gebhart/patrepeval huggingface dataset:
Three classes of ligands each bind to distinct sites on the orphan G protein-coupled receptor GPR84 (2017)

Medium chain fatty acids can activate the pro-inflammatory receptor GPR84 but so also can molecules related to 3,3'-diindolylmethane. 3,3'-Diindolylmethane and decanoic acid acted as strong positive allosteric modulators of the function of each other and analysis showed the affinity of 3,3'-diindolylmethane to be at least 100 fold higher. Methyl decanoate was not an agonist at GPR84. This implies a key role in binding for the carboxylic acid of the fatty acid. Via homology modelling we predicted and confirmed an integral role of arginine<sup>172</sup>, located in the 2nd extracellular loop, in the action of decanoic acid but not of 3,3'-diindolylmethane. Exemplars from a patented series of GPR84 antagonists were able to block agonist actions of both decanoic acid and 3,3'-diindolylmethane at GPR84. However, although a radiolabelled form of a related antagonist, [<sup>3</sup>H]G9543, was able to bind with high affinity to GPR84, this was not competed for by increasing concentrations of either decanoic acid or 3,3'-diindolylmethane and was not affected adversely by mutation of arginine<sup>172</sup>. These studies identify three separable ligand binding sites within GPR84 and suggest that if medium chain fatty acids are true endogenous regulators then co-binding with a positive allosteric modulator would greatly enhance their function in physiological settings.
Analysis of ku80-Mutant Mice and Cells with Deficient Levels of p53 (2000)

Absence of Ku80 results in increased sensitivity to ionizing radiation, defective lymphocyte development, early onset of an age-related phenotype, and premature replicative senescence. Here we investigate the role of p53 on the phenotype of ku80-mutant mice and cells. Reducing levels of p53 increased the cancer incidence for ku80(-/-) mice. About 20% of ku80(-/-) p53(+/-) mice developed a broad spectrum of cancer by 40 weeks and all ku80(-/-) p53(-/-) mice developed pro-B-cell lymphoma by 16 weeks. Reducing levels of p53 rescued populations of ku80(-/-) cells from replicative senescence by enabling spontaneous immortalization. The double-mutant cells are impaired for the G(1)/S checkpoint due to the p53 mutation and are hypersensitive to gamma-radiation and reactive oxygen species due to the Ku80 mutation. These data show that replicative senescence is caused by a p53-dependent cell cycle response to damaged DNA in ku80(-/-) cells and that p53 is essential for preventing very early onset of pro-B-cell lymphoma in ku80(-/-) mice.
Characterizing Extravascular Fluid Transport of Macromolecules in the Tumor Interstitium by Magnetic Resonance Imaging (2005)

Noninvasive imaging techniques to image and characterize delivery and transport of macromolecules through the extracellular matrix (ECM) and supporting stroma of a tumor are necessary to develop treatments that alter the porosity and integrity of the ECM for improved delivery of therapeutic agents and to understand factors which influence and control delivery, movement, and clearance of macromolecules. In this study, a noninvasive imaging technique was developed to characterize the delivery as well as interstitial transport of a macromolecular agent, albumin-GdDTPA, in the MCF-7 human breast cancer model in vivo, using magnetic resonance imaging. The transport parameters derived included vascular volume, permeability surface area product, macromolecular fluid exudate volume, and drainage and pooling rates. Immunohistochemical staining for the lymphatic endothelial marker LYVE-1 was done to determine the contribution of lymphatics to the macromolecular drainage. Distinct pooling and draining regions were detected in the tumors using magnetic resonance imaging. A few lymphatic vessels positively stained for LYVE-1 were also detected although these were primarily collapsed and tenuous suggesting that lymphatic drainage played a minimal role, and that the bulk of drainage was due to convective transport through the ECM in this tumor model.
IR-Spectroscopic Study of Complex Formation of Nitrogen Oxides (NO, N2O) with Cationic Forms of Zeolites and the Reactivity of Adsorbed Species in CO and CH4 Oxidation (2021)

