gebhart/patrepeval huggingface dataset:
Editorial: Low-dimensional structures, nanoparticles, and optical measurements (2022)

EDITORIAL article Front. Phys., 29 November 2022Sec. Optics and Photonics Volume 10 - 2022 | https://doi.org/10.3389/fphy.2022.1094822
Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF<sup>V600E</sup> Conformation (2016)

The BRAF kinase, within the mitogen activated protein kinase (MAPK) signaling pathway, harbors activating mutations in about half of melanomas and to a significant extent in many other cancers. A single valine to glutamic acid substitution at residue 600 (BRAF<sup>V600E</sup>) accounts for about 90% of these activating mutations. While BRAF<sup>V600E</sup>-selective small molecule inhibitors, such as debrafenib and vemurafenib, have shown therapeutic benefit, almost all patients develop resistance. Resistance often arises through reactivation of the MAPK pathway, typically through mutation of upstream RAS, downstream MEK, or splicing variants. RAF kinases signal as homo- and heterodimers, and another complication associated with small molecule BRAF<sup>V600E</sup> inhibition is drug-induced allosteric activation of a wild-type RAF subunit (BRAF or CRAF) of the kinase dimer, a process called "transactivation" or "paradoxical activation." Here, we used BRAF<sup>V600E</sup> and vemurafenib as a model system to develop chemically linked kinase inhibitors to lock RAF dimers in an inactive conformation that cannot undergo transactivation. This structure-based design effort resulted in the development of Vem-BisAmide-2, a compound containing two vemurafenib molecules connected by a bis amide linker. We show that Vem-BisAmide-2 has comparable inhibitory potency as vemurafenib to BRAF<sup>V600E</sup> both in vitro and in cells but promotes an inactive dimeric BRAF<sup>V600E</sup> conformation unable to undergo transactivation. The crystal structure of a BRAF<sup>V600E</sup>/Vem-BisAmide-2 complex and associated biochemical studies reveal the molecular basis for how Vem-BisAmide-2 mediates selectivity for an inactive over an active dimeric BRAF<sup>V600E</sup> conformation. These studies have implications for targeting BRAF<sup>V600E</sup>/RAF heterodimers and other kinase dimers for therapy.
Increased expression of granzymes A and B in fatal asthma (2015)

Inflammatory mediators other than the classic T-helper cell type 2 (Th2)-related pathway play a role in asthma, especially in severe asthma and in exacerbations [1]. Recent studies have suggested a role for cytotoxic CD8 T-cells in lung function impairment [2], lung function decline [3] and smoking-associated asthma [4]. Increased numbers of GzmA+ and GzmB+ cells in the airways and lung parenchyma of subjects who died from asthma <http://ow.ly/IcKV7> We would like to thank G.M. Möller (Ziekenhuis Rivierenland Tiel, The Netherlands) for helpful suggestions during the study.
New Host-Vector System for <i>Thermus</i> spp. Based on the Malate Dehydrogenase Gene (2001)

A Thermus thermophilus HB27 strain was constructed in which the malate dehydrogenase (mdh) gene was deleted. The Deltamdh colonies are recognized by a small-colony phenotype. Wild-type phenotype is restored by transformation with Thermus plasmids or integration vector containing an intact mdh gene. The wild-type phenotype provides a positive selection tool for the introduction of plasmid DNA into Thermus spp., and because mdh levels can be readily quantified, this host-vector system is a convenient tool for monitoring gene expression.
Factors involved in specific transcription by mammalian RNA polymerase II. Transcription factor IIS stimulates elongation of RNA chains. (1987)

A factor that stimulates random transcription of purified DNAs by RNA polymerase II has been partially purified and analyzed with respect to its possible role in specific transcription from class II promoters. Studies of the effect of this factor (transcription factor IIS) on transcription from the adenovirus major late promoter in a system reconstituted with RNA polymerase II and purified factors (IIA, IIB, IIE, and IID) indicated that it acted subsequent to the initiation step and that it stimulated the rate of elongation. Kinetic experiments indicated that the factor affected the efficiency with which the RNA polymerase II passed through pausing sites. The relationship of transcription factor IIS to a protein previously purified from Erlich ascites tumor cells (Sekimizu, K., Nakanishi, Y., Mizuno, D., and Natori, S. (1979) Biochemistry 18, 1582-1588) was also studied.
How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior (2006)

