gebhart/patrepeval huggingface dataset:
Inhibition of Cdc7/Dbf4 kinase activity affects specific phosphorylation sites on MCM2 in cancer cells (2008)

Abstract The Cdc7/Dbf4 kinase is required for initiation of DNA replication and also plays a role in checkpoint function in response to replication stress. Exactly how Cdc7/Dbf4 mediates those activities remains to be elucidated. Cdc7/Dbf4 physically interacts with and phosphorylates the minichromosome maintenance complex (MCM), such as MCM2, MCM4 and MCM6. Cdc7/Dbf4 activity is required for association of Cdc45 followed by recruitment of DNA polymerase on the chromatin. Using high resolution mass spectrometry, we identified six phosphorylation sites on MCM2, two of them have not been described before. We provide evidence that Cdc7/Dbf4 mediates phosphorylation on serine 108 and serine 40 on human MCM2 in vitro and in vivo in cancer cells in the absence of DNA damage. Antibodies specific to pS108 or pS40 confirmed the sites and established useful read‐outs for inhibition of Cdc7/Dbf4. This report demonstrates the utility of an in vitro to in vivo workflow utilizing immunoprecipitation and mass spectrometry to map phosphorylation sites on endogenous kinase substrates. The approach can be readily generalized to identify target modulation read‐outs for other potential kinase cancer targets. J. Cell. Biochem. 104: 1075–1086, 2008. © 2008 Wiley‐Liss, Inc.
Exploring Electrochemical C(sp 3 )–H Oxidation for the Late-Stage Methylation of Complex Molecules (2022)

The "magic methyl" effect, a dramatic boost in the potency of biologically active compounds from the incorporation of a single methyl group, provides a simple yet powerful strategy employed by medicinal chemists in the drug discovery process. Despite significant advances, methodologies that enable the selective C(sp<sup>3</sup>)-H methylation of structurally complex medicinal agents remain very limited. In this work, we disclose a modular, efficient, and selective strategy for the α-methylation of protected amines (i.e., amides, carbamates, and sulfonamides) by means of electrochemical oxidation. Mechanistic analysis guided our development of an improved electrochemical protocol on the basis of the classic Shono oxidation reaction, which features broad reaction scope, high functional group compatibility, and operational simplicity. Importantly, this reaction system is amenable to the late-stage functionalization of complex targets containing basic nitrogen groups that are prevalent in medicinally active agents. When combined with organozinc-mediated C-C bond formation, our protocol enabled the direct methylation of a myriad of amine derivatives including those that have previously been explored for the "magic methyl" effect. This synthesis strategy thus circumvents multistep <i>de novo</i> synthesis that is currently necessary to access such compounds and has the potential to accelerate drug discovery efforts.
Isolation of "Campylobacter hyointestinalis" from a human (1986)

We isolated "Campylobacter hyointestinalis" from the rectal culture of a homosexual man with proctitis. Phenotypic characterization of the isolate was confirmed by DNA hybridization by using the taxonomic spot blot. "C. hyointestinalis" was previously isolated only from animals but should be considered in the identification of Campylobacter species isolated from humans.
Enantioselective Synthesis of 12-Amino Alkylidenecyclopentenone Prostaglandins (2002)

An enantioselective synthesis of new 12-amino alkylidenecyclopentenone prostaglandins is reported. The key step of the synthesis involved a [3.3] sigmatropic rearrangement of an asymmetric allylic cyanate to elaborate an asymmetric 5-amino-1,6-diene which was further transformed into cyclopentenone by successive ring-closing metathesis reaction catalyzed by the Grubbs reagent and one-pot oxidation. A palladium-catalyzed cross-coupling reaction on a 5-iodo-1,5-diene allowed the synthesis of prostanoids with variable Rw side chains. These new compounds exhibit high cytotoxic activities.
Ionometrie (1979)

Ionometrische Verfahren beruhen auf der Wechselwirkung energiereicher Ionen mit den Atomen von Festkörpern. Dabei können sowohl aus der Veränderung der Energie, der Anzahl und der Richtung der eingeschossenen Ionen nach dem Wechselwirkungsprozeß als auch aus den Kenngrößen der Sekundärstrahlung, die bei der Wechselwirkung erzeugt wird (Teilchenstrahlung oder elektromagnetische Strahlung), Rückschlüsse auf physikalische Eigenschaften der Festkörper gezogen werden. Für die Untersuchung kristalliner Festkörper ergaben sich prinzipiell neue Möglichkeiten durch die Entdeckung des Kanalisierungs- und Blockierungseffekts [1–5].
GW0742, a High Affinity PPAR-β/δ Agonist Reduces Lung Inflammation Induced by Bleomycin Instillation in Mice (2010)

