gebhart/patrepeval huggingface dataset:
Complementarity of passive samplers and biomonitoring tools to evaluate surface water contamination by pesticides in agricultural catchments (2015)

Grab sampling may be scarcely adequate to evaluate the impact on surface waters of pesticide used in agriculture because of its poor spatiotemporal representativeness compared to the high variability of the contamination patterns. Indeed, it is still not easy to link the effect of agricultural practice changes to water quality at the catchment scale. Furthermore, biological indicators may also be useful in addition to pesticide concentration determination to evaluate their impact on ecosystems. In this way, the contribution of new integrative tools has been evaluated. Passive samplers and biological indicators have been applied together at the catchment scale so as to identify their coherence and complementarity. The tested chemical tools are the passive-SBSE (Stir Bar Sorptive Extraction) dedicated to hydrophobic to moderately hydrophilic compounds and the POCIS (Polar Organic Chemical Integrative Sampler) dedicated to hydrophilic compounds. As concerns biological approach, it consisted in the in situ deployment of i) caging methodology with a highly ecological relevant amphipod species, Gammarus fossarum, coupled to the measurement of toxicity markers (acetylcholine esterase inhibition, feeding rate) and ii) the study of microbial and macro-invertebrate communities (measurement of leaf decomposition rates) as well as phototrophic periphytic communities (measurement of Pollution Induced Community Tolerance). These tools have been applied during june 2014 (corresponding to vineyard and corn period of application) in two contrasted agricultural catchments. The Ardières basin situated in the Beaujolais region (France) is submitted to viticulture pressure and a marked pesticide contamination has already been highlighted. Three measurement stations have been chosen so as to search for a contamination gradient from upstream to downstream. The Coise basin is located in the Monts du Lyonnais (France) in a zone of mixed farming breeding with a predominance of meadows, corn and cereals. Three measurement stations have been selected on three sub-catchments corresponding to differentiated pesticide use. In total, 49 pesticides (28 herbicides, 9 fungicides and 12 insecticides) have been analyzed as well as potential confusing parameters (metal(oïd)s, nutrients, temperature, luminosity, water flow). Results show the high coherence of chemical and biological tools responses. All of them were able to reflect the spatial contamination gradients as well as the specific contamination and impact associated to each agro-pedo-climatical context. A weekly exposure also permitted to take into account the temporal variability of the contamination according to flood occurrence. Finally, their sensitivity, reactivity and integration capacity make these tools relevant and promising to assess agricultural pesticide impact on surface water in addition to grab sampling.
Association of somatic ERCC2 mutations with cisplatin sensitivity in muscle-invasive urothelial carcinoma. (2014)

4510 Background: Cisplatin-based combination chemotherapy is the standard of care for patients with muscle invasive urothelial carcinoma. Pathologic downstaging to pT0/pTis after neoadjuvant cisplatin-based chemotherapy is associated with improved survival, although the molecular determinants of cisplatin sensitivity are incompletely understood. Recent reports have identified somatic mutations in ERCC2, a nucleotide excision repair gene, in 7-12% of bladder cancers. Preclinical evidence suggests that defects in the nucleotide excision repair (NER) pathway mediate cisplatin sensitivity. Methods: We performed whole exome sequencing of pre-treatment tumor and germline DNA from 51 patients with muscle invasive urothelial carcinoma who received neoadjuvant cisplatin-based chemotherapy followed by cystectomy (26 pT0/pTis “responders”, 25 pT2+ “non-responders”). Computational methods were employed to identify somatic mutations that occurred preferentially in cisplatin responders. Functional validation of significantly enriched mutations was performed using cellular cisplatin and UV sensitivity assays. Results: Somatic ERCC2 mutations were observed in 38.5% of responders and 0% of non-responders (q < 0.01). ERCC2 was the only gene enriched in the cisplatin responders compared with non-responders. ERCC2 mutations clustered within or near conserved helicase domains required for ERCC2 function. Expression of the identified ERCC2 mutants in an ERCC2-deficient cell line failed to rescue cisplatin and UV sensitivity compared to wild-type ERCC2. Conclusions: Somatic ERCC2 mutation is associated with cisplatin sensitivity in muscle invasive urothelial carcinoma. These results may inform the use of cisplatin-containing regimens in muscle invasive urothelial carcinoma, and potentially other ERCC2-mutated tumors.
Association studies and gene expression analyses of the DISC1‐interacting molecules, pericentrin 2 (PCNT2) and DISC1‐binding zinc finger protein (DBZ), with schizophrenia and with bipolar disorder (2009)

