gebhart/patrepeval huggingface dataset:
Quantitative tomographic imaging of intermolecular FRET in small animals (2012)

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule.
Sister chromatid exchanges, chromosomal aberrations, and cytotoxicity produced by antitumor topoisomerase II inhibitors in sensitive (DC3F) and resistant (DC3F/9-OHE) Chinese hamster cells. (1988)

4'-(9-Acridinylamino)methanesulfon-m-anisidide, etoposide, and 2-methyl-9-hydroxyellipticinium are antitumor topoisomerase II (topo II) inhibitors. The relationship between drug-induced sister chromatid exchanges (SCEs) or chromosomal aberrations and cytotoxicity was investigated in Chinese hamster cells sensitive (DC3F) and resistant (DC3F/9-OHE) to topo II inhibitors. Thirty-min drug treatments produced SCEs and chromosomal aberrations in sensitive (DC3F) cells, 4'-(9-acridinylamino)methanesulfon-m-anisidide being more potent than etoposide or 2-methyl-9-hydroxyellipticinium at equimolar concentrations. Comparable treatments of resistant (DC3F/9-OHE) cells did not produce chromosomal damage. The cytotoxicity of 4'-(9-Acridinylamino)-methanesulfon-m-anisidide was also greater than that of etoposide or 2-methyl-9-hydroxyellipticinium in DC3F cells, and no cytotoxicity was observed in DC3F/9-OHE at drug concentrations that produced more than two logs of cell kill in DC3F cells. A plot of cytotoxicity versus SCEs showed a good correlation between the two parameters. Therefore, short treatments of mammalian cells with topo II inhibitors produce reversible topo II-mediated DNA breaks which are associated with chromosomal aberrations and SCEs whose number correlates with cytotoxicity. In addition, topo II mutant DC3F/9-OHE cells were more sensitive than DC3F cells to the chromosomal, DNA cross-linking and cytotoxic effects of mitomycin C and were equally sensitive to the cytotoxic effect of camptothecin.
Synthesis and EPR Studies of Radicals and Biradical Anions of C<sub>60</sub> Nitroxide Derivatives (1997)

A series of C60 derivatives substituted with the nitroxide group 2,2,6,6-tetramethylpiperidine-1-oxyl have been synthesized. A detailed EPR and ENDOR study of the neutral radicals and of their reduction products is reported. All the neutral species give EPR spectra consisting of a main triplet of lines with ∼15 G splitting by the 14N nucleus, typical of nitroxide radicals. Some of them show additional well-resolved splittings by methyl and methylene protons, which are discussed in relation to the conformation of the nitroxide ring. When the compounds are progressively reduced under vacuum by contact with an alkali metal mirror, new EPR lines are observed; a 1:1:1 triplet with a splitting constant half that of a nitroxide radical and g = 2.0030 is attributed to biradical anions where one electron is located in the fullerene moiety and experiences a strong exchange coupling with the nitroxide unpaired electron. Frozen solution spectra of these species allow the determination of the electron−electron dipolar interaction parameters which are compared with theoretical MO calculations. The experimental values agree with a spin distribution of one unpaired electron mostly in the equatorial plane of the fullerene. Another single line which appears in the spectrum as the reduction proceeds further on (g = 1.9999) is attributed to a new species: possibly a substituted fullerene radical anion in which the nitroxide group is irreversibly reduced.
Hybrid tactile probe for damage detection and material recognition (2003)