The formation of complexes and disproportionation of nitrogen oxides (NO, N<sub>2</sub>O) on cationic forms of LTA, FAU, and MOR zeolites was investigated by diffuse-reflectance IR spectroscopy. N<sub>2</sub>O is adsorbed on the samples under study in the molecular form and the frequencies of the first overtone of the stretching vibrations ν<sup>1</sup><sub>0-2</sub> and the combination bands of the stretching vibrations with other vibrational modes for N<sub>2</sub>O complexes with cationic sites in zeolites (ν<sup>3</sup><sub>0-1</sub> + ν<sup>1</sup><sub>0-1</sub>, ν<sup>1</sup><sub>0-1</sub> + δ<sub>0-2</sub>) are more significantly influenced by the nature of the zeolite. The presence of several IR bands in the region of 2400-2600 cm<sup>-1</sup> (the ν<sup>1</sup><sub>0-1</sub> + δ<sub>0-2</sub> transitions) for different zeolite types was explained by the availability of different localization sites for cations in these zeolites. The frequencies in this region also depend on the nature of the cation (its charge and radius). The data can be explained by the specific geometry of the N<sub>2</sub>O complex formed, presumably two-point adsorption of N<sub>2</sub>O on a cation and a neighboring oxygen atom of the framework. Adsorption of CO or CH<sub>4</sub> on the samples with preliminarily adsorbed N<sub>2</sub>O at 20-180 °C does not result in any oxidation of these molecules. NO<sup>+</sup> and N<sub>2</sub>O<sub>3</sub> species formed by disproportionation of NO are capable of oxidizing CO and CH<sub>4</sub> molecules to CO<sub>2</sub>, whereas NO<sub>x</sub> is reduced simultaneously to N<sub>2</sub> or N<sub>2</sub>O. The peculiarities in the behavior of cationic forms of different zeolites with respect to adsorbed nitrogen oxides determined by different density and localization of cations have been established.
International round-robin experiment for angle-resolved light scattering measurement (2019)

An international round-robin experiment has been conducted to test procedures and methods for the measurement of angle-resolved light scattering. ASTM E2387-05 has been used as the main guide, while the experience gained should also contribute to the new ISO standard of angle-resolved scattering currently under development (ISO/WD 19986:2016). Seven laboratories from Europe and the United States measured the angle-resolved scattering from Al/SiO<sub>2</sub>-coated substrates, transparent substrates, volume diffusors, quasi-volume diffusors, white calibration standards, and grating samples at laser wavelengths in the UV, VIS, and NIR spectra. Results were sent to Fraunhofer IOF, which coordinated the experiments and analyzed the data, while ESA-ESTEC, as the project donor, defined conditions and parameters. Depending mainly on the sample type, overall good to reasonable agreements were observed, with largest deviations at scattering angles very close to the specular beam. Volume diffusor characterization unexpectedly turned out to be challenging. Not all participants provided measurement uncertainty ranges according to the Guide to the Expression of Uncertainty in Measurement; often, a single general scatterometer-related measurement uncertainty value was stated. Although relative instrument measurement uncertainties close to 1% are sometimes claimed, the comparison results did not support these claims for specular scattering samples as mirrors, substrates, or gratings.
Supplementary Figure 6 from Chk2 Phosphorylation of Survivin-ΔEx3 Contributes to a DNA Damage–Sensing Checkpoint in Cancer (2023)

&lt;p&gt;PDF file - 271K, Correlation between survivin and activated Chk2 expression during colorectal tumorigenesis, in vivo. A. Patient-derived surgical or endoscopic specimens representative of progressive stages of the colorectal adenoma-to-carcinoma transition (normal mucosa, hyperplasia, moderate dysplasia, severe dysplasia and adenocarcinoma) were analyzed for expression of Thr68-phosphorylated (T68) Chk2, survivin, p53, or Chk2, by immunohistochemistry. B. Tissue slides representative of the indicated histologic diagnoses (20 cases/each) were scored for positively stained cells using a 5% cutoff. IHC, immunohistochemistry.&lt;/p&gt;
Effectors in Plant–Microbe Interactions (2011)