Disrupted-in-Schizophrenia 1 (DISC1) and its molecular cascade have been implicated in the pathophysiology of major psychoses. Previously, we identified pericentrin 2 (PCNT2) and DISC1-binding zinc finger protein (DBZ) as binding partners of DISC1; further, we observed elevated expression of PCNT2 in the postmortem brains and in the lymphocytes of bipolar disorder patients, compared to controls. Here, we examined the association of PCNT2 with schizophrenia in a case-control study of Japanese cohorts. We also examined the association of DBZ with schizophrenia and with bipolar disorder, and compared the mRNA levels of DBZ in the postmortem brains of schizophrenia, bipolar and control samples. DNA from 180 schizophrenia patients 201 controls were used for the association study of PCNT2 and DBZ with schizophrenia. Association of DBZ with bipolar disorder was examined in DNA from 238 bipolar patients and 240 age- and gender-matched controls. We observed significant allelic and genotypic associations of the PCNT2 SNPs, rs2249057, rs2268524, and rs2073380 (Ser/Arg) with schizophrenia; the association of rs2249057 (P = 0.002) withstand multiple testing correction. Several two SNP- and three SNP-haplotypes showed significant associations; the associations of haplotypes involving rs2249057 withstand multiple testing correction. No associations were observed for DBZ with schizophrenia or with bipolar disorder; further, there was no significant difference between the DBZ mRNA levels of control, schizophrenia and bipolar postmortem brains. We suggest a possible role of PCNT2 in the pathogenesis of schizophrenia. Abnormalities of PCNT2, the centrosomal protein essential for microtubule organization, may be suggested to lead to neurodevelopmental abnormalities.
Optimal Cooperative Power Allocation for Energy Harvesting Enabled Relay Networks (2014)

In this paper, we present a new power allocation scheme for a decode-and-forward (DF) relaying-enhanced cooperative wireless system. While both source and relay nodes may have limited traditional brown power supply or fixed green energy storage, the hybrid source node can also draw power from the surrounding radio frequency (RF) signals. In particular, we assume a deterministic RF energy harvesting (EH) model under which the signals transmitted by the relay serve as the renewable energy source for the source node. The amount of harvested energy is known for a given transmission power of the forwarding signal and channel condition between the source and relay nodes. To maximize the overall throughput while meeting the constraints imposed by the non-sustainable energy sources and the renewable energy source, an optimization problem is formulated and solved. Based on different harvesting efficiency and channel condition, closed form solutions are derived to obtain the optimal source and relay power allocation jointly. It is shown that instead of demanding high on-grid power supply or high green energy availability, the system can achieve compatible or higher throughput by utilizing the harvested energy.
Aberrant Cyclization Affords a C-6 Modified Cyclic Adenosine 5′-Diphosphoribose Analogue with Biological Activity in Jurkat T Cells (2012)

Two nicotinamide adenine dinucleotide (NAD(+)) analogues modified at the 6 position of the purine ring were synthesized, and their substrate properties toward Aplysia californica ADP-ribosyl cyclase were investigated. 6-N-Methyl NAD(+) (6-N-methyl nicotinamide adenosine 5'-dinucleotide 10) hydrolyzes to give the linear 6-N-methyl ADPR (adenosine 5'-diphosphoribose, 11), whereas 6-thio NHD(+) (nicotinamide 6-mercaptopurine 5'-dinucleotide, 17) generates a cyclic dinucleotide. Surprisingly, NMR correlation spectra confirm this compound to be the N1 cyclic product 6-thio N1-cIDPR (6-thio cyclic inosine 5'-diphosphoribose, 3), although the corresponding 6-oxo analogue is well-known to cyclize at N7. In Jurkat T cells, unlike the parent cyclic inosine 5'-diphosphoribose N1-cIDPR 2, 6-thio N1-cIDPR antagonizes both cADPR- and N1-cIDPR-induced Ca(2+) release but possesses weak agonist activity at higher concentration. 3 is thus identified as the first C-6 modified cADPR (cyclic adenosine 5'-diphosphoribose) analogue antagonist; it represents the first example of a fluorescent N1-cyclized cADPR analogue and is a new pharmacological tool for intervention in the cADPR pathway of cellular signaling.
Photon-efficient quantum key distribution using time–energy entanglement with high-dimensional encoding (2015)