Two health monitoring systems for damage detection in composite structures have been developed. First, a magnetic probe measures the magnetic field reflection during a frequency exploration. The local electrical conductivity of the structure is deduced from the cut-off frequency of the transfer function. Secondly, a probe with piezoelectric elements analyzes the local visco-elastic response of the structure produced at the moment of touching and stressing it. The same piezoceramic elements induces the mechanical solicitation and senses the response signal. The probes are compared in the analysis of damages induced in a coupon of quasi isotropic Carbon-epoxy material by various aggressions: 4 J- and 2 J-impacts inducing delaminations, a local burning by contact with a hot body and a simulated lightning impact by electric spark. Both probes show sensitivities to these various types of damage. For the piezoelectric probe, a "real-time" strategy, based on the processing of spectral power densities of the sensor signals, leads to an automatic measuring system classifying the damages. A software, based on fuzzy logic and implemented on a dedicated micro controller, elaborates the input data in order to realize the material damages classification. Combination the two techniques in a hybrid probe and use of the fuzzy logic procedure to the full signals to classify the structure response in a more subtle and extended way is the starting point of the design of a multisensor tactile probe able to recognize damages for a given material (NDE) or several classes of materials (robotized examinations in hostile environments).
NAD(P)+–NAD(P)H Models. 86. Nonsteric Stereochemistry in Hydride-Transfer to Sulfinylpyridinium Ion (1996)

Abstract The molecular structure of an enantiomer of nicotinamide coenzyme analog 1 has been determined by X-ray crystallography with the absolute configuration being established by the anomalous dispersion effects of all non-hydrogen atoms: (+)-1 exhibits (S)-form sticking the sulfinyl S–O out of the re face. The stereochemistry of the hydride-transfer reaction between the chiral coenzyme analogs, 1 and MenPNPH, was studied. The hydride from (S)- or (R)-MenPNPH, respectively, transfers to (S)- or (R)-1, affording the dihydropyridine compound syn-2 predominantly: That is, the reaction takes place in the face occupied by the sulfinyl oxygen. On the other hand, the transfer to (R)- or (S)-1 mainly takes place so as to afford anti-2. It has been deduced that (S)-1 reacts with (S)-MenPNPH more than twice as fast as (R)-1 does or vice versa. It has also been elucidated that the amide oxygen in MenPNPH points to 1 exclusively at the transition state of the reaction, regardless the configuration of the reagents. The intermolecular arrangement at the transition state of the reaction is discussed.
Variable Volumes of Resected Bone Resulting From Different Total Ankle Arthroplasty Systems (2016)

Primary bone resection associated with different implant hardware systems varied more on the talar side of the articulation, and the stemmed prosthesis did not result in dramatic increases in periarticular bone resection. Clinicians should weigh the effects of greater or lesser bone resection associated with various implant designs against other factors used for hardware selection.
Design Of Pre-Coding And Combining In Hybrid Analog-Digital Massive Mimo With Phase Noise (2017)

The design of massive MIMO, especially at millimeter waves, requires a trade-off between cost and power consumption, balancing the complexity and the performance in terms of achievable rate. A recent trend in the design is to<br> split the pre-coding at the transmitter and the combining at the receiver into a digital and analog part, with hybrid analog-digital schemes. In this paper the effect of phase noise is considered in the design of different hybrid analog-digital alternatives to implement massive MIMO, in particular at very high frequencies.Its effect depending on the number of RF chains, oscillators, and<br> groups of antennas is analyzed providing some insights for the system design. In order to limit the penalty introduced by the phase noise to values below 6 dB, with a number of antennas around 64, the value of phase noise increment variance should be limited below 0.005. This limit is slightly lower in a simplified architecture with more blocks driven by independent oscillators.
A Markov Model of Gap Occurrence in Continuous Glucose Monitoring Data for Realistic in Silico Clinical Trials (2023)

A Markov model describing CGM gaps was developed and validated on two real datasets. The model describes well the number of gaps for each sensor, the gap distribution over monitoring days, and the gap durations. Such a model can be integrated into existing diabetes simulators to realistically simulate CGM gaps in ISCTs and thus enable the development of more effective and robust diabetes management strategies.
Total zinc absorption in young women, but not fractional zinc absorption, differs between vegetarian and meat-based diets with equal phytic acid content (2006)

