gebhart/patrepeval huggingface dataset:
Total Synthesis of (±)-Deethyleburnamonine and Vindeburnol (RU 24722) with the Corresponding Nitriles as Starting Material (1999)

Cyclisation occurred during base treatment of cis-nitrile (5).The resulting new imine (6) was converted into the therapeutically important deethyleburnamonine (4).Total synthesis of vindeburnol (RU 24722) (3), another important drug, was achieved in one step starting from the trans-nitrile (9).(+)-Vincamine (1)' and (+)-eburnamonine (2), as well as the optical antipode of 2, (-)-eburnamonine, all possessing an ethyl group at C-20, have been recognised world-wide as important pharmacological compounds and are clinically used in many countries.'It has been demonstrated during the last decade that the ethyl group is not alone responsible for the activity.In fact, some unnatural 20-deethyl derivatives of 1 and 2 also display interesting pharmaceutical activities.Both vindeburnol (3)' and (+)deethyleburnamonine (4)' belong to that group.Many synthetic studies have'been dedicated to the total synthesis of 3 and 4 7 but the procedures suggested have tended to be long and tedious.Our continuous interest in natural products, and in achieving better yields and lower cost for the synthesis of key compounds, led us to focus on the nitriles, which are both stable and easily prepared.In this publication, we show that appropriate nitriles can be used as precursors for vindebumol (3) and (*)- deethyleburnamonine (4).
245-GHz InAlN/GaN HEMTs With Oxygen Plasma Treatment (2011)

We report lattice-matched In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.17</sub> Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.83</sub> N/GaN high-electron mobility transistors on a SiC substrate with a record current gain cutoff frequency ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fT</i> ). The key to this performance is the use of an oxygen plasma treatment to form a thin oxide layer on the InAlN barrier and to reduce the gate leakage current by more than two orders of magnitude. In addition, the RF transconductance ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ) collapse is reduced in the O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -treated devices, which results in a significant improvement in the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> . In a transistor with a gate length of 30 nm, an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> of 245 GHz is achieved, the highest value ever reported in GaN-based field-effect transistors.
Immunochemical studies of fibroblasts from patients with methylmalonyl-CoA mutase apoenzyme deficiency: detection of a mutation interfering with mitochondrial import. (1987)

Methylmalonyl-CoA mutase (2-methylmalonyl-CoA CoA-carbonylmutase, EC 5.4.99.2) is a mitochondrial enzyme whose deficiency in man leads to several biochemically and clinically heterogenous++ forms of methylmalonic acidemia. Intact fibroblasts from 21 patients with mutase apoenzyme deficiency have been pulse-labeled with [3H]leucine or [35S]methionine to determine how amounts of newly synthesized mutase recovered from these cells by immunoprecipitation compare with the amounts of steady-state crossreacting material previously determined. Ten lines (3 mut-, 7 mut 0 ), previously shown to have detectable steady-state crossreacting material, had amounts of newly synthesized mutase that varied from similar (7 lines) to considerably greater than (3 lines) the steady-state amounts. Of 11 lines that had no detectable steady-state crossreacting material, 6 had no detectable newly synthesized mutase, and 5 had amounts of mutase ranging from just detectable to almost half that of control. This result suggests that, at least for this latter group, one effect of the mutation in the mutase gene is to reduce the stability of the mutase protein. We examined fibroblasts from 48 patients with mutase apoenzyme deficiency to determine the sizes of the mature mutase subunit and the mutase precursor accumulated in the presence of the mitochondrial transport inhibitor rhodamine 6G. Of the 38 lines that had detectable newly synthesized mutase, only 2, lines 437 and 552, showed a pattern different from that generated by the normal precursor and mature subunits. Line 437 had two immunoprecipitable precursor proteins in the presence of rhodamine, each of which appeared to be transported and processed in the cells to produce two distinct mature proteins. Line 552 also had two anti-mutase reactive proteins in the presence of rhodamine, but each was smaller than the normal mature subunit and neither appeared to be proteolytically processed. The defect in line 552 is almost certainly an amino-terminal deletion that removes the leader peptide necessary for proper uptake and cleavage of the mutase precursor; this represents a clear example of a natural human mutation that interferes with mitochondrial transport of a protein.
A cellular automata simulation of atomic layer etching (2018)