Peroxisome Proliferator-Activated Receptor β/δ belongs to a family of ligand-activated transcription factors. Recent data have clarified its metabolic roles and enhanced the potential role of this receptor as a pharmacological target. Moreover, although its role in acute inflammation remains unclear, being the nuclear receptor PPAR β/δ widely expressed in many tissues, including the vascular endothelium, we assume that the infiltration of PMNs into tissues, a prominent feature in inflammation, may also be related to PPAR β/δ. Mice subjected to intratracheal instillation of bleomycin (BLEO, 1 mg/kg), a glycopeptide produced by the bacterium Streptomyces verticillus, develop lung inflammation and injury characterized by a significant neutrophil infiltration and tissue oedema. Therefore, the aim of this study is to investigate the effects of GW0742, a synthetic high affinity PPAR β/δ agonist, and its possible role in preventing the advance of inflammatory and apoptotic processes induced by bleomycin, that long-term leads to the appearance of pulmonary fibrosis. Our data showed that GW0742-treatment (0.3 mg/Kg, 10 percent DMSO, i.p.) has therapeutic effects on pulmonary damage, decreasing many inflammatory and apoptotic parameters detected by measurement of: 1) cytokine production; 2) leukocyte accumulation, indirectly measured as decrease of myeloperoxidase (MPO) activity; 3) IkBα degradation and NF-kB nuclear translocation; 4) ERK phosphorylation; 5) stress oxidative by NO formation due to iNOS expression; 6) nitrotyrosine and PAR localization; 7) the degree of apoptosis, evaluated by Bax and Bcl-2 balance, FAS ligand expression and TUNEL staining. Taken together, our results clearly show that GW0742 reduces the lung injury and inflammation due to the intratracheal BLEO--instillation in mice.
Mathematical analysis of the static solar concentrator with cascading right-angle prisms (2014)

Welcome to the WIT Press eLibrary - the home of the Transactions of the Wessex Institute collection, providing on-line access to papers presented at the Institute's prestigious international conferences and from its State-of-the-Art in Science & Engineering publications.
Selective breeding of miniature swine leads to an increased rate of acceptance of MHC-identical, but not of class I-disparate, renal allografts (1992)

Previous work from this laboratory demonstrated that tolerance to MHC-identical or class I-disparate renal allografts develops in approximately one third of miniature swine without exogenous immunosuppression. A back-cross study indicated that rejection of MHC-identical transplants due to minor Ag was controlled by one or possibly two non-MHC-linked, autosomal dominant Ir genes. According to this hypothesis, and assuming complete penetrance, graft acceptors would be homozygous recessive at the relevant Ir loci, as would their offspring. Alternatively, if the gene(s) were incompletely penetrant, then two acceptors could give rise to a rejector. However, a high rate of MHC-identical graft acceptance would still be expected in the offspring of acceptors even if the Ir gene(s) were incompletely penetrant. To test this hypothesis and to obtain a higher frequency of acceptor animals for studies of tolerance, a program of selective breeding of renal allograft acceptors was begun. In the present paper, we assess the effect of selective breeding on renal graft acceptance. The analysis indicates a marked increase in the rate of MHC-identical graft acceptance, from 27.3% (n = 24) for the earliest of the four chronologic subgroups assessed to 64.5% (n = 33) for the most recent subgroup (p less than 0.0001). Calculations of kinship revealed that the increased acceptance of MHC-identical grafts was not the result of differences between acceptors and rejectors in donor/recipient consanguinity. Class I-disparate grafts (n = 128) were similarly stratified chronologically and compared. Unlike MHC-identical grafts, the rate of acceptance of class I-disparate grafts has not changed over time. We conclude that rejector/acceptor status with respect to class I MHC incompatibility is determined by genetic factors in addition to those that control responses to minor antigen incompatibilities only.
Catalytic Effects of Silver in Iodine Reactors for Dissolved Used Nuclear Fuel (2022)