Zn bioavailability is often lower in vegetarian diets mainly due to low Zn and high phytic acid contents. The objective of the present study was to determine the fractional and total absorption of Zn from a vegetarian diet in comparison with meat diets with equal concentrations of phytic acid. A randomized cross-over design, comprising three whole-day diet periods of 5 d each, with a vegetarian diet or diets containing Polish-produced meat or Danish-produced meat, was conducted. Twelve healthy female subjects completed the study. All diets had a high content of phytic acid (1250 micromol/d) and in the meat diets the main meals contained 60 g pork meat. All main meals were extrinsically labelled with the radioactive isotope 65Zn and absorption of Zn was measured in a whole-body counter. The mean Zn content of the whole-day diet was: Polish meat diet 9.9 (SE 0.14) mg, Danish meat diet 9.4 (SE 0.19) mg and vegetarian diet 7.5 (SE 0.18) mg. No difference was observed in the fractional absorption of Zn (Polish meat diet: 27 (SE 1.2) %, Danish meat diet: 27 (SE 1.9) % and vegetarian diet: 23 (SE 2.6) %). A significantly lower amount of total Zn was absorbed from the vegetarian diet (mean Zn absorption of Polish meat diet: 2.7 (SE 0.12) mg/d (P<0.001), Danish meat diet: 2.6 (SE 0.17) mg/d (P=0.006) and vegetarian diet: 1.8 (SE 0.20) mg/d). In conclusion, the vegetarian diet compared with the meat-based diets resulted in lower amounts of absorbed Zn due to a higher content of Zn in the meat diets, but no difference was observed in the fractional absorption of Zn.
Wafer-Scale Fabrication of Nanofluidic Arrays and Networks Using Nanoimprint Lithography and Lithographically Patterned Nanowire Electrodeposition Gold Nanowire Masters (2012)

Wafer scale (cm(2)) arrays and networks of nanochannels were created in polydimethylsiloxane (PDMS) from a surface pattern of electrodeposited gold nanowires in a master-replica process and characterized with scanning electron microscopy (SEM), atomic force microscopy (AFM), and fluorescence imaging measurements. Patterns of gold nanowires with cross-sectional dimensions as small as 50 nm in height and 100 nm in width were prepared on silica substrates using the process of lithographically patterned nanowire electrodeposition (LPNE). These nanowire patterns were then employed as masters for the fabrication of inverse replica nanochannels in a special formulation of PDMS. SEM and AFM measurements verified a linear correlation between the widths and heights of the nanowires and nanochannels over a range of 50 to 500 nm. The PDMS replica was then oxygen plasma-bonded to a glass substrate in order to create a linear array of nanofluidic channels (up to 1 mm in length) filled with solutions of either fluorescent dye or 20 nm diameter fluorescent polymer nanoparticles. Nanochannel continuity and a 99% fill success rate was determined from the fluorescence imaging measurements, and the electrophoretic injection of both dye and nanoparticles in the nanochannel arrays was also demonstrated. Employing a double LPNE fabrication method, this master-replica process was also used to create a large two-dimensional network of crossed nanofluidic channels.
Thymoquinone challenges UHRF1 to commit auto-ubiquitination: a key event for apoptosis induction in cancer cells (2018)

Down-regulation of UHRF1 (Ubiquitin-like containing PHD and Ring Finger 1) in Jurkat cells, induced by natural anticancer compounds such as thymoquinone, allows re-expression of tumor suppressor genes such as <i>p73</i> and <i>p16</i><sup><i>INK4A</i></sup> . In order to decipher the mechanisms of UHRF1 down-regulation, we investigated the kinetic of expression of HAUSP (herpes virus-associated ubiquitin-specific protease), UHRF1, cleaved caspase-3 and p73 in Jurkat cells treated with thymoquinone. We found that thymoquinone induced degradation of UHRF1, correlated with a sharp decrease in HAUSP and an increase in cleaved caspase-3 and p73. UHRF1 concomitantly underwent a rapid ubiquitination in response to thymoquinone and this effect was not observed in the cells expressing mutant UHRF1 RING domain, suggesting that UHRF1 commits an auto-ubiquitination through its RING domain in response to thymoquinone treatment. Exposure of cells to Z-DEVD, an inhibitor of caspase-3 markedly reduced the thymoquinone-induced down-regulation of UHRF1, while proteosomal inhibitor MG132 had no such effect. The present findings indicate that thymoquinone induces in cancer cells a fast UHRF1 auto-ubiquitination through its RING domain associated with HAUSP down-regulation. They further suggest that thymoquinone-induced UHRF1 auto-ubiquitination followed by its degradation is a key event in inducing apoptosis through a proteasome-independent mechanism.
Imaging by Elemental and Molecular Mass Spectrometry Reveals the Uptake of an Arsenolipid in the Brain of <i>Drosophila melanogaster</i> (2016)

