gebhart/patrepeval huggingface dataset:
Prediction of Solvation Sites at the Interface of Src SH2 Domain Complexes Using Molecular Dynamics Simulations (2007)

Src Homology 2 (SH2) domains are approximately 100 amino acid domains that mediate recognition of tyrosine-phosphorylated sites by signalling proteins. Structures of SH2 domains with bound ligands indicate a potentially important role of water in influencing the binding thermodynamics. In this study, we used molecular dynamics (MD) simulation methods to evaluate solvation sites at the binding interface of the Src SH2 domain. We designed a software, WaRP (Water Residency Potential), to compute the positions of hydration sites from coordinates data of MD simulations and studied the impact of the computed positions on the prediction of the thermodynamics of Src SH2 domain binding to phosphorylated peptides using a method based on accessible surface area buried upon association. Two dually phosphorylated ligands and one monophosphorylated ligand were studied. We showed that the software predicted between 70% and 85% of the crystallographic water molecules depending on complexes. Comparison of the predicted water structures of both the bound and unbound binding partners led to a thorough evaluation of water behaviour during the binding reaction. We also showed that the predicted water structures of all ligand-SH2 domain structures investigated may be used to derive the entropy change provided that the heat capacity change is known. This study is the first to examine the dynamics of the water structure around the SH2 domain binding interface and contributes to our understanding of binding thermodynamics in SH2 domains.
Graft Ischemia Correlates with Urinary Excretion of the Proximal Marker Enzyme Fructose-1,6-Bisphosphatase in Human Kidney Transplantation (1997)

This study was undertaken to test the hypothesis that ischemia prior to transplantation causes tubular damage without clinical evidence of graft dysfunction. The urinary excretion of fructose-1,6-bisphosphatase (EC 3.1.3.11, FBPase), a cytosolic enzyme located exclusively in the proximal tubules, and the lysosomal enzyme N-acetyl-beta-D-glucosaminidase (EC 3.2.1.30) were measured daily between postoperative days 1 and 4 in 25 renal cadaveric graft recipients who enjoyed an entirely uncomplicated first postoperative month. During the first 4 posttransplant days urinary FBPase excretion was 0.9 +/- 0.5 U/g (0.1 +/- 0.06 U/mmol) urinary creatinine [+/-SD; range 0.2-2.1 U/g (0.02-0.24 U/mmol)]. Cold ischemia time was 20.6 +/- 8.4 h (median 22 h, range: 3-32 h). Multiple regression revealed a significant correlation between cold ischemia time and posttransplant urinary FBPase excretion (multiple R = 0.65, p < 0.001). There were no confounding effects of recipient's age and gender, number of previous transplants, cyclosporin A levels, warm ischemia time, anastomosis time, donor age and gender. Urinary FBPase excretion was significantly lower in grafts stored for a shorter time than the median cold ischemia time of 22 hours (0.69 +/- 0.42 U/g, n = 13) as compared to those stored for a longer period of time (1.13 +/- 0.56 U/g; n = 12; p = 0.035). These results indicate that graft injuries occur even in the absence of graft dysfunction and that the duration of cold ischemia itself correlates with a degree of tubular cell damage as defined by urinary FBPase excretion.
Alkyl Sulfides as Promising Sulfur Sources: Metal‐Free Synthesis of Aryl Alkyl Sulfides and Dialkyl Sulfides by Transalkylation of Simple Sulfides with Alkyl Halides (2018)

A site-selective metal-free dealkylative approach to synthesize aryl alkyl and symmetrical dialkyl sulfides has been developed. This procedure is convenient and has wide functional group tolerance giving rise to sulfides carrying various alkyl chains from simple alkyl sulfides and alkyl halides in good to excellent yields. This transalkylation proceeds by an ionic mechanism via sulfonium intermediates and it was proposed that dimethylacetamide (DMAC) may participate in part to promote the reaction.
Supplementary Figure 6 from Myeloid-Derived Suppressor Cells Function as Novel Osteoclast Progenitors Enhancing Bone Loss in Breast Cancer (2023)

&lt;p&gt;PDF file - 108K, In vivo bone destruction mediated by MDSC requires NO production&lt;/p&gt;
Synthese und Kristallstruktur von Tribrommethyltriphenylphosphonium-bromid und Bis(tribrommethyltriphenylphosphonium)-tribroniid-bromid / Synthesis and Crystal Structure of Tribromomethyltriphenylphosphonium Bromide and Bis(tribromomethyltriphenylphosphonium) Tribromide Bromide (1995)