Eukaryotic plant pathogens, such as oomycetes and fungi, cause highly destructive diseases that negatively impact commercial and subsistence agriculture worldwide. These pathogens secrete an arsenal of effector proteins to modulate plant innate immunity and enable parasitic infection. Deciphering the biochemical activities of effectors to understand how pathogens successfully colonize and reproduce on their host plants became a driving paradigm in the field. This presentation will focus on effectors of oomycetes, such as the Irish potato famine pathogen Phytophthora infestans. Tremendous progress has been made recently in understanding the biology of oomycete effectors. Two classes of effectors target distinct sites in the host plant: apoplastic effectors are secreted into the plant extracellular space, while cytoplasmic effectors are translocated inside the plant cell, where they target different subcellular compartments. Of particular interest are the RXLR and Crinkler host-translocated (cytoplasmic) effectors that are characterized by conserved motifs following the signal peptide. The RXLR domain is functionally interchangeable with a malaria host targeting domain and functions in delivery into host cells. The recent completion of several oomycete genome sequences enabled genome-wide cataloguing of the effector secretome revealing hundreds of candidate effectors. Effectors are frequently organized in clusters of paralogous genes that localize in expanded, repeat-rich and gene-sparse regions of the genome. Many effector genes exhibit hallmarks of positive selection probably as a result of a coevolutionary arms race with host factors. We also utilized the discovered RXLR effectors in highthroughput in planta expression assays to screen for avirulence and virulence activities. The perturbations caused by these effectors is helping to elucidate the mechanisms of pathogenicity as well as further illuminate mechanisms of plant defense and innate immunity.
Cryptococcus neoformans responds to mannitol by increasing capsule size in vitro and in vivo (2010)

The polysaccharide capsule of the fungus Cryptococcus neoformans is its main virulence factor. In this study, we determined the effects of mannitol and glucose on the capsule and exopolysaccharide production. Growth in mannitol significantly increased capsular volume compared with cultivation in glucose. However, cells grown in glucose concentrations higher than 62.5 mM produced more exopolysaccharide than cells grown in mannitol. The fibre lengths and glycosyl composition of capsular polysaccharide from yeast grown in mannitol was structurally different from that of yeast grown in glucose. Furthermore, mannitol treatment of mice infected intratracheally with C. neoformans resulted in fungal cells with significantly larger capsules and the mice had reduced fungal dissemination to the brain. Our results demonstrate the capacity of carbohydrate source and concentration to modify the expression of a major virulence factor of C. neoformans. These findings may impact the clinical management of cryptococcosis.
ChemInform Abstract: EIN NEUES FURAN‐DIMERES (1973)

Abstract Hydroxy‐aceton (I) reagiert mit Malodinitril (II) nur intermediär zum Furan (III), das sofort in einer Diels‐Alder‐Reaktion in (IV) übergeht.
Multiple scattering mechanisms causing interference effects in the differential cross sections of H + D2 → HD(v′ = 4,  j′) + D at 3.26 eV collision energy (2016)

Differential cross sections (DCSs) for the H + D2 → HD(v' = 4, j') + D reaction at 3.26 eV collision energy have been measured using the photoloc technique, and the results have been compared with those from quantum and quasiclassical scattering calculations. The quantum mechanical DCSs are in good overall agreement with the experimental measurements. In common with previous results at 1.97 eV, clear interference patterns which appear as fingerlike structures have been found at 3.26 eV but in this case for vibrational states as high as v' = 4. The oscillatory structure is prominent for low rotational states and progressively disappears as j' increases. A detailed analysis, similar to that carried out at 1.97 eV, shows that the origin of these structures could be traced to interferences between well defined classical mechanisms. In addition, at this energy, we do not observe the anomalous positive j'-θ trend found for the v' = 4 manifold at lower collision energies, thus reinforcing our explanation that the anomalous distribution for HD(v' = 4, j') at 1.97 eV only takes place for those states associated with low product recoil energies.
Accurate Junction-Depth Measurements Using Chemical Staining (1989)

The techniques of chemical staining, spreading resistance, and secondary-ion mass spectrometry (SIMS) have been used in the determination of the depth of diffused and ion-implanted junctions in an effort to estimate the accuracy of the staining method. Computer simulations were also used to study the behaviour of charge carriers in the semiconductor under illumination, and the accuracy of the junction depth obtained from raw spreading resistance data. It was observed that it is possible to measure junction depth reproducibly, to within 200 Å of the metallurgical junction depth, by carefully controlling the surface preparation of the sample and the lighting conditions under which the staining takes place.
Verbesserte Pharmakodynamik und Pharmakokinetik nach intravenöser Applikation von Peg-Interferon alfa-2a bei Patienten mit Hepatitis C Genotyp 1 und Null Response auf eine Therapie mit Peg-Interferon alfa/Ribavirin (IVAN-Studie) (2013)