The dissolution of used nuclear fuel generates a variety of off-gasses including flammable hydrogen and other species that are a concern for environmental release. The H-Canyon facility at the Savannah River Site is currently dissolving aluminum-clad research reactor fuel from material test reactors and the High Flux Isotope Reactor (HFIR) using a mercury-catalyzed nitric acid flowsheet. Savannah River National Laboratory recently developed and deployed a Raman spectrometer to monitor the off-gas stream from the dissolution process. Results from these measurements indicated a lack of the expected hydrogen, nitrous oxide, and nitric oxide in the off-gas stream. It was proposed that the silver on the silver nitrate–coated berl saddles present in the reactors for iodine capture were acting as a catalytic hydrogen recombiner. Nitric oxide is readily oxidized to nitrogen dioxide under normal conditions, but it was unclear what happened to the nitrous oxide. A laboratory-scale iodine reactor was assembled and filled with silver nitrate–coated berl saddles to help ascertain the fate of nitrous oxide and hydrogen. Testing with this laboratory-scale reactor observed the recombination of hydrogen when a simulated dissolver off-gas was passed through the reactor containing silver nitrate–coated berl saddles at the approximate temperatures seen in H-Canyon. However, the nitrous oxide concentration was unchanged, suggesting a more complex process occurring within the off-gas stream before it reaches the iodine reactors at H-Canyon.
AudioBIFS: Describing audio scenes with the MPEG-4 multimedia standard (1999)

We present an overview of the AudioBIFS system, part of the Binary Format for Scene Description (BIFS) tool in the MPEG-4 International Standard. AudioBIFS is the tool that integrates the synthetic and natural sound coding functions in MPEG-4. It allows the flexible construction of soundtracks and sound scenes using compressed sound, sound synthesis, streaming audio, interactive and terminal-dependent presentation, three-dimensional (3-D) spatialization, environmental auralization, and dynamic download of custom signal-processing effects algorithms. MPEG-4 sound scenes are based on a model that is a superset of the model in VRML 2.0, and we describe how MPEG-4 is built upon VRML and the new capabilities provided by MPEG-4. We discuss the use of structured audio orchestra language, the MPEG-4 SAOL, for writing downloadable effects, present an example sound scene built with AudioBIFS, and describe the current state of implementations of the standard.
Dimorphism in the P2Y1 ADP Receptor Gene Is Associated With Increased Platelet Activation Response to ADP (2004)

A common genetic variant at the P2Y1 locus is associated with platelet reactivity to ADP. This genotype effect partly explains the interindividual variation in platelet response to ADP and may have clinical implications with regard to thrombotic risk.
Antiparallel dimer structure of CELSR cadherin in solution revealed by high-speed atomic force microscopy (2023)

Cadherin EGF LAG seven-pass G-type receptors (CELSR) cadherins, members of the cadherin superfamily, and adhesion G-protein-coupled receptors, play a vital role in cell-cell adhesion. The mutual binding of the extracellular domains (ectodomains) of CELSR cadherins between cells is crucial for tissue formation, including the establishment of planar cell polarity, which directs the proper patterning of cells. CELSR cadherins possess nine cadherin ectodomains (EC1-EC9) and noncadherin ectodomains. However, the structural and functional mechanisms of the binding mode of CELSR cadherins have not been determined. In this study, we investigated the binding mode of CELSR cadherins using single-molecule fluorescence microscopy, high-speed atomic force microscopy (HS-AFM), and bead aggregation assay. The fluorescence microscopy analysis results indicated that the <i>trans</i>-dimer of the CELSR cadherin constitutes the essential adhesive unit between cells. HS-AFM analysis and bead aggregation assay results demonstrated that EC1-EC8 entirely overlap and twist to form antiparallel dimer conformations and that the binding of EC1-EC4 is sufficient to sustain bead aggregation. The interaction mechanism of CELSR cadherin may elucidate the variation of the binding mechanism within the cadherin superfamily and physiological role of CELSR cadherins in relation to planar cell polarity.
On the potential biological impact of radiation-induced acoustic emissions during ultra-high dose rate electron radiotherapy: a preliminary study (2023)

Ionizing radiation pulses delivered at ultra-high dose rates in emerging FLASH radiotherapy can result in high-intensity low-frequency thermoacoustic emissions that may have a biological impact. This study aims at providing insights into the thermoacoustic emissions expected during FLASH radiotherapy and their likelihood of inducing acoustic cavitation. The characteristics of acoustic waves induced by the energy deposition of a pulsed electron beam similar to previous pre-clinical FLASH radiotherapy studies and their propagation in murine head-like phantoms are investigated in-silico. The results show that the generated pressures are sufficient to produce acoustic cavitation due to resonance in the irradiated object. It suggests that thermoacoustics may, in some irradiation scenarios, contribute to the widely misunderstood FLASH effect or cause adverse effects if not taken into account at the treatment planning stage.
Oxytocin/Vasopressin-Related Peptides Have an Ancient Role in Reproductive Behavior (2012)