Tribromotriphenylphosphonium bromide 1 has been prepared by the reaction of triphenylphosphine with tetrabromomethane in dichloromethane. Colourless crystals were obtained by recrystallization from the same solvent. The light-sensitive crystals change colour to yellow. The crystals are triclinic, space group P1̄ , Z = 4, a = 1008.6(5), b = 1357.8(6), c = 1560.7(7) pm, α = 106.61(4), β = 91.80(4), γ = 93.88(4)°. In the solid state there are discrete monomeric (C 6 H 5 ) 3 PCBr 3 + cations and Br - anions. The cation has a slightly irregular tetrahedral geometry around the P atom. The crystals contain one molecule CH 2 C 12 per four molecules (C 6 H 5 ) 3 PCBr 4 . Bis(tribromomethyltriphenylphosphonium) tribromide bromide 2 can be obtained as a byproduct of the reaction of (C 6 H 5 ) 3 P with CBr 4 by variation of the reaction conditions. Red light-stable crystals are obtained by recrystallization from CH 2 C 12 . The crystals are monoclinic, space group C2/c, Z = 8, a = 2231.5(7), b = 1532.7(7), c = 1556.9(6) pm, β = 129.69(2)°. In the solid state bis(tribromomethyltriphenylphosphonium) tribromide bromide exists as discrete monomeric (C 6 H 5)3 PCBr 3 + cations and Br - and Br 3 - anions. The Br anion and the central Br of Br 3 - anion lie on crystallographic twofold axes. The cation has also a slightly irregular tetrahedral geometry around the P atom, with a long P-CBr 3 bond.
Synthesis and Morpholinolysis of N,N-diethyl Carbamate Derivatives of 4- HOAt, 7-HOAt and HOBt (2007)

N,N-Diethyl carbamates of 1-hydroxy-7-azabenzotriazole (7-HOAt), 1-hydroxy-4-azabenzotriazole (4-HOAt), 1-hydroxybenzotriazole (HOBt), and 1-hydroxypyrrolidine-2,5-dione have been synthesised. The reactivities of these active esters have been determined by studying the kinetics and mechanism of their morpholinolysis in acetonitrile at different temperatures.
Steady‐State D‐C Polarization Characteristics of the  O 2, Pt/Stabilized Zirconia Interface (1980)

Four‐probe d‐c polarization studies were carried out on the Pt/stabilized zirconia interface between 600° and 900°C in the presence of 10−6–1 atm of oxygen partial pressure. Three types of polarization effects were observed. At high currents, the oxygen flux density is limited by diffusion of molecular oxygen in the gas phase through a boundary layer near the interface. At intermediate currents, porous Pt electrodes are almost completely non‐blocking to oxygen, and the primary impedance present is due to ionic resistivity in the electrolyte. At low overvoltages, a limiting current plateau is observed at 600° and 700°C, which disappeared completely at 800°C and above. Two alternative mechanisms involving slow diffusion of either atomic oxygen or an electronic species are proposed to account for the observed behavior.
A novel strategy for segmentation of magnetic resonance (MR) images corrupted by intensity inhomogeneity artifacts (2006)

Magnetic resonance images are often corrupted by intensity inhomogeneity (i.e., bias field effects), which manifests itself as slow intensity variations over the image domain. Such shading artifacts must be corrected before performing computerized analyses such as intensity-based segmentation and quantitative analysis. In this paper, we present a novel strategy in the fuzzy c-means (FCM) framework that simultaneously estimates the bias field while segmenting the image. An additive field term that models the bias field is incorporated into the FCM objective function. We propose a new term based on the spectral parameterization (i.e., wavelet coefficients) of the bias field that serves as a regularizer to enforce the smoothness of the estimated bias field. We also introduce a second regularization term that causes the labeling of each pixel to be influenced by its immediate neighborhood pixels. The latter regularization term renders the algorithm less sensitive to noise. We show that the novel objective functional could be optimized efficiently using an iterative process. The efficacy of the algorithm is demonstrated on synthesized images as well as on clinical breast MR images. With the synthesize images, segmentation accuracy using standard FCM is 89.07% while segmentation accuracy with the proposed algorithm is 99.95%.
Comparison of High Performance Liquid Chromatography and Immunoassay Methods for Measurement of Cyclosporine A Blood Concentrations After Feline Kidney Transplantation (1998)