Conventional quantum key distribution (QKD) typically uses binary encoding based on photon polarization or time-bin degrees of freedom and achieves a key capacity of at most one bit per photon. Under photon-starved conditions the rate of detection events is much lower than the photon generation rate, because of losses in long distance propagation and the relatively long recovery times of available single-photon detectors. Multi-bit encoding in the photon arrival times can be beneficial in such photon-starved situations. Recent security proofs indicate high-dimensional encoding in the photon arrival times is robust and can be implemented to yield high secure throughput. In this work we demonstrate entanglement-based QKD with high-dimensional encoding whose security against collective Gaussian attacks is provided by a high-visibility Franson interferometer. We achieve unprecedented key capacity and throughput for an entanglement-based QKD system because of four principal factors: Franson interferometry that does not degrade with loss; error correction coding that can tolerate high error rates; optimized time–energy entanglement generation; and highly efficient WSi superconducting nanowire single-photon detectors. The secure key capacity yields as much as 8.7 bits per coincidence. When optimized for throughput we observe a secure key rate of 2.7 Mbit s ^−1 after 20 km fiber transmission with a key capacity of 6.9 bits per photon coincidence. Our results demonstrate a viable approach to high-rate QKD using practical photonic entanglement and single-photon detection technologies.
Fluorescence Image Histology Pattern Transformation using Image Style Transfer (2019)

Confocal laser endomicroscopy (CLE) allow on-the-fly in vivo intraoperative imaging in a discreet field of view, especially for brain tumors, rather than extracting tissue for examination ex vivo with conventional light microscopy. Fluorescein sodium-driven CLE imaging is more interactive, rapid, and portable than conventional hematoxylin and eosin (H&amp;E)-staining. However, it has several limitations: CLE images may be contaminated with artifacts (motion, red blood cells, noise), and neuropathologists are mainly trained on colorful stained histology slides like H&amp;E while the CLE images are gray. To improve the diagnostic quality of CLE, we used a micrograph of an H&amp;E slide from a glioma tumor biopsy and image style transfer, a neural network method for integrating the content and style of two images. This was done through minimizing the deviation of the target image from both the content (CLE) and style (H&amp;E) images. The style transferred images were assessed and compared to conventional H&amp;E histology by neurosurgeons and a neuropathologist who then validated the quality enhancement in 100 pairs of original and transformed images. Average reviewers' score on test images showed 84 out of 100 transformed images had fewer artifacts and more noticeable critical structures compared to their original CLE form. By providing images that are more interpretable than the original CLE images and more rapidly acquired than H&amp;E slides, the style transfer method allows a real-time, cellular-level tissue examination using CLE technology that closely resembles the conventional appearance of H&amp;E staining and may yield better diagnostic recognition than original CLE grayscale images.
Glycoconjugate vaccines: Principles and mechanisms (2018)

Bacterial conjugate vaccines are used in infants, adolescents, and the elderly, and they are among the safest and most successful vaccines developed during the last 40 years. Conjugation of polysaccharides to proteins provides T cell epitopes that are necessary in the germinal centers for the affinity maturation of polysaccharide-specific B cells. Collective analysis of data from animal experiments and clinical trials, reviewed with current knowledge of immunology, revealed possible mechanistic explanations that may improve our understanding of conjugate vaccines. Key conclusions are that naïve infants respond differently from adolescents and adults and that most of recommended schedules generate only 10 to 35% of the maximal antibody titer that the vaccine can induce, indicating that the full potential of glycoconjugate vaccines has not yet been reached.
Virus-Specific Cytotoxic CD4+ T Cells for the Treatment of EBV-Related Tumors (2010)

