gebhart/patrepeval huggingface dataset:
Metabolic Activation and Major Protein Target of a 1-Benzyl-3-carboxyazetidine Sphingosine-1-phosphate-1 Receptor Agonist (2012)

1-{4-[(4-Phenyl-5-trifluoromethyl-2-thienyl)methoxy]benzyl}azetidine-3-carboxylic acid (MRL-A) is a potent sphingosine-1-phosphate-1 receptor agonist, with potential application as an immunosuppressant in organ transplantation or for the treatment of autoimmune diseases. When administered orally to rats, radiolabeled MRL-A was found to undergo metabolism to several reactive intermediates, and in this study, we have investigated its potential for protein modification in vivo and in vitro. MRL-A irreversibly modified liver and kidney proteins in vivo, in a dose- and time-dependent manner. The binding was found to occur selectively to microsomal and mitochondrial subcellular fractions. Following a nonspecific proteolytic digestion of liver and kidney proteins, a single major amino acid adduct was observed. This adduct was characterized with LC/MS/UV and NMR spectroscopy and was found to be the product of an unprecedented metabolic activation of the azetidine moiety leading to the formation of a ring-opened α,β-unsaturated imine conjugated to the ε-amino group of a lysine residue. The formation of this adduct was not inhibited when rats were pretreated with 1-aminobenzotriazole, indicating that P450 enzymes were not involved in the metabolic activation of MRL-A. Rather, our findings suggested that MRL-A underwent bioactivation via a β-oxidation pathway. Several other minor adducts were identified from protein hydrolysates and included lysine, serine, and cysteine conjugates of MRL-A. These minor adducts were also detected in microsomal incubations fortified with the cofactors for acyl-CoA synthesis and in hepatocytes. Trypsin digestion of crude liver homogenates from rats treated with radiolabeled MRL-A led to the identification of a single radioactive peptide. Its sequence, determined by LC/MS analysis, revealed that the target of the major reactive species of MRL-A in vivo is Lys676 of long chain acyl-CoA synthetase-1 (ACSL1). This lysine residue has been found to be critical for ACSL1 activity, and its modification has the potential to lead to biological consequences such as cardiac hypertrophy or thermogenesis dysregulation.
Production of agaro- and carra-oligosaccharides by partial acid hydrolysis of galactans (2011)

Agaro- and carra-oligosaccharides were produced by partial acid hydrolysis of commercial agarose and kappa-carrageenan. Di- and tetrasaccharides were purified by gel filtration chromatography and characterized by NMR (1D and 2D) spectroscopy and ESIMS. The following oligosaccharides were obtained: agarobiose, agarotetraose, kappa-carrabiose and kappa-carratetraose. Agarobiose and agarotetraose were used as standards to develop a high performance size exclusion chromatography (HPSEC) method which was utilized to study the hydrolysis rate of agarose and oligosaccharide production. Six hours of hydrolysis (0.1 M TFA, 65 ºC) produced mainly di- and tetrasaccharides. The methodology for oligosaccharide production and evaluation developed in the present work shows good potential for the production of bioactive oligosaccharides.
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology (2010)

The software is available at http://icorn.sourceforge.net
Scalable Coating and Properties of Transparent, Flexible, Silver Nanowire (2010)

We report a comprehensive study of transparent and conductive silver nanowire (Ag NW) electrodes,includingascalablefabricationprocess,morphologies,andoptical,mechanicaladhesion,andflexibility properties, and various routes to improve the performance. We utilized a synthesis specifically designed for long andthinwiresforimprovedperformanceintermsofsheetresistanceandopticaltransmittance.Twenty/sqand 80% specular transmittance, and 8 ohms/sq and 80% diffusive transmittance in the visible range are achieved, whichfallinthesamerangeasthebestindiumtinoxide(ITO)samplesonplasticsubstratesforflexibleelectronics andsolarcells.TheAgNWelectrodesshowopticaltransparenciessuperiortoITOfornear-infraredwavelengths(2- foldhighertransmission).Owingtolightscatteringeffects,theAgNWnetworkhasthelargestdifferencebetween diffusive transmittance and specular transmittance when compared with ITO and carbon nanotube electrodes, a propertywhichcouldgreatlyenhancesolarcellperformance.AmechanicalstudyshowsthatAgNWelectrodeson flexiblesubstratesshowexcellentrobustnesswhensubjectedtobending.Wealsostudytheelectricalconductance ofAgnanowiresandtheirjunctionsandreportafacileelectrochemicalmethodforaAucoatingtoreducethewire- to-wire junction resistance for better overallfilm conductance. Simple mechanical pressing was also found to increasetheNWfilmconductanceduetothereductionofjunctionresistance.Theoverallpropertiesoftransparent Ag NW electrodes meet the requirements of transparent electrodes for many applications and could be an immediate ITO replacement forflexible electronics and solar cells.
Fiber Bragg Gratings embedded inside 3D-printed Patches – sensor design and mechanical characterization (2023)