Objective —To compare two methods of whole blood cyclosporine A (CsA) measurement in cats. Study Design —Whole blood samples were analyzed for CsA concentrations with use of high performance liquid chromatography (HPLC) and monoclonal immunoassay methods. Animals —Blood (n = 36 samples) was obtained from six cats after renal transplantation. Methods —Results were compared by linear regression analysis using both pooled and individual patient data. Eight samples were off‐scale on the immunoassay and were excluded. Results —There was significant correlation between CsA measured using HPLC and immunoassay methods ( P &lt; .001; r = .942; r 2 = .887). However, individuals varied nonrandomly from the mean pooled patient data. Correlation between the assay methods was higher for individual patients using data only from that specific individual (mean r value = .976; r 2 = .955). Clinical utility of the immunoassay (ie, results would prompt an appropriate CsA dosage adjustment) was good when based on individually derived conversion factors (27 of 28 [96.5%] of decision events). Conclusion—HPLC is superior for measurement of blood CsA concentrations in cats after kidney transplantation. However, an immunoassay may provide reliable information for CsA management if a comparative database (HPLC v immunoassay) has been previously determined in a specific patient. Clinical Relevance —Locally available monitoring of CsA by immunoassay in cats may provide significant advantages when shipping of blood samples to distant locations is required to obtain analysis by HPLC. These advantages may include cost and timeliness of results in circumstances where daily blood CsA concentrations may be desired, such as when managing an acute rejection reaction.
Long-Chain-Branching Index for Essentially Linear Polyethylenes (1999)

Low levels of long-chain branching (LCB) in an otherwise linear polyethylene, such as HDPE or LLDPE, are known to affect dramatically the polymer melt rheological properties. However, reliable techniques to detect and quantify LCB at these levels (i.e., ≪1 LCB/1000 C) have not been available. In this work, the long-chain-branching index (LCBI) is developed for essentially linear, polydisperse polyethylenes, which are those containing a small level of LCB, such that the measured intrinsic viscosity is the same, within experimental error, to that calculated from MWD data, assuming the resins are linear. The long-chain-branching index (LCBI) is fundamentally related to the viscosity enhancement due to long-chain branching, and it is independent of molecular weight (MW) and molecular weight distribution (MWD). It is given by the relation: LCBI = ηo0.179/4.8[η] − 1, where ηo (P) is the zero shear viscosity at 190 °C, and [η] (dL/g) is the intrinsic viscosity in trichlorobenzene at 135 °C. A suitable average molecular weight could substitute the intrinsic viscosity in this relation, if so desired. The numerical factors in the defining relation are derived on fundamental grounds such that the lowest value of 0.0 represents perfectly linear polyethylene. Various measures of LCB that have appeared in the literature, including the Dow rheology index (DRI) and those based on the activation energy of viscous flow, are critically examined and their limitations identified. The new index proposed here overcomes these limitations, as illustrated with a vast number of examples with commercial polyethylenes. The applicability of the LCBI for distinguishing LCB levels within conventional, free-radical polymerized LDPEs is also investigated.
NEW GLOBAL SAFE/ECONOMICAL NUCLEAR ENERGY INDUSTRY-THORIUM MOLTEN-SALT NUCLEAR ENERGY SYNERGETICS- (2023)

To solve the global energy/environmental problems in the next century a huge-size Fission Industry should be prepared in high public acceptance. It seems to be established by THORIMS-NES(Thorium Molten-Salt Nuclear Energy Synergetics) composed of simple Molten-Salt Fission Reactors (MSR FUJI-series) and <sup>233</sup>U producing Accelerator Molten-Salt Breeders (AMSB). These new Th facilities will be developed by utilizing/eliminating the "excess Pu" separated from Pu weapon-heads and the spent-fuel of U-Pu reactors. THORIMS-NES will have big advantages not only in safety and radio waste issues, but also in nuclear-proliferation/terrorism and economy issues.
CMET-01. CLINICAL AND DOSIMETRIC FACTORS RELATED TO RADIATION NECROSIS AFTER FIVE FRACTION RADIOSURGERY FOR RESECTED BRAIN METASTASES (2018)