Although adoptive immunotherapy with CD8(+) CTL is providing clinically relevant results against EBV-driven malignancies, the effector role of CD4(+) T cells has been poorly investigated. We addressed this issue in a lymphoblastoid cell line-induced mouse model of posttransplant lymphoproliferative disease (PTLD) by comparing the therapeutic efficacy of EBV-specific CD4(+) and CD8(+) T cell lines upon adoptive transfer. CD4(+) T cells disclosed a long-lasting and stronger proliferative potential than CD8(+) T cells, had a similar activation and differentiation marker profile, efficiently killed their targets in a MHC class II-restricted manner, and displayed a lytic machinery comparable to that of cognate CD8(+) T cells. A detailed analysis of Ag specificity revealed that CD4(+) T cells potentially target EBV early lytic cycle proteins. Nonetheless, when assessed for the relative therapeutic impact after in vivo transfer, CD4(+) T cells showed a reduced activity compared with the CD8(+) CTL counterpart. This feature was apparently due to a strong and selective downmodulation of MHC class II expression on the tumor cells surface, a phenomenon that could be reverted by the demethylating agent 5-aza-2'-deoxycytidine, thus leading to restoration of lymphoblastoid cell line recognition and killing by CD4(+) T cells, as well as to a more pronounced therapeutic activity. Conversely, immunohistochemical analysis disclosed that HLA-II expression is fully retained in human PTLD samples. Our data indicate that EBV-specific cytotoxic CD4(+) T cells are therapeutic in mice bearing PTLD-like tumors, even in the absence of CD8(+) T cells. These findings pave the way to use cultures of pure CD4(+) T cells in immunotherapeutic approaches for EBV-related malignancies.
Butane Hydroisomerisation Using Pt‐Promoted OSDA‐Free Zeolite Beta (2023)

Abstract Hydroisomerisation of n ‐butane to isobutane is a challenging reaction, even for Pt‐loaded zeolites with strong acid sites. In comparison with 10‐membered ring (10MR) zeolites, 12‐membered ring (12MR) zeolites give consistently higher isomerisation yields. We report that besides the known catalysts with *BEA topology, also three‐dimensional frameworks with MSE and YFI topologies (with Si/Al∼10) are suitable to obtain high isobutane selectivities and yields. As an alternative to Beta zeolites obtained via templated synthesis, Beta zeolites prepared via a template‐free synthesis proved to be more active at lower temperatures and delivered higher isobutane yields in such conditions. Side reactions such as the Pt‐catalysed hydrogenolysis were successfully suppressed by decreasing the Pt content, even in hydrogen‐rich conditions. Isobutane yields up to 31 % were achieved in a single pass.
Ultra wideband transparent RF aperture for electro-optical integration (2010)

RF sensors can provide a suitable foundation in developing combined RF/optical imaging apertures. The paper describes an ultra wideband RF aperture as an enabler in a combined conformal Radio Frequency (RF) and Electro-Optical (EO) aperture. The proposed aperture is intended for RF to Mid-IR operation. The RFEO aperture is based on a novel, planar, Interweaved SPiral Array (ISPA). The paper presents a 19:1 bandwidth aperture printed using optically transparent conductor (OTC) on a glass superstrate placed conformally on a ground plane. The OTC enables vertical integration of the EO and RF (with the RF aperture above the EO layer). Multiple RF aperture layers can be used to achieve 1-180 GHZ operation.
Cardiac Safety Pharmacology Modeling (2020)

Mathematical models of cardiac electrophysiology have a long and illustrious history for gaining an increased understanding of underlying biological mechanisms in the cardiomyocyte. Their use has provided insights into the interplay of ion channels, pumps and exchangers that modify the concentrations of ions on either side of cell membrane to generate a membrane potential. More recently the models have been put forward as a method in supporting decision making within the pharmaceutical industry, and even to support regulatory recommendations as to the possible outcomes of a novel compound׳s impact on the whole heart when these compounds bind and modify the behavior of these proteins. When experiments that assess the impact of compounds against more than one biological driver of membrane potential are conducted, then a requirement exists for summation of these experimental inputs, which can often be non-linear and occasionally non-intuitive. Therefore, computational models offer a more systematic and reproducible interpretation that can be readily assessed for their accuracy based on the analysis of known compounds, with known cardiac outcomes. However, the level of complexity and detail that is required has been a source of debate, together with the level of variance and reproducibility in the experimental measurements. The article introduces the brief history of the field together with the current state of art. The approach and application of computational models in this context provides a compelling and important insight for wider adoption of in-silico approaches.
2-[(7R,9S,10R,12E)-4,9-Dihydroxy-10-methyl-5-oxo-7,8,9,10,11,14-hexahydro-5H-6-oxa-benzocyclododecen-7-yl]ethyl octanoate (2002)

