gebhart/patrepeval huggingface dataset:
Formation of Signal Transfer Complexes between Stem Cell and Platelet-Derived Growth Factor Receptors and SH2 Domain Proteins in Vitro (1995)

Cellular growth and differentiation signals are generated and defined by the interaction of specific phosphotyrosine residues of activated receptor tyrosine kinases (RTKs) and src homology-2 (SH2) domain-containing intracellular signal transducers. This appears to involve for both the p145c-kit and beta platelet-derived growth factor receptor (PDGF-R) cytoplasmic domains the formation of multiprotein signal transfer complexes, which include combinations of noncatalytic and enzymatically active subunits of phosphatidylinositol 3'-kinase (PI3'-K), phospholipase C-gamma (PLC gamma), and guanosine trisphosphatase activating protein (GAP). In vitro association experiments indicate that PLC gamma and PI3'-K bind the beta PDGF-R simultaneously, while these two SH2 proteins compete for association to p145c-kit binding sites, with p85/PI3'-K exhibiting higher affinity. Interestingly, GAP and p85/PI3'-K binding to distinct p145c-kit phosphotyrosines is cooperative, enhancing formation of a heterotetrameric signaling complex, which may include different combinations of p85 alpha and p85 beta with p110, p112, and p116 by interaction with the same tyrosine 721 docking site. The diversity of molecular interactions observed for PDGF-R and p145c-kit suggests a new mode of signal definition and modulation.
The creation of drops in T-shaped microfluidic devices with the ‘modified’ laser–LIGA technique: I. Fabrication (2005)

Surface effects are crucial in multiphase microfluidics, particularly in drop creation, where solid surface properties are a determining factor in a successful creation of micro- and nanodrops. Often, drops cannot be created due to the modification of solid surface properties as a result of the chosen microfabrication method. A novel micromachining technique is demonstrated, which combines nickel template fabrication and replication of microstructures on polymer substrates for mass production of microfluidic devices. The 'modified' laser-LIGA technique eliminates surface wetting problems and the occurrence of a deeper joint section resulting from traditional excimer laser ablation based methods. It is shown in this work that monodisperse microdrops can be successfully created in T-shaped microchannels fabricated with this technique. An investigation of shear-induced drop formation from the resulting T-shaped fluidic devices has shown that drop size decreases with increasing shear and that there exists a maximum in drop productivity for a given dispersed phase flowrate. The experimental data can be produced with high levels of certainty and repeatability, which again demonstrates the robustness of this technique.
Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The “Undoing” of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network (2019)

Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen-deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein-solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.
Supplementary Methods, Figures 1-2 from Frizzled 4 Regulates Stemness and Invasiveness of Migrating Glioma Cells Established by Serial Intracranial Transplantation (2023)

Supplementary Methods, Figures 1-2 from Frizzled 4 Regulates Stemness and Invasiveness of Migrating Glioma Cells Established by Serial Intracranial Transplantation
A compact, high-speed, wearable sensor network for biomotion capture and interactive media (2007)

In this paper, we present a wireless sensor platform designed for processing multipoint human motion with low latency and high resolution. One application considered here is interactive dance, in which a choreographer wishes to translate the movements of multiple dancers into real-time audio or video content to accompany the performance. This can only be accomplished using a distributed measurement system capable of responding quickly with enough information to describe the expressive movements of multiple people. Similar requirements exist for biomechanical analysis, especially in the context of athletic training, where high resolution is demanded, and instant feedback is also desirable. Our approach to addressing such aggressive requirements involves a high-speed wireless network of compact inertial measurement units (IMUs) that can be worn at various locations on the body. Each device is equipped with its own 1Mbps radio link and a full six-axis IMU, as well as a capacitive node-to-node proximity sensor. Currently, the system supports real-time data collection and processing for up to 25 nodes with 100Hz full state updates, thereby handling much higher data rates than its predecessors. With locally buffered data, sample rates of up to 1kHz have been achieved successfully. Early results discussed here demonstrate the feasibility of our design through testing with both dancers and professional athletes.
An algorim for quantification of hemodynamic properties in murine dorsal window chamber video images (2011)

We have developed a computational algorithm for the quantification of hemodynamic parameters from video‐rate images of blood flow in a dorsal window chamber model. This method analyses local correlations in pixel intensity fluctuations due to single erythrocyte movement to determine flow rates and direction of movement. The ability to quantify these parameters is of major importance in assessing vascular remodeling in tumor models. Since vascular oxygen/nutrient/drug transport dynamics play a major role in determining tumor progression and response to treatment, the ability to automatically quantify treatment induced effects is an invaluable asset to the dorsal window chamber model. Whereas earlier efforts to quantify flow dynamics relied heavily upon manual vessel identification and sampling of segments of interest, this method provides an entirely automated method by which values for relative velocity and direction of movement can be assigned to every pixel in the field of view. This advancement in analysis will facilitate much more rapid and less biased data generation than currently available image analysis techniques.
Amide proton transfer (APT) imaging of brain tumors at 7 T: The role of tissue water T<sub>1</sub>-Relaxation properties (2016)

The strong correlation of MTR<sub>Rex</sub> and MTR<sub>asym</sub> with T<sub>1wat</sub> and the absence thereof in AREX suggests that much of APT contrast in tumors for the low-power, 3D-acquisition scheme at 7 T originates from the inherent tissue water T<sub>1</sub> -relaxation properties. Magn Reson Med 77:1525-1532, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Die Verwendung von Lewis-Säuren bei Reaktionen freier Radikale (1998)

Ihr Schattendasein überwunden haben freie Radikale in den vergangenen Jahren, und sie gelten schon längst nicht mehr nur als interessante reaktive Zwischenstufen mit begrenztem präparativem Nutzen. Neue Möglichkeiten für die Synthesechemie eröffnet die Durchführung von Radikalreaktionen in Gegenwart von Lewis-Säuren. In einzigartiger Weise kann die Reaktionsgeschwindigkeit der radikalischen Addition an Olefine erhöht und der stereochemische Verlauf solcher Reaktionen kontrolliert werden. Jüngere Beispiele für enantioselektive Radikalreaktionen und Perspektiven für Anwendungen in der Katalyse werden vorgestellt.
The effect of sample size on polygenic hazard models for prostate cancer (2019)

Abstract We aimed to determine the effect of sample size on performance of polygenic hazard score (PHS) models in predicting the age at onset of prostate cancer. Age and genotypes were obtained for 40,861 men from the PRACTICAL consortium. The dataset included 201,590 SNPs per subject, and was split into training (34,444 samples) and testing (6,417 samples) sets. Two PHS model-building strategies were investigated. Established-SNP model considered 65 SNPs that had been associated with prostate cancer in the literature. A stepwise SNP selection was used to develop Discovery-SNP models. The performance of each PHS model was calculated for random sizes of the training set (1 to 30 thousand). The performance of a representative Established-SNP model was estimated for random sizes of the testing set (0.5 to 6 thousand). Mean HR 98/50 (hazard ratio of top 2% to the average in the test set) of the Established-SNP model increased from 1.73[95%CI: 1.69-1.77] to 2.41[2.40-2.43] when the number of training samples was increased from 1 to 30 thousand. The corresponding HR 98/50 of the Discovery-SNP model increased from 1.05[0.93-1.18] to 2.19[2.16-2.23]. HR 98/50 of a representative Established-SNP model using testing set sample sizes of 0.6 and 6 thousand observations were 1.78[1.70-1.85] and 1.73[1.71-1.76], respectively. We estimate that a study population of 20 to 30 thousand men is required to develop Discovery-SNP PHS models for prostate cancer. The required sample size could be reduced to 10 thousand samples, if a set of SNPs associated with the disease has already been established. Author summary Polygenic hazard scores represent a recent advancement in polygenic prediction to model the age of onset of various diseases, such as Alzheimer’s disease or prostate cancer. These scores accumulate small effect sizes from several tens of genetic variants and can be used to establish an individual’s risk of experiencing an event relative to a control population across time. The largest barrier to the development of polygenic hazard scores is the large number of study subjects needed to develop the underlying models. We sought to understand the effect of varying the total number of samples on the performance of a polygenic hazard score in the context of prostate cancer. We found that the performance of the score did not appreciably change beyond 20 to 30 thousand observations when developing the model from scratch. However, when the discovery of the genetic variants can be borrowed from those already identified in the literature to be associated with the disease, the required number of samples is reduced to 10 thousand with no appreciable detriment in performance. We hope that these results can guide the design of future studies of polygenic scores in other diseases and demonstrate the importance of genome-wide association studies.
Experimental Comparison of Low-Load Piston Compounding Deactivation for the DBDC+EC Engine Architecture (2021)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;An experimental piston compounded engine was designed with guidance from thermodynamic modeling, then was built and tested to compare the model predictions to measured results. This Downsized Boosted Dilute Combustion, Exhaust Compounded (DBDC+EC) engine concept has shown great potential for improvements in efficiency at high loads through extended second expansion process, but suffered from excessive expander cylinder pumping and low exhaust temperatures at low loads. Four expander operating strategies were experimentally tested and simulated at a range of engine speeds and loads to determine the most efficient method to deactivate the piston compounding at low loads. The most effective method involved deactivating all the expander valves and operating it as an air-spring while diverting power cylinder exhaust gasses through a separate bypass port. While this method requires some unique hardware development to enable on-the-fly actuation, it offers 15% to 22% improvements in low-load BSFC over the active expander method while improving exhaust temperatures by 100° to 150°C.&lt;/div&gt;&lt;/div&gt;
Supplementary Data from Stromal LRP1 in Lung Adenocarcinoma Predicts Clinical Outcome (2023)

&lt;p&gt;Supplementary Figures S1-S7; Supplementary Tables S1-S6.&lt;/p&gt;
ChemInform Abstract: The Enantioselective Synthesis of the Potent Dopamine D1 Agonist (1R, 3S)‐3‐(1′‐Adamantyl)‐1‐(aminomethyl)‐3,4‐dihydro‐5,6‐dihydroxy‐1H‐2‐ benzopyran (A77636) (1993)

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.
Outcomes following cholecystectomy in human immunodeficiency virus-positive patients treated with antiretroviral therapy: A retrospective cohort study (2022)

The number of the human immunodeficiency virus (HIV)-positive patients are increasing worldwide, and more HIV-positive patients are undergoing urgent or elective cholecystectomy. There is still insufficient evidence on the relationship between surgical complications of cholecystectomy and antiviral status in HIV-positive patients. The purpose of the present study is to evaluate surgical outcomes after cholecystectomy in HIV-positive patients. Records of consecutive HIV-positive patients who underwent cholecystectomy between January 2010 and December 2020 were reviewed retrospectively. Patients were divided into urgent and elective surgery groups. Urgent surgery was defined as surgery within 48 hours of admission. Postoperative complications were evaluated according to the Clavien-Dindo classification. A total of 30 HIV-positive patients underwent urgent (<i>n</i> = 7) or elective (<i>n</i> = 23) cholecystectomy. Four complications (13.3%) occurred, and the rate was significantly higher in the urgent group than in the elective group (<i>p</i> = 0.008). However, all complications were minor (3 cases of grade I and one case of grade II), and there were no severe postoperative complications. There was no significant difference in CD4+ lymphocyte status in all patients and between the 2 groups before and after surgery (<i>p</i> = 0.133). No cases of postoperative deterioration in the control of HIV infection were observed. In conclusion, cholecystectomy in HIV-positive patients with controlled HIV under recent antiretroviral therapy may be performed safely even in an emergency situation.
Light-Activated Desorption of Photoactive Polyelectrolytes from Supported Lipid Bilayers (2005)

Phospholipid vesicles and supported bilayers have emerged as a promising platform for the development of biorecognition devices. To expand the capabilities of such biochips, it becomes desirable to direct and control the assembly of lipid structures into more sophisticated architectures. As one step toward this goal, we demonstrate the photoregulated desorption of a new class of polymer from lipid bilayers. The neutral, hydrophobic polymer resides within the bilayer under mild pH and ambient conditions. However, it contains side groups that can undergo excited state proton transfer (ESPT). The polymer therefore behaves as a polyelectrolyte when exposed to UV light. With the ensuing increase in hydrophilicity, the molecule is spontaneously ejected from the bilayer. Quartz crystal microbalance measurements with dissipation monitoring (QCM-D) have recorded this process and have shown that a rapid buffer exchange during light exposure results in efficient removal of the polymer from the system. Three polymers were tested in all: a polyanion, a polycation, and a polyzwitterion. A one-step approach to the synthesis of the monomer, performed under relatively mild reaction conditions, made it possible to synthesize each polymer in one step.
Advanced 3D eWLB-SiP (embedded Wafer Level Ball Grid Array – System in Package) Technology (2017)

FO-WLP (Fan-Out Wafer Level Packaging) has been established as one of the most versatile packaging technologies in the recent past and is already accounting for a market value of over 1 billion USD due to its unique advantages. The technology combines high performance, increased functionality with a high potential for heterogeneous integration and reduce the total form factor as well as cost-effectiveness. The emerging of advanced of silicon node technology down to 10 nanometer (nm) in support of higher performance, bandwidth and better power efficiency in mobile products pushes the boundaries of emerging packaging technologies to smaller form-factor packaging designs with finer line/spacing as well as improved thermal electrical/performance and integration of SiP or 3D capabilities. Advanced eWLB FO-WLP technology provides a versatile platform for the semiconductor industry's technology evolution from single or multi-die 2D package designs to 2.5D interposers and 3D System-in-Package (SiP) configurations. This paper reports developments that extend multi-die and 3D SiP applications with eWLB technology, including ultra thin devices or/and with an interposer substrate attachment. Test vehicles have been designed and fabricated to demonstrate and characterize integrated packaging solutions for network, mobile products including IoT and wearable electronics. The test vehicles have ranged from ~30mm2 to large sizes up to ~230mm2 and 0.4mm ball pitch. Assembly process details including 3D vertical interconnect, laser ablation, RDL processes and mechanical reliability characterizations are to be discussed with component and board level reliability results. In addition, warpage behavior and the PoP stacking process will also be presented. Innovative structure optimization that provides dual advantages of both height reduction and enhanced package reliability are reported. To enable higher interconnection density and signal routing, packages with multiple redistribution layers (RDL) and fine line/width spacing are fabricated and implemented on the eWLB platform. Successful reliability and electrical characterization results on multi-die and 3D eWLB-SiP configurations are reported as an enabling technology for highly integrated, miniaturized, low profile and cost effective solutions.
Preparation and Photophysical Properties of <i>Bis</i>(tridentate) Iridium(III) Emitters: Pincer Coordination of 2,6-Di(2-pyridyl)phenyl (2020)

The way to prepare molecular emitters [5t + 4t'] of iridium(III) with a 5t ligand derived from the abstraction of the hydrogen atom at position 2 of the aryl group of 1,3-di(2-pyridyl)benzene (dpybH) is shown. In addition, the photophysical properties of the new emitters are compared with those of their counterparts resulting from the deprotonation of 1,3-di(2-pyridyl)-4,6-dimethylbenzene (dpyMebH), at the same position, which are also synthesized. Treatment of 0.5 equiv of the dimer [Ir(μ-Cl)(η<sup>2</sup>-COE)<sub>2</sub>]<sub>2</sub> (COE = cyclooctene) with 1.0 equiv of Hg(dpyb)Cl leads to the iridium(III) derivative IrCl<sub>2</sub>{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyb)}(η<sup>2</sup>-COE) (<b>3</b>), which reacts with 2-(1<i>H</i>-imidazol-2-yl)-6-phenylpyridine (HNImpyC<sub>6</sub>H<sub>5</sub>) and 2-(1<i>H</i>-benzimidazol-2-yl)-6-phenylpyridine (HNBzimpyC<sub>6</sub>H<sub>5</sub>) in the presence of Na<sub>2</sub>CO<sub>3</sub> to give Ir{κ<sup>3</sup>-<i>C</i>,<i>N</i>,<i>N</i>-(NImpyC<sub>6</sub>H<sub>4</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyb)} (<b>4</b>) and Ir{κ<sup>3</sup>-<i>C</i>,<i>N</i>,<i>N</i>-(NBzimpyC<sub>6</sub>H<sub>4</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyb)} (<b>5</b>), respectively. Similar reactions of the Williams's dimer [IrCl(μ-Cl){κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyMeb)}]<sub>2</sub> with HNImpyC<sub>6</sub>H<sub>5</sub> and HNBzimpyC<sub>6</sub>H<sub>5</sub> in the presence of Na<sub>2</sub>CO<sub>3</sub> afford the dimethylated counterparts Ir{κ<sup>3</sup>-<i>C</i>,<i>N</i>,<i>N</i>-(NImpyC<sub>6</sub>H<sub>4</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyMeb)} (<b>6</b>) and Ir{κ<sup>3</sup>-<i>C</i>,<i>N</i>,<i>N</i>-(NBzimpyC<sub>6</sub>H<sub>4</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyMeb)} (<b>7</b>), whereas 2-(6-phenylpyridine-2-yl)-1<i>H</i>-indole (HIndpyC<sub>6</sub>H<sub>5</sub>) initially gives IrH{κ<sup>2</sup>-<i>N</i>,<i>N</i>-(IndpyC<sub>6</sub>H<sub>5</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyMeb)} (<b>8</b>) and subsequently Ir{κ<sup>3</sup>-<i>C</i>,<i>N</i>,<i>N</i>-(IndpyC<sub>6</sub>H<sub>4</sub>)}{κ<sup>3</sup>-<i>N</i>,<i>C</i>,<i>N</i>-(dpyMeb)} (<b>9</b>). Complexes <b>4</b>-<b>7</b> are phosphorescent green emitters (λ<sub>em</sub> 490-550 nm), whereas <b>9</b> is greenish yellow emissive (λ<sub>em</sub> 547-624 nm). They display lifetimes in the range 0.5-9.7 μs and quantum yields in both doped poly(methyl)methacrylate films and in 2-methyltetrahydrofuran at room temperature depending upon the ligands: 0.5-0.7 for <b>6</b> and <b>7</b>, about 0.4 for <b>4</b> and <b>5</b>, and 0.3-0.2 for <b>9</b>.
X-Linked Agammaglobulinemia Patients Are Not Infected with Epstein-Barr Virus: Implications for the Biology of the Virus (1999)

Epstein-Barr virus (EBV) infects both B lymphocytes and squamous epithelial cells in vitro, but the cell type(s) required to establish primary and persistent infection in vivo has not been definitively elucidated. The aim of this study was to investigate a group of individuals who lack mature B lymphocytes due to the rare heritable disorder X-linked agammaglobulinemia in order to determine the role of the B cell in the infection process. The results show that none of these individuals harbored EBV in their blood or throat washings. Furthermore, no EBV-specific memory cytotoxic T lymphocytes were found, suggesting that they had not undergone infection in the past. In contrast, 50% of individuals were found to carry human herpesvirus 6, showing that they are infectible by another lymphotropic herpesvirus. These results add weight to the theory that B lymphocytes, and not oropharyngeal epithelial cells, may be required for primary infection with EBV.
Advances in Optical Waveguide Engineering (2003)

This PDF file contains the editorial “Advances in Optical Waveguide Engineering” for OE Vol. 42 Issue 10
Immunological responses and viral modulatory effects of vaccination with recombinant modified vaccinia virus Ankara (rMVA) expressing structural and regulatory transgenes of simian immunodeficiency virus (SIVmac32H/J5M) (2007)

Improved combinations of viral vectors are required to elicit appropriate immune responses to control viral replication.