Stereotactic Radiosurgery (SRS) is increasingly utilized in the management of resected brain metastases (rBM). A significant complication is radiation necrosis (RN) due to larger target size. Despite dose de-escalation and hypofractionation, rates of RN after SRS to rBM remain high. The aim of this analysis is to evaluate dosimetric parameters associated with RN for rBM. From 2008–2016, 55 rBM in 52 patients at a single institution that were treated with 5 fraction LINAC based SRS (25-35Gy) with a minimum 3 months follow-up were evaluated. For each lesion, variables including clinical target volume (CTV), dose and location/magnitude of hot spots were recorded. Hot spot location was stratified as either within tumor bed (CTV) or within the PTV expansion margin (PTV minus CTV). Overall survival (OS) estimated using Kaplan-Meier method. Cumulative incidence with competing risks was used to estimate rates of RN and local recurrence (LR). Optimal cut-points predicting for RN for hotspot magnitude based on location were identified via maximization of the log-rank test statistic. Median age and OS for all patients was 58.5 years and 16.2 months, respectively. For all targets, the median CTV was 17.53 cc, and mean max hotspot was 113%. At 1 year, cumulative incidence of RN and LR for all patients was 21.8% and 13.1%. Univariate analysis showed max hot spot (hazard ratio (HR): 3.28, p=0.045) and hot spots within PTV expansion margin of 105%, 110% and 111% predicted for RN with HRs of 3.64, 8.47, and 6.90 respectively (all p<0.05), but hot spots within the CTV did not. To our knowledge, this is the first study that investigated dosimetric factors that predict for RN after hypofractionated SRS to rBM. Hot spot location and magnitude appear important for predicting RN risk, suggesting these parameters should be considered during treatment planning.
Addition of conductive particles to improve the performance of activated carbon air-cathodes in microbial fuel cells (2017)

Inexpensive carbon black combined with heat-treatment produced the most effective activated carbon catalyst for improving microbial fuel cell cathode performance.
Solenoid: universal tool for measuring beam parameters (2019)

Solenoids are frequently used for focusing of the low energy electron beams. In this paper we focus on using these magnets as a nearly universal tool for measuring beam parameters including energy, emittance, and the beam position and angle with respect to the solenoid axis. We describe in detail corresponding procedures as well as experimental results of such measurements.
Supplementary Figures 1 through 5 and Supplementary Figure Legends from p53 Loss in MYC-Driven Neuroblastoma Leads to Metabolic Adaptations Supporting Radioresistance (2023)

&lt;p&gt;Supplementary Figure 1. The p53 pathway is functional in Th-MYCN neuroblastomas. Supplementary Figure 2. Immunohistochemical analysis of Th-MYCN mice. Supplementary Figure 3. Restoration of p53 has no effect on tumor growth rate or penetration in Th-MYCN/Trp53KI/KI mice. Supplementary Figure 4. Th-MYCN/Trp53KI/KI pups display increased percentage of neoplastic islands compared to Th-MYCN/Trp53WT/WT pups. Supplementary Figure 5. Figure S5 Th-MYCN/Trp53WT/WT and Th-MYCN/Trp53KI/K tumors are similar in their basal DNA damage levels.&lt;/p&gt;
Fliih, a Gelsolin-Related Cytoskeletal Regulator Essential for Early Mammalian Embryonic Development (2002)

The Drosophila melanogaster flightless I gene is required for normal cellularization of the syncytial blastoderm. Highly conserved homologues of flightless I are present in Caenorhabditis elegans, mouse, and human. We have disrupted the mouse homologue Fliih by homologous recombination in embryonic stem cells. Heterozygous Fliih mutant mice develop normally, although the level of Fliih protein is reduced. Cultured homozygous Fliih mutant blastocysts hatch, attach, and form an outgrowing trophoblast cell layer, but egg cylinder formation fails and the embryos degenerate. Similarly, Fliih mutant embryos initiate implantation in vivo but then rapidly degenerate. We have constructed a transgenic mouse carrying the complete human FLII gene and shown that the FLII transgene is capable of rescuing the embryonic lethality of the homozygous targeted Fliih mutation. These results confirm the specific inactivation of the Fliih gene and establish that the human FLII gene and its gene product are functional in the mouse. The Fliih mouse mutant phenotype is much more severe than in the case of the related gelsolin family members gelsolin, villin, and CapG, where the homozygous mutant mice are viable and fertile but display alterations in cytoskeletal actin regulation.
Degradation Mechanisms of Electric Double Layer Capacitors with Activated Carbon Electrodes on High Voltage Exposure (2015)