Our understanding of social insect behavior has significantly influenced artificial intelligence (AI) and multirobot systems' research (e.g., ant algorithms and swarm robotics). In this work, however, we focus on the opposite question: "How can multirobot systems research contribute to the understanding of social animal behavior?" As we show, we are able to contribute at several levels. First, using algorithms that originated in the robotics community, we can track animals under observation to provide essential quantitative data for animal behavior research. Second, by developing and applying algorithms originating in speech recognition and computer vision, we can automatically label the behavior of animals under observation. In some cases the automatic labeling is more accurate and consistent than manual behavior identification. Our ultimate goal, however, is to automatically create, from observation, executable models of behavior. An executable model is a control program for an agent that can run in simulation (or on a robot). The representation for these executable models is drawn from research in multirobot systems programming. In this paper we present the algorithms we have developed for tracking, recognizing, and learning models of social animal behavior, details of their implementation, and quantitative experimental results using them to study social insects
Symptoms at presentation to the emergency department: Predicting outcomes and changing clinical practice? (2017)

The number of symptoms did not correlate with the main adverse outcomes (ICU-admission and in-hospital mortality). However, clinical practice was influenced by the nature and number of symptoms. This was shown by associations with hospitalisation, length-of-stay, use of resources and follow-up presentations. Furthermore, the number of symptoms correlated with the caregivers' disease severity ratings and the attributed triage categories. This may indicate that caregivers respond to the number of symptoms by a higher investment in their immediate work-ups and later follow-ups.
Enhanced Light Emission of Germanium Light-Emitting-Diode on 150 mm Germanium-On-Insulator (GOI) (2023)

Germanium-on-insulator (GOI) has become a novel platform for Ge-based electronic and photonic applications. Discrete photonic devices such as waveguides, photodetectors, modulators, and optical pumping lasers have been successfully demonstrated on this platform. To realize electric injection emitting is highly desirable towards integrated photonics. In this work, we report for the first time the Ge p−i−n light-emitting-diodes (LEDs) on the GOI substrate. The high-quality Ge LED on a 150-mm diameter GOI substrate was fabricated via direct wafer bonding followed by ion implantations. As a tensile strain of 0.19% has been introduced during the GOI fabrication process resulting from thermal mismatch, the LED devices exhibit a dominant direct bandgap transition peak near 0.785 eV (~1,580nm) at room temperature. In sharp contrast to conventional III-V LEDs, we found that the electroluminescence/photoluminescence (EL/PL) spectra show enhanced intensities as raising the temperature from 300 to 450 K as a consequence of higher occupation of direct bandgap. The maximum enhancement in EL intensity is a factor of 140% near 1,635 nm due to the improved optical confinement offered by the bottom insulator layer. This work potentially broadens the GOI's functional variety for applications in near-infrared sensing, electronics, and photonics.
Crystallization and preliminary x-ray investigation of sarcoplasmic calcium-binding protein from Nereis diversicolor. (1987)

Crystals of sarcoplasmic calcium-binding proteins from Nereis diversicolor have been grown from solutions of ammonium sulfate. The crystals are monoclinic, space group P2(1); the axes are a = 43.65 (1), b = 56.05 (1), c = 65.77 (1) A, and beta = 92.58 (2) degrees. The crystals are quite stable to x-rays and diffract beyond 2.5 A resolution. The asymmetric unit contains two protein molecules.
Use of Systematic Biopsy Results to Predict Pathologic Stage in Patients with Clinically Localized Prostate Cancer: A Preliminary Report (1998)

The pathologic features of cancer in systematic needle biopsy specimens more accurately predicts which patients have advanced stage cancer than standard clinical tests alone.
Results of a round-robin experiment in multiple-pulse LIDT measurement with ultrashort pulses (2004)

For the development of standard measurement procedures in optics characterization, comparative measurement campaigns (Round-robin experiments) are indispensable. Within the framework of the CHOCLAB project in the mid-90s, several international Round-robins were successfully performed qualifying procedures for e. g. 1 on 1-LIDT, laser-calorimetry and total scattering. During the recent years, the demand for single pulse damage investigations has been overtaken by the more practically relevant S on 1-LIDT. In contrast to the industrial needs, the comparability of the multiple-pulse LIDT has not been proven by Round-robin experiments up to now. As a consequence of the current research activities on the interaction of ultra-short pulses with matter as well as industrial applications, numerous fs-laser systems become available in universities and research institutes. Furthermore, special problems for damage testing may be expected because of the intrinsic effects connected with the interaction of ultrashort pulses with optical materials. Therefore, a Round-robin experiment on S on 1-damage testing utilizing fs-pulses was conducted within the framework of the EUREKA-project CHOCLAB II. For this experiment, seven parties investigated different types of mirrors and windows. Most of the partners were guided by the International Standard ISO 11254-2, but one partner employed his own damage testing technique. In this presentation, the results of this comparative experiment are compiled demonstrating the problems induced by special effects of damage testing in the ultra-short pulse regime.
Influence of Steel Fibre Reinforcement on the Shear Resistance and Crack Pattern Formation of Self-Compacting Concrete Beams (2010)