A two-dimensional, cellular automata model for atomic layer etching (ALE) is presented and used to predict the etch rate and the evolution of the roughness of various surfaces as a function of the efficiencies or probabilities of the adsorption and removal steps in the ALE process. The atoms of the material to be etched are initially placed in a two-dimensional array several layers thick. The etch follows the two step process of ALE. First, the initial reaction step (e.g., Cl reacting with Si) is assumed to occur at 100% efficiency activating the exposed, surface atoms; that is, all exposed atoms react with the etching gas. The second reaction step (e.g., Ar ion bombardment or sputtering) occurs with efficiencies that are assumed to vary depending on the exposure of the surface atoms relative to their neighbors and on the strength of bombardment. For sufficiently high bombardment or sputtering, atoms below the activated surface atoms can also be removed, which gives etch rates greater than one layer per ALE cycle. The bounds on the efficiencies of the second removal step are extracted from experimental measurements and fully detailed molecular dynamics simulations from the literature. A trade-off is observed between etch rate and surface roughness as the Ar ion bombardment is increased.
Heterogeneous Kinetics of H 2 O, HNO 3 and HCl on HNO 3 hydrates (α-NAT, β-NAT, NAD) in the range 175–200 K (2016)

Abstract. Experiments on the title compounds have been performed using a multidiagnostic stirred-flow reactor (SFR) in which the gas- as well as the condensed phase has been simultaneously investigated under stratospheric temperature conditions in the range 175–200 K. Wall interactions of the title compounds have been taken into account using Langmuir adsorption isotherms in order to close the mass balance between deposited and desorbed (recovered) compounds. Thin solid films at 1 micron or so typical thickness have been used as a proxy for atmospheric ice particles and have been deposited on a Si window of the cryostat where the optical element was the only cold point in the deposition system. FTIR absorption spectrometry in transmission as well as partial and total pressure measurement using residual gas MS and sensitive pressure gauges have been employed in order to monitor growth and evaporation processes as a function of temperature using both pulsed gas admission and continuous monitoring under SFR conditions. Thin solid H2O ice films were used as the starting point throughout, with the initial formation of α-NAT followed by the gradual transformation of α → β-NAT starting at 185 K. NAD was formed at once at somewhat larger partial pressures of HNO3 deposited on pure H2O ice. In contrast to published reports the formation of α-NAT proceeded without prior formation of an amorphous HNO3/H2O layer and always resulted in β-NAT. For α- and β-NAT the temperature dependent accommodation coefficient α(H2O) and α(HNO3), the evaporation flux Jev(H2O) and Jev(HNO3) and the resulting saturation vapor pressure Peq(H2O) and Peq(HNO3) were measured and compared to binary phase diagrams of HNO3/H2O in order to afford thermochemical control of the kinetic parameters. The resulting kinetic and thermodynamic parameters of activation energies for evaporation (Eev) and standard heats of evaporation ΔHev0 of H2O and HNO3 for α- and β-NAT, respectively, led to an estimate for the relative standard enthalpy difference between α- and β-NAT of −6.0 ± 20 kJ/mol in favor of β-NAT, as expected, despite a significantly larger value of Eev for HNO3 in α-NAT. This in turn implies a substantial activation energy for HNO3 accommodation in α- compared to β-NAT where Eacc(HNO3) is essentially zero. The kinetic (α(HCl), Jev(HCl)) and thermodynamic (Peq(HCl)) parameters of HCl-doped α – and β-NAT have been determined under the assumption that HCl adsorption did not significantly affect α(H2O) and α(HNO3) as well as the evaporation flux Jev(H2O). Jev(HCl) and Peq(HCl) on both α- and β-NAT are larger than the corresponding values for HNO3 across the investigated temperature range but significantly smaller than the values for pure H2O ice. This means that once contaminated with HCl the "impurity" HCl will persist along with HNO3 upon complete evaporation of the atmospheric ice particle. We comment on recent laboratory results involving the HNO3/H2O system using Chilled Mirror Hygrometers (CMH) in light of the present kinetic results.
The ontogeny of discourse structure mimics the development of literature (2016)