Degradation mechanism of electrochemical double layer capacitors on high-voltage exposure is examined. Capacitance loss for positive electrodes is significantly accelerated above 4.5 V (vs. Li/Li+) whereas that of negative electrodes occurs on the electrochemical cycles down to 1.2 V. The surface of positive electrodes is covered with decomposition products of propylene carbonate used as electrolyte solution, and therefore high-voltage exposure increases impedance of electrodes. In contrast, the degradation of negative electrodes is triggered by the decomposition reaction of electrolyte salts, resulting in the formation of radical species. It is proposed that the radical species attack fluorinated polymer used as a binder, leading to the defluorination of binders and thus increase in polarization on electrochemical cycles.
Revealing the role of electron-electron correlations by mapping dissociation of highly excited <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow><mml:msub><mml:mi mathvariant="normal">D</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow><mml:mo>+</mml:mo></mml:msup></mml:math> using ultrashort XUV pulses (2018)

Understanding electron-electron correlations in matter ranging from atoms to solids represents a grand challenge for both experiment and theory. These correlations occur on attosecond timescales and have only recently become experimentally accessible. In the case of highly excited systems, the task of understanding and probing correlated interactions is even greater. In this work, we combine state-of-the-art light sources and advanced detection techniques with ab initio calculations to unravel the role of electron-electron correlation in ${\mathrm{D}}_{2}$ photoionization by mapping the dissociation of a highly excited ${{\mathrm{D}}_{2}}^{+}$ molecule. Correlations between the two electrons dictate the pathways along which the molecule dissociates and lead to a superposition of excited ionic states. Using 3D Coulomb explosion imaging and electron-ion coincidence techniques, we assess the relative contribution of competing parent ion states to the dissociation process for different orientations of the molecule with respect to the laser polarization, which is consistent with a shake-up ionization process. As a step toward observing coherent superposition experimentally, we map the relevant nuclear potentials using Coulomb explosion imaging and show theoretically that such an experiment could confirm this coherence via two-path interference.
Regulator of G protein Signaling 14 (RGS14) Interacts with 14‐3‐3 via an H‐Ras and Gαi‐dependent Mechanism (2015)

RGS14 is a multifunctional protein scaffold that is known to interact with active Gαi/o via its RGS domain, Raf and active H‐Ras‐GTP via its R1 Ras binding domain (RBD), and inactive Gαi 1/3 via its G protein regulatory (GPR; also known as GoLoco) domain. RGS14 has been shown to suppress long term potentiation (LTP) in the CA2 region of the hippocampus, thereby regulating hippocampal‐based learning and memory. The 14‐3‐3 family of proteins has recently been shown to be necessary for hippocampal LTP and associative learning and memory. Here we show evidence for an H‐Ras and Gαi‐dependent interaction between RGS14 and 14‐3‐3. Following overexpression of FLAG‐RGS14 and 14‐3‐3γ in HEK293T cells and pull‐down of FLAG‐RGS14, we observed an interaction between RGS14 and 14‐3‐3γ only in the presence of Gαi and/or the constitutively active form of H‐Ras(G12V). This interaction appears to occur within the R1 domain of RGS14, and is corroborated by mass spectrometry analysis of proteins recovered from intact cells. RGS14 interaction with 14‐3‐3γ does not appear to be due to direct binding of Gαi or H‐Ras(G12V) to RGS14. Ongoing studies will further elucidate the nature and physiological function of this interaction between RGS14 and 14‐3‐3γ, which may give insight into the functions of both RGS14 as well as 14‐3‐3 in their roles in modulating synaptic plasticity in the hippocampus. Studies supported by R01‐NS037112‐15 (JRH) and T32‐GM008602 (KJG).
Radiographic Sagittal Tibio-Talar Offset in Ankle Arthrodesis—Accuracy and Reliability of Measurements (2020)

Radiographic outcome assessment of ankle arthrodesis (AA) requires accurate measurement techniques. This study aimed to identify the most reliable methods for sagittal tibio-talar alignment measurements with regard to the tibio-talar offset after AA. Lateral weight-bearing radiographs of 38 fused ankles were selected for retrospective review. The sagittal tibio-talar angle (STTA), the modified tibio-talar ratio (mT-T ratio) and the sagittal tibio-talar offset (tibCOR, procLAT) were measured by three independent observers. Intra- and interobserver correlation coefficients (ICC) and mean measurement differences were calculated to assess measurement reliability and accuracy. By defining the talar longitudinal axis as a line from the inferior aspect of the posterior tubercle of the talus to the most inferior aspect of the talar neck, STTA showed excellent (ICC 0.924; CI 95% 0.862-0.959) and mTT-ratio provided high (ICC 0.836; CI 95% 0.721-0.909) interobserver reliability, respectively. For tibio-talar offset measurement the tibCOR method showed superior reliability and better interobserver agreement compared to the procLAT technique. The STTA and a modified T-T ratio are recommended for future scientific radiographic measurements in AA.