The application of optical fibers with fiber Bragg gratings (FBG) in the civil, biomedical and robotics fields presents several challenges related to the positioning and gluing of the sensor to the surface to be monitored. For this reason, the development of 3D-printed patches that embed optical fibers has become relevant in recent years. The studies existing in the literature focus on some specific process parameters, like the infill density and the choice of the material of the patch. However, a systematic analysis regarding the interaction between the material of the patch material and the embedded fiber coating to secure adhesion and strain transfer is still missing. This preliminary study aims at assessing the performances of 3D-printed patches embedding optical fibers in different combinations of filament materials and coatings of the fiber. Two sensors per combination of filament material (ABS, PLA) and coating of the fiber (acrylate, polyimide) are fabricated and mechanically tested. The results indicate that the fabrication process is more reliable when using polyimide-coated fibers, and the measurements of the resulting sensors are more repeatable.
Construction of a Prediction Model for Taste of Miso (Japanese Fermented Soybean Paste) Using Metabolic Profiling and Quantitative Descriptive Analyses (2019)

Various types of miso are manufactured in Japan, which results in diverse flavors. However, the number of miso engineers who understand the variety of miso tastes has decreased due to decreases in the miso market. To solve this problem, we examined the potential to characterize various miso tastes using mainly low-molecular-weight hydrophilic component data by metabolic profiling. Analysis was performed by orthogonal partial least squares analysis, the relative intensity data for annotated compounds as explanatory variables and the data obtained by sensory evaluation as objective variables. The OPLS prediction model of taste had high accuracy and stability, and the components important for each taste were reasonable. From the results of model construction, we also found galactose correlated to umami. These results suggested that sensory evaluations of various types of miso may be in part replaced with instrumental analyses in the future.
Abstract 13470: RV Ejection Efficiency Measured in the Phasic Pulmonary Flow; a CMR Approach in PAH (2015)

Introduction: Measurements of RV function, such as RVEF and RV-measured ventricular-vascular coupling (VVC), maybe important in predicting survival in PAH, but are dependent on load and mathematical assumptions. However, independent measures, such as flow efficiency (FEI) within the main PA may be better predictors. FEI is dependent on the natural ratio between MPA area to pulsatile blood wavelength (λ), where λ is proportional to the product of λ velocity and the pulse time, but is difficult to measure directly. Hypothesis: We hypothesize pulmonary FEI will correlate with the VVC and RVEF. Methods: CMR was performed on 18 pts with PAH to assess RV function. Eight pts additionally underwent RV CMR during physiologic stressors: 1) inhaled NO 2) dobutamine (20μ/kg/min) and 3) volume challenge (500ml NaCl). MPA flow was measured via phase velocity mapping (PVM). The RVEF, VVC ratio and ejection time (ET) were calculated from CMR. The MPA area was measured from the PVM images along with avg velocity (Vel avg . Pulmonary FEI = (average Vel avg x ET) / MPA area. Results: A total of 38 unique measures of RVEF (52±12%), VVC (0.89±.3) and MPA flow conditions were measured: Vel avg (49±15cm/s), MPA area (51±11mm 2 ) and ET (295±61ms). The FEI correlated with RVEF and VVC via log term: RVEF = 11.5 log nat (FEI) + 37.2; and VVC = 0.34 log nat (FEI) + 1.17.Bland-Altman analysis of the measured RVEF vs. the FEI modeled RVEF (Fig 1) has an offset bias of 0, a four SD range of ±14.4; r=0. 0.8, while the measured VVC vs. modeled has a bias of 0 and a 4 SD range of ± 0.45; r = 0.74. Conclusions: The linear combination of average pulmonary blood velocity, ejection time and MPA area combine to form a pulmonary FEI that strongly correlates with RVEF and VVC. Importantly, it is devoid of the afterload/preload assumptions of RVEF and the multitude of assumptions of V 0 and RVEDP in VVC. As such, this index may provide additional clinical value since it reflects the directly measured intrinsic efficiency of integrated RV-PA conditions.
Adenosine A2Aand A2Breceptors in cultured human and porcine coronary artery endothelial cells (2000)