This paper presents the results of experimental tests carried out on steel fibre reinforced self-compacting concrete (SFR-SCC) beams without stirrups. Sixteen beams are cast using four mixtures of SCC with different steel fibre content, while the longitudinal reinforcement is kept constant in all test members. The beams are subjected to four point bending tests at a shear span-to-depth ratio of 2. The ultimate shear stress is recorded, as well as the crack pattern and the mid-span beam deflection. Test results show that as fibre content increases, higher ultimate shear stresses are achieved. When fibres are included, test members exhibit an increase in ductility and a more extensive crack pattern is observed. The experimental values of the ultimate shear stresses are also compared with theoretical values as given by empirical expressions in literature.
Flow-Induced Patterning of Langmuir Monolayers (2004)

Insoluble monolayers on water have been patterned at the macroscopic scale (i.e., at the centimeter scale of the flow apparatus) as well as the mesoscopic scale (i.e., down to the micron scale resolvable via optical microscopy). The macroscopic patterning at the air/water interface results from a hydrodynamic instability leading to a steadily precessing flow pattern. The velocity field is measured, and the associated shear stress at the interface is shown to be locally amplified by the flow pattern. The resulting hydrodynamic effects on two different monolayer systems are explored: (1) the pattern in a model monolayer consisting of micron-size, surface-bound particles is visualized to show that the particles are concentrated into isolated regions of converging flow with high shear, and (2) Brewster angle microscopy of a Langmuir monolayer (vitamin K1) shows not only that the monolayer is patterned at the macroscopic scale but also that the localized high-shear flow further patterns the monolayer at the mesoscale.
Assessment of the role of activin A and transforming growth factor β in the regulation of AML12 cell growth (1997)

The present study was conducted to determine the role of two autocrine factors, activin A and transforming growth factor beta (TGF-beta), in the growth regulation of AML12 hepatocytes. We overexpressed truncated type II activin and/or TGF-beta receptors in AML12 cells. In AML12 cells overexpressing truncated type II activin receptors (AML-tAR cells), the inhibitory effect of activin A on DNA synthesis was completely blocked. AML-tAR cells proliferated faster than parental cells, both in the presence and absence of epidermal growth factor (EGF). However, AML-tAR cells could not grow in soft agar. Follistatin augmented EGF-induced DNA synthesis in AML12 cells, whereas it was ineffective in AML-tAR cells. In AML12 cells overexpressing truncated type II TGF-beta receptor (AML-tTR cells), the inhibitory effect of TGF-beta on DNA synthesis was blocked. AML-tTR cells proliferated faster than parental cells, both in the presence and absence of EGF, but at a slower rate than that of AML-tAR cells. AML-tTR cells did not grow in soft agar. The growth rate of cells overexpressing both types of truncated receptors was identical to that of AML-tAR cells, and these cells did not grow in soft agar. These results indicate that both activin A and TGF-beta act as autocrine inhibitors of DNA synthesis in AML12 cells, and that the blocking of the actions of two factors does not lead to transformation. Activin A is a predominant autocrine factor in these cells.
ChemInform Abstract: (1,2)‐Wittig Rearrangement of Enantio‐Defined α‐ Alkoxyalkyllithiums: Stereochemistry at the Li‐Bearing Terminus and Mutual Recognition of Enantiomers During the Radical Recombination. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fröhlich interaction dominated by a single phonon mode in CsPbBr3 (2021)