The structure of the title compound, C26H38O6, is described. Two mol­ecules of the title compound are related by a twofold non-crystallographic symmetry operation. There is an extensive hydrogen-bonding network, as well as van der Waals interactions between alkyl groups.
Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers (2023)

<i>Sphingobium</i> sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of <i>erythro</i>-DGPD was reported in SYK-6, but the catabolic pathway for <i>threo</i>-DGPD was as yet unknown. Here, we elucidated the catabolism of <i>threo</i>-DGPD, which proceeds through conversion to <i>erythro</i>-DGPD. When <i>threo</i>-DGPD was incubated with SYK-6, the Cα hydroxy groups of <i>threo</i>-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD<sup>+</sup>-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to <i>erythro</i>-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and <i>ldpA</i>-neighboring SDR genes. The gene products of SLG_12690 (<i>ldpC</i>) and SLG_12640 (<i>ldpB</i>) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that <i>ldpC</i> and <i>ldpB</i> are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of <i>threo</i>-DGPD with a net stereoinversion using multiple dehydrogenases. <b>IMPORTANCE</b> In many catalytic depolymerization processes of lignin polymers, aryl-ether bonds are selectively cleaved, leaving carbon-carbon bonds between aromatic units intact, including dimers and oligomers with β-1 linkages. Therefore, elucidating the catabolic system of β-1-type lignin-derived compounds will aid in the establishment of biological funneling of heterologous lignin-derived aromatic compounds to value-added products. Here, we found that <i>threo</i>-DGPD was converted by successive stereoselective oxidation and reduction at the Cα position by multiple alcohol dehydrogenases to <i>erythro</i>-DGPD, which is further catabolized. This system is very similar to that developed to obtain enantiopure alcohols from racemic alcohols by artificially combining two enantiocomplementary alcohol dehydrogenases. The results presented here demonstrate that SYK-6 has evolved to catabolize all four stereoisomers of DGPD by incorporating this stereoinversion system into its native β-1-type dimer catabolic system.
Interaction of Epothilone B (Patupilone) with Microtubules as Detected by Two‐Dimensional Solid‐State NMR Spectroscopy (2010)

Die Apoptose von Krebszellen ist die Folge, wenn Epothilone wie Patupilon nach einem bislang unbekannten Mechanismus die Polymerisation von αβ-Tubulindimeren zu Mikrotubuli auslösen. Durch Festkörper-NMR-Spektroskopie von Mikrotubuli-gebundenem Patupilon wurden nun Atompositionen des Wirkstoffs identifiziert, deren chemische Verschiebungen durch den Bindevorgang deutlich verändert werden (siehe Korrelationsspektren von freiem (schwarz) und komplexiertem Patupilon (rot)).
Leveraging Millimeter Waves for Security (2018)

The fact that Millimeter Wave (mmWave) communication needs to be directional is usually perceived as a challenge; in this paper we argue that it enables efficient secret key sharing that are unconditionally secure from passive eavesdroppers, by building on packet erasures. We showcase the potential of our approach in two setups: beam sweeping to align receiver/transmitter pairs, and vehicle platooning. We show that in the first case, we can establish a few hundred secret bits at virtually no additional transmission cost; and in the second case, we can potentially establish keys in the order of tenths of Mbps. These first results are based on some simplifying assumptions, yet we believe they give incentives to further explore such techniques.
High performance lasers on Si (2019)

We review our recent progress on high performance heterogeneously integrated and directly grown semiconductor light sources on Si, with an emphasis on sub-kilohertz narrow linewidth lasers and high-channel-count comb lasers.