We investigated the role of the cAMP link to the signal transduction mechanism coupled with adenosine A(2A) and A(2B) receptors in cultured human coronary artery endothelial cells (HCAEC) and porcine coronary artery endothelial cells (PCAEC). 2-[4-[2-¿2-[(4-aminophenyl)methylcarbonylamino]ethylaminocarbon yl¿eth yl]phenyl]ethylamino-5'- ethylcarboxamidoadenosine ((125)I-PAPA-APEC) (PAPA-APEC) was used to demonstrate the specific binding in PCAEC membranes. The specific binding was saturable and reversible with a maximal number of binding sites (B(max)) of 240 fmol/mg protein, and scatchard analysis revealed a single class of binding site with an equilibrium dissociation constant (K(d)) of 1. 17 +/- 0.035 nM. In competition experiments, adenosine receptor agonists showed the following order of potency (based on IC(50)): 5'-(N-ethylcarboxamido)adenosine (NECA) >/= CGS-21680 > 2-chloroadenosine. This order appears to be consistent with the A(2) adenosine receptor classification. We also studied the effects of adenosine agonists on the accumulation of cAMP as an indirect approach to show the presence of functional A(2) receptors. Similarly, the same adenosine agonists (10(-7)-10(-4) M) elicited the production of cAMP in intact endothelial cells in a dose-dependent manner, exhibiting consistently with the A(2) adenosine receptor classification. A selective A(2A) adenosine receptor antagonist (ZM-241385, 10(-8) M) significantly inhibited the effect of CGS-21680 on cAMP but only partly inhibited the effect of NECA, suggesting the presence of both A(2A) and A(2B) receptors. Western blot analysis further showed the immunoreactivity of A(2A) and A(2B) receptor at 45 and 36 kDa, respectively, in both HCAEC and PCAEC. Direct evidence for the presence of A(2A) and A(2B) receptors in cultured HCAEC and PCAEC by reverse transcription-polymerase chain reaction (RT-PCR), revealed expected PCR product sizes (205 and 173 bp) for A(2A) and A(2B) receptors in HCAEC and PCAEC, respectively. The data show that adenylate cyclase-coupled adenosine A(2A) and A(2B) receptors are present in coronary endothelial cells.
Optical encoder based on the Lau effect (2000)

Daniel CrespoJose´AlonsoDepartamento de O´pticaUniversidad Complutense de MadridFacultad de Ciencias Fi ´sicasCiudad Universitaria, s/nMadrid 28040, SpainToma´s MorlanesDepartamento de I1DFagor Automation S. CoopBarrio de San Andre´s s/nP.O. Box 194Mondrago´n 20500, Guipuzcoa, SpainEusebio BernabeuDepartamento de O´pticaUniversidad Complutense de MadridFacultad de Ciencias Fi´sicasCiudad Universitaria, s/nMadrid 28040, SpainAbstract. An optical encoder based on the Lau effect is presented. It isshown that this system has several advantages over standard opticalencoders based on the moire´effect, such as smaller sensitivity to varia-tions in the gap between gratings and higher design simplicity. Problemsdue to the quality of the collimated beam, which are present in moire-effect-based encoders, are also avoided. Two different optimized de-signs for different resolutions are presented. Experimental measure-ments, in good agreement with the model developed by us, arepresented.
Topical Pimecrolimus and Tacrolimus and the Risk of Cancer (2007)