Discourse varies with age, education, psychiatric state and historical epoch, but the ontogenetic and cultural dynamics of discourse structure remain to be quantitatively characterized. To this end we investigated word graphs obtained from verbal reports of 200 subjects ages 2-58, and 676 literary texts spanning ~5,000 years. In healthy subjects, lexical diversity, graph size, and long-range recurrence departed from initial near-random levels through a monotonic asymptotic increase across ages, while short-range recurrence showed a corresponding decrease. These changes were explained by education and suggest a hierarchical development of discourse structure: short-range recurrence and lexical diversity stabilize after elementary school, but graph size and long-range recurrence only stabilize after high school. This gradual maturation was blurred in psychotic subjects, who maintained in adulthood a near-random structure. In literature, monotonic asymptotic changes over time were remarkable: While lexical diversity, long-range recurrence and graph size increased away from near-randomness, short-range recurrence declined, from above to below random levels. Bronze Age texts are structurally similar to childish or psychotic discourses, but subsequent texts converge abruptly to the healthy adult pattern around the onset of the Axial Age (800-200 BC), a period of pivotal cultural change. Thus, individually as well as historically, discourse maturation increases the range of word recurrence away from randomness.
THYROXINE 5′-DEIODINASE ACTIVITY IN BROWN ADIPOSE TISSUE (1983)

Homogenates of rat brown adipose tissue (BAT) and epididymal fat pad (EPI) catalyze the 5'-deiodination of 3,3',5'-triiodothyronine (rT3) in the presence of dithiothreitol. BAT, but not EPI, catalyzes the 5'-deiodination of thyroxinE (T4) generating equal amounts of 3,5,3'-triiodothyronine (T3) and iodide. BAT 5'-deiodinase activity was unaffected by propylthiouracil (PTU) and was elevated in hypothyroid rats, whereas EPI 5'-deiodinase was totally inhibited by PTU and was depressed in hypothyroidism. These results indicate that type II (PTU-insensitive) 5'-iodothyronine deiodinase activity is present in BAT.
Nanocapsules for the co-delivery of selol and doxorubicin to breast adenocarcinoma 4T1 cells in vitro (2017)

Nanocapsules (NCS-DOX) with an oily core of selol and a shell of poly(methyl vinyl ether-co-maleic anhydride) covalently conjugated to doxorubicin were developed. These nanocapsules are spherical, with an average hydrodynamic diameter of about 170 nm, and with negative zeta potential. NCS-DOX effectively co-delivered the selol and the doxorubicin into 4T1 cells and changed the intracellular distribution of DOX from the nuclei to the mitochondria. Moreover, a significantly increased cytotoxicity against 4T1 cells was observed, which is suggestive of additive or synergic effect of selol and doxorubicin. In conclusion, PVM/MA nanocapsules are suitable platforms to co-deliver drugs into cancer cells.
Conformité, microstructure et purété de films d'aluminium déposés sur substrats de Si patternés. Etude comparative selon le procédé de dépôt : pulvérisation plasma, ablation laser, dépôt chimique en phase vapeur (2010)

National audience
Plant‐Based Anticancer Molecules: A Chemical and Biological Profile of Some Important Leads (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Characterization of Interactions between the Anti-apoptotic Protein BAG-1 and Hsc70 Molecular Chaperones (1998)