Many biological functions are conserved, but the extent to which conservation applies to integrative behaviors is unknown. Vasopressin and oxytocin neuropeptides are strongly implicated in mammalian reproductive and social behaviors, yet rodent loss-of-function mutants have relatively subtle behavioral defects. Here we identify an oxytocin/vasopressin-like signaling system in Caenorhabditis elegans, consisting of a peptide and two receptors that are expressed in sexually dimorphic patterns. Males lacking the peptide or its receptors perform poorly in reproductive behaviors, including mate search, mate recognition, and mating, but other sensorimotor behaviors are intact. Quantitative analysis indicates that mating motor patterns are fragmented and inefficient in mutants, suggesting that oxytocin/vasopressin peptides increase the coherence of mating behaviors. These results indicate that conserved molecules coordinate diverse behavioral motifs in reproductive behavior.
SINGLE STEP PATTERNING OF MOLECULARLY IMPRINTED POLYMERS FOR LARGE SCALE FABRICATION OF BIOCHIPS (2008)

International audience
Hydrogen Absorption in Cathodically Polarized Titanium Alloys (2002)

Cathodic polarisation may cause hydrogen absorption and embrittlement of titanium alloys. There is no need to protect titanium in seawater, but polarisation is inevitable when titanium components are connected to steel that is cathodically protected. The risk of hydrogen embrittlement of risers and other heavily loaded components rouse a need to quantify the amount of hydrogen that titanium alloys may absorb as a function of alloy composition, polarisation potential, temperature, cold working and time. The test program included Ti-3Al-2.5V and Ti-6Al-4V alloys that are candidate materials for risers. The hydrogen uptake was measured over a 3 years period in natural seawater. The results show that titanium absorbs hydrogen when it is polarised to potentials less than −0.8V vs. Ag/AgCl in seawater, but the absorption rate decreased with time. The maximum hydrogen loading measured after three years exposure at −1.04 V vs. Ag/AgCl was 150 ppm. A calcareous deposit built up on all surfaces and limited the hydrogen evolution and thereby the hydrogen uptake. Ti-3Al-2.5V alloys picked up less hydrogen than Ti-6Al-4V alloys, and palladium or ruthenium enhanced hydrogen uptake to some extent. Welding or cold working did not influence hydrogen uptake of the alloys included in the tests. Temperature had little effect, and thermal gradients in the titanium materials had no measurable influence. The effect of hydrogen on the mechanical properties of the alloys was not studied in detail in these experiments, but most specimens were tensioned C-rings with permanent strain. Neither of these developed cracks or other signs of embrittlement during the tests.
(Digital Presentation) Multimodal Encapsulation of p-SnOx to Engineer the Carrier Density for Thin Film Transistor Applications (2022)