Die Gründe des Nichtansprechens einer Peg-Interferon (Peg-IFNa) basierten Therapie bei chronischer Hepatitis C sind nicht gut verstanden. Die Peg IFNa-Plasmaspiegel zeigen nach subcutaner (s.c.) Applikation eine signifikante interindividuelle Variabilität. Eine unzureichende Peg-IFNa Resorption nach s.c. Applikation könnte einen Faktor für die Nonresponse darstellen, und durch einen Wechsel der Applikationsart auf eine intravenöse (i.v.) Gabe überwunden werden. Ziel unserer Studie war der Vergleich der Pharmakodynamik und -kinetik einer s.c. vs. i.v. Peg-IFNa Applikation.
Yonsei Experience in Robotic Urologic Surgery - Application in Various Urological Procedures (2008)

Based on our experience at a single-institution, robot system can be used both safely and efficiently in many areas of urologic surgeries including prostatectomy. Once this system is familiar to surgeons, it will be used in a wide range of urologic surgery.
Discrete versus Infinite Molecular Self-Assembly:  Control in Crystalline Hydrogen-Bonded Assemblies Based on Resorcinol (2001)

Cocrystallization of 1,2-bis(4-pyridyl)ethane (4,4'-bipyeth) with resorcinol (res), 4-chlororesorcinol (4-Cl-res), and 4,6-dichlororesorcinol (4,6-di-Cl-res) yields molecular solids (4,4'-bipyeth).(res) 1a, 2(4,4'-bipyeth).2(4-Cl-res) 1b, and 2(4,4'-bipyeth).2(4,6-di-Cl-res) 1c with components held together by O-H...N hydrogen bonds. In 1a the components form an infinite 1D polar array, whereas in 1b and 1c the components form 0D four-component complexes. Formation of the discrete assemblies is attributed to peripheral steric effects, which block the solid-state polymerization. [reaction: see text]
A K-band monolithic CPW oscillator co-integrated with a buffer amplifier (2002)

This paper describes the design approach, fabrication process, and performance of a monolithic CPW oscillator incorporating a buffer amplifier on the same chip, for K-band wireless network applications. At 21 GHz, the output power of the oscillator recorded 17 dBm with an overall DC-RF efficiency of 22%. By changing the length of a source feedback line, the oscillation frequency was varied up to 26 GHz. For all cases, the output power remained higher than 16 dBm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Implications of proxy caching for provisioning networks and servers (2002)

In this paper, we examine the potential benefits of Web proxy caches in improving the effective capacity of servers and networks. Since networks and servers are typically provisioned based on a high percentile of the load, we focus on the effects of proxy caching on the tail of the load distribution. We find that, unlike their substantial impact on the average load, proxies have a diminished impact on the tail of the load distribution. The exact reduction in the tail and the corresponding capacity savings depend on the nature of the workload and the percentile of the load distribution chosen for provisioning networks and servers-the higher the percentile, the smaller the savings. For workloads considered in this study, compared with over a 50% reduction in the average load, the savings in network and server capacity was only 20%-35% for the 99th percentile of the load distribution. We also find that while proxies can be somewhat useful in smoothing out some of the burstiness in Web workloads; the resulting workload continues, however, to exhibit substantial burstiness and a heavy-tailed nature. We identify one-time requests for large objects to be the limiting factor that diminishes the impact of proxies on the tail of load distribution. We conclude that, while proxies are immensely useful to users due to the reduction in the average response time, they are less effective in improving the capacities of networks and servers.
[Correlation between respiration and heart rate in 12- to 14-year-old children during sleep and wakefulness]. (1995)

The coupling of respiratory and cardiac rhythm is determined by interactions of oscillating brain stem centers and external physical and psychical influences. Not well known are effects of sleep and wakefulness which will be investigated over the day. From the ECG and respirogram of 42 healthy children (11 female, 31 male, 12 to 14 years) during 24 h the time series of instantaneous heart rate (HR) and respiratory rhythm and from this by FFT the density spectra of power, the maximal power and related frequency in the respiratory range were ascertained. Differences between nonREM sleep and wakefulness and the strength of coupling were determined by coherence analysis. In all probands the maximal power of HR and of the coherence were higher during nonREM sleep than in wakefulness. Both values were stable during each state. The maximum related frequencies of HR and respiration shifted parallel between sleep and wakefulness. The results mean augmentation in nonREM sleep following to improved transfer of respiratory activity to the control of HR. The increased coherence hints at a stronger linear coupling which is stable during each state. The changes of cardiorespiratory coupling may be effected by stronger non-linear parts in the interactions during wakefulness.
Differential excretory/secretory proteome of the adult female and male stages of the human blood fluke, Schistosoma mansoni (2022)

