gebhart/patrepeval huggingface dataset:
Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling (2021)

Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.
Spectrally selective tinoxide and indiumoxide coatings (1989)

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A novel gradient adaptive step size LMS algorithm with dual adaptive filters (2013)

Least mean square (LMS) adaptive filter has been used to extract life signals from serious ambient noises and interferences in biomedical applications. However, a LMS adaptive filter with a fixed step size always suffers from slow convergence rate or large signal distortion due to the diversity of the application environments. An ideal adaptive filtering system should be able to adapt different environments and obtain the useful signals with low distortion. Adaptive filter with gradient adaptive step size is therefore more desirable in order to meet the demands of adaptation and convergence rate, which adjusts the step-size parameter automatically by using gradient descent technique. In this paper, a novel gradient adaptive step size LMS adaptive filter is presented. The proposed algorithm utilizes two adaptive filters to estimate gradients accurately, thus achieves good adaptation and performance. Though it uses two LMS adaptive filters, it has a low computational complexity. An active noise cancellation (ANC) system with two applications for extracting heartbeat and lung sound signals from noises is used to simulate the performance of the proposed algorithm.
Communication—Solvate Ionic Liquid Incorporating Lithium Nitrate as a Redox Mediator for Lithium-Oxygen Batteries (2019)

A solvate ionic liquid (SIL) of highly concentrated 4.0 M lithium nitrate (LiNO3) in a dimethylsulfoxide solution is introduced for lithium-oxygen batteries. As a redox mediator (RM), highly concentrated LiNO3 in the SIL works more effectively than the lower concentrated one to decompose lithium peroxide (Li2O2) on the cathode with an extremely low charging voltage of 3.6 V. In addition, X-ray photoelectron spectroscopy analysis confirms that side products during discharging and charging are markedly restricted in the SIL. The low solubility of Li2O2 intermediate (LiO2) in the SIL may be an important reason for the restriction of side products.
Towards Stable and Conductive Titanium Oxynitride High‐Surface‐Area Support for Iridium Nanoparticles as Oxygen Evolution Reaction Electrocatalyst (2019)

Abstract The rational design of electrochemical oxygen evolution reaction (OER) electrocatalyst is essential for the development of efficient and sustainable electrochemical energy conversion, storage and electrolysis applications. One of the remaining limitations of the low‐temperature electrolyzers is the large amounts of highly scarce and expensive iridium used as the OER electrocatalysts. This could be solved by applying much smaller amounts of iridium on efficient and stable support. Here we present a very promising functionality of titanium oxynitride (TiON x ) high‐surface‐area support that effectively disperses the iridium nanoparticles, exhibits good intrinsic electrical conductivity and stability and thus promises efficient reduction of the noble‐metal loading in electrolyzers gas diffusion electrodes. The new nanocomposite made of approximately 3 nm‐sized iridium nanoparticles finely dispersed on TiON x support is produced using a novel synthetic route. Extensive characterization shows that the new composites exhibit an electronic interaction with the support and, ultimately, a high OER performance in acidic media.
Flow induced crystallization prevents melt fracture of HDPE in uniaxial extensional flow (2018)

This work concerns extension induced crystallization of a commercial high density polyethylene above the equilibrium melting temperature. We compare the nonlinear response during uniaxial elongation to the morphology obtained in the quenched fibers after cessation of the flow at a Hencky strain of 5. At 12 °C above the melting temperature, the samples undergo brittle fracture. Samples stretched at 2 and 6 °C above the melting temperature remain intact throughout the entire course of deformation and exhibit a strain hardening behavior that does not follow time temperature superposition. We propose that stabilization of the filament at lower temperatures, as well as the failure of time temperature superposition, is caused by flow-induced nucleation and growth of shish structures oriented along the flow direction. Further justification is obtained from small-angle X-ray scattering performed on the quenched filament showing an increased formation of shish with an increase in the deformation rate. We find the critical Hencky strain for the onset of the shish formation to be between 0 and 0.6, which is significantly lower than the values reported in the existing literature. We model the influence of shish nucleation on the rheological response in an extension using the hierarchical multimode stress function, which is modified to include the stretched network assumption.
Pre-operative Machine Learning for Heart Transplant Patients Bridged with Temporary Mechanical Circulatory Support (2022)