In this review the controversy regarding the association between topical pimecrolimus and tacrolimus and the development of tumors is unfolded. After reviewing the literature we conclude that, currently, there is no scientific evidence of an increased incidence of skin cancer, lymphomas or systemic immunosuppression in those patients that use or have used topical calcineurin inhibitors. Published studies lack adequate number of patients and/or the follow-up time is short enough to conclude that topical use of calcineurin inhibitors might be associated with the reported cases of skin cancer and lymphoma. Nevertheless the possibility of long term cutaneous and/or systemic side effects cannot be excluded.
Daxx regulates mitotic progression and prostate cancer predisposition (2012)

Mitotic progression of mammalian cells is tightly regulated by the E3 ubiquitin ligase anaphase promoting complex (APC)/C. Deregulation of APC/C is frequently observed in cancer cells and is suggested to contribute to chromosome instability and cancer predisposition. In this study, we identified Daxx as a novel APC/C inhibitor frequently overexpressed in prostate cancer. Daxx interacts with the APC/C coactivators Cdc20 and Cdh1 in vivo, with the binding of Cdc20 dependent on the consensus destruction boxes near the N-terminal of the Daxx protein. Ectopic expression of Daxx, but not the D-box deleted mutant (DaxxΔD-box), inhibited the degradation of APC/Cdc20 and APC/Cdh1 substrates, leading to a transient delay in mitotic progression. Daxx is frequently upregulated in prostate cancer tissues; the expression level positively correlated with the Gleason score and disease metastasis (P = 0.027 and 0.032, respectively). Furthermore, ectopic expression of Daxx in a non-malignant prostate epithelial cell line induced polyploidy under mitotic stress. Our data suggest that Daxx may function as a novel APC/C inhibitor, which promotes chromosome instability during prostate cancer development.
Effet de la microflore colique humaine sur le devenir métabolique de la catéchine, un composé polyphénolique majeur du vin (1998)

Affiche N 254
An automatic procedure to construct the optimal soft-decision quantizers and branch metrics for Viterbi decoders (2002)

An automatic procedure is developed to construct the optimal soft-decision quantizer and branch metric, based on the cutoff rate criterion that determines the optimal soft-decision vector quantization regions, for the Viterbi (1967) decoder over any memoryless channel. As only samples of the received symbols are required, this procedure finds applications in many practical channels.
Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose (2014)

A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.
Bitstream-based feature extraction for wireless speech recognition (2002)

In this paper, we propose a feature extraction method for a speech recognizer that operates in digital communication networks. The feature parameters are basically extracted by converting the quantized spectral information of a speech coder into a cepstrum. We also combine the voiced/unvoiced information obtained from the bitstream of the speech coder into the recognition feature set. From speaker-independent connected digit HMM recognition, we find that the speech recognition system employing the proposed bitstream-based front-end gives superior word and string accuracies over a recognizer constructed from decoded speech signals. Its performance is comparable to that of the wireline recognition system that uses only the cepstrum as a feature set.
The Fourier reconstruction of a head section (1974)

The Fourier reconstruction may be viewed simply in the spatial domain as the sum of each line integral times a weighting function of the distance from the line to the point of reconstruction. A modified weighting function simultaneously achieves accuracy, simplicity, low computation time, as well as low sensitivity to noise. Using a simulated phantom, the authors compare the Fourier algorithm and a search algorithm. The search algorithm required 12 iterations to obtain a reconstruction of accuracy and resolution comparable to that of the Fourier reconstruction, and was more sensitive to noise. To speed the search algorithm by using fewer interactions leaves decreased resolution in the region just inside the skull which could mask a subdural hematoma.
Synthesis and Structures of Steroidal Oxathiolanes (1981)

Abstract Synthesis of isomeric oxathiolanes from 6-oxosteroids is described. Configurations at spirocyclic carbon in these compounds have been established on the basis of CD and NMR spectra with the use of shift reagent [Eu(dpm)3].
Peptides genetically selected for NF-κB activation cooperate with oncogene Ras and model carcinogenic role of inflammation (2014)