Arsenic-containing lipids (arsenolipids) are natural products of marine organisms such as fish, invertebrates, and algae, many of which are important seafoods. A major group of arsenolipids, namely, the arsenic-containing hydrocarbons (AsHC), have recently been shown to be cytotoxic to human liver and bladder cells, a result that has stimulated interest in the chemistry and toxicology of these compounds. In this study, elemental laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS) and molecular matrix-assisted laser desorption/ionization (MALDI-)MS were used to image and quantify the uptake of an AsHC in the model organism Drosophila melanogaster. Using these two complementary methods, both an enrichment of arsenic and the presence of the AsHC in the brain were revealed, indicating that the intact arsenolipid had crossed the blood-brain barrier. Simultaneous acquisition of quantitative elemental concentrations and molecular distributions could allow new insight into organ-specific enrichment and possible transportation processes of arsenic-containing bioactive compounds in living organisms.
A Nonribosomal Peptide Synthetase-Derived Iron(III) Complex from the Pathogenic Fungus<i>Aspergillus fumigatus</i> (2013)

Small molecules (SMs) play central roles as virulence factors of pathogenic fungi and bacteria; however, genomic analyses suggest that the majority of microbial SMs have remained uncharacterized. Based on microarray analysis followed by comparative metabolomics of overexpression/knockout mutants, we identified a tryptophan-derived iron(III)-complex, hexadehydro-astechrome (HAS), as the major product of the cryptic has nonribosomal peptide synthetase (NRPS) gene cluster in the human pathogen Aspergillus fumigatus. Activation of the has cluster created a highly virulent A. fumigatus strain that increased mortality of infected mice. Comparative metabolomics of different mutant strains allowed to propose a pathway for HAS biosynthesis and further revealed cross-talk with another NRPS pathway producing the anticancer fumitremorgins.
Amyloid-β Aggregates Cause Alterations of Astrocytic Metabolic Phenotype: Impact on Neuronal Viability (2010)

Amyloid-beta (Abeta) peptides play a key role in the pathogenesis of Alzheimer's disease and exert various toxic effects on neurons; however, relatively little is known about their influence on glial cells. Astrocytes play a pivotal role in brain homeostasis, contributing to the regulation of local energy metabolism and oxidative stress defense, two aspects of importance for neuronal viability and function. In the present study, we explored the effects of Abeta peptides on glucose metabolism in cultured astrocytes. Following Abeta(25-35) exposure, we observed an increase in glucose uptake and its various metabolic fates, i.e., glycolysis (coupled to lactate release), tricarboxylic acid cycle, pentose phosphate pathway, and incorporation into glycogen. Abeta increased hydrogen peroxide production as well as glutathione release into the extracellular space without affecting intracellular glutathione content. A causal link between the effects of Abeta on glucose metabolism and its aggregation and internalization into astrocytes through binding to members of the class A scavenger receptor family could be demonstrated. Using astrocyte-neuron cocultures, we observed that the overall modifications of astrocyte metabolism induced by Abeta impair neuronal viability. The effects of the Abeta(25-35) fragment were reproduced by Abeta(1-42) but not by Abeta(1-40). Finally, the phosphoinositide 3-kinase (PI3-kinase) pathway appears to be crucial in these events since both the changes in glucose utilization and the decrease in neuronal viability are prevented by LY294002, a PI3-kinase inhibitor. This set of observations indicates that Abeta aggregation and internalization into astrocytes profoundly alter their metabolic phenotype with deleterious consequences for neuronal viability.
Measuring Similarity Between Any Pair of Passengers Using Smart Card Usage Data (2021)

