized HER kinase inhibitors to block activation of the receptors. In multiple xenograft tumor models, PI3K-AKT inhibition resulted in potent RTK induction in vivo and combined inhibition of the HER kinases and AKT resulted in improved antitumor effects with tumor regressions observed in several cases. We conclude that the PI3K-AKT pathway feedback regulates RTK expression through a FOXO-dependent induction of RTK transcripts. This reactivation of upstream RTK signaling is likely to attenuate the effects of AKT inhibition. Blockade of feedback-upregulated RTKs may significantly improve the antitumor effects of PI3K-AKT inhibitors and is a potential combination strategy for PI3K-AKT driven cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4690. doi:10.1158/1538-7445.AM2011-4690
Screening of Ionic Liquid/H2O Working Pairs for Application in Low Temperature Driven Sorption Heat Pump Systems (2015)

Due to the known corrosion and crystallization issues of LiBr/H2O, the state-of-the-art working pair in sorption heat pump (SHP) systems, research into alternative working pairs is of high practical relevance. We have studied a wide range of ionic liquids (ILs) for this application in order to find potential new systems with enhanced performance. The screening was conducted with a focus on vapor pressure measurements of, in total, 74 examined working pairs. As common vapor–liquid-equilibrium measurements are very precise but rather time-consuming, we developed a new setup allowing a fast relative determination of humidities with very small sample volumes for screening purposes. By this method we identified seventeen IL/H2O working pairs fulfilling the technical relevant criterion of a water vapor pressure pH2O ≤ 10 mbar at T = 308 K with an IL content of less than 80 wt % (wIL < 0.8). Further evaluation of these candidates with respect to their thermal stability and viscosity allowed us to identify [MMIM][HCOO]/H2O, [MMIM][OAc]/H2O, [MMIM][C2H5COO]/H2O, [Me4N][HCOO]/H2O, [Me4N][OAc]/H2O and [Me4N] [C2H5COO]/H2O as the most promising IL/H2O systems for a possible application in SHP systems.