Chronic inflammation is associated with increased cancer risk. Furthermore, the transcription factor NF-κB, a central regulator of inflammatory responses, is constitutively active in most tumors. To determine whether active NF-κB inherently contributes to malignant transformation, we isolated a set of NF-κB-activating genetic elements and tested their oncogenic potential in rodent cell transformation models. Genetic elements with desired properties were isolated using biologically active selectable peptide technology, which involves functional screening of lentiviral libraries encoding 20 or 50 amino acid-long polypeptides supplemented with endoplasmic reticulum-targeting and oligomerization domains. Twelve NF-κB-activating selectable peptides (NASPs) representing specific fragments of six proteins, none of which was previously associated with NF-κB activation, were isolated from libraries of 200,000 peptides derived from 500 human extracellular proteins. Using selective knockdown of distinct components of the NF-κB pathway, we showed that the isolated NASPs act either via or upstream of TNF receptor-associated factor 6. Transduction of NASPs into mouse and rat embryo fibroblasts did not, in itself, alter their growth. However, when coexpressed with oncogenic Ras (H-Ras(V12)), NASPs allowed rodent fibroblasts to overcome H-Ras(V12)-mediated p53-dependent senescence and acquire a transformed tumorigenic phenotype. Consistent with their ability to cooperate with oncogenic Ras in cell transformation, NASP expression reduced the transactivation activity of p53. This system provides an in vitro model of NF-κB-driven carcinogenesis and suggests that the known carcinogenic effects of inflammation may be at least partially due to NF-κB-mediated abrogation of oncogene-induced senescence.
Five Solid Forms of a Potent Imidazopyridazine Antimalarial Drug Lead: A Preformulation Study (2019)

A novel antimalarial drug lead, 6-(3-(methylsulfonyl)phenyl)-3-(4-(methylsulfonyl)phenyl)-imidazo[1,2-b]pyridazine (MMV652103), with good in vitro and in vivo antiplasmodial effects but poor aqueous solubility was investigated for preformulation beneficiation by supramolecular methods. Three polymorphs (Forms 1–3), an amorphous phase (Form 4), and a monohydrate (Form 5) were discovered and characterized by thermal analytical methods including hot stage microscopy, differential scanning calorimetry, and thermogravimetric analysis, complemented by variable-temperature powder X-ray diffraction. Single crystals of polymorphic Form 1, Form 2, and a monohydrate of the drug lead were isolated, and their structures were elucidated by X-ray diffraction, which enabled the respective molecular conformations, inter- and intramolecular interactions, and packing arrangements to be determined. A schematic energy–temperature diagram incorporating the polymorphic forms and the amorphous form of the drug lead was constructed using data gleaned from thermal analysis, kinetic solubility experiments, and observations of solvent-mediated transitions. The amorphous form of the drug lead displayed a significant increase in dissolution rate, yielding a maximum concentration of 3–4 times those of the crystalline forms after 1 h.
[Cutaneous alternariosis. Clinical diagnosis and therapeutic options]. (2004)

Localized skin infections caused by the pigmented fungi of the genus Alternaria are being increasingly observed. In the past, primarily patients receiving long-term glucocorticoid therapy were likely to have this mycosis, which is commonly traumatic, but now it is frequently encountered in organ transplantation patients. Possible therapeutic options and differential diagnosis are discussed by means of two case reports--a female renal transplant patient infected by A. alternata and a patient with iatrogenic Cushing syndrome infected by A. infectoria. Histopathological differentiation from other fungal infections may be difficult but is of therapeutic and prognostic significance. Finding short hyphae in tissue sections is an important clue. Since A. infectoria shows little conidial growth in culture, rDNA ITS sequencing offers another diagnostic possibility. Therapy has not yet been standardized. Along with surgical intervention, systemic itraconazole is the usual choice.
Robust metric velocity estimation for non-overlapping camera systems (2014)

This paper introduces a novel, robust and efficient approach for metric velocity estimation using multiple cameras with no overlapping fields of view. By incorporating rotation priors, the metric velocity estimation problem reduces to solving a set of linear equations. To determine the metric velocity, a total of three temporal point correspondences provided by at least two cameras are required. This enables the use of a 3-point RANSAC algorithm for robust outlier rejection. To enable the use of the algorithm on platforms with different computational budgets, we present three approaches with increasing computational requirements to solve for the metric velocity. The scheme can detect if the motion of the camera system is close to degeneracy and degrades gracefully. The proposed scheme is evaluated using synthetic image sequences.