The anti-cell death protein BAG-1 binds to 70-kDa heat shock proteins (Hsp70/Hsc70) and modulates their chaperone activity. Among other facilitory roles, BAG-1 may serve as a nucleotide exchange factor for Hsp70/Hsc70 family proteins and thus represents the first example of a eukaryotic homologue of the bacterial co-chaperone GrpE. In this study, the interactions between BAG-1 and Hsc70 are characterized and compared with the analogous GrpE-DnaK bacterial system. In contrast to GrpE, which binds DnaK as a dimer, BAG-1 binds to Hsc70 as a monomer with a 1:1 stoichiometry. Dynamic light scattering, sedimentation equilibrium, and circular dichroism measurements provided evidence that BAG-1 exists as an elongated, highly helical monomer in solution. Isothermal titration microcalorimetry was used to determine the complex stoichiometry and an equilibrium dissociation constant, KD, of 100 nM. Kinetic analysis using surface plasmon resonance yielded a KD consistent with the calorimetrically determined value. Molecular modeling permitted a comparison of structural features between the functionally homologous BAG-1 and GrpE proteins. These data were used to propose a mechanism for BAG-1 in the regulation of Hsp70/Hsc70 chaperone activity.
Network Coding-Aware Queue Management for Unicast Flows over Coded Wireless Networks (2010)

We are interested in unicast flows over wireless networks with intersession network coding (such as COPE). TCP flows over coded wireless networks do not fully exploit network coding opportunities due to their bursty behavior and to the fact that TCP is agnostic to the underlying network coding. In this paper, we take the following steps. First, we formulate congestion control for unicast flows over coded wireless networks as a network utility maximization problem and we present a distributed solution. Second, by mimicking the structure of the optimal solution, we propose a "network-coding aware" queue management scheme (NCAQM) at intermediate nodes. We make no changes to TCP or MAC protocols. We demonstrate, via simulation, that TCP over NCAQM performs significantly better than TCP over COPE.
Sonochemical Insertion of Silver Nanoparticles into Two-Dimensional Mesoporous Alumina (2007)

Nanocomposites of Ag nanoparticles/mesoporous γ-Al2O3 were synthesized by sonochemical treatment of the precursors. The sonicated product consisted of Ag nanoparticles dispersed in the bayerite [Al(OH)3]/boehmite [AlO(OH)] matrix. Upon calcination under argon, the Ag nanoparticles were found to be incorporated in a mesoporous structure of γ-Al2O3. For a solid containing 3.7 wt % Ag nanoparticles, the nanoparticles remained on the surface of mesoporous alumina and hence BET surface area increased as compared to pristine γ-Al2O3, whereas for 10.5 wt % Ag nanoparticles, the surface area decreased. HRTEM studies corroborated this fact and showed that, at higher Ag concentrations, Ag nanoparticles blocked the pores and also increased the diameter of the pores of mesoporous alumina. The products with the 3.7 wt % silver concentration had uniform pores with narrow pore size distribution of the pores, although the TEM pictures indicated wormhole channel motifs. The formation of the mesoporous structure was governed by the templating behavior of the organic groups (mainly formic acid) attached to the alumina nanoparticles. The shape of the pores closely resembled the two-dimensional hexagonal mesoporous structure with the P6mm space group, as observed from small-angle X-ray diffraction experiments. Diffuse reflection optical spectra at 27 °C showed an absorption band (419−424 nm) due to the surface plasmon of Ag inside the ceramic matrix.
Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome (2005)

The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In this study, we have evaluated the reproducibility of the SAGE method and identified the factors that affect it. The determination coefficient (R2 ) for the reproducibility of SAGE is 0.96. However, there are some factors that can affect the reproducibility of SAGE, such as the replication of concatemers and ditags, the number of sequenced tags and double PCR amplification of ditags. Thus, corrections for these factors must be made to ensure the reproducibility and accuracy of SAGE results. A bioinformatic analysis of SAGE data is also presented in order to eliminate these artifacts. Finally, the current study shows that increasing the number of sequenced tags improves the power of the method to detect transcripts and their regulation by experimental conditions.
Phase transitions in stochastic self-organizing maps (1997)