Recent years have witnessed considerable progress in the application of Internet of Things (IoT) technology in smart transportation systems. The wider presence of Wi-Fi networks in subway gates allows passengers to use the quick response (QR) code of mobile phone applications for entrance. The network established by gates has become a medium which connects stations and passengers. However, in addition to directly monitoring the passenger flow, the potential application of the smart card usage data collected by the gates remains an open topic. Although there are several clustering-based works devoted to revealing passengers’ travel behavior patterns, research on the social attributes of subway passengers is very limited. To fill the gap, this article proposes a novel method to mine similarity information of passengers by leveraging passengers’ communication behaviors hidden in subway card usage data. Passengers are first organized as a graph, which not only reflects the interactions between them but also incorporates the context information of subway stations. Then, the node embedding is used to encode the information contained in the graph and with the use of cosine similarity, the similarity between two passengers is measured. Extensive experiments on two real-world location-based social network data sets and extended experiments on a Shanghai subway data set are conducted. The results show that the proposed method can effectively improve the accuracy of similarity measurement and provide social features that are distinguishable from travel behavior patterns.
Techniques for automatic digital video composition (1999)

Recent developments in digital technology have enabled a class of video-based applications that were not previously viable. However, digital video production systems face the challenge of accessing the inherently linear and time-dependent media of audio and video, and providing effective means of composing them into a cohesive piece for presentation. Moreover, there are no appropriate metrics that allow for assessment of the quality of an automatically-composed video piece. Techniques presently available are limited in scope, and do not account for all the features of a composition. This dissertation presents metrics that evaluate the quality of a video composition. In addition, it proposes techniques for automatic composition of video presentations as well as improvements in access to digital video data. Yet another challenge faced by video production systems is the customization of the presentation to suit user profiles. For instance, certain elements of video compositions, such as v...
Genetic dissection of lupus pathogenesis: a recipe for nephrophilic autoantibodies (1999)

Sle1 and Sle3 are 2 loci that confer susceptibility to lupus nephritis in the NZM2410 strain of mice. Our previous work has shown that B6.NZMc1 mice, congenic for Sle1, exhibit loss of tolerance to chromatin but do not develop any pathogenic autoantibodies or disease. B6.NZMc7 mice, congenic for Sle3, exhibit low-grade polyclonal B- and T-cell activation, elevated CD4/CD8 ratios, and mildly penetrant glomerulonephritis. In contrast to these monocongenics, the present study reveals that B6.NZMc1|c7 mice, bicongenic for Sle1 and Sle3, exhibit splenomegaly, significantly expanded populations of activated B and CD4(+) T cells, and a robust, variegated IgG autoantibody response targeting multiple components of chromatin (including double-stranded DNA), intact glomeruli, and basement membrane matrix antigens. As one might predict, these mice, particularly the females, exhibit highly penetrant glomerulonephritis. These findings lend strong support to a two-step epistatic model for the formation of pathogenic, nephrophilic autoantibodies in lupus. Whereas loci such as Sle1 may serve to breach tolerance to chromatin, full-blown pathogenic maturation of the autoantibody response appears to require additional input from other loci (such as Sle3) and gender-based factors.
The Role of Laparoscopy in Pediatric Urology (2003)

Laparoscopy (and minimally invasive surgery in general) has been slower to gain acceptance among pediatric urologists than among many other specialists. This is largely because of the reconstructive rather than extirpative focus of pediatric urology, as well as the small size of our patients. Recent advances in technology, as well as innovative thinking regarding applications for laparoscopy, have begun to change the situation. For example, laparoscopy has been used for more than 20 years as a diagnostic adjunct in the management of the nonpalpable testicle [1]. With the introduction of cord clipping for a first-stage Fowler-Stephens operation [2] and then laparoscopic orchidopexy [3], the era of therapeutic laparoscopy in pediatric urology was born. Today, laparoscopic orchidopexy is a well-accepted part of the urologist’s repertoire for dealing with high testicles [4–8].