<b>Background:</b> Existing prediction models for post-transplant mortality in patients bridged to heart transplantation with temporary mechanical circulatory support (tMCS) perform poorly. A more reliable model would allow clinicians to provide better pre-operative risk assessment and develop more targeted therapies for high-risk patients. <b>Methods:</b> We identified adult patients in the United Network for Organ Sharing database undergoing isolated heart transplantation between 01/2009 and 12/2017 who were supported with tMCS at the time of transplant. We constructed a machine learning model using extreme gradient boosting (XGBoost) with a 70:30 train:test split to predict 1-year post-operative mortality. All pre-transplant variables available in the UNOS database were included to train the model. Shapley Additive Explanations was used to identify and interpret the most important features for XGBoost predictions. <b>Results:</b> A total of 1584 patients were included, with a median age of 56 (interquartile range: 46-62) and 74% male. Actual 1-year mortality was 12.1%. Out of 498 available variables, 43 were selected for the final model. The area under the receiver operator characteristics curve (AUC) for the XGBoost model was 0.71 (95% CI: 0.62-0.78). The most important variables predictive of 1-year mortality included recipient functional status, age, pulmonary capillary wedge pressure (PCWP), cardiac output, ECMO usage, and serum creatinine. <b>Conclusions:</b> An interpretable machine learning model trained on a large clinical database demonstrated good performance in predicting 1-year mortality for patients bridged to heart transplantation with tMCS. Machine learning may be used to enhance clinician judgement in the care of markedly high-risk transplant recipients.
ChemInform Abstract: Synthesis of Polyfluoroalkoxylated Pyrimidines and Pyrazoles by Using Novel β‐Polyfluoroalkoxy Vinamidinium Salts. (1998)

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.
Azure A chloride: computational and spectroscopic study (2008)

Abstract Fourier transform Raman and IR as well as UV–visible spectra of the phenothiazine dye Azure A chloride, 3‐amino‐7‐(dimethylamino) phenothiazin‐5‐ium chloride were recorded and analyzed. The spectral interpretation was done following full structure optimization and vibrational wavenumber calculations based on the density functional theory (DFT) using the standard B3LYP/6‐31G(d) basis set. The NH stretching wavenumber is found to be lowered owing to intermolecular NH···S hydrogen bonding. The downshift of CH stretching wavenumber is discussed. The first hyperpolarizability of the dye is calculated. Time‐dependent density functional theory (TD‐DFT) calculations of electronic spectra were performed on the optimized structure and compared with the experimental UV–visible spectrum. The atomic net charges of the molecule reveal the M effect of the nitrogen atoms in the molecule. Stability of the molecule arising from hyperconjugative interactions leading to its nonlinearity and bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Copyright © 2008 John Wiley &amp; Sons, Ltd.
On-chip food safety monitoring: multi-analyte screening with imaging surface plasmon resonance-based biosensor (2010)

If I knew I would find you all in Wageningen, I would have moved years ago.Thanks for all the lunches, BBQs, parties, dinners, trips, chit-chats, philosophical discussions, coffees & drinks and for just hanging around.Thanks for taking care of my plants, dog, husband, kids and me.You made Wageningen feel like home to me.Last but not least-my dear family.My parents
Human Herpesvirus 8 (Kaposi's Sarcoma–Associated Herpesvirus) Infection in Men Receiving Treatment for HIV-1 Infection (1999)

Although antibodies to HHV-8 are common among HIV-1-infected men, detection of HHV-8 DNA in PBMC is uncommon and is associated with a diagnosis of Kaposi's sarcoma.
Superradiant Emission of Ultra-Bright Photon Pairs in Doppler-Broadened Atomic Ensemble (2016)

With a recent rising interest of single photon superradiance due to its potential usefulness for efficient collection of single photon from an atomic ensemble, bright and narrow photon pair source is a key component in realization of quantum communication and quantum computer based on coherent interaction between light and atomic ensemble. We report the superradiant emission of ultra-bright photon pairs with a coincidence counting rate per input power of 64,600 cps/mW via spontaneous four-wave mixing in a thermal vapour cell. The photon-pair generation rate is enhanced by the contribution of two-photon coherence of almost atomic velocity groups in the Doppler-broadened ladder-type atomic system. The quadratic proportionality of the probability of detecting a heralded single photon as a function of the optical depth clarifies that the ultra-brightness results from the superradiance. In addition, a single photon superradiant beating at a high optical depth of the atomic ensemble is observed for the first time.
Effect of Foam on Liquid Phase Mobility in Porous Media (2016)