The excellent optoelectronic performance of lead halide perovskites has generated great interest in their fundamental properties. The polar nature of the perovskite lattice means that electron-lattice coupling is governed by the Fröhlich interaction. Still, considerable ambiguity exists regarding the phonon modes that participate in this crucial mechanism. Here, we use multiphonon Raman scattering and THz time-domain spectroscopy to investigate Fröhlich coupling in CsPbBr<sub>3</sub>. We identify a longitudinal optical phonon mode that dominates the interaction, and surmise that this mode effectively defines exciton-phonon scattering in CsPbBr<sub>3</sub>, and possibly similar materials. It is additionally revealed that the observed strength of the Fröhlich interaction is significantly higher than the expected intrinsic value for CsPbBr<sub>3</sub>, and is likely enhanced by carrier localization in the colloidal perovskite nanocrystals. Our experiments also unearthed a dipole-related dielectric relaxation mechanism which may impact transport properties.
Supplementary Table 2 from Phase I, Dose-Escalation Study of the Targeted Cytotoxic LHRH Analog AEZS-108 in Patients with Castration- and Taxane-Resistant Prostate Cancer (2023)

&lt;p&gt;Supplemental Table 2. Grade 1, 2, 3 and 4 adverse events including all cohorts (n=18). Toxicities defined as not related to treatment were excluded.&lt;/p&gt;
Investigation of Lattice Mismatch in Rhenium Containing Nickel-Base Superalloys (1986)

In this study, three techniques for measuring gamma/gamma prime lattice mismatch were examined on two alloys, each of which had two different ageing heat treatments, i.e. standard age and overaged. Each alloy contained a different Re content so that the effect of this element on lattice mismatch also could be investigated. The techniques used for measuring lattice mismatch were x-ray diffraction, convergent beam electron diffraction and interface dislocation analysis. Additionally, the electron microprobe was used to examine bulk homogeneity and a scanning transmission electron microscope equipped with a Kevex X-ray EDS system was used to examine phase compositions. From this study it was determined that the x-ray diffraction data and the CBED data yield the same results for room temperature lattice mismatch, although CBED requires a significant amount of data in order to be useful due to the scatter in the technique. The dislocation analysis technique gave larger negative values of mismatch. It is believed that these latter values represent those which exist at the aging temperature (1079°C). No effect of Re on lattice mismatch was observed, possibly due to the fact that the lower Re alloy contained more W.
The impact of delayed treatment of uncomplicated P. falciparum malaria on progression to severe malaria: A systematic review and a pooled multicentre individual-patient meta-analysis (2020)

Our results quantify the relationship between rapid access to treatment and reduced risk of severe disease, which was particularly strong for SMA. There was some evidence to suggest that progression to other severe phenotypes may also be prevented by prompt treatment, though the association was not as strong, which may be explained by potential selection bias, sample size issues, or a difference in underlying pathology. These findings may help assess the impact of interventions that improve access to treatment.
Double-Kissing Nanocrush for Bifurcation Lesions: Development, Bioengineering, Fluid Dynamics, and Initial Clinical Testing (2019)

The DK nanocrush technique may represent the ultimate refinement of the original crush technique with a number of practical and theoretical advantages. It remains to be tested against other bifurcation techniques in prospective trials.
Induction of Tolerance for Long-Term Liver Allograft Survival Without Immunosuppression in Cynomolgus Monkeys (2018)

Background Spontaneous liver tolerance occurs only in highly selected patients with stable liver function for several years. There is an unmet need for a safe and reliable regimen allowing rapid immunosuppression (IS) withdrawal. Herein, we investigated if tolerance to liver allografts can be achieved in cynomolgus macaques using four different non-myeloablative preparative regimens. Methods Nine combined liver and bone marrow cell transplants were performed in cynomolgus monkeys, using three various conditioning regimens (group A, B, C). All animals received total body irradiation (1.5 Gy), thymic irradiation (7 Gy), and ATGAM (50 mg/kg) prior to the transplant. Rituximab (20 mg/kg), anti-CD40 (50 mg/kg), and anti-CD2 (1-2 mg/kg) monoclonal antibodies were given according to Table 1. Four additional livers (group D) were transplanted with the same protocol as in group C, but BMT was omitted. All IS was completely discontinued by day 55. Results All recipients developed multilineage mixed chimerism. Group A showed severe rejection with CD8+ T effector memory (Tmem) cell expansion. Improved pretransplant host Tmem depletion using anti-CD2 in group B resulted in prolonged multlineage MC and graft acceptance. Animal B(2), however, developed grade 1 GVHD in skin and rectum. The addition of post-transplant anti-CD2 in group C depleted donor Tmem, prevented GVHD, while permitting prolonged MC and extended IS-free graft survival. With the exclusion of BMT (group D), passenger leukocytes in the liver promoted transient MC. Even when chimerism was lost and memory T cells recovered, group D maintained normal graft function without any inflammation seen in protocol biopsies beyond six months. The percentage of Tregs in total CD4 were elevated over baseline during the period of stable graft function in Groups C and D animals.Conclusions This is the first proof of concept study demonstrating long-term stable liver allograft function in nonhuman primates using a non-myeloablative treatment regimen to facilitate rapid IS withdrawal. The results demonstrate the ability of anti-CD2 to control Tmem responses, and that liver transplantation alone (without infusion of DBM cells) generates MC and is associated with long-term graft survival after complete IS withdrawal. NIAID R56AI122332-01A1. AASLD Career Development Award in the Memory of the University of Michigan Transplant Team. Columbia University Irving Institute for Clinical Research.
Mo<sup>V</sup>−Mo<sup>VI</sup> Mixed Valence Polyoxometalates for Facile Synthesis of Stabilized Metal Nanoparticles:  Electrocatalytic Oxidation of Alcohols (2007)