It has been challenging to synthesize p-type SnO x (1≤x&lt;2) and engineer the electrical properties such as carrier density and mobility due to the narrow processing window and the localized oxygen 2p orbitals near the valence band. We recently reported on the processing of p-type SnOx and an oxide-based p-n heterostructures, demonstrating high on/off rectification ratio (&gt;10 3 ), small turn-on voltage (&lt;0.5 V), and low saturation current (~1×10 -10 A) 1 . In order to further understand the p-type oxide and engineer the properties for various electronic device applications, it is important to identify (or establish) the dominating doping and transport mechanisms. The low dopability in p-type SnOx, of which the causation is also closely related to the narrow processing window, needs to be mitigated so that the electrical properties of the material are to be adequately engineered 2, 3 . Herein, we report on the multifunctional encapsulation of p-SnO x to limit the surface adsorption of oxygen and selectively permeate hydrogen into the p-SnO x channel for thin film transistor (TFT) applications. Time-of-flight secondary ion mass spectrometry measurements identified that ultra-thin SiO 2 as a multifunctional encapsulation layer effectively suppressed the oxygen adsorption on the back channel surface of p-SnO x and augmented hydrogen density across the entire thickness of the channel. Encapsulated p-SnO x -based TFTs demonstrated much-enhanced channel conductance modulation in response to the gate bias applied, featuring higher on-state current and lower off-state current. The relevance between the TFT performance and the effects of oxygen suppression and hydrogen permeation is discussed in regard to the intrinsic and extrinsic doping mechanisms. These results are supported by density-functional-theory calculations. Acknowledgement This work was supported by the U.S. National Science Foundation (NSF) Award No. ECCS-1931088. S.L. and H.W.S. acknowledge the support from the Improvement of Measurement Standards and Technology for Mechanical Metrology (Grant No. 20011028) by KRISS. K.N. was supported by Basic Science Research Program (NRF-2021R11A1A01051246) through the NRF Korea funded by the Ministry of Education. References Lee, D. H.; Park, H.; Clevenger, M.; Kim, H.; Kim, C. S.; Liu, M.; Kim, G.; Song, H. W.; No, K.; Kim, S. Y.; Ko, D.-K.; Lucietto, A.; Park, H.; Lee, S., High-Performance Oxide-Based p–n Heterojunctions Integrating p-SnOx and n-InGaZnO. ACS Applied Materials &amp; Interfaces 2021, 13 (46), 55676-55686. Hautier, G.; Miglio, A.; Ceder, G.; Rignanese, G.-M.; Gonze, X., Identification and design principles of low hole effective mass p-type transparent conducting oxides. Nat Commun 2013, 4 . Yim, K.; Youn, Y.; Lee, M.; Yoo, D.; Lee, J.; Cho, S. H.; Han, S., Computational discovery of p-type transparent oxide semiconductors using hydrogen descriptor. npj Computational Materials 2018, 4 (1), 17. Figure 1
Oxidative polymerization of catecholamines: structural access by high-resolution mass spectrometry (2017)

We introduce an avenue for the structural elucidation of bio-inspired functional poly(catecholamines) <italic>via</italic> high-resolution electrospray ionization mass spectrometry.
Alar Rim Lowering (1987)

A technique for the lowering of the alar rim is presented. The indications for this technique, originally presented by Meyer and Kesselring, have been expanded to other related nasal deformities, including the high-arched nostril, the asymmetrical nostril, the Mestizo nose, and the hanging columella, in which the surgeon feels that total nasal length should not be sacrificed. The technique consists of an incision parallel to the alar rim and an unfurling of the vestibular mucosa caudally. A cartilage graft from the septum, lowering lateral cartilage, or other source is placed between the two layers at the newly proposed alar height. Through-and-through sutures hold the graft and alar rim in place.
Tribochemical Reactions at the Water-Lubricated Silicon Nitride Interface: Gel Formation Mechanism (2005)

Silicon-based ceramics such as silicon nitride can be very effectively lubricated by water under certain conditions (1–3). After a wear-in period a condition of very low friction coefficient (&lt;0.01) can be achieved for average contact pressures of 40 MPa and lower. Tomizawa &amp; Fischer (1) proposed a chemomechanical polishing mechanism to reduce surface roughness enabling the onset of hydrodynamic lubrication by water. We suggest that there is an additional soft hydrated silica gel layer adhering to the rubbing surfaces that provides a deformable protective film to enable effective hydrodynamic lubrication of water and protect the surfaces from occasional asperity contacts. The existence of such films was indicated by the nanomechanical data performed on worn surfaces.
Plasma process induced physical damages on multilayered magnetic films for magnetic domain wall motion (2014)

The effect of ion irradiation on magnetic domain wall motion (DWM) in a perpendicularly magnetized Co/Ni multilayered film was investigated. The DWM in the Co/Ni multilayered film was sometimes inhibited owing to damage in Co/Ni induced by ion irradiation from Ar/NH 3 /CO plasma during the etching of the upper layer of a Co/Pt multilayered film depending on the etched depth over Co/Ni. When the DWM was disturbed, modifications of crystallinity were observed by transmission electron microscopy (TEM) near the etched surface region of Co/Ni. Also, the segregation of Pt which was knocked on from the upper layer of Co/Pt, was observed by energy dispersive X-ray line-scan analysis by TEM (TEM–EDX). In contrast to that, the sample which had fine DWM property showed clear lattice image of Co/Ni. A Monte Carlo simulation of Ar + ion irradiation predicted an atom-displacement range of about 3.5 nm depth from the etching surface when the ion acceleration voltage was 900 V. It was deep enough to degrade the area near the top region of the Co/Ni multilayered magnetic thin film. Eliminating these physical modifications during the etching process would be the key to the fabrication of reliable nonvolatile devices using domain wall motion.