We describe the development of neighborhood-preserving stochastic maps in terms of a probabilistic clustering problem. Starting from a cost function for central clustering that incorporates distortions from channel noise, we derive a soft topographic vector quantization algorithm (STVQ) which is based on the maximum entropy principle, and which maximizes the corresponding likelihood in an expectation-maximization fashion. Among other algorithms, a probabilistic version of Kohonen's self-organizing map (SOM) is derived from STVQ as a computationally efficient approximation of the $E$ step. The foundation of STVQ in statistical physics motivates a deterministic annealing scheme in the temperature parameter $\ensuremath{\beta}$, and leads to a robust minimization algorithm of the clustering cost function. In particular, this scheme offers an alternative to the common stepwise shrinking of the neighborhood width in the SOM, and makes it possible to use its neighborhood function solely to encode the desired neighborhood relations between the clusters. The annealing in $\ensuremath{\beta}$, which corresponds to a stepwise refinement of the resolution of representation in data space, leads to the splitting of an existing cluster representation during the ``cooling'' process. We describe this phase transition in terms of the covariance matrix C of the data and the transition matrix H of the channel noise, and calculate the critical temperatures and modes as functions of the eigenvalues and eigenvectors of C and H. The analysis is extended to the phenomenon of the automatic selection of feature dimensions in dimension-reducing maps, thus leading to a ``batch'' alternative to the Fokker-Planck formalism for on-line learning. The results provide insights into the relation between the width of the neighborhood and the temperature parameter $\ensuremath{\beta}$: It is shown that the phase transition which leads to the representation of the excess dimensions can be triggered not only by a change in the statistics of the input data but also by an increase of $\ensuremath{\beta}$, which corresponds to a decrease in noise level. The theoretical results are validated by numerical methods. In particular, a quantity equivalent to the heat capacity in thermodynamics is introduced to visualize the properties of the annealing process.
Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis (2015)

Periodontitis is a common oral disease. Although it can be treated, the disease may reoccur without obvious symptoms. Current clinical examination parameters are useful in disease diagnosis but cannot adequately predict the outcome of individual tooth sites after treatment. A link between the subgingival microbiota and periodontitis was identified previously; however, it remains to be investigated whether the microbiome can serve as a diagnostic and prognostic indicator. In this study, for the first time, we characterized the subgingival microbiome of individual tooth sites before and after treatment using a large-scale metagenomic analysis. Our longitudinal study revealed changes in the microbiota in taxonomic composition, cooccurrence of subgingival microorganisms, and functional composition. Using the microbiome profiles, we were able to classify the clinical states of subgingival plaque samples with a high accuracy. Follow-up clinical examination of sampled sites indicates that the subgingival microbiome profile shows promise for the development of diagnostic and prognostic tools.
Supplementary Table 5 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome (2023)

Supplementary Table 5 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome
Video time-lapse microscopy of phagocytosis and intracellular fate of crystalline nickel sulfide particles in cultured mammalian cells. (1982)

The endocytosis and intracellular distribution of carcinogenic crystalline nickel sulfide (NiS) particles in Chinese hamster ovary cells were studied using time-lapse video recording with phase-contrast and bright-field optics. Crystalline NiS particles were phagocytosedd by Chinese hamster ovary cells in regions of membrane ruffling. While these particles may remain bound to the cell surface for variable time intervals (min to hr), their internalization generally required only 7 to 10 min. Endocytosed crystalline NiS particles exhibited saltatory motion, and lysosomes were observed to interact repeatedly with the particles in a manner similar to that observed during the digestion of macropinosomes. Particles were never observed to be exocytosed from the cell, and with time, most of the internalized particles aggregated in the region around the nucleus. After 24 to 48 hr, particle saltation decreased to a point where the particle position became relatively fixed in the perinuclear region, and in some instances, this was associated with a conspicuous vacuole formation around the particles. It is concluded that the uptake and distribution of crystalline NiS particles occur by normal endocytic and saltatory processes as occur during the formation and breakdown of macropinosomes. The observed lysosomal interaction with phagocytoses cytoplasmic NiS may accelerate particulate nickel dissolution allowing entry of ionic nickel into the nucleus.