We investigate the validity of the assumption that foam in porous media reduces the mobility of gas phase only and does not impact the liquid-phase mobility.The foam is generated by simultaneous injection of nitrogen gas and a surfactant solution into sandstone cores and its strength is varied by changing surfactant type and concentration.We find, indeed, that the effect of foam on liquid-phase mobility is not pronounced and can be ignored.Our new experimental results and analyses resolve apparent discrepancies in the literature.Previously, some researchers erroneously applied relative permeability relationships measured at small to moderate capillary numbers to foam floods at large capillary number.Our results indicate that the water relative permeability in the absence of surfactant should be measured with the capillary pressure ranging up to values reached during the foam floods.This requires conducting a steady-state gas/water core flood with capillary numbers similar to that of foam floods or measuring the water relative-permeability curve using a centrifuge.
Sampling Efficacy for the Red Imported Fire AntSolenopsis invicta(Hymenoptera: Formicidae) (2011)

Cost-effective detection of invasive ant colonies before establishment in new ranges is imperative for the protection of national borders and reducing their global impact. We examined the sampling efficiency of food-baits and pitfall traps (baited and nonbaited) in detecting isolated red imported fire ant (Solenopsis invicta Buren) nests in multiple environments in Gainesville, FL. Fire ants demonstrated a significantly higher preference for a mixed protein food type (hotdog or ground meat combined with sweet peanut butter) than for the sugar or water baits offered. Foraging distance success was a function of colony size, detection trap used, and surveillance duration. Colony gyne number did not influence detection success. Workers from small nests (0- to 15-cm mound diameter) traveled no >3 m to a food source, whereas large colonies (>30-cm mound diameter) traveled up to 17 m. Baited pitfall traps performed best at detecting incipient ant colonies followed by nonbaited pitfall traps then food baits, whereas food baits performed well when trying to detect large colonies. These results were used to create an interactive model in Microsoft Excel, whereby surveillance managers can alter trap type, density, and duration parameters to estimate the probability of detecting specified or unknown S. invicta colony sizes. This model will support decision makers who need to balance the sampling cost and risk of failure to detect fire ant colonies.
Semantic data fusion through visually-enabled analytical reasoning (2014)

Investigating terrorist activity patterns and predicting threats involve collecting and analyzing data from both hard sensors and humans as part of analysts' reasoning process (evidence building, hypothesis creation and testing and decision making). Although automated data fusion methods have been proposed in previous studies, they tend to operate on low-level linguistic features of events and fail to connect to high-level conceptual categories that analysts need to make judgment. This paper argues for extending data fusion models and architecture with an explicit component of visual analytics that integrates human and machine analytical capability through interactive visual analysis. We motivate this argument by the need for human-driven analytical reasoning in counter-intelligence investigation domain. Our extended data fusion architecture follows the sensemaking theory of Pirolli and Card, which provides a framework for understanding specific details on how investigative analysis weave computation, visualization and human reasoning to support coherent analytics. The feasibility of this data fusion architecture is demonstrated through an Analysts' Workbench that allows analysts to construct intelligence reports through discovering, assessing, and associating evidences.
Discovery of Small Molecule Entry Inhibitors Targeting the Fusion Peptide of SARS-CoV-2 Spike Protein (2021)

SARS-CoV-2 entry into host cells relies on the spike (S) protein binding to the human ACE2 receptor. In this study, we investigated the structural dynamics of the viral S protein at the fusion peptide (FP) domain and small molecule binding for therapeutics development. Following comparative modeling analysis and docking studies of our previously identified fusion inhibitor chlorcyclizine, we performed a pharmacophore-based virtual screen and identified two novel chemotypes of entry inhibitors targeting the FP. The compounds were evaluated in the pseudoparticle viral entry assay and SARS-CoV-2 cytopathic effect assay and showed single-digital micromole inhibition against SARS-CoV-2 as well as SARS-CoV-1 and MERS. The characterization of the FP binding site of SARS-CoV-2 S protein provides a promising target for the structure-based development of small molecule entry inhibitors as drug candidates for the treatment of COVID-19.
Synthesis and properties of novel hole transport materials for electroluminescent devices (1998)

Abstract We synthesized low molecular weight triphenyldiamines (TPDs), novel 1,3,5‐tris(diarylamino)benzenes (TDABs), polymeric triphenyldiamines and insoluble triphenylamine networks based on tris(4‐ethynylphenyl)amine as hole transport materials for electroluminescent displays. The HOMO energy values as determined from cyclic voltammetry measurements for TPDs and TDABs are between −4.97 and −5.16 eV. By using a polymeric TPD as hole transport layer and tris(8‐quinolinolato) aluminium as emitter, LEDs with an onset voltage of 3V and a luminance up to 900 cd/m 2 were obtained under ambient conditions.
Recent advances in diagnosis and treatment of pheochromocytoma. (2003)