Mo&lt;sup&gt;V&lt;/sup&gt;−Mo&lt;sup&gt;VI&lt;/sup&gt; mixed valence polyoxometalates (POMs), H&lt;sub&gt;7&lt;/sub&gt;[β-P(Mo&lt;sup&gt;V&lt;/sup&gt;)&lt;sub&gt;4&lt;/sub&gt;(Mo&lt;sup&gt;VI&lt;/sup&gt;)&lt;sub&gt;8&lt;/sub&gt;O&lt;sub&gt;40&lt;/sub&gt;] (&lt;b&gt;1&lt;/b&gt;), (NH&lt;sub&gt;4&lt;/sub&gt;)&lt;sub&gt;10&lt;/sub&gt;[(Mo&lt;sup&gt;V&lt;/sup&gt;)&lt;sub&gt;4&lt;/sub&gt;(Mo&lt;sup&gt;VI&lt;/sup&gt;)&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;14&lt;/sub&gt;(O&lt;sub&gt;3&lt;/sub&gt;PCH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;(H&lt;sub&gt;2&lt;/sub&gt;OPCH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;]·15H&lt;sub&gt;2&lt;/sub&gt;O (&lt;b&gt;2&lt;/b&gt;), and [ε-P(Mo&lt;sup&gt;V&lt;/sup&gt;)&lt;sub&gt;8&lt;/sub&gt;(Mo&lt;sup&gt;VI&lt;/sup&gt;)&lt;sub&gt;4&lt;/sub&gt;O&lt;sub&gt;36&lt;/sub&gt;(OH)&lt;sub&gt;4&lt;/sub&gt;{La(H&lt;sub&gt;2&lt;/sub&gt;O)&lt;sub&gt;2.5&lt;/sub&gt;Cl&lt;sub&gt;1.25&lt;/sub&gt;}&lt;sub&gt;4&lt;/sub&gt;]·27H&lt;sub&gt;2&lt;/sub&gt;O (&lt;b&gt;3&lt;/b&gt;), respectively, were selected because they possess built-in reducing abilities. They were used for\nthe synthesis of Pt&lt;sup&gt;0&lt;/sup&gt; and Pd&lt;sup&gt;0&lt;/sup&gt; nanoparticles (NPs) in water at room temperature without UV irradiation. Small\nsize NPs (1.7−4 nm) were obtained, their stabilization following the order &lt;b&gt;1&lt;/b&gt; &gt; &lt;b&gt;2&lt;/b&gt; ≫ &lt;b&gt;3&lt;/b&gt;. They were characterized\nby transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and electrochemistry.\nDetection of molybdenum in XPS and electrochemistry supports the hypothesis that each polyoxometalate\nserves both as a reductant and as a protective layer, in agreement with the propensity, particularly of Mo-based POMs, to self-assemble on metal and other solid surfaces. The Pt&lt;sup&gt;0&lt;/sup&gt; and Pd&lt;sup&gt;0&lt;/sup&gt; NPs were tested for the\nelectrocatalytic oxidation of methanol and ethanol, respectively, and proved efficient for these processes. In\naddition, Pt&lt;sup&gt;0&lt;/sup&gt; was resistant to poisoning during methanol oxidation. The synthesis of these stabilized nanoparticles\nis facile and provides materials that show promise for use in fuel cells.