Abstract Intricate molecular communication between the schistosome (flatworms) and its mammalian host, as well as between paired male and female schistosomes has shaped the secreted proteome of these flatworms. Whereas the schistosome egg is responsible for the disease manifestations of chronic schistosomiasis, the long lived, adult female and male stages also release mediators that facilitate their long-lived intra-vascular existence in a hostile niche where they are bathed in immune cells and effector molecules. However, despite their importance, no studies have focused on analysing the excretory/secretory products (ESPs) from adult schistosomes. Herein, ESPs from cultured Schistosoma mansoni male or female adult worms were identified, quantified, compared and contrasted using a label-free proteomic approach. Approximately 1,000 proteins were identified, from which almost 800 could be finally quantified. Considering the proteins uniquely identified and proteins with a significantly regulated expression pattern in male or female flukes, a total of 370 and 140 proteins were more abundantly secreted by males and females, respectively. Using functional analysis networks showing the gene ontology terms and KEGG pathways with the highest significance, we observed that male schistosomes secrete proteins related to carbohydrate metabolism, cytoskeletal organisation more abundantly than females, while female worms secreted more hydrolases and proteins involved in cellular homeostasis than males. This analysis doubles the number of previously reported ESPs from S. mansoni , contributing to a better understanding of the host-parasite dynamic interactions. Furthermore, these findings expand potential vaccine and diagnostic candidates for this neglected tropical disease pathogen, which will enable deeper understanding of the molecular communication critical to parasitism.
Directed Denaturation:  Room Temperature and Stoichiometric Unfolding of Cytochrome c by a Metalloporphyrin Dimer (2003)

Using circular dichroism, UV-vis, and trypsin proteolysis, we have shown how a metalloporphyrin dimer induces the unfolding of a protein, cytochrome c, under physiologically relevant conditions and accelerates its rate of proteolytic degradation.
Sub-2-cycle laser-driven wakefield electron acceleration (2013)

Summary form only given. The idea of electron acceleration by laser wakefield in plasma has been suggested [1] and proved [2] to give an accelerating gradient up to several orders of magnitude higher than conventional RF based linac. The unique property of laser plasma not only offers the opportunity to build a compact X-ray source [3] but also can be used as an electron diffraction source with high temporal resolution and brightness due to the natural property of laser plasma wave.We report on experimental results of electron acceleration with LWS-20 (Light Wave Synthesizer-20) [4], which is a sub-5 fs, 16 TW OPCPA system. LWS-20 is the world's first multi-TW sub-2-cycle light source. Our target is a supersonic He nozzle combined with shock-front injection [5]. The nozzle gives a plateau-like density profile with gas density on the order of few times 1019 cm 3, and the shock front was generated by a razor blade put into supersonic flow. The target is designed as an energy tuneable electron source by changing injection position with the blade position. The laser pulses are focused by an f/4 off-axis parabolic mirror which generates on target peak intensity of about 1019 Wcm 2. The total charge, beam profile and divergence were detected by a scintillating screen imaged onto a CCD, while the electron spectra were measured by using a carefully calibrated permanent magnet equipped with scintillating screens as detectors.Laser plasma acceleration was achieved after optimizing the most important laser and plasma parameters such as pulse duration, energy, focusing, plasma density, shock front position, etc. In a certain range of these parameters we obtained electron beams with 2.5 Hz repetition rate. We got a few pC of charge per shot within 1/e2 of electron distribution with about 25 mrad divergence in this unique regime. Typical single shot electron spectrum shows a mono-energetic dark-current-free feature with tuneable peak energy about 8-11 MeV and about 30% energy spread as shown in Fig. 1. Such an electron source has high potential for many applications such as time-resolved electron diffraction [6] or external injection source of a cascaded electron accelerator.
svmPSF quickstart manual (2020)

This user manual explains how to install and use the svmPSF plugins for Fiji/ImageJ. The svmPSF plugin models a spatially variant PSF into a series of spatially invariant PSFs for image deconvolution.