Pheochromocytomas are rare tumours of catecholamine-producing chromaffin cells leading to hypertension and symptoms of catecholamine excess. They can be benign or malignant, sporadic or familial tumours. Genetic syndromes associated with pheochromocytoma are MEN II, VHL disease and neurofibromatosis type 1. Usually, pheochromocytomas occur in the adrenal medulla. Clinical manifestations include hypertension (which can be intermittent, stable or in the form of hypertensive peaks) and symptoms related to catecholamine excess such as headache, palpitations and tachycardia, pallor, anxiety and nervousness, nausea, vomiting, weight loss. This clinical syndrome can be mimicked by various hyperkinetic and hyperadrenergic states. When pheochromocytoma is suspected, the first diagnostic step is represented by the measurement of catecholamines and their metabolites (metanephrines) in urine and plasma. Chro-mogranin A measurement can be useful. The clonidine suppression test may be helpful in ruling out other conditions that may elevate catecholamines and metanephrines. Localiza-tion and staging of pheochromocytoma is based on MRI, which is more sensitive than CT scan, and (131)I-MIBG scintiscan. The best therapeutic option for pheochromocytoma is surgery with a laparoscopic approach. An appropriate pre-, intra- and postoperative medical management of the patient is mandatory. In the absence of optimal medical treatment, intraoperative mortality reaches 50%.
Coupling of column liquid chromatography and thermospray mass spectrometry via phase-system switching with an ion-exchange trapping column (1992)

A benzenesulphonic acid-type cation exchanger (pKa < 1) is used as trapping-column material in a phase-system switching for the on-line coupling of column liquid chromatography and thermospray mass spectrometry. Phase-system switching is used to remove non-volatile constituents from the mobile phase, so that eluents containing non-volatile buffers and ion-pairing agents can be used without contaminating the mass spectrometer. The total analytical system is optimized using four benzalkonium test compounds (quaternary ammonium compounds). The reversed-phase separation of the test compounds as well as the parameters involved in the sorption on and desorption from the trapping column are studied. Important parameters during sorption are the concentration of the phosphate buffer and the percentage of acetonitrile in the mobile phase. During desorption of the test compounds from the ion-exchanger the percentage of acetonitrile in the desorption eluent and the pH are the most important factors. As an example, the analysis of domiphen in nasal drops is shown.
Electrophoretic and cytochemical characterization of alpha-naphthyl acetate esterases in acute myeloid leukemia: relationships with membrane receptor and monocyte-specific antigen expression (1984)

Alpha-naphthyl acetate esterases (ANAE) were examined by cytochemical and isoelectric focusing (IEF) techniques in 48 cases of acute myeloid leukemia that were classified by conventional morphological criteria. Four main types of ANAE isoenzyme patterns were found by IEF, and comparisons with the expression of membrane receptors (Fc-IgG and C3b) and monocyte-specific antigens (UCHM1, UCHALF, and E11) suggest relationships between ANAE isoenzyme synthesis and distinct myeloid maturational stages. The results further indicate that the blast cells of acute myelomonocytic leukemia (AMML) may represent an immature variant of monocytic leukemia (AMoL) and that morphological examination alone is inadequate in the assessment of monocytic differentiation in acute myeloid leukemias. Inhibition studies of cytochemical ANAE activity with sodium fluoride (NaF) show that the presence of NaF-sensitive or NaF-resistant ANAE enzymes is often unrelated to the diagnostic category of acute leukemia. The results of this study are examined in relation to current concepts of myeloid differentiation, and the application of these findings to the subclassification of acute myeloid leukemias is discussed.
Concise Chemoenzymatic Three‐Step Total Synthesis of Isosolenopsin through Medium Engineering (2013)

A short and efficient total synthesis of the alkaloid isosolenopsin and its enantiomer has been achieved. In the key step, a ω-transaminase catalyzed the regioselective mono-amination of the diketone pentadecane-2,6-dione which was obtained in a single step via Grignard reaction. Initial low conversions in the biotransformation could be overcome by optimisation of the reaction conditions employing suitable cosolvents. In the presence of 20 vol% DMF or <i>n</i>-heptane best results were obtained employing two enantio-complementary ω-transaminases originating from <i>Arthrobacter</i> between 30-40 °C; under these conditions conversions of >99% and perfect stereocontrol (<i>ee</i> > 99%) were achieved. Diastereostelective chemical reduction (H<sub>2</sub>/Pd/C) of the biocatalytic product gave the target compound. The linear three step synthesis provided the natural product isosolenopsin in diastereomerically pure form (<i>ee</i> > 99%, d.r. = 99:1) with